title: Single cell transcriptomics reveal type-2 inflammatory gene regulation in airway epithelium driven by allergen-specific immunotherapy

city: Garching

first: Maren

last: Büttner

address: Ingolstädter Landstr. 1

country: Germany

institute: Helmholtz Zentrum München

summary:
Background: Airway epithelium in patients with allergic airway disease actively releases and is subjected to the influence of type-2 cytokines with observable changes in basal epithelial cells. Symptoms that grass pollen-allergic patients experience due to this priming can be controlled by allergen-specific immunotherapy (AIT). However, the impact of AIT on type-2 related mediators of airway epithelial cells is unknown.
Methods: Protein levels of type-2 cytokines in nasal secretions of grass pollen-allergic patients were analyzed during 3-year AIT-regimen using multiplex-ELISA. Source and IL-4-dependence of type-2 cytokines were examined in IL-4-primed primary ALI cultures using single-cell transcriptomics.
Results: Type-2 cytokines CCL-26 and POSTN oscillated seasonally, derived from basal epithelial cells and were induced by IL-4-priming. In contrast, TSLP and IL-33 derived from basal cells, albeit independently of IL-4. POSTN and IL-24 nasal levels changed corresponding to 3-year AIT progression. Four characteristic epithelial type-2 cytokines stood out: IL-33 changed independent of season, IL-4-exposure, or AIT; CCL-26 was triggered upon IL-4-priming and was induced during pollen season, but not influenced by AIT; IL-24 decreased following three years of AIT; and POSTN, which was increased in IL-4-primed basal epithelial cells and oscillated during pollen season, also responded to long-term AIT.
Conclusions: Atopic reprogramming of type-2 epithelial cytokines seems to persist despite long-term AIT, which may be one mechanism explaining why AIT only restores allergen tolerance for seven to ten years. Type-2 related epithelial cytokines are differentially expressed which may relate to the distinct expression of basal as opposed to differentiated secretory or ciliated epithelial cells.

overall_design: The single-cell suspension was subjected to library preparation for single-cell 5’ gene expression analysis using the Chromium Next GEM Single Cell 5ʹ Library Kit v1.1 (10x Genomics, Leiden, The Netherlands), the Chromium Next GEM Single Cell Gel Bead Kit v1.1 (10x Genomics), and the single-cell partitioning instrument Chromium Controller (10x Genomics) according to the manufacturer’s instructions. The Bioanalyzer High Sensitivity DNA Analysis (Agilent, Waldbronn, Germany) and KAPA Library Quantification Kit (Hoffmann-La Roche, Basel, Switzerland) were used to control the quality and quantity of the libraries prior to submission for sequencing.

first: Ulrich

last: Zissler

first: Adam

last: Chaker

first: Amanda

last: Hornick

first: Madlen

last: Oelsner

last: Erb

first: Martin

last: Feuerherd

first: Lisa

last: Pechtold

first: Lynn

last: zur Bonsen

first: Mirjam

last: Plaschke

first: Josephine

last: Kau

first: Miodrag

last: Davidovic

first: Ulrike

last: Protzer

first: Simon

last: Blank

first: Benjamin

last: Schubert

first: Jose

last: Ordovas-Montanes

first: Carsten

middle: B

last: Schmidt-Weber

first: Constanze

last: Jakwerth


title: Integrated miRNAs profiling, DNA methylation, and RNA expression in gastroenteropancreatic neuroendocrine neoplasias

status: Public on Mar 31 2023

city: Madrid

first: GarciaCarbonero

last: Lab

state: Comunidad de Madrid

address: Av/ Córdoba s/n

department: Centro de Oncología Experimental

country: Spain

institute: Instituto de Investigación Hospital 12 de Octubre

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: The ASC-1 complex promotes translation initiation of the scanning ribosomes

city: Chikusa-ku, Nagoya, Aichi

first: Kazuya

last: Ichihara

address: Furo-cho

country: Japan

institute: Nagoya University

type: Expression profiling by high throughput sequencing

summary: Translation is initiated by binding of the eIF4F complex to the 5' cap of the mRNA, which is followed by scanning of the initiation codon by scanning ribosomes. Here we demonstrate that the ASC-1 complex (ASCC), which was previously shown to promote the dissociation of colliding 80S ribosomes, associates with the scanning ribosomes to regulate translation initiation. Sel-TCP-seq analysis revealed that ASCC3, a subunit of ASCC with a helicase domain, localizes predominantly to the 5' untranslated region of mRNAs. Knockdown of ASCC3 resulted in reduced translation efficiency associated with reduced 43S preinitiation complex (PIC) loading and a reduced speed of scanning ribosomes. In addition, depletion of the ubiquitin ligase ZNF598, a sensor of collided 80S ribosomes, also reduces the PIC loading and speed of scanning ribosomes. Our results have thus revealed that ASCC is required not only for dissociation of colliding 80S ribosomes, but also for efficient translation initiation by scanning ribosomes.

overall_design: Translational dynamics regulated by eIF4F or ASC-1 complex

first: Y

last: Kito

first: K

first: A

last: Matsumoto

last: Nakayama


title: Self-maintenance of Cardiac Resident Reparative Macrophages Attenuates Doxorubicin-induced Cardiomyopathy through the SR-A1-c-Myc Axis

city: Nanjing

first: Qi

last: Chen

state: Jiangsu Province

address: 101 Longmian Avenue

department: Department of Pathophysiology

country: China

institute: Nanjing Medical University

summary:
Rationale: Doxorubicin-induced cardiomyopathy (DiCM) is a significant cause of heart failure and mortality in cancer patients, in which macrophage-orchestrated inflammation serves as an essential pathogenic mechanism. However, the specific roles of tissue-resident and monocyte-derived macrophages in DiCM remain poorly understood.
Objective: Uncovering the origins, phenotypes, and functions of proliferative cardiac resident macrophages and mechanistic insights into the self-maintenance of cardiac macrophage during DiCM progression.
Methods and Results: Mice were administrated with doxorubicin to induce cardiomyopathy. Dynamic changes of resident and monocyte-derived macrophages were examined by lineage tracing, parabiosis, and bone marrow transplantation. We found that the monocyte-derived macrophages primarily exhibited a pro-inflammatory phenotype that dominated the whole DiCM pathological process and impaired cardiac function. In contrast, cardiac resident macrophages were vulnerable to doxorubicin insult. The survived resident macrophages exhibited enhanced proliferation and conferred a reparative role. Global or myeloid specifically ablation of class A1 scavenger receptor (SR-A1) inhibited proliferation of cardiac resident reparative macrophages and therefore exacerbated cardiomyopathy in DiCM mice. Importantly, the detrimental effect of macrophage SR-A1 deficiency was confirmed by transplantation of GFP+ wild type bone marrow. At the mechanistic level, we show that c-Myc, a key transcriptional factor for the SR-A1-P38-SIRT1 pathway, mediated the effect of SR-A1 in reparative macrophage proliferation in DiCM.
Conclusions: The SR-A1-c-Myc axis may represent a promising target to treat DiCM through augmentation of cardiac resident reparative macrophage proliferation.

overall_design: Examination of heart mRNA profiles in 5  different treated mice types.

first: Hanwen

last: Zhang


title: Disruption of sensory plastid-associated PPD3 triggers plant growth- and defense-related epigenetic responses in Arabidopsis [RNA-Seq 2]

city: University Park

first: Hardik

last: Kundariya

state: PA

address: 361 N. Frear

country: USA

institute: The Pennsylvania State University

summary: RNA sequencing of PPD3-RNAi transgene-positive (T+) dwarf and large and wild type.

overall_design: Aboveground tissues were collected at bolting stage. Three biological replicates for each, T+ dwarf and large

first: Ha

middle: E

last: Jeh

first: Sally

last: Mackenzie


title: Disruption of sensory plastid-associated PPD3 triggers plant growth- and defense-related epigenetic responses in Arabidopsis [Bisulfite-Seq]

type: Methylation profiling by high throughput sequencing

summary: DNA bisulfide sequencing of PPD3-OX transgene-positive (T+) dwarf and large, Gen1 memory dwarf, Gen2 memory dwarf and large, wild type.

overall_design: Aboveground tissues were collected at bolting stage. Three biological replicates for each, T+ and Gen1 were siblings and Gen2 is progeny of Gen1.


title: Disruption of sensory plastid-associated PPD3 triggers plant growth- and defense-related epigenetic responses in Arabidopsis [RNA-Seq]

summary: RNA sequencing of PPD3-OX transgene-positive (T+) dwarf and large, Gen1 memory dwarf, Gen2 memory dwarf and large, wild type.


title: Disruption of sensory plastid-associated PPD3 triggers plant growth- and defense-related epigenetic responses in Arabidopsis


title: Transcriptome analysis of human maturing macula

city: Tokyo

first: Taku

last: Tanaka

address: 2-10-1 Okura, Setagaya

department: Ophthalmology

institute: National Center for Child Health and Development

summary: The macula is an essential region of the retina responsible for visual acuity. Abnormalities in development of the fovea at the center of the macula lead to severe diseases. To identify macula-specific differentially expressed genes in maturing stage of macular development, we compared the gene expression profiles of the macular and peripheral region of the pediatric retina.

overall_design: Retinas were collected from six cases of retinoblastoma and peters pnomaly and were divided into macular region and peripheral region. Using RNAs extracted from these six tissues, the expression profiles of macula and peripheral retina were compared by microarray analysis.

first: Tadashi

last: Yokoi

first: Noriyuki

last: Azuma


title: Integrated miRNAs profiling, DNA methylation, and RNA expression in gastroenteropancreatic neuroendocrine neoplasias [miRNA]

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

summary:
Background: Neuroendocrine neoplasms (NENs) are mutationally quiet, and epigenetic mechanisms drive their development and progression. We aim to comprehensively characterize the microRNA (miRNA) profile of NENs, and explore downstream targets and their epigenetic modulation.
Material and Methods: In total, 84 cancer-related miRNAs were analyzed in 84 NEN samples from lung and gastroenteropancreatic GEP origin, and their prognostic value was evaluated by univariate and multivariate models. Transcriptomics (N=63) and methylomics (N=30) were performed to predict miRNA target genes, signaling pathways and regulatory CpG sites. Findings were validated in The Cancer Genome Atlas (TCGA) cohorts and in NEN cell lines.
Results: We identified a signature of eight miRNAs that stratified patients in three prognostic groups (5-year survival of 80%, 66% and 36%). Expression of the eight-miRNA gene signature correlated with 71 target genes involved in PI3K-Akt and TNFα-NF-kB signaling. Of these, 28 were associated with survival and validated in silico and in vitro. Finally, we identified five CpG sites involved in the epigenetic regulation of these eight miRNAs.
Conclusion: In brief, we identified an 8-miRNA signature able to predict survival of patients with GEP and lung NENs, and identified genes and regulatory mechanisms driving prognosis in NEN patient.

overall_design:
This study includes 85 paired tumor and non-tumor samples from 85 lung and GEP NEN patients. miRNAs profiling was performed in 84 patients, DNA methylation in 30 patients and RNA expressión in 63 patients.
This dataset includes the miRNA data.

