title: 4DNESLQDCU1A - Replicate experiments of RNA-seq on RUES2 differentiated to endothelial cell

last: DCIC

address: 10 Shattuck St

institute: 4D Nucleome - Data Coordination and Integration Center

summary: Vascular endothelial cells are a mesoderm-derived lineage with many essential  functions, including angiogenesis and coagulation. The gene-regulatory mechanisms  underpinning endothelial specialization are largely unknown, as are the roles of  chromatin organization in regulating endothelial cell transcription. To  investigate the relationships between chromatin organization and gene expression,  we induced endothelial cell differentiation from human pluripotent stem cells and  performed Hi-C and RNA-sequencing assays at specific time points. Long-range  intrachromosomal contacts increase over the course of differentiation,  accompanied by widespread heteroeuchromatic compartment transitions that are  tightly associated with transcription. Dynamic topologically associating domain  boundaries strengthen and converge on an endothelial cell state, and function to  regulate gene expression. Chromatin pairwise point interactions (DNA loops)  increase in frequency during differentiation and are linked to the expression of  genes essential to vascular biology. Chromatin dynamics guide transcription in  endothelial cell development and promote the divergence of endothelial cells from  cardiomyocytes.

overall_design:
lab: Chuck Murry, UW
award: 1U54DK107979-01
accession: 4DNESLQDCU1A
condition: endothelial cell - day 14
submitted_by: Kris Alavattam
dataset_label: RNA-seq on human iPSCs differentiated to endothelium
contributing_labs: William Noble, UW
experiment_type: RNA-seq
url: https://data.4dnucleome.org/experiment-set-replicates/4DNESLQDCU1A/
number_of_experiments: 2

experiment: 4DNEXCBSYZBN; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXMH7P7QL; replicate_number: Biorep 2, Techrep 1


title: 4DNESVIKXE89 - Replicate experiments of RNA-seq on RUES2 differentiated to endothelial progenitor cell

status: Public on Jan 18 2023

city: Boston

state: MA

country: USA

type: Expression profiling by high throughput sequencing

overall_design:
lab: Chuck Murry, UW
award: 1U54DK107979-01
accession: 4DNESVIKXE89
condition: endothelial progenitor - day 6
submitted_by: Kris Alavattam
dataset_label: RNA-seq on human iPSCs differentiated to endothelium
contributing_labs: William Noble, UW
experiment_type: RNA-seq
url: https://data.4dnucleome.org/experiment-set-replicates/4DNESVIKXE89/
number_of_experiments: 2

experiment: 4DNEX58A4SPS; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXI4ZEEMG; replicate_number: Biorep 2, Techrep 1


title: 4DNESX5HHBRP - Replicate experiments of DNase Hi-C on RUES2 differentiated to mesoderm with DNaseI

overall_design:
lab: Chuck Murry, UW
award: 1U54DK107979-01
accession: 4DNESX5HHBRP
condition: mesoderm - day 2
submitted_by: Kris Alavattam
dataset_label: DNase Hi-C on human iPSCs differentiated to endothelium
contributing_labs: William Noble, UW
experiment_type: DNase Hi-C
url: https://data.4dnucleome.org/experiment-set-replicates/4DNESX5HHBRP/
number_of_experiments: 2

experiment: 4DNEXY9AKMVH; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXAIR7YJB; replicate_number: Biorep 2, Techrep 1