first: Beatriz

last: Soldevilla

first: Alberto

last: Lens-Pardo

first: Paula

last: Espinosa-Olarte

first: Carlos

last: Carretero-Puche

first: Sonia

last: Molina-Pinelo

last: Robles

first: Marta

last: Benavent

first: Lourdes

last: Gomez-Izquierdo

last: Fierro-Fernández

first: Patricia

last: Morales-Burgo

last: Jimenez-Fonseca

last: Anton-Pascual

first: Yolanda

last: Rodríguez-Gil

first: Ana

last: Teijó-Quintants

first: Anna

last: La Salvia

last: Rubio-Cuesta

first: Maria

middle: D

last: Riesco-Martinez

first: Rocio

last: Garcia-Carbonero


title: Gene expression profile at single cell level of muscle cells from the main electric organ (EO) in the electric eel

status: Public on Mar 30 2023

city: Guangzhou

first: Xidong

last: Mu

address: No.1 Xingyu Road

institute: Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences

summary: Electrocytes are the cellular basis of electrogenesis. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of cells in the muscle from the main EO of the elctric eel and the distribution and abundance of electrocytes.

overall_design: The muscle sample from the main EO were analyzed using scRNAseq to find out electrocytes.

first: Yuanyuan

last: Wang

first: Yi

last: Liu

first: Yexin

last: Yang

first: Chao

first: Yang

last: Zhang

last: Bian


title: Molecular Markers for Predicting Treatment Outcome in Patients with Rectal Cancer: A Comprehensive Analysis from the German Rectal Cancer Trials

city: Göttingen

first: Tim

last: Beissbarth

address: Humboldtallee 32

department: Medical Statistics

institute: University Medical Center Göttingen

summary: Background: Validated markers to predict outcome in rectal cancer patients treated with multimodal therapy remain elusive. Identifying molecular profiles for disease prognosis would be required for the design of clinical trials aimed at optimizing risk-adapted therapies. We have therefore used whole genome expression profiling of tumors of a large cohort of patients enrolled in the multicenter trials of the German Rectal Cancer Study Group (GRCSG) to identify molecular profiles for individualized therapy.  Methods: We prospectively collected pretherapeutic biopsies from patients (n=300) treated according to the GRCSG trial guidelines from seven different German surgical departments using rigid quality controls. These samples were profiled by global gene expression analysis and a classifier developed to predict postoperative lymph node status and Disease Free Survival (DFS). The performance of the classifier was validated with an independent, prospectively collected set of samples.  Findings: The final training and test set included 198 patients. Analyzes for postoperative nodal status and DFS revealed 69 and 674 differentially regulated genes, respectively. Depending on the classifier the accuracy to predict lymph node status ranged from 64% to 69% with negative predictive values between 72% and 74%. Stratification according to DFS resulted in a good (n=99), bad (n=96) and a small very bad prognosis group (n=3). Based on linear discriminant analysis the classifier for positive lymph node status was validated in 47 independent patients and revealed an accuracy of 72% and a positive predictive value of 100%. Thereby, prediction based on molecular profiling is superior to prediction based on conventional clinical markers.  Interpretation: Whole genome expression analysis of pretherapeutical biopsies resulted in a molecular classifier of disease prognosis. This classifier was successfully validated. The high positive predictive value for post therapeutic lymph node status allows identification of patients requiring alternative or intensified treatment protocols. These data are currently validated for their clinical applicability and should be taken as basis for future molecular driven clinical trials to develop risk-adapted treatments.

overall_design: Tumor samples from a total of 245 patients (198 samples for classifier training and 47 samples for validation)

first: Jochen

last: Gaedcke

first: Peter

last: Jo

first: Klaus

last: Jung

first: Marian

last: Grade

first: Julia

last: Kitz

first: Hendrik

middle: A

last: Wolff

first: Gabriela

last: Salinas-Riester

first: Ulrich

last: Sax

first: Lena

middle: C

last: Conradi

first: Josef

last: Rüschoff

last: Matzel

first: Verena

last: Grünewald

first: Dirk

last: Schrader

first: Ina

last: Burkowski

last: Weyhe

first: Rudolph

last: Hesterberg

last: Kania

first: Werner

last: Hohenberger

first: Heinz

last: Becker

first: Rolf

last: Sauer

first: Clemens

middle: F

last: Hess

first: Claus

last: Rödel

first: Thomas

last: Ried

first: Thorsten

last: Liersch

last: Beißbarth

first: Michael

last: Ghadimi


title: Effect of FDX1 overexpression on gene expression in SUDHL-4 cells upon elesclomol stimulation

city: Shanghai

first: Yuhang

last: Jiang

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences

summary: To investigate the function FDX1 in the regulation of elesclomol (ES)-induced cell death, we established SUDHL-4 cell lines in which the full-length coding sequence of FDX1 was overexpressed (FDX1-OE), we then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells (control and FDX1-OE SUDHL-4) with or without elsclomol treatment

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control and FDX1-OE SUDHL-4 cells.

first: Qi

last: Wang

first: Weifeng

last: Chen

first: Xiaoting

last: Feng


title: Effect of FDX1 overexpression on gene expression in WSU-DLCL2 cells upon elesclomol stimulation

summary: To investigate the function FDX1 in the regulation of elesclomol (ES)-induced cell death, we established WSU-DLCL2 cell lines in which the full-length coding sequence of FDX1 was overexpressed (FDX1-OE), we then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells (control and FDX1-OE WSU-DLCL2) with or without elsclomol treatment

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control and FDX1-OE WSU-DLCL2 cells.


title: Accurate circadian time prediction from a single bulk and single-cell transcriptomic data by tauFisher

city: Irvine

first: Bogi

last: Andersen

address: Sprague Hall Rm 206

institute: University of California, Irvine

summary: As the circadian clock regulates fundamental biological processes, disrupted clocks are often observed in patients and diseased tissues. Determining the circadian time of the patient or the tissue of focus is essential in circadian medicine and research. Here we present tauFisher, a computational pipeline that accurately predicts circadian time from a single transcriptomic sample. We demonstrate tauFisher’s outstanding performance in both bulk and single cell transcriptomic data collected from multiple tissue types and experimental settings. Application of tauFisher at a cell-type level in a single cell RNA-seq dataset collected from mouse dermal skin implies that greater circadian phase heterogeneity may explain the dampened rhythm of collective core clock gene expression in dermal immune cells compared to dermal fibroblasts. Given its robustness and generalizability across assay platforms, experimental setups, and tissue types, as well as its potential application in single cell RNA-seq data analysis, tauFisher is a promising tool that facilitates circadian medicine and research.

overall_design: Dermal cells were collected from WT C57BL/6J mouse dorsal skin every four hours for three days under the 12:12 light-dark cycle. The Chromium Single Cell 3' v3 (10x Genomics) libraries were prepared and sequenced with Illumina NovaSeq6000.

first: Junyan

last: Duan

first: Michelle

middle: N

last: Ngo

first: Satya

middle: S

last: Karri

first: Babak

last: Shahbaba

first: John

last: Lowengrub


title: Dissecting cell-type specific pathophysiological changes in human type-2 diabetic pancreatic islets using single-cell transcriptomic data

city: Farmington

first: Efthymios

last: Motakis

state: CT

address: 10 Farmington Drive

department: Computational Sciences

institute: The Jackson Laboratory

summary: Pancreatic islet (dys)function is central to glucose homeostasis and type 2 diabetes (patho)physiology. Human islets consist of multiple endocrine (alpha, beta, delta, gamma), endothelial, and resident/inflitrating immune cells whose coordinated functions modulate glucose mobilization or disposal. Single cell transcriptome profiling (scRNA-seq) studies have been applied to dissect human islet cellular heterogeneity, identify islet cell (sub)populations, and define their molecular repertoire. However, precise understanding of cell type-specific alterations in type 2 diabetic vs. non-diabetic individuals is lacking, due in part to the limited number of individuals or single cell transcriptomes per individual profiled for comparison. Here, we create a comprehensive single cell transcriptome atlas of 245,878 human islet cells from 48 individuals spanning non-diabetic (ND), pre-diabetic (PD), and type 2 diabetic (T2D) states and matched for sex, age, and ancestry and define marker gene sets that are robustly expressed across disease states for each of the 14 cell types identified. We observe significant decreases in the number of beta cells sampled from T2D vs. ND or PD donors. Two of eight putative beta cell subpopulations, with ‘high functioning’ and ‘senescent’ cell gene signatures, increase and decrease in T2D donor islets, respectively. Importantly, we identify 511 differentially expressed genes in beta cells from T2D vs. ND donors. This includes monogenic and type 2 diabetes effector genes, such as HNF1A, DGKB, ST6GAL1, and FXYD2, for which genetic and environmental effects on their expression is concordant.  Human beta cell and islet knockdown of selected newly-identified down-regulated genes impairs beta cell viability or function. Together, this study provides new and robust, cell type-resolved insights on the cellular and molecular changes in healthy vs. diabetic human islets and represents a valuable resource to the islet biology and type 2 diabetes communities.

overall_design:
Pancreatic islets from 17 type 2 diabetic (T2D), 17 non-diabetic (ND) and 14 prediabetic (PD) cadaveric organ donors were dissociated to single cell suspension and captured/profiled using 10x Genomics single-cell RNA-seq platform
ND: Islet29, Islet34, Islet37, Islet38, Islet42, Islet45, Islet47, Islet54, Islet57, Islet59, Islet61, Islet68, Islet73, Islet80, Islet104, Islet107, Islet123
PD: Islet40, Islet50, Islet53, Islet55, Islet56, Islet58, Islet62, Islet63, Islet70, Islet85, Islet89, Islet101, Islet118, Islet127
T2D:  Islet28, Islet30, Islet31, Islet32, Islet33, Islet39, Islet41, Islet44, Islet48, Islet52, Islet60, Islet71, Islet84, Islet91, Islet126, Islet119, Islet128

first: Siddhi

last: Nargund

first: Romy

last: Kursawe

first: Nathan

last: Lawlor

first: Sai

last: Krishnan

first: Vijay

last: Selvam

middle: L

last: Stitzel


title: Adaptation strategies of Pseudothermotoga species to hydrostatic pressure by transcriptional analyses

city: Marseille

first: Romain

last: Fenouil

address: Parc Scientifique et Technologique de Luminy - Case 906

department: CIML

country: France

institute: CNRS

summary: Pseudothermotoga elfii strain DSM9442 and P. elfii subsp. lettingae strain TMOT are hyperthermophilic bacteria. P. elfii is a moderate piezophile, isolated from an oil-producing well in Africa at a depth of more than 1600 m. P. lettingae is piezotolerant, isolated from a thermophilic bioreactor fed with methanol as the sole carbon and energy source. In this study, we analysed these bacteria at the genomic and transcriptomic levels. According to the hydrostatic pressure growth conditions the transcriptomic analyses revealed differentially expressed genes emphasizing amino acid and sugars metabolism and transport as the major hydrostatic pressure responding processes. Notably, this work highlights the central role of the amino acid aspartate as key intermediate of the pressure adaptation mechanisms of the deep strain P. elfii DSM 9442. In addition, several differentially expressed genes involved in the membrane and cell wall biosynthesis pathways may be linked to the chain formation morphotype previously described at high pressure for strain P. elfii DSM9442.

sample_organism: Pseudothermotoga elfii DSM 9442 = NBRC 107921

overall_design: Pseudothermotoga cells were grown  in 120 mL flasks at the desired hydrostatic pressure (0.1, 20, 30 and 40 MPa for Pseudothermotoga elfii strain DSM9442 and 0.1 and 20 MPa for P. elfii subsp. lettingae strain TMOT) until reaching mid-exponential growth. Then, cells were harvested by centrifugation at 6800g for 15 min at 4°C; the pellet was resuspended in 400 µL of 10 mM Tris-HCl (pH 8.0) and spun for 2 min at 12000g. The supernatant was removed and the pellet frozen in liquid nitrogen before being placed in -80°C storage until use for RNA-seq analyses.

first: Nathalie

last: Pradel

first: Hassiba

last: Belhabib

first: Marie

last: Roumagnac

first: Manon

last: Bartoli

first: Wajdi

last: Hania

first: Yann

last: Denis

first: Marc

last: Garel

first: Christian

last: Tamburini

first: Bernard

last: Ollivier

first: Zara

last: Summers

first: Fabrice

last: Armougom

first: Alain

last: Dolla


title: Gene expression profile of kidneys from mice at post-natal day 2

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

summary: To investigate the role of Tfeb/Tfe3 in the transcriptional alterations of kidney-specific Flcn-KO mice.

overall_design: Total RNA was extracted from mouse kidneys.

first: R

first: C

last: Di Malta


title: Establishment and Function of Chromatin Organization at Replication Origins

city: Planegg-Martinsried

first: Erika

last: Chacin

address: Grosshaderner Strasse 9

institute: BMC - Ludwig-Maximilians-Universität München

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The Origin Recognition Complex (ORC) is essential for the initiation of eukaryotic chromosome replication as it loads the replicative helicase, the minichromosome maintenance (MCM) complex, at replication origins. Origins display a stereotypic chromatin structure with nucleosome depletion at ORC binding sites and flanking arrays of regularly spaced nucleosomes. Although discovered long ago, it is unknown how this chromatin struture is established and if it matters for replication. By genome-scale biochemical reconstitution we screened ~300 origins and 17 purified budding yeast chromatin factors and found that ORC established nucleosome depletion over origins and flanking nucleosome arrays by orchestrating the chromatin remodelers INO80, ISW1a, ISW2 and Chd1. The functional importance of ORC’s chromatin organizing activity was directly demonstrated by ORC mutations that maintained classical MCM loader activity but lost array generation activity. These mutations impaired replication through chromatin in vitro and were lethal in vivo. Our results establish that ORC, besides its canonical role as MCM loader, has a second essential function as master regulator of the origin chromatin structure that is a crucial prerequisite for efficient chromosome replication.

overall_design: We in vitro reconstituted the chromatin landscape of origins of replication with purified components. We used in vivo and in vitro approaches to show that ORC is a master regulator of this process and that regular spaced nucleosomal arrays are important for replication efficiency.

first: Karl-Uwe

last: Reusswig

first: Jessica

last: Furtmeier

first: Priyanka

last: Bansal

first: Leonhard

last: Karl

first: Boris

last: Pfander

first: Tobias

last: Straub

first: Philipp

last: Korber

first: Christoph

last: Kurat


title: Gas lean obob GRf/fGRmKO

first: Hiroki

last: Yamazaki

address: 35 Shinanomachi, Shinjuku-ku

department: Department of Biochemistry

institute: Keio University School of Medicine

summary: Muscle glucocorticoid receptor (GR) signaling regulates gene expressions in skeletal muscle. To reveal the roles of muscle GR in systemic metabolism in obesity, ob/ob background muscle-specific GR knockout (ob/ob GRmKO) mice were generated.

overall_design: GR Flox+/+ Cre-/- Lep+/+ (lean GRf/f), GR Flox+/+ Cre+/- Lep+/+ (lean GRmKO), GR Flox+/+ Cre-/- Lepob/ob (ob/ob GRf/f), and GR Flox+/+ Cre+/- Lepob/ob (ob/ob GRmKO) were compared. Gastrocnemius muscle from 7-week-old male mice was excised and analyzed. We used pooled RNA samples (n = 3).

first: Masaaki

last: Uehara

first: Noritada

last: Yoshikawa

first: Akiko

last: Kuribara-Souta

first: Motohisa

last: Yamamoto

first: Yasuko

last: Hirakawa

first: Yasuaki

last: Kabe

first: Makoto

last: Suematsu

first: Hirotoshi

last: Tanaka


title: GasLiverWAT GRf/fGRmKO vehicleCORT

summary: Muscle glucocorticoid receptor (GR) signaling regulates gene expressions in skeletal muscle and promotes protein catabolism. To reveal the roles of muscle GR in systemic metabolism, corticosterone was chronically administered to GR-floxed (GRf/f) or muscle-specific GR knockout (GRmKO) mice, and metabolic changes were analyzed.

overall_design: The drinking water of 8-week-old GRf/f or GRmKO male mice was replaced with a 1% ethanol solution containing 100 μg/mL CORT or a vehicle. After 4-week treatment, gastrocnemius muscle, liver, and gonadal white adipose tissue were excised and analyzed. We used pooled RNA samples (n = 3).


title: TRained Immunity induced by Bcg in UroThElial carcinoma (Tribute) associated RNA-seq analysis

city: Parkville

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

summary: Trained immunity is the phenomenon whereby innate immune cells such as monocytes or macrophages undergo functional reprogramming after exposure to certain microbial components, altering their responses to future exposures. Intravesical instillation with Bacillus Calmette-Guérin (BCG) is the most effective adjuvant therapy in patients with high-risk non-muscle invasive bladder cancer (HR-NMIBC). HR-NMIBC is associated with a high risk of tumor recurrence and progression to muscle-invasive bladder cancer. The precise immunological mechanisms through which BCG mediates anti-tumor immunity are still unclear. The aim of our study was to investigate the (long-term) induction of trained immunity by repeated BCG instillations in NMIBC patients and elucidate the immunological and epigenetic mechanisms that are involved. Another aim was to assess the relationship between trained immunity response and clinical response of NMIBC patients, in terms of recurrence free survival and progression free survival. To determine whether BCG instillations induce trained immunity in peripheral blood mononuclear cells (PBMCs) we performed a prospective cohort study (‘Tribute’) and isolated PBMCs collected before BCG therapy and at 8 time points during BCG therapy. A total of 17 BCG-naïve HR-NMIBC patients were included. After isolation of PBMCs, monocytes were further purified using an isolation procotol with a percoll gradient. RNA was isolated from these purified monocytes were and used as input for RNA-seq analysis.

overall_design: Blood was collected using venapuncture and PBMCs were isolated at three time points during the BCG induction cycle: pre-BCG1, BCG2 and BCG6; and two time points during each subsequent BCG maintenance cycle: pre-BCG7, BCG9, pre-BCG10, BCG12, pre-BCG13 and BCG15. For each donor one replicate for each time point was included. RNA from purified monocytes was isolated for the time points pre-BCG1, BCG6, and pre-BCG7 and the RNA-seq data was analysed. For some patients RNA-seq data for the pre-BCG10 time point was also available, but this time point was not included in the analysis because not every patient had data available for this time point. Comparisons for differentially expressed genes were made using the pre-BCG1 time point as a reference.

first: Jelmer

last: van Puffelen

first: Liesbeth

last: van Emst

first: Denise

last: Kooper

first: Tahlita

last: Zuiverloon

first: Ursula

last: Oldenhof

first: Alfred

last: Witjes

first: Tessel

last: Galesloot

first: Alina

last: Vrieling

first: Katja

last: Aben

first: Lambertus

last: Kiemeney

first: Egbert

last: Oosterwijk

first: Mihai

last: Netea

first: Joost

last: Boormans

first: Antoine

last: van der Heijden

first: Leo

last: Joosten

first: Sita

last: Vermeulen


title: Transcriptomic responses of bat cells to European bat lyssavirus 1 infection under conditions simulating euthermia and hibernation

status: Public on Mar 29 2023

city: Paris

first: Hugo

last: Varet

address: 28 rue du Docteur Roux

institute: Institut Pasteur

summary: Background: Coevolution between pathogens and their hosts decreases host morbidity and mortality. Bats can tolerate viruses which can be lethal to other vertebrate orders, including humans. Bat adaptations to infection include localized immune response, early pathogen sensing, high interferon expression without pathogen stimulation, and regulated inflammatory response. The immune reaction is costly, and bats suppress high-cost metabolism during torpor. In the temperate zone, bats hibernate in winter, utilizing a specific behavioural adaptation to survive detrimental environmental conditions and lack of energy resources. Hibernation torpor involves major physiological changes that pose an additional challenge to bat-pathogen coexistence. Here, we compared bat cellular reaction to viral challenge under conditions simulating hibernation, evaluating the changes between torpor and euthermia.     Results: We infected the olfactory nerve-derived cell culture of Myotis myotis with an endemic bat pathogen, European bat lyssavirus 1 (EBLV-1). After infection, the bat cells were cultivated at two different temperatures – 37 ◦ C and 5 ◦ C - to examine the cell response during conditions simulating euthermia and torpor, respectively. The mRNA isolated from the cells was sequenced and analysed for differential gene expression attributable to the temperature and/or infection treatment. In conditions simulating euthermia, infected bat cells produce an excess signalling by multitude of pathways involved in apoptosis and immune regulation influencing proliferation of regulatory cell types which can, in synergy with other produced cytokines, contribute to viral tolerance. We found no up- or downregulated genes expressed in infected cells cultivated at conditions simulating torpor compared to non-infected cells cultivated under the same conditions. When studying the reaction of uninfected cells to the temperature treatment, bat cells show an increased production of heat shock proteins (HSPs) with chaperone activity, improving the bat’s ability to repair molecular structures damaged due to the stress related to the temperature change.     Conclusions: The lack of bat cell reaction to infection in conditions simulating hibernation may contribute to the virus tolerance or persistence in bats. Together with the cell damage repair mechanisms induced in response to hibernation, the immune regulation may promote bats’ ability to act as reservoirs of zoonotic viruses such as lyssaviruses.

overall_design: Comparative gene expression in infected olfactory nerve-derived cell culture of Myotis myotis with an endemic bat pathogen, European bat lyssavirus 1 (EBLV-1) cultivated at two different temperatures – 37 ◦ C and 5 ◦ C - to examine the cell response during conditions simulating euthermia and torpor, respectively. The dataset includes sequencing data of 12 samples, technical triplicates from a different laboratory session of each treatment conditions – Infected at 37°C, Infected at 5°C, Non-infected at 37°C, Non-infected at 5°C.

first: Markéta

last: Harazim

first: Laurent

last: Dacheux

first: Juliette

last: Perrot


title: TRained Immunity induced by Bcg in UroThElial carcinoma (Tribute)

first: Boris

last: Novakovic

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

overall_design: Refer to individual Series


title: Epigenetic profiling of cycling endometrium at single-cell resolution

city: Coventry

first: Jan

middle: J

last: Brosens

address: University Hospital Coventry and Warwickshire

department: Warwick Medical School

country: United Kingdom

institute: University of Warwick

summary: The human menstrual cycle can be divided into two major phases by the event of ovulation. Before ovulation, in the proliferative or follicular phase, the endometrium proliferates under the influence of estradiol produced by growing ovarian follicles. After ovulation, in the secretory or luteal phase, ovarian progesterone produced by the newly formed corpus luteum drives a process of differentiation during which the endometrium becomes competent to receive and support the growth of the embryo. Single-cell analyses at the RNA level from our group and others have begun to decipher cell-type specific expression in the endometrium. How these events are controlled at the chromatin level remains elusive, however. In this study, we applied single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) to profile the epigenetic landscapes of human endometrial samples across the menstrual cycle.

overall_design: Twelve timed endometrial biopsies were processed as described in detail elsewhere (Brighton et al., 2017) and subjected to single-cell ATAC-seq.

first: Pavle

last: Vrljicak

first: Emma

last: Lucas

first: Sascha

last: Ott


title: Effect of intransal C3a treatment on gene expression in mouse brain cortex in the post-acute phase of ischemic stroke.