Series supplementary files:
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/3bc27771-c927-4989-97b1-8419cce5a7d1/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFIUM3G3AS.pairs.gz, 4DNFIXBHYYOM.pairs.gz
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-combined
file_format: pairs
file name: 4DNFI2849Y4V.pairs.gz
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/3bc27771-c927-4989-97b1-8419cce5a7d1/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFIUM3G3AS.pairs.gz, 4DNFIXBHYYOM.pairs.gz
description: This is an output file of the Hi-C processing pipeline
file_type: contact matrix
file_format: mcool
file name: 4DNFITDFDM7G.mcool
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/957e0544-7b71-4a34-976f-51a6849f2085/
genome_assembly: GRCh38
derived_from: 4DNFITDFDM7G.mcool
description: Boundaries calls on Hi-C contact matrices
file_type: boundaries
file_format: bed
file name: 4DNFIV6FC82G.bed.gz
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/957e0544-7b71-4a34-976f-51a6849f2085/
genome_assembly: GRCh38
derived_from: 4DNFITDFDM7G.mcool
description: Diamond insulation scores calls on Hi-C contact matrices
file_type: insulation score-diamond
file_format: bw
file name: 4DNFI4ODUZA1.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/8c20d591-6f65-45c7-ae78-5714d7acc9c1/
genome_assembly: GRCh38
derived_from: 4DNFITDFDM7G.mcool, 4DNFI7MCA4R6.bedGraph.gz
description: Compartments signals on Hi-C contact matrices
file_type: compartments
file_format: bw
file name: 4DNFIXYRPAMB.bw


title: 4DNESXR4J4MS - Replicate experiments of RNA-seq on RUES2 differentiated to mesoderm

overall_design:
lab: Chuck Murry, UW
award: 1U54DK107979-01
accession: 4DNESXR4J4MS
condition: mesoderm - day 2
submitted_by: Kris Alavattam
dataset_label: RNA-seq on human iPSCs differentiated to endothelium
contributing_labs: William Noble, UW
experiment_type: RNA-seq
url: https://data.4dnucleome.org/experiment-set-replicates/4DNESXR4J4MS/
number_of_experiments: 2

experiment: 4DNEXNQUX8R8; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXV26Q4OX; replicate_number: Biorep 2, Techrep 1


title: 4DNES6MT2D6K - Replicate experiments of DNase Hi-C on RUES2 differentiated to endothelial progenitor cell with DNaseI

overall_design:
lab: Chuck Murry, UW
award: 1U54DK107979-01
accession: 4DNES6MT2D6K
condition: endothelial progenitor - day 6
submitted_by: Kris Alavattam
dataset_label: DNase Hi-C on human iPSCs differentiated to endothelium
contributing_labs: William Noble, UW
experiment_type: DNase Hi-C
url: https://data.4dnucleome.org/experiment-set-replicates/4DNES6MT2D6K/
number_of_experiments: 2

experiment: 4DNEXMBTNXDO; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEX1G8JPA2; replicate_number: Biorep 2, Techrep 1

Series supplementary files:
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/e5aa930c-3432-4241-afbc-e16825a67abd/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFIA8K6KY2.pairs.gz, 4DNFI1CFBP14.pairs.gz
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-combined
file_format: pairs
file name: 4DNFITUM51JH.pairs.gz
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/e5aa930c-3432-4241-afbc-e16825a67abd/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFIA8K6KY2.pairs.gz, 4DNFI1CFBP14.pairs.gz
description: This is an output file of the Hi-C processing pipeline
file_type: contact matrix
file_format: mcool
file name: 4DNFI3CTXDI2.mcool
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/7ce02156-7855-42b4-99d4-518d05bf3442/
genome_assembly: GRCh38
derived_from: 4DNFI3CTXDI2.mcool
description: Boundaries calls on Hi-C contact matrices
file_type: boundaries
file_format: bed
file name: 4DNFI7TJG9K9.bed.gz
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/7ce02156-7855-42b4-99d4-518d05bf3442/
genome_assembly: GRCh38
derived_from: 4DNFI3CTXDI2.mcool
description: Diamond insulation scores calls on Hi-C contact matrices
file_type: insulation score-diamond
file_format: bw
file name: 4DNFI51TV9E1.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/a3af3d78-fc80-45bd-b01f-3c03e5d3f530/
genome_assembly: GRCh38
derived_from: 4DNFI3CTXDI2.mcool, 4DNFI7MCA4R6.bedGraph.gz
description: Compartments signals on Hi-C contact matrices
file_type: compartments
file_format: bw
file name: 4DNFIYKU74YL.bw


title: 4DNES8R5RDVD - Replicate experiments of DNase Hi-C on RUES2 with DNaseI

overall_design:
lab: Chuck Murry, UW
award: 1U54DK107979-01
accession: 4DNES8R5RDVD
condition: undifferentiated - day 0
submitted_by: Kris Alavattam
dataset_label: DNase Hi-C on human iPSCs differentiated to endothelium
contributing_labs: William Noble, UW
experiment_type: DNase Hi-C
url: https://data.4dnucleome.org/experiment-set-replicates/4DNES8R5RDVD/
number_of_experiments: 2

experiment: 4DNEXGWVDZL5; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEX561P4FA; replicate_number: Biorep 2, Techrep 1