city: Vestec

first: Lukas

last: Valihrach

address: Prumyslova 595

country: Czech Republic

institute: Institute of Biotechnology, Czech Academy of Science

summary:
The goal of this study was to gain insight into possible mechanisms of improved neural plasticity and functional recovery folowing ischemic stroke in mice confered by a delayed intranasal treatment with complement peptide C3a (reported previously in Stokowska et al., Brian, 2017).
Differential expression analysis revealed that daily intranasal treatment between day 7 and 14 post-stroke is associated with downregualtion of genes involved in inflammatory responses and glial cells reactivity, primarily astrocytes.  Further, cellular deconvolution analysis pointed to C3a-dependent reduction of fraction of astrocytes with gene expression profile charcterisitc for potentially neurotoxic disease-associated  astrocytes (DAAs, orignially descreibed in Alzheimer disease) and increse in fraction of homeostatic astrocytes, with expression profile indicating supportive role for neuronal function and plasticity.
We conclude that the C3a-C3aR signalling modulates post-stroke reactive astrogliosis in the manner favouring neural plasticity the peri-lesional cortex.

overall_design: Time-course analysis of gene expression in cerebral cortex after ischemic stroke (photothrombosis). Samples were collected from  ipsilesional (i.e., peri-infarct) and corresponding contralesional cortex or homotopic regions in naive (no storke) mice - encomapssing primary motor and somatosensory upper limb area. Samples were taken at baseline (naive), 7 days after stroke, i.e. before treatment initiation as well as at 14 days post-stroke, i.e. after one weak-long daily intransal treatment with C3a or PBS (vehicle); 4 mice per time-point or treatment group.

first: Anna

last: Cisowska

first: Pavel

last: Abaffy

first: Daniel

last: Žucha

first: Lukáš

first: Milos

last: Pekny

first: Marcela

last: Pekna


title: Tumor-specific CD8+ T cells

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

institute: Chiba univercity


title: Large neutral amino acid levels tune perinatal neuronal excitability and survival

city: Klosterneuburg

first: Lisa

middle: Sophie

last: Knaus

address: Am Campus 1

country: Austria

institute: IST Austria

summary: Surprisingly little is known about the critical metabolic changes that neural cells have to undergo during development and how even mild, temporary shifts in this program can influence brain circuitries and behavior. Inspired by the discovery that mutations in SLC7A5, a transporter of metabolically-essential large neutral amino acids (LNAAs), lead to autism, we employed metabolomic profiling to study the metabolic states of the cerebral cortex across different developmental stages. We found that the forebrain undergoes significant metabolic remodeling throughout development, with certain groups of metabolites showing stage-specific changes. But what are the consequences of interfering with this metabolic program? By manipulating Slc7a5 expression in neural cells, we found that the metabolism of LNAAs and lipids are interconnected in the cortex. Deletion of Slc7a5 in neurons perturbs specifically the postnatal metabolic state leading to a shift in lipid metabolism and a stage- and cell-type-specific alteration in neuronal activity patterns, resulting in a long-term circuit dysfunction.

overall_design: Bulk RNA-sequencing for wild type and Slc7a5fl/fl;Emx1-Cre+ mice.  Cortical tissue samples (age P2), three biological replicates each.

first: Gaia

last: Novarino


title: RNA-seq of tumor-specific CD8+ T cells

summary: Tumor-specific CD8+ T cells are heterogeneous; Tcf1+ stem-like CD8+ T cells give rise to cytotoxic Tim-3+ terminally differentiated CD8+ T cells. The goal of this study is to determine the capacity of CD69 to regulate differentiation of tumor-specific CD8+ T cells in the tumor microenvironment and tumor-draining lymph nodes. Our single-cell RNA-seq and RNA-seq analyses of tumor-specific CD8+ T cells reveal the important function of CD69 in anti-tumor CD8+ T cell immunity. Thus, CD69 is an attractive target for cancer immunotherapy.

overall_design: AH1 tetramer+ CD8+ T cell subpopulations were sorted and subjected to RNA-seq.

first: Ryo

last: Koyama-Nasu

first: Motoko

middle: Y

last: Kimura

first: Ami

last: Aoki

first: YangSong

last: Wang

first: Yukiyoshi

last: Mita

first: Ichita

last: Hasegawa

first: Yukihiro

last: Endo

first: Atsushi

last: Onodera

first: Kiyoshi

last: Hirahara

first: Shinichiro

last: Motohashi

first: Toshinori

last: Nakayama


title: Gene expression in cancerous and paraneoplastic tissues of patients with head and neck squamous cell carcinoma.

status: Public on Mar 28 2023

city: Yantai

first: Xicheng

last: Song

address: No.20, Yuhuangding East Road, Zhifu District, Yantai City, Shandong Province

department: Department of Otorhinolaryngology, Head and Neck Surgery

institute: Qingdao University Affiliated Yantai Yuhuangding Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: We performed whole-transcriptome sequencing to identify dysregulated circRNAs and identified circRNA/miRNA/mRNA ceRNA networks of HNSCC.

overall_design: Comparative gene expression profiling of RNA-seq data from cancerous and paraneoplastic tissues of patients with head and neck squamous cell carcinoma.


title: scRNA-seq of tumor-specific CD8+ T cells

overall_design: AH1 tetramer+ CD8+ T cells were sorted and subjected to scRNA-seq.


title: Effect of frataxin silencing by RNAi on 4, 7 and 14 days old worms

status: Public on Mar 27 2023

city: Düsseldorf

first: Natascia

last: Ventura

address: Auf'm Hennekamp 50

institute: Heinrich Heine University  and the IUF- Leibniz Research Institute for Environmental Medicine

summary: The study aimed to investigate the mechanisms that promote compensatory pro-longevity responses during mild mitochondrial stress in Caenorhabditis elegans.   This was achieved by performing a DNA microarray analysis to compare gene expression profiles of wild-type and mild mitochondrial-stressed long-lived worms at days 4, 7, and 14 after birth, in five replicates.    The worms were fed with either an empty-vector control (pL4440) or vector-expressing dsRNA against nematode frataxin (frh-1) to induce mild mitochondrial stress, for 3 consecutive generation starting from eggs.

overall_design: frh-1 silenced and control group were collected at  days 4, 7, and 14 after birth in 5 independent replicates.

first: Alfonso

last: Schiavi


title: Genome-wide gene expression responses to experimental manipulation of Saccharomyces cerevisiae Repressor Activator Protein 1 (Rap1) expression level

status: Public on Mar 24 2023

city: Middletown

first: Joseph

last: Coolon

address: 52 Lawn Avenue

department: Biology

institute: Wesleyan University

summary: We analyze genome-wide gene expression response of Saccharomyces cerevisiae to sequential reduction of RAP1 levels.

overall_design: We compared yeast with wildtype RAP1 level with yeast with three levels of decreased RAP1 expression using the TET off system and differing amounts of doxycycline in the growth media.

first: Siddhant

last: Kalra

first: Rubye

last: Peyser

first: Josephine

last: Ho

first: Charlotte

last: Babbin

first: Neil

last: Bohan

first: Alyssa

last: Cortes

first: Jake

last: Erley

first: Manaal

last: Fatima

last: Flinn

first: Emma

last: Horwitz

first: Rachel

last: Hsu

first: Won

last: Lee

first: Vivian

last: Lu

first: Alaa

last: Narsh

first: Donatto

last: Navas

first: Kalu

last: Okoroafor

first: Elizabeth

last: Ouanemalay

first: Sophie

last: Ross

first: Funke

last: Sowole

last: Specht

first: Joshua

last: Woo

first: Kristina

last: Yu


title: The role of ESX-1 on infected and uninfected neutrophils in Mycobacterium marinum infection

city: Lyngby

first: Line

last: Wulff

address: Kemitorvet, Building 204

department: Health Technology

country: Denmark

institute: Technical University of Denmark

summary: Mice were infected with wild type or ESX-1-deficient (deltaRD1) Mycobacterium marinum. 14 days post infection, infected and uninfected neutrophils from the infected tissue were sorted for single cell RNA sequencing analysis.

overall_design: single cell RNA sequencing analysis of infected or bystander (noninfected) neutrophils during M. marinum infection

first: Julia

last: Lienard

last: Munke

first: Clément

last: Da Silva

first: Julien

last: Vandamme

first: Katie

last: Laschanzky

first: Thorsten

last: Joeris

first: William

last: Agace

first: Fredric

last: Carlsson


title: UHMK1 is a splicing regulatory kinase

city: Munich

first: Vanessa

last: Arfelli

state: Bavaria

address: Max-Lebsche-Platz 30

department: Medical Clinic and Polyclinic III

institute: Munich University Hospital, Ludwig-Maximilians University (LMU)

summary: The U2AF Homology Motif Kinase 1 (UHMK1) is the only kinase that contains the U2AF homology motif (UHM), a common protein interaction domain among splicing factors. Through this motif, UHMK1 interacts with the splicing factors SF1 and SF3B1, known to participate in early steps of spliceosome assembly and 3’ splice site recognition. Also, UHMK1 phosphorylates these splicing factors in vitro. Despite that, the involvement of UHMK1 in RNA processing has never been demonstrated. Here, we submitted UHMK1-overexpressing or -depleted NIH3T3 cells RNAseq analysis to evaluate UHMK1 contribution to gene expression and splicing.

overall_design: RNA-seq of UHMK1-overexpressing and -depleted (knockdown) NIH3T3 cells

first: Arfelli

last: Vanessa

first: Bagnoli

middle: W

last: Johannes

first: Kerbs

last: Paul


title: Time-course transcriptome analysis of TF-induced iPSC neurons

status: Public on Mar 23 2023

city: Kawasaki

first: Waka

last: Lin

state: Kanagawa

address: 3-25-22, Tonomachi

institute: Ricoh Company, Ltd.

summary: We report on a comprehensive time-course study of transcription factor (TF)-induced iPSC neurons cultured in vitro through an intrinsic maturation program following neurogenesis. Combining the present RNA-seq study with immunocytochemistry and electrophysiological analyses, we determined the transcriptional and morphological sequences of key developmental events associated with postnatal brain-like transition and spinogenesis. TF-induced iPSC neurons successfully acquired structural and functional synaptic maturity, which will critically expand their utility in modeling higher brain functions and disorders.

overall_design: Comparative gene expression profiling analysis by RNA-Seq of TF-induced iPSC-derived neurons at day 0, 10, 32, 57, and 88 of culture after induction of differentiation.

first: Shusaku

last: Shiomoto

first: Yuichi

last: Eguchi

first: Yudai

last: Kawashima


title: Comparative Gene Expression During Sinoatrial Node and Atrial Development

status: Public on Mar 22 2023

city: Chapel Hill/ 27599

first: Michael

last: Bressan

state: NC

address: 100 Mason Farm Rd

department: Cell Biology and Physiology

institute: University of North Carolina Chapel Hill

summary: To determine pathways activated during sinoatrial node morphogenesis we conducted bulk RNA sequencing on functionally validated tissue preps of embryonic sinoatrial node and atria.

overall_design: Gene expression analysis was preformed on RNAseq data obtained from 3 pooled samples of sinoatrial node tissue and 3 pooled samples of atrial tissue isolated HH stage 30 chick hearts (each sample pool was assembled from ~20 indivudal hearts)

first: Bressan

last: Michael

first: Easterling

last: Marrietta


title: Defining a molecular signature of  breast cancer circulating tumor cells using an in vitro model

city: Silver Spring

first: Julianne

last: Twomey

state: MD

address: 10903 New Hampshire Ave. Building 71-2260

department: CDER/OPQ/OBP

institute: Food and Drug Administration

summary: In this study, we have developed an in vitro model of CTCs by using non-adherent suspension culture. We used this model to study a group of breast cancer cell lines with distinct molecular subtypes (TNBC and ER+/PR+).