Series supplementary files:
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/c091e2ab-51df-4bfe-aebe-bebc5f79e87e/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFI7DIPZH6.pairs.gz, 4DNFIZU6KA1G.pairs.gz
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-combined
file_format: pairs
file name: 4DNFI9G526S3.pairs.gz
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/c091e2ab-51df-4bfe-aebe-bebc5f79e87e/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFI7DIPZH6.pairs.gz, 4DNFIZU6KA1G.pairs.gz
description: This is an output file of the Hi-C processing pipeline
file_type: contact matrix
file_format: mcool
file name: 4DNFIOML8JZK.mcool
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/7a0376ad-efca-4ac0-b9ae-ec5fba386a87/
genome_assembly: GRCh38
derived_from: 4DNFIOML8JZK.mcool
description: Boundaries calls on Hi-C contact matrices
file_type: boundaries
file_format: bed
file name: 4DNFIGKQQYO6.bed.gz
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/7a0376ad-efca-4ac0-b9ae-ec5fba386a87/
genome_assembly: GRCh38
derived_from: 4DNFIOML8JZK.mcool
description: Diamond insulation scores calls on Hi-C contact matrices
file_type: insulation score-diamond
file_format: bw
file name: 4DNFI6LFESL2.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/0632d35f-9799-4258-a23f-7ca1edefd294/
genome_assembly: GRCh38
derived_from: 4DNFIOML8JZK.mcool, 4DNFI7MCA4R6.bedGraph.gz
description: Compartments signals on Hi-C contact matrices
file_type: compartments
file_format: bw
file name: 4DNFI7QUHGB5.bw


title: 4DNESNTQV8XL - Replicate experiments of RNA-seq on RUES2

overall_design:
lab: Chuck Murry, UW
award: 1U54DK107979-01
accession: 4DNESNTQV8XL
condition: undifferentiated - day 0
submitted_by: Kris Alavattam
dataset_label: RNA-seq on human iPSCs differentiated to endothelium
contributing_labs: William Noble, UW
experiment_type: RNA-seq
url: https://data.4dnucleome.org/experiment-set-replicates/4DNESNTQV8XL/
number_of_experiments: 2

experiment: 4DNEX2Y8O58V; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEX9TQ4UM5; replicate_number: Biorep 2, Techrep 1


title: 4DNES2D4WOKP - Replicate experiments of DNase Hi-C on RUES2 differentiated to endothelial cell with DNaseI

overall_design:
lab: Chuck Murry, UW
award: 1U54DK107979-01
accession: 4DNES2D4WOKP
condition: endothelial cell - day 14
submitted_by: Kris Alavattam
dataset_label: DNase Hi-C on human iPSCs differentiated to endothelium
contributing_labs: William Noble, UW
experiment_type: DNase Hi-C
url: https://data.4dnucleome.org/experiment-set-replicates/4DNES2D4WOKP/
number_of_experiments: 2

experiment: 4DNEXCJ14SGJ; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXT2XYQBB; replicate_number: Biorep 2, Techrep 1

Series supplementary files:
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/519d66c0-5095-462a-9b0c-f4626747903a/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFI9DDJXER.pairs.gz, 4DNFIMKBHA9W.pairs.gz
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-combined
file_format: pairs
file name: 4DNFIPKTDXSP.pairs.gz
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/519d66c0-5095-462a-9b0c-f4626747903a/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFI9DDJXER.pairs.gz, 4DNFIMKBHA9W.pairs.gz
description: This is an output file of the Hi-C processing pipeline
file_type: contact matrix
file_format: mcool
file name: 4DNFIAGGRHEX.mcool
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/8fc3a52b-205c-4aa0-9958-97aaa7b8701f/
genome_assembly: GRCh38
derived_from: 4DNFIAGGRHEX.mcool
description: Boundaries calls on Hi-C contact matrices
file_type: boundaries
file_format: bed
file name: 4DNFI4RWUV7C.bed.gz
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/8fc3a52b-205c-4aa0-9958-97aaa7b8701f/
genome_assembly: GRCh38
derived_from: 4DNFIAGGRHEX.mcool
description: Diamond insulation scores calls on Hi-C contact matrices
file_type: insulation score-diamond
file_format: bw
file name: 4DNFIR1DN1Q3.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/51be66ff-4aa6-4869-b792-6e08ca4acbf2/
genome_assembly: GRCh38
derived_from: 4DNFIAGGRHEX.mcool, 4DNFI7MCA4R6.bedGraph.gz
description: Compartments signals on Hi-C contact matrices
file_type: compartments
file_format: bw
file name: 4DNFIRVPMNWY.bw


title: The microRNomes of Chinese Hamster Ovary (CHO) cells and their extracellular vesicles, and how they respond to osmotic and ammonia stress

city: Newark

first: Jessica

last: Belliveau

state: DE

department: Dept. of Chemical and Biomolecular Engineering

institute: University of Delaware

type: Non-coding RNA profiling by high throughput sequencing

summary: A new area of focus in Chinese Hamster Ovary (CHO) biotechnology is the role of small (exosomes) and large (microvesicles or microparticles) extracellular vesicles (EVs). CHO cells in culture exchange large quantities of proteins and RNA through these EVs, yet the content and role of these EVs remain elusive. MicroRNAs (miRs) are central to adaptive responses to stress and more broadly to changes in culture conditions. Given that EVs are highly enriched in miRs, and that EVs release large quantities of miRs both in vivo and in vitro, EVs and their miR content likely play an important role in adaptive responses. Here we report the miRNA landscape of CHO cells and their EVs under normal culture conditions and under ammonia and osmotic stress. We show that both cells and EVs are highly enriched in five miRs (among over 600 miRs) that make up about half of their total miR content, and that these highly enriched miRs differ significantly between normal and stress culture conditions. Notable is the high enrichment in mir-92a and miR-23a under normal culture conditions, in contrast to the high enrichment in let-7 family miRs (let-7c, let-7b and let-7a) under both stress conditions. The latter suggests a preserved stress-responsive function of the let-7 miR family, one of the most highly preserved miR families across species, where among other functions, let-7 miRs regulate core oncogenes, which, depending on the biological context, may tip the balance between cell cycle arrest and apoptosis. While the expected –based on their profound enrichment – important role of these highly enriched miRs remains to be dissected, our data and analysis constitute an important resource for exploring the role of miRs in cell adaptation as well as for synthetic applications.

overall_design: Examination of small RNA profile of Chinese Hamster Ovary (CHO) cells, microparticles, and exosomes derived from standard and stressed (osmotic and ammonia) cultures via small RNA-Sequencing

first: Belliveau

last: Jessica

first: Papoutsakis

last: ET


title: The HAPSTR2 retrogene buffers stress signaling and resilience in mammals

city: Chicago

first: Marc

last: Mendillo

state: IL

address: 303 E Superior St

institute: Northwestern University

summary: We recently identified HAPSTR1 (C16orf72) as a key component in a novel pathway which regulates the cellular response to molecular stressors, such as DNA damage, nutrient scarcity, and protein misfolding. Here, we identify a functional paralog to HAPSTR1: HAPSTR2. HAPSTR2 formed early in mammalian evolution, via genomic integration of a reverse transcribed HAPSTR1 transcript, and has since been preserved under purifying selection. HAPSTR2, expressed primarily in neural and germline tissues and a subset of cancers, retains established biochemical features of HAPSTR1 to achieve two functions. In normal physiology, HAPSTR2 directly interacts with HAPSTR1, markedly augmenting HAPSTR1 protein stability in a manner independent from HAPSTR1's canonical E3 ligase, HUWE1. Alternatively, in the context of HAPSTR1 loss, HAPSTR2 expression is sufficient to buffer stress signaling and resilience. Thus, we discover a mammalian retrogene which safeguards fitness.