overall_design: MCF7 and MB-231 cells were cultured in either a monolayer or a non-adherent suspension culture for seven days at 37°C/ 5% CO2  prior to harvest. One experiment was performed for each culture condition (MCF7-Monolayer (M7M), MCF7-Suspension (M7S), MB-231-Monolayer (M231M), MB-231 Suspension (M231S).


title: Transcriptional changes of adult liver biliary epithelial cells in vivo upon high-fat diet

city: Lausanne

first: Gaby

last: El Alam

state: Vaud

address: Station 15

department: SV LISP

country: Switzerland

institute: École polytechnique fédérale de Lausanne

summary:
Background and Aims: During severe or chronic hepatic injury, biliary epithelial cells (BECs), also known as cholangiocytes, undergo rapid reprogramming and proliferation, a process known as ductular reaction (DR), and allow liver regeneration by differentiating into both functional cholangiocytes and hepatocytes. While DR is a hallmark of chronic liver diseases, including advanced stages of non-alcoholic fatty liver disease (NAFLD), the early events underlying BEC activation are largely unknown. Since NAFLD initiates with increased lipid accumulation, a stage called steatosis; we hypothesized that BECs isolated directly from steatotic livers might address current knowledge gaps in early BEC activation.
Approach and Results: Here, we used methods allowing isolation and extensive transcriptional characterization of BECs from chow diet (CD)- and high-fat diet (HFD)-fed mice livers. We demonstrate that BECs readily accumulate lipids during HFD feeding and that lipid overload induces the conversion of adult cholangiocytes into active BECs through upregulation of the cell cycle and DNA replication signature. This event is accompanied by significant downregulation of extracellular matrix organization in BECs derived from HFD-fed mice livers but not CD-fed mice livers. Mechanistically, we found that lipid overload unleashes the activation of the E2F transcription factors in BECs, which drives cell cycle progression.

overall_design: BECs isolated from 5 healthy livers (CD) and 7 steatotic livers (HFD) by FACS were subjected to RNA seq.

first: Ece

last: Yildiz

first: Kristina

last: Schoonjans


title: Microarray expression data of NCI-H1975 cells treated with osimertinib, alpelisib, or combination of these in the presence or absence of L-histidinol.

city: Koto-ku

first: Hitomi

last: Shirahama

state: Tokyo

address: Ariake 3-8-31

institute: Japanese Foundation for Cancer Research

summary:
Oncogenic signals often activate abnormal proliferation, while simultaneously activate stress-adaptive mechanisms such as the integrated stress response (ISR) to ensure rapid growth under intrinsic and extrinsic stress conditions. In this study, we investigated the involvement of EGFR-PI3K pathway in the regulation of ISR in EGFR-mutant NSCLC cell lines under amino acid deprivation. We found that the third generation EGFR inhibitor osiemrtinib suppressed induction of activation transcription factor 4 (ATF4), the key ISR effector, in EGFR mutant cells, while the effect was to a less extent in cells harboring PIK3CA-co-alteration. PI3K inhibitors including P110a-specific inhibitor alpelicib markedly suppress ATF4 induction in PIK3CA-mutant cell lines. To further explore the role of EGFR-PI3K, transcriptome analysis was performed in EGFR- and PIK3CA-mutated NCI-H1975 cells treated with osimertinib, alpelisib, or combination of these in the absence or presence of histidyl-tRNA inhibitor L-histidinol (His), mimicking amino acid deprived conditions. Among His-induced genes, either osimertinib or alpelisib partially, but the combination dramatically suppressed a cluster of genes targeted by ATF4. Furthermore, combination of osimertinib and alpelisib increased apoptotic cells under amino acid deprived conditions. These results indicate that oncogenic EGFR-PI3K pathway contributes to cellular adaptation to stress conditions through ATF4.
We used microarrays to identify genes whose expression is up- or down-regulated by inhibition of EGFR, PI3K, or both under amino acid deprivation.

overall_design: NCI-H1975 cells were treated with DMSO, osimertinib (10 nM), alpelisib (1 µM), or a combination of these in the presence or absence of L-histidinol (2 mM) for 24 hours.

first: Mizuki

last: Takahashi

first: Yuka

last: Okamoto

first: Yu

last: Kato

first: Satomi

last: Tsukahara

first: Yoshikazu

last: Sugimoto

first: Akihiro

last: Tomida


title: Transcriptomic profles of the ruminal wall in Italian Mediterranean dairy bufaloes fed green forage

status: Public on Mar 21 2023

city: Barcelona

first: Riccardo

last: Aiese Cigliano

address: Calle Comte D'Urgell 240

institute: Sequentia Biotech SL

summary: Feed regimens have a pivotal role in modulating the transcriptional programs that, in turns, have an impact on many biological processes, including metabolism, health and development. Green feed diet in ruminant exerts a beneficial effect on rumen metabolism and enhances the content of health-promoting biomolecules in the milk. However, a comprehensive analysis focused to the identification of genes, and therefore, biological processes modulated by the green feed diet in buffalo rumen has never been reported so far. In this regard, to highlight the impact of the green feed diet on ruminal transcriptomic profiles, we performed RNA-sequencing in buffaloes fed a total mixed ratio (TMR) + the inclusion of 30% of ryegrass green feed (treated group) in comparison with buffaloes fed a dry TMR diet (control group).

overall_design: Comparative gene expression analysis of control and green forage fed animals

first: Angela

last: Salzano

first: Salvatore

last: Fioriniello

first: Nunzia

last: D'Onofrio

first: Maria

last: Balestrieri

first: Gianluca

last: Neglia

first: Floriana

last: Della Ragione

first: Giuseppe

last: Campanile


title: Functional switching of the peritumoral cutaneous Schwann cells in melanoma

city: Pittsburgh

first: Uma

last: Chandran

address: 5607 Baum Blvd.

department: Department of Biomedical Informatics

institute: University of Pittsburgh

summary: We utilize Plp1-CreERT/Rosa26Stopt-tdTomato mice to purify by flow cytometry the peritumoral skin Schwann cells from melanoma-bearing mice, and compare them to skin Schwann cells from tumor-free mice by RNA-sequencing.

overall_design: mRNA profile of purified cutaneous peritumoral Schwann cells from B16F10-bearing Plp1-CreERT/Rosa26Stop-tdTomato mice versus cutaneous Schwann cells from tumor-free mice.

first: Yuri

last: Bunimovich

first: Vishal

last: Soman

first: Kavita

last: Vats


title: Single-cell analysis of shared signatures and transcriptional diversity during zebrafish development

city: Bethesda

first: Jeffrey

middle: Allen

last: Farrell

address: 6 Center Drive (6A/1A06)

department: Division of Developmental Biology

institute: National Institute of Child Health and Human Development

summary: We generated an atlas of 489,686 single-cell transcriptomes from 62 closely spaced developmental stages spanning the first 5 days of zebrafish development, encompassing the first transcriptional events after zygotic genome activation to a freely-swimming, feeding animal.

overall_design: To profile the molecular cell states that occur during wild-type zebrafish development, we generated single-cell transcriptomes from entire wild-type (TL/AB) zebrafish embryos and larvae across 50 closely spaced developmental stages ranging from 14–120 hours post-fertilization (hpf). To capture underrepresented populations and allow robust cluster identification, we sampled heavily every 12 hours; to maintain temporal continuity necessary to investigate gene expression dynamics, we additionally sampled smaller cell numbers every 2 hours (Fig. 1a). In order to profile a large number of cells at an acceptable cost, we employed the cell hashing technique MULTI-seq (McGinnis et al. 2019), which barcodes cells prior to sample collection. Input cell concentrations were then increased, which profiled more cells, but at the cost of increased artefactual cell doublets (where multiple cells are incorrectly identified as ‘one cell’). The MULTI-seq hashing allowed computational identification and removal of doublets, which had multiple barcodes. We mapped reads to the GRCz11 genome, annotated using the Lawson Lab Zebrafish Transcriptome Annotation (v4.3.2) that harmonizes Ensembl and Refseq annotations, includes improved 3’ UTR models, and proposes additional gene models (Lawson et al. 2020). We remapped published single-cell data from wildtype (TL/AB) zebrafish encompassing 3–12 hpf (Farrell et al. 2018) and merged the two datasets to generate a continuous single-cell time-course of 489,686 cells from 62 closely-spaced developmental stages spanning 3 to 120 hpf.

first: Abhinav

last: Sur

first: Yiqun

last: Wang

first: Gennady

last: Margolin


title: Metabolic and transcriptomic signatures of the acute psychological stress response in the mouse brain

status: Public on Mar 20 2023

city: Daejeon

first: Seyun

last: Kim

address: Daehak-ro 291

country: South Korea

institute: KAIST

summary: The acute stress response triggers various physiological responses such as energy mobilization to meet metabolic demands. However, the underlying molecular changes in the brain remain largely obscure. Here, we use a brief water avoidance stress (WAS) to elicit an acute stress response in mice. By employing RNA-sequencing and metabolomics profiling, we investigate the acute stress-induced molecular changes in the mouse whole brain. Aberrant expression of 60 genes was detected in the brain tissues of WAS-exposed mice. Functional analyses showed that the aberrantly expressed genes were enriched in various processes such as superoxide metabolism. In our global metabolomic profiling, total 43 brain metabolites were significantly altered by acute WAS. Metabolic pathways upregulated from WAS-exposed brain tissues relative to control samples included lipolysis, eicosanoid biosynthesis, and endocannabinoid synthesis. Acute WAS also elevated levels of branched-chain amino acids, 5-aminovalerates, 4-hydroxy-nonenal-glutathione, as well as mannose, suggesting complex metabolic changes in the brain. The observed molecular events in the present study provide a valuable resource that can help us better understand how acute psychological stress impacts neural functions.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for one hemisphere of the forebrain tissue of 1 h water avoidance stressed mouse and its control.

first: Haein

last: Lee

first: Jina

last: Park


title: A nutrient information pathway links diet to taste (DNA-Seq II)

city: Ann Arbor

first: Monica

last: Dus

state: Michigan

address: 1105 N University, 4224

institute: University of Michigan

summary: We report the application of targeted DNA Adenine Methyltransferase identification DNA sequencing technology for high-throughput profiling of Pcl occupancy in the Gr5a cells of male Drosophila melanogaster adults. By expressing the UAS-LT3-Dam::Pcl and UAS-LT3-Dam transgene using the Gr5a-GAL4;tubulinGAL80ts driver.

overall_design: 3 replicates from the Gr5a cells  per dietary condition per genotype is obtained using the illumna NextSeq-500 platform

first: Anoumid

last: Vaziri


title: A nutrient information pathway links diet to taste (RNA-Seq)

summary: We report the application of ribosomal profiling based RNA sequencing technology for high-throughput profiling of the Gr5a cells of male Drosophila melanogaster adults. By expressing the UAS-Rpl3-3XFLAG transgene using the Gr5a-GAL4 driver.

overall_design: 2-3 replicates from both the Gr5a and input fraction per dietary condition is obtained using the illumna NextSeq-500 platform. The dietary conditions include control and sugar diet (30% sucrose) supplemented with 10uM OSMI-1.


title: A nutrient information pathway links diet to taste (DNA-Seq I)

summary: We report the application of targeted DNA Adenine Methyltransferase identification DNA sequencing technology for high-throughput profiling of OGT occupancy in the Gr5a cells of male Drosophila melanogaster adults. By expressing the UAS-LT3-Dam::Pcl and UAS-LT3-Dam transgene using the Gr5a-GAL4;tubulinGAL80ts driver.