overall_design: Comparative RNA-seq profiling of two cell lines after siRNA knockdown of HAPSTR1 and/or HAPSTR2, with or without overexpression of HAPSTR2

first: Amici

last: David

first: Mendillo

last: Marc


title: Preclinical optimization of a GPC2-targeting CAR T cell therapy for neuroblastoma

city: Bethesda

first: Yingying

last: Cao

address: 9000 Rockville pike

institute: National Institutes of Health

summary: Background: Although most patients with newly diagnosed high-risk neuroblastoma (NB) achieve remission after initial therapy, more than 50% experience late relapses caused by minimal residual disease (MRD) and succumb to their cancer. Therapy strategies to target MRD may benefit these children. We developed a new chimeric antigen receptor (CAR) targeting glypican (GPC)2 and conducted iterative preclinical engineering of the CAR structure to maximize its anti-tumor efficacy before clinical translation.  Methods: We evaluated different GPC2-CAR constructs by measuring the CAR activity against several NB cell lines in vitro. NOD-SCID mice engrafted with human NB cell lines or orthotopic patient-derived xenograft (PDX) and treated with human CAR T cells served as in vivo models. Mechanistic studies were performed using single-cell RNA-sequencing.  Results: Applying stringent in vitro assays and orthotopic in vivo NB models, we demonstrated that our single-chain variable fragment, CT3, integrated into a CAR backbone with a CD28 hinge, CD28 transmembrane, and 4-1BB co-stimulatory domain elicits the best preclinical anti-NB activity compared to other tested CAR constructs. This enhanced activity was associated with an enrichment of CD8+ effector T cells in the tumor-microenvironment and upregulation of several effector molecules such as GNLY, GZMB, ZNF683, and HMGN2. Finally, we also showed that the CT3.28H.BBζ CAR was more potent than a recently clinically tested GD2-targeted CAR to control NB in vivo.   Conclusion: Given the robust preclinical activity of CT3.28H.BBζ, these promising results warrant further clinical testing in children with NB.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 2 donors, 3 GPC2-CAR constructs and one untransduced control. We manufactured the cells and performed single-cell RNA-seq after cell manufacturing. We then injected the cells into tumor-bearing mice and harvested tumors to perform the same analysis on cells from the TME.

first: Ming

last: Sun

first: Carol

middle: J

last: Thiele

first: Rosa

last: Nguyen


title: Effect of STm-delta-aroA on CD4+ T cell activation

city: Birmingham

first: David

last: Bending

address: IBR

department: Institute of Immunology and Immunotherapy

country: United Kingdom

institute: University of Birmingham

summary: The experiment was designed to test how tumour conditoned media from STm-delta-aroA infected tumour organoids would modulate T cell activation. Using splenocytes from Nr4a3-Tocky Great Smart-17A mice, T cells were activated with soluble anti-CD3 and anti-CD28 antibodies. At 4 and 16 h live CD4+ T cells were FACS sorted and RNA extracted. Analysis revealed that T cells exposed to STm-delta-aroA conditioned tumor medium failed to upregulate metabolic pathways associated with canonical T cell activation.

overall_design: Tumour organoids (colonic and small intestinal) derived from APCmin mice were cultured in Matrigel and infected with either an attenuated STm mutant (aroA, containing a deletion in the shikimate pathway) or left non-infected (non-treated) for 2 hours. After 2 hours, the organoids were washed twice with PBS and then re-cultured in fresh media containing gentamicin, in order to kill any extracellular bacteria. Tumours were incubated at 37C for 48hours, after which time the tumour-conditioned media (TCM) was aspirated and pooled. Meanwhile, splenocytes from Nr4a3-Tocky-GS mice were isolated and seeded into a 96-well plate. Splenocytes (1x10^6/well) were cultured in 100ul TCM from non-treated or STm-infected tumours for 4 and 16h, with 1 ug/mL a-CD3 and 5 ug/mL a-CD28 antibodies added to each well to induce T cell activation. Live CD4+ T cells were then FACS-sorted and RNA extracted. Libraries were made using Lexogen's Quant-Seq 3' mRNA FWD UMI kits according to the manufacturer's instructions. Libraries were pooled and sequenced on a NextSeq 500 machine.