title: Gene expression and identification of japanese quail embryonic forebrain cells.

city: Haifa

first: Michael

last: Andreyanov

state: Israel

address: Efron 1

department: Medicine

country: Israel

institute: Technion - Israel Institute of Technology

summary: We used single cell RNAseq to identify the populations and identity of cells present in the japanese quail forebrain during its embryonic stages.

overall_design: Japanese quail embryo forebrains were extracted and grown in vitro, from multiple quails onto multiple neuronal culture plates, infected with an AAV expressing YFP. Cultured japanese quail neuronal forebrain cells were collected and analyzed using scRNAseq.

first: Shaden

last: Zoabi

first: Shai

last: Berlin


title: Genome-scale CRISPR screen reveals neddylation to contribute to cisplatin resistance of testicular germ cell tumors II

city: Bonn

first: Kai

last: Funke

state: NRW

address: Venusberg-Campus 1

department: Pathology, Developmental Pathology

institute: University Hospital Bonn

summary: Type II testicular germ cell tumors (TGCT) are the most prevalent tumors in young men. Patients suffering from cisplatin resistant TGCTs are facing very poor prognosis demanding novel therapeutic options. Neddylation is a known posttranslational modification mediating many important biological processes including tumorigenesis. Overactivation of neddylation pathway promotes carcinogenesis and tumor progression in various entities by inducing proteasomal degradation of tumor suppressors (e.g., p21, p27). We used a genome-scale CRISPR/Cas9 activation screen to identify cisplatin resistance factors. TGCT cell lines were treated with the neddylation inhibitor (MLN4924)/cisplatin/combination and investigated for changes in viability (XTT assay), apoptosis/cell cycle (flow cytometry) as well as in the transcriptome (3’mRNA sequencing). NAE1 overexpression was detected in cisplatin resistant colonies from the CRISPR screen. Inhibition of neddylation using MLN4924 increased cisplatin cytotoxicity in TGCT cell lines and sensitized cisplatin resistant cells towards cisplatin. Apoptosis, G2/M-phase cell cycle arrest, gH2A.X/P27 accumulation and mesoderm/endoderm differentiation was observed in TGCT cells while fibroblast cells were unaffected. We identified overactivation of neddylation as a factor for cisplatin resistance in TGCTs and highlighted the additive effect of NAE1 inhibition by MLN4924 in combination with cisplatin as a novel treatment option for TGCTs.

overall_design: A genome scale CRISPR/Cas9 activation screen was performed in the two TGCT cell lines JAR and 2102EP. After cisplatin treatment, surviving cells were recovered and genomic DNA was isolated. The sgRNA encoding regions were amplified with primers connected to illumina adapter sequences. The products were used for next generation sequencing. Total 2 samples with n=1 for each cell line.

first: Ulf

last: Einsfelder

first: Aylin

last: Hansen

first: Lena

last: Arévalo

first: Simon

last: Schneider

first: Daniel

last: Nettersheim

first: Valentin

last: Stein

first: Hubert

last: Schorle


title: Bulk RNA-seq on  CTNNB1 mutation CRISPR-corrected ASD iPSC-derived neural progenitor cells  as well as one matched control iPSC-derived neural progenitor cells to study the effects of autism genetic background

city: Cleveland

first: Shuai

last: Fu

state: OH

address: 10900 Euclid Avenue

department: Department of Genetics and Genome Sciences

institute: Case Western Reserve University

summary: Alterations in cortical neurogenesis are implicated in neurodevelopmental disorders including autism spectrum disorders (ASDs). Many ASD risk genes have been identified as critical for brain development, but the contribution of genetic backgrounds, although inferred in complex genetic disorders such as ASD, remains unclear. Here, using isogenic induced pluripotent stem cell (iPSC)-derived neural progenitor cells (NPCs) and cortical organoid models, we report that a heterozygous PTEN p.I135L mutation found in an ASD patient with macrocephaly dysregulates cortical neurogenesis in an ASD genetic background-dependent fashion. We found that this PTEN p.I135L mutation led to overproduction of NPC subtypes as well as neuronal subtypes including both deep and upper layer neurons in its ASD background, but not when introduced into a control genetic background. ASD and control background differences in neurogenesis, neural development and synapse signaling were also observed. These findings provide experimental evidence that both a PTEN p.I135L mutation and ASD genetic background contribute to cellular features consistent with ASD associated with macrocephaly.

overall_design: We compared  RNA-Seq libraries of neural progenitor cells Arch CTNNB1 WT/WT vs Chap CTNNB1 WT/WT to study the effect of ASD genetic bakcground on gene expression profiles in the neural progenitor cells. Libraries for each genotype include three independent cell culture replicates and three separate passages

first: Anthony

last: Wynshaw-Boris


title: Single cell gene expression profiles for iPSC-derived cortical organoids

overall_design: one control and one CTNNB1 mutation corrected ASD patient iPSC-derived cortical organoids at week 10  were processed and used for scRNA-seq analysis.


title: Single cell gene expression profiles for isogenic PTEN panel iPSC-derived cortical organoids

overall_design: Isogenic PTEN panel cortical organoids at week 10 and week 21 were processed and used for scRNA-seq analysis.


title: DNA methylation analysis of cellular senescence

city: Bologna

first: Paolo

last: Garagnani

state: BO

address: Via San Giacomo 12

department: Department of Medical and Surgical Sciences (DIMEC)

institute: Univeristy of Bologna

summary: The aim of the present study was to provide a comprehensive characterization of whole genome DNA methylation patterns in replicative and ionizing irradiation- or doxorubicin-induced premature senescence, exhaustively exploring epigenetic modifications in three different human cell types: in somatic diploid skin fibroblasts and in bone marrow- and adipose-derived mesenchymal stem cells. With CpG-wise differential analysis three epigenetic signatures were identified: a) cell type- and treatment-specific signature; b) cell type-specific senescence-related signature; and c) cell type-transversal replicative senescence-related signature. Cluster analysis revealed that only replicatively senescent cells created a distinct group reflecting notable alterations in the DNA methylation patterns accompanying this cellular state. Replicative senescence-associated epigenetic changes seemed to be of such an extent that they surpassed interpersonal dissimilarities. Enrichment in pathways linked to the nervous system and involved in the neurological functions was shown after pathway analysis of genes involved in the cell type-transversal replicative senescence-related signature. Although DNA methylation clock analysis provided no statistically significant evidence on epigenetic age acceleration related to senescence, a persistent trend of increased biological age in replicatively senescent cultures of all three cell types was observed. Overall, this work indicates the heterogeneity of senescent cells depending on the tissue of origin and the type of senescence inducer that could be putatively translated to a distinct impact on tissue homeostasis.

overall_design: Bisulphite converted DNA from 48 samples were hybridised to the Illumina Infiniun MethylationEPIC v1.0 BeadChip following manufacture's protocols.

first: Katarzyna

middle: M

last: Kwiatkowska


title: Effect of Notch4 deletion on pancreatic tumorigenesis in mice

city: New York

first: Richard

last: Friedman

state: NY

address: 1130 St. Nicholas Av

institute: Columbia University Irving  Medical Center

summary:
The gene expression of
N4-/-PKC (Notch4 -/-; p16fl/fl;LSL-KrasG12D;p48-Cre) mouse pancreatic tumor cell lines was compared to that of
PKC ( p16fl/fl; LSL-KrasG12D;p48-Cre) mouse pancreatic tumor cell lines

overall_design:
A. PKC mice (n=3)
B. N4-/-PKC mice (n=2)

first: Kiyoshi

last: Saeki

first: Wanglong

last: Qiu

first: Carrie

last: Shawber

first: Jan

last: Kitajewski

first: Jianhua

last: Hu

first: Gloria

middle: H

last: Su


title: Role of the RNA-binding protein ZC3H41 in the regulation of ribosomal protein messenger RNAs in trypanosomes.

city: Armilla

first: Antonio

last: Estevez

state: Granada

address: Avda. del Conocimiento 17

department: Lopez-Neyra

institute: CSIC

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

overall_design: Refer to individual Series


title: Bulk RNA-seq on isogenic PTEN panel iPSC-derived neural progenitor cells to study the effect of ASD specific PTEN mutation and the effects of autism genetic background

overall_design: We compared  RNA-Seq libraries of neural progenitor cells Apex WT/I135L vs Apex WT/WT, Chap WT/I135L vs Chap WT/WT to study the effect of PTEN WT/I135L in either control genetic background or ASD genetic background, we then compared Apex WT/WT vs Chap WT/WT; Apex WT/I135L vs Chap WT/I135L and Apex KO/KO vs Chap KO/KO to study the effect of ASD genetic bakcground with different PTEN genotypes.  Libraries for each genotype include three independent cell culture replicates and three separate passages


title: Expression data from Arabidopsis thaliana mutants and treatments

status: Public on Mar 19 2023

city: Saint Lucia

first: Alicia

middle: May

last: Hellens

state: Queensland

address: Mansfield Place

department: School of Biological Sciences

institute: The University of Queensland

summary:
Plants need to be able to respond to changes quickly due to the inability of a plant to change location. Hormones within the plant signal for these transcriptional changes that will affect the plant's ability to survive. Strigolactone is a plant hormone that was more recently discovered so has a less detailed understanding of what genes it regulates, compared to other plant hormones. First published in Brewer et al 2016, PNAS
We used microarrays to determine transcriptional responses in strigolactone mutants and in wild-type plants with various physiological treatment which affect hormone levels over 24 hours.

overall_design: Two-week old Arabidopsis thaliana plants were either kept intact, decapitated (shoot tip was removed), decapitated and treated with IAA, treated with NPA. Additionally Arabidopsis thaliana plants with mutations in the MAX1, MAX2, or MAX3 gene were profiled. Plant hypocotyls were harvested 24 h after treatment and 120-150 individual hypocotyls were harvested for one biological replicate. Three biological replicates were conducted for each of the seven conditions

first: Tinashe

middle: G

last: Chabikwa

first: Franziska

last: Fichtner

first: Philip

last: Brewer

first: Christine

last: Beveridge


title: Nutrigenomic regulation of sensory plasticity

first: Monica

last: Dus


title: Genome-scale CRISPR screen reveals neddylation to contribute to cisplatin resistance of testicular germ cell tumors

first: Kai

last: Funke

overall_design: Total RNA obtained from cell lines treated for 48 hours with MLN4924 only/cisplatin only/combination (MLN4924 and cisplatin) compared to DMSO/DMF/combination (DMSO and DMF) treated control cells. Total 36 samples with n=3 for each condition.

first: Ulf

last: Einsfelder

first: Aylin

last: Hansen

first: Lena

last: Arévalo

first: Simon

last: Schneider

first: Daniel

last: Nettersheim

first: Valentin

last: Stein

first: Hubert

last: Schorle


title: Adenine Base Editing of Hematopoietic Stem Cells Rescues T-Cell Development for CD3δ Severe Combined Immune Deficiency

city: Los Angeles

first: Gay

last: Crooks

state: CA

address: 610 CHARLES E. YOUNG DRIVE EAST

department: Department of Pathology & Lab Medicine

institute: University of California, Los Angeles (UCLA)

summary: CD3δ SCID is a devastating inborn error of immunity caused by mutations in CD3D, encoding the invariant CD3δ chain of the CD3/TCR complex necessary for normal thymopoiesis. We demonstrate an adenine base editing (ABE) strategy to restore CD3δ in autologous hematopoietic stem and progenitor cells (HSPC). Delivery of mRNA encoding a laboratory-evolved ABE and guide RNA into CD3δ SCID patient’s HSPCs resulted in 71.2±7.85% (n=3) correction of the pathogenic mutation. Edited HSPCs differentiated in artificial thymic organoids produced mature T cells exhibiting diverse TCR repertoires and TCR-dependent functions. Edited human HSPCs transplanted into immunodeficient mice showed 88% reversion of the CD3D defect in human CD34+ cells isolated from mouse bone marrow after 16 weeks, indicating correction of long-term repopulating HSCs. These findings demonstrate preclinical efficacy of ABE in HSPC for the treatment of CD3δ SCID, providing a foundation for the development of a one-time treatment for CD3δ  SCID patients.

overall_design: scRNA-sequencing of HSPC-derived T-lineage

first: Grace

middle: E

last: McAuley

last: Yiu

first: Patrick

last: Chang

first: Gregory

last: Newby

first: Beatriz

last: Campo-Fernandez

first: Sorel

middle: T

last: Fitz-Gibbon

first: Xiaomeng

last: Wu

first: Sung-Hae

last: Kang

first: Amber

last: Garibay

first: Jeffrey

last: Butler

first: Valentina

last: Christian

first: Ryan

last: Wong

first: Kelcee

last: Everette

first: Anthony

last: Azzun

first: Hila

last: Gelfer

first: Christopher

last: Seet

first: Aru

last: Narendran

first: Luis

last: Murguia-Favela

first: Zulema

last: Romero

first: Nicola

last: Wright

first: David

middle: R

last: Liu

first: Donald

middle: B

last: Kohn


title: Transcriptomic study on human skin samples: identification of actinic keratoses two risk classes.

city: Vandœuvre-lès-Nancy

first: Hélène

last: Dubois-Pot-Schneider

address: Site CRAN/Faculté de Médecine - Bâtiment D, 1er étage 9 avenue de la Forêt de Haye, BP 184

department: CRAN

institute: Université de Lorraine - UMR7039 CRAN

summary: Gene expression profile analysis allowed to identify 2 classes of AK.

overall_design: A total of 72 tissue samples (24 NL, 23 L, 4 PL and 21 AK) were isolated from 24 patients. For each patient, samples were acquired on the lesion (L or AK), on the perilesional (PL) i.e. safety surgical margin area (often containing AK) and/or on the non-lesional (NL) parts of the elliptical surgical excision.

first: Marine

last: Amouroux


title: Pleomorphic Variants of Borreliella (syn. Borrelia) burgdorferi Express Evolutionary Distinct Transcriptomes

status: Public on Mar 17 2023

city: Zagreb

first: Tomislav

last: Domazet-Loso

state: Grad Zagreb

address: Bijenička cesta 54

department: Division of Molecular Biology

country: Croatia

institute: Institut Rudjer Bošković

summary: The objective of the study was to uncover the transcriptional differences between B. burgdorferi pleomorphic forms (spirochetes, round bodies, blebs and biofilms).

overall_design: Spirochetes were raised in BSK-H medium containing 6% rabbit serum in conical tubes with a tightly closed lid. Round bodies were gained by resuspending and incubating spirochetes in molecular-biology grade water for 10-30 minutes. Blebs were raised by adding spirochetes into conical tubes with a vented lid. Biofilms were induced by cultivation of spirochetes in tissue-culture dishes. Each sample was represented in three replicates, except the bleb samples which were represented in two replicates.

first: Nina

last: Čorak

first: Sirli

last: Anniko

first: Christina

last: Daschkin-Steinborn

first: Viktoria

last: Krey

first: Sara

last: Koska

first: Momir

last: Futo

first: Tin

last: Široki

first: Innokenty

last: Woichansky

first: Luka

last: Opašić

first: Domagoj

last: Kifer

first: Anja

last: Tušar

first: Horst-Günter

last: Maxeiner

first: Mirjana

last: Domazet-Lošo

first: Carsten

last: Nicolaus


title: HypoSUMOylation in embryonic stem cells generate head-trunk embryo-like structures [ChIP-seq]

city: Paris

first: Yann

last: Loe-Mie

address: 25 rue du Dr Roux

department: Computational Biology

institute: Institut Pasteur

summary: Numerous models of synthetic embryos have recently been established to simulate mammalian development. Two main strategies have been developed to build mouse or human embryo-like structures (ELS): by assembling embryonic and extraembryonic stem cells or by challenging embryonic stem cells (ESCs) with a pulse of WNT agonist. However, both models did not fully recapitulate early organogenesis, particularly the emergence of brain derivatives. SUMOylation was recently identified as a general barrier to cell fate transitions. Here, we show that mouse ESCs exposed to a small-molecule inhibitor of SUMOylation alone generate adherent spheroids which, once in suspension, self-organize in gastrulating structures containing cell types spatially and functionally-related to embryonic and extraembryonic compartments. Alternatively, spheroids cultured in an optimized droplet-microfluidic device form elongated ELS characterized by a multi-axial organization of the body plan reminiscent of natural embryo morphogenesis. Single-cell transcriptomics further revealed various cell types including anterior neuronal cell types, Schwann cell precursors and somites. Mechanistically, transient SUMOylation repression gradually increases the global level of DNA methylation, which in turn represses transcription of Nanog and other pluripotency-associated genes, enhancing cellular plasticity of ESCs. Our morphogen-free protocol constitutes a new facet to study regulative mechanisms of early development by targeting reprogramming roadblocks to shape multicellular architecture.

overall_design: Examination of SUMO-2_3, Kap1 and Zfp57 landscapes in control ES cells (D1) and in ES cells after SUMO recovery (D8), in duplicate, using Illumina Illumina Hiseq 4000.

first: Jack-Christophe

last: Cossec

first: Tatiana

last: Traboulsi


title: NF-κB/p52 augments ETS1 binding genome-wide to promote glioma progression

city: Singapore

first: Yinghui

last: Li

state: Singapore

address: 60 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

summary: Gliomas are among the most invasive and chemo-resistant cancers, making them challenging to treat. Chronic inflammation is one of the key drivers of glioma progression as it promotes the aberrant activation of inflammatory pathways such as NF-κB signalling which drives cancer cell invasion, angiogenesis and tissue remodelling. NF-κB factors typically dimerize with its own family members, but emerging evidence of their promiscuous interactions with other oncogenic factors have been reported to activate the transcription of new target genes and function. Here, we show that non-canonical NF-κB activation directly regulates p52 at the ETS1 promoter to activate its expression. This in turn impacts the genomic and transcriptional landscape of ETS1 in a glioma-specific manner. We further show that enhanced non-canonical NF-κB signalling promotes the co-localization of p52 and ETS1, resulting in the transcriptional activation of non-κB and/or non-ETS glioma-promoting genes. We conclude that p52-induced ETS1 overexpression in glioma cells remodels the genome-wide regulatory network of p52 and ETS1 to transcriptionally drive cancer progression

overall_design:
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for p52 and ETS1 in control and ETS1 knockdown U-87 MG cells, with and without TWEAK stimulation

Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for RNApol2 in control, ETS1 and NFKB2 knockdown U-87 MG cells, with and without TWEAK stimulation

RNA-sequencing on control untreated, control TWEAK treated, ETS1 knockdown TWEAK treated and NFKB2 knockdown TWEAK treated U87-MG cells

first: Nicholas

last: Sim


title: The small and large intestine contain transcriptionally related mesenchymal subsets that derive from embryonic Gli1+ mesothelial cells

city: Lyngby

first: Line

last: Wulff

address: Kemitorvet, Building 204

department: Health Technology

institute: Technical University of Denmark


title: HypoSUMOylation in embryonic stem cells generates head-and-trunk embryo-like structure [ChIP-Seq]

summary: Recent advances in synthetic mammalian embryo models have opened new avenues to understand the complex events controlling lineage decisions and morphogenetic processes occurring during peri-implantation and early organogenesis. Two main strategies have been developed to build embryo-like structures (ELS): by assembling extraembryonic and embryonic stem cells (ESCs) or by subjecting ESCs to various morphogens. Here, we show that mouse ESCs solely exposed to chemical inhibition of SUMOylation, a posttranslational modification which acts as a general barrier to cell-fate transitions, generates early ELSs comprising both anterior neural and trunk-associated regions. HypoSUMOylated ESCs give rise to adherent spheroids which, once in suspension, self-organize into gastrulating structures containing cell types spatially and functionally related to embryonic and extraembryonic compartments. Alternatively, spheroids cultured in an optimized droplet-microfluidic device form elongated structures characterized by a multi-axial organization reminiscent of natural embryo morphogenesis. Single-cell RNA-sequencing further revealed a variety of cellular lineages including properly positioned anterior neuronal cell types, Schwann cell precursors and paraxial mesoderm segmented into somite-like structures. Mechanistically, transient SUMOylation suppression gradually increases DNA methylation genome-wide and repressive marks deposition at Nanog, enhancing ESC plasticity. Our approach provides a proof of principle for a potential new strategy to study early embryogenesis by targeting reprogramming roadblocks to shape multicellular architecture.

overall_design: Examination of 3 different histone modifications and SUMO-1 in ES cells treated or not with the SUMO inhibitor, in duplicate, using Illumina Illumina Hiseq 4000.


title: HypoSUMOylation in embryonic stem cells generates head-and-trunk embryo-like structure [RNA-Seq]

overall_design: mRNA profiles of mouse ES cells treated or not with the inhibitor of SUMOylation were generated by deep sequencing, in duplicate, using Illumina Illumina Hiseq 4000.

last: Loe Mie


title: HypoSUMOylation in embryonic stem cells generates head-and-trunk embryo-like structure [Methyl-seq]

overall_design: Examination of the level of methylation in ES cells treated or not with the SUMO inhibitor, in triplicate, using Illumina Illumina Hiseq 4000.


title: Transcriptomic changes in the mouse brain in response to short-term high-fat metabolic stress

status: Public on Mar 16 2023

first: Seyun

last: Kim

summary: To investigate the transcriptomic changes of brain tissue by short term high fat diet. After 10 days exposing of high fat diet, whole mouse brains were extracted.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NCD and HFD.

first: Kim

last: Seyun

first: Kin

last: Ji Kwang

first: Hong

last: Sehoon

first: Park

last: Jina


title: Single-walled vs. Multi-walled Carbon Nanotubes: Influence of Physico-Chemical Properties on Toxicogenomics Responses in Mouse Lungs

city: Ottawa

first: Sabina

last: Halappanavar

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Healthy Environments and Consumer Safety Branch

country: Canada

institute: Health Canada

summary: Transcriptional profiling of mouse lung tissue comparing control vs exposure to different carbon nanotubes. The aim was to determine if the physico-chemical properties influence the genotoxic, inflammatory and pro-fibrotic responses.

overall_design: Purified and extracted RNA from lung tissue of female mice C57BL/6J BomTac aged 6-7 weeks exposed for 24 hours to different single-walled carbon nanotubes (SWCNTs) or multi-walled carbon nanotubes (MWCNTs) by single intratracheal instillation of 6, 18 or 54 μg/mouse. n= 8 control group, n=5 each dose group.

first: Silvia

last: Solorio-Rodriguez


title: N-acetylcysteine overcomes NF1-loss driven resistance to PI3K alpha inhibition in breast cancer

city: Basel

first: Mohamed

last: Bentires-Alj

address: Hebelstrasse 20

department: DBM

institute: University Hospital Basel

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: HypoSUMOylation in embryonic stem cells generates head-and-trunk embryo-like structure


title: Analysis of LAMPS-induced chromatin accessibility and interactions

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital


title: ATAC-seq analysis of HeLa stable cells expressing LAMPS targeting the HS2 enhancer

summary: We describe that light-activated phase separation at the targeted HS2 enhancer increases chromatin accessibility

overall_design: ATAC-seq was performed to determine chromatin accessibility in HeLa stable cells expressing LAMPS fused with BRD4 or FUSN IDR with blue light illumination for 5min (Light) or without (Dark)

first: YoonJung

first: Yuannyu

last: Zhang


title: ChIP-seq analysis of dCas9 chromatin occupancy in HeLa cells expressing LAMPS

summary: Significant enrichment of dCas9 chromatin occupancy at the targeted HS2 enhancer was observed in cells expressing LAMPS under the dark condition and after blue light illumination.

overall_design: ChIP-seq was performed to determine the chromatin occupancy of biotinylated dCas9 in cells expressing target-specific sgRNAs or no sgRNA control.


title: CAPTURE-3C-seq analysis of locus-specific long-range DNA interactions in HeLa stable cells expressing LAMPS and sgHS2

summary: We demonstrate that LAMPS-mediated LLPS induces the formation of long-range chromatin interactions

overall_design: We combined the chromatin interaction assays (Chromatin Conformation Capture or 3C) with the high affinity dCas9 purification approach to identify locus-associated long-range interactions (CAPTURE-3C-seq).


title: High-throughput single cardiomyocyte transcriptomics identify novel gene programs underlying the normal developmental process of terminal cardiomyocyte differentiation

city: Odense M

first: Ditte

middle: Caroline

last: Andersen

address: Campusvej 55

department: Clinical Research

institute: University of Southern Denmark

summary: It is generally accepted that G2M cell cycle arrest occurs around birth (P3 in mice) as a natural process of cardiomyocyte (CM) terminal differentiation resulting in binucleation/polyploidization that renders the mammalian heart non-regenerative after damage. Mechanisms underlying this postnatal switch in CM proliferation remain unclear. Herein, we developed a novel approach combining fluorescence-activated cell sorting (FACS) with single cell RNA sequencing (scRNA-seq) of fixed CMs and specifically identified transcription factors (TFs) involved in G2M cell cycle completion of mouse CMs.

overall_design: Samples for scRNA-seq were collected at E16.5, P1, and P5 by dissociation of the left ventricle of the heart whereafter fixed cardiomyocytes were selectively enriched and divided into diploid and tetraploid fractions using FACS of fixed cardiac cells.

first: Sara

last: Bak

first: Eva

last: Harvald

first: Mark

last: Burton

first: Mads

last: Thomassen

first: Christina

middle: D

last: Fenger

middle: C


title: Expression of mRNA in  intestinal tissue samples from IBS-D patients and healthy subjects

status: Public on Mar 15 2023

city: zhengzhou

first: Yao

last: Lu

state: henan province

address: 1 Jianshe Dong Lu, Zhengzhou City, Henan Province, China

institute: zhengzhou university

summary: IBS-D is a disease with multi-factor interaction between environment, central system, gut and gene, and its pathogenesis is relatively complex. In order to find the regulation of mRNA in the pathogenesis of IBS-D, intestinal tissue samples of IBS-D patients and healthy subjects were obtained (5 IBS-D patients,5 healthy subjects)， Changes in mRNA expression profiles were detected by high-throughput sequencing.

overall_design: Comparative gene expression profiling analysis of miRNA-seq/mRNA-seq data for Intestinal biopsies from IBS-D patients and healthy subjects

first: Yaoyao

first: Yuna

last: Chai


title: Multiple omics analysis indicated the potential role of miRNAs and target genes in visceral hypersensitivity in IBS-D

summary: IBS-D is a disease with multi-factor interaction between environment, central system, gut and gene, and its pathogenesis is relatively complex. In order to find the regulation of miRNA in the pathogenesis of IBS-D, intestinal tissue samples of IBS-D patients and healthy subjects were obtained (5 IBS-D patients,5 healthy subjects)， Changes in miRNA expression profiles were detected by high-throughput sequencing.


title: Effects of Cinnamomum ramulus (CR) on expression profiles effects of cancer cell lines

status: Public on Mar 13 2023

city: Shenzhen

first: Huang

last: Hsien-Da

address: 2001 Longxiang Boulevard, Longgang District

institute: CUHKSZ

summary: Cinnamomi ramulus (CR) is one of the most widely used traditional Chinese medicine (TCM) with anti-cancer effects. Analyzing transcriptomic responses of different human cell lines to TCM treatment is a promising approach to understand the unbiased mechanism of TCM. This study treated ten cancer cell lines with different CR concentrations, followed by mRNA sequencing.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of 10 different cells lines treated with three CR concentrations (L-low dosage, M-medium dosage, H-high dosage).

first: Jing

last: Li

first: Hsi-Yuan

last: Huang

first: Yang-Chi-Dung

last: Lin

first: Yun

last: Tang


title: RBBP4 regulates pluripotent-to-2C-like state transition through modulating heterochromatin assembly

city: Guangzhou

first: Wang

middle: Fang

last: Ping

state: Guangdong

address: 190 Kaiyuan Avenue

department: Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

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

overall_design: Refer to individual Series


title: BULK RNA SEQ OF HUVEC - NON-TARGETING AND SUN1, STATIC AND FLOW

city: WAUWATOSA

first: ZIQING

last: LIU

state: WI

address: 8701 W Watertown Plank Rd, BSB 5320

department: Biology

institute: Medical College of Wisconsin

summary: The nuclear membrane protein SUN1 promotes blood vessel formation and barrier function by stabilizing endothelial cell-cell junctions. Communication between SUN1 and endothelial cell junctions relies upon proper microtubule dynamics and Rho signaling, revealing long-range cellular communication from the nucleus to the cell periphery that is important for vascular development and function.

overall_design: Comparative gene expression analysis for RNA-seq data for HUVEC exposed to 72h shear stress or static conditions, as well as control and SUN1 KD (siRNA depletion) conditions

first: Danielle

last: Buglak

first: Ariel

last: Gold

first: Molly

last: Kulikauskas

first: Shea

last: Ricketts

first: Allison

last: Marvin

first: Andrew

last: Burciu

first: Natalie

last: Tanke

first: Ziqing

last: Liu

first: Karina

last: Kinghorn

first: Morgan

last: Oatley

first: Bryan

last: Johnson

first: Pauline

last: Bougaran

first: Celia

last: Shiau

first: Stephen

last: Rogers

first: Victoria

last: Bautch


title: RPL3L-containing ribosomes determine translation elongation dynamics required for cardiac function

city: Chikusa-ku, Nagoya, Aichi

first: Kazuya

last: Ichihara

address: Furo-cho

institute: Nagoya University

summary: Although several ribosomal protein (RP) paralogs are expressed in a tissue-specific manner, how these proteins affect translation and why they are required only in certain tissues have remained unclear. Here we show that RPL3L, a paralog of RPL3 specifically expressed in heart and skeletal muscle, influences translation elongation dynamics. Deficiency of RPL3L-containing ribosomes (RPL3L-ribosomes) in RPL3L knockout male mice resulted in impaired cardiac contractility. Ribosome occupancy at mRNA codons was found to be altered in the RPL3L-deficient heart, and the changes were negatively correlated with those observed in myoblasts overexpressing RPL3L. RPL3L-ribosomes were less prone to collisions compared with RPL3-containing canonical ribosomes. Although the loss of RPL3L-ribosomes altered translation elongation dynamics for the entire transcriptome, its effects were most pronounced for transcripts related to cardiac muscle contraction and dilated cardiomyopathy, with the abundance of the encoded proteins being correspondingly decreased. Our results provide new insight into the mechanisms and physiological relevance of tissue-specific translational regulation.

overall_design: Translational dynamics regulated by Rpl3l-containing ribosomes

first: C

last: Shiraishi

first: K

first: A

last: Matsumoto

last: Nakayama


title: Osr1 controls the pro-regenerative response of Fibro-Adipogenic Progenitors

city: Berlin

first: Georgios

last: Kotsaris

address: Thielallee, 63

country: Germany

institute: Freie Universität Berlin

summary:
Purpose: To study the requirement of Osr1 expression for FAP function during skeletal muscle regeneration.
Methods: We sequenced total mRNAs isolated from adult FAPs FACS sorted from 3 and 7 day post injured hindlimb skeletal muscle of Ctrl (Osr1flox/+ CAGG Cre+) and Osr1 cKO (Osr1flox/flox CAGG Cre+) mice.
Results: Loss of Osr1 leads to pro-fibrotic orientation of FAPs and impairs both FAP-macrophage and FAP-MuSCs communication network resulting in impaired regenerative myogenesis and persistent fibrosis.
Conclusions: Osr1 is a key transcriptional regulator of FAP regenerative function protecting FAPs from assuming a detrimental pro-fibrotic and anti-myogenic state.

overall_design: Sequencing was performed on RNAs isolated from adult FAPs FACS sorted from 3 and 7 days post injured hindlimb skeletal muscle of Ctrl (Osr1flox/+ CAGG Cre+) and Osr1 cKO (Osr1flox/flox CAGG Cre+) mice.

first: Sigmar

last: Stricker


title: IFN-gamma signature-driven neoadjuvant domatinostat, nivolumab and ipilimumab in stage III melanoma – the DONIMI trial

city: Amsterdam

first: PETROS

last: DIMITRIADIS

email: p.dimitriadis@nki.nl, d.rao@nki.nl

state: Noord-Holland

address: Plesmanlaan 121

country: Netherlands

institute: NETHERLANDS CANCER INSTITUTE - NKI

summary: Low baseline Interferon gamma (IFNg) response signature is associated with lack of response to neo-adjuvant anti-PD1 + anti-CTLA4 therapy in patients with melanoma. Domatinostat, a class I specific histone deacetylase inhibitor is known to induce IFNg response in patients with advanced stage melanoma. Thus, addition of domatinostat to anti-PD1 + anti-CTLA4 might result in increased response to treatment. However, the effect of this combination therapy on tumor growth has not been evaluated in the pre-clinical setting. We therefore evaluated whether addition of domatinostat results in immune modulation and tumor growth control in the MeVa2.1.dOVA murine melanoma model. We provide pre-clinical evidence to use this combination in melanoma patients.

overall_design: 8-week-old female C57BL/6 mice were injected s.c with MeVa2.1.dOVA cell line in the right flank. When average tumor volume reached 100 mm3, mice were randomized into treatment arms based on tumor volume. Mice received vehicle control, domatinostat, antiPD1 + anti-CTLA4, or  domatinostat + antiPD1 + anti-CTLA4. Domatinostat (20 mg/kg) was administered twice daily via oral gavage. Anti-PD1 (100 ug per mouse) and anti-CTLA4 (50 ug per mouse) were administered two times per week intraperitoneal. Mice were sacrificed after 13 days of treatment and tumors were harvested for RNA seq analysis (n=4 mice per arm were used for RNA seq analysis).

first: Petros

last: Dimitriadis

first: Disha

last: Rao

first: Christian

middle: U

last: Blank


title: Saturating mutagenesis of the GADD45A intron 3 enhancer using STARRseq

status: Public on Mar 12 2023

city: Albany

middle: A

last: Sammons

address: 1400 Washington Ave, Life Sciences 2075

department: Biological Sciences

institute: University at Albany - SUNY

summary: Assessment of individual nucleotide impact on overall GADD45A enhancer activity, dependency on p53 and/or activation through inegrated stress response (ISR).

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Massively parallel reporter assay (MPRA) testing every nucleotide substitution or deletion within the GADD45A intron 3 enhancer

first: Gabriele

last: Baniulyte