first: Alastair

last: Copland

first: Kendle

middle: M

last: Maslowski


title: Fluoropyrimidine-induced cardiotoxicity in colorectal cancer patients

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

summary: Fluoropyrimidines (FP) are the backbone chemotherapy in colorectal cancer (CRC) treatment; however, their use is associated with cardiotoxicity, which is underreported. In the present study, we aimed to prospectively determining the incidence rates and related risk factors of FP-induced cardiotoxicity (FIC) in CRC patients and at identifying predictive biomarkers.  One hundred and twenty-nine consecutive previously untreated CRC patients underwent active cardiological monitoring, including 5-items simplified questionnaire on symptoms, electrocardiogram (ECG) and plasma sample collection during FP chemotherapy. FIC was defined as the presence of ECG alterations and/or the arising of at least one symptom of chest pain, dyspnoea, palpitations or syncope. The primary objective was the evaluation of FIC incidence. Secondary objectives were the correlation of FIC with well-known cardiological risk factors and the identification of circulating biomarkers (serum levels of TnI, proBNP; miRNA analysis) as predictors of FIC.  Twenty out of 129 (15.5%) patients experienced FIC. The most common symptoms were dyspnoea (60%) and chest pain (40%), while only 15% of patients presented ECG alterations, including one acute myocardial infarction. Retreatment with FP was attempted in 90% of patients with a favourable outcome. Despite 48% of patients having cardiological comorbidities, we did not observe an increased FIC in this subgroup. Only the subgroup of females with the habit of alcohol consumption showed an increased risk of FIC. None of the circulating biomarkers evaluated demonstrated a clinical utility as FIC predictors.   FIC can be an unexpected, life-threatening adverse event that can limit the subsequent treatment choices in CRC patients.   In this prospective study, well-known cardiological comorbidities were not related to higher FIC risk and circulating biomarkers predictive of toxicity could not be found. With careful monitoring, mainly based on symptoms, almost all patients completed the FP treatment.

overall_design: Baseline circulating miRNA profiling in the plasma of 8 CRC patients who experienced a cardiovascular event was compared with that of 16 patients without cardiovascular event.

first: Pasquale

last: Lombardi

first: Giacomo

last: Aimar

first: Caterina

last: Peraldo-Neia

first: Alessandro

last: Bonzano

first: Ilaria

last: Depetris

first: Elisabetta

last: Fenocchio

first: Roberto

last: Filippi

first: Virginia

last: Quarà

first: Michela

last: Milanesio

first: Giuliana

last: Cavalloni

first: Loretta

last: Gammaitoni

first: Marco

last: Basiricò

first: Celeste

last: Cagnazzo

first: Giovanna

last: Chiorino

first: Massimo

last: Aglietta

first: Francesco

last: Leone


title: Dynamic chromatin organization and regulatory interactions in human endothelial cell differentiation

last: DCIC

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

overall_design: Refer to individual Series


title: Epigenetic signature of ionizing radiation in therapy-related AML patients

city: Gliwice

first: Agnieszka

last: Cecotka

address: Kozielska, 9/8

department: Department of Data Science and Engineering

country: Poland

institute: Politechnika Śląska

summary: Therapy-related acute myeloid leukaemia (t-AML) is a late adverse effect of previous chemotherapy(ct-AML) and/or radiotherapy (rt-AML) or immunosuppressive treatment. t-AMLs represent ~10-20% of all AML cases, are extremely aggressive and have a poor prognosis in comparison to de novo AML. We hypothesised that in rt-AML, exposure to radiation leads to genome-wide epigenetic modifications. An epigenome-wide association study was conducted, measuring over 850K methylation sites across the whole genome in 14 donors. We focused on 94K sites lying in CpG-rich gene promoter regions. Overall, we found genome-wide hypo-methylation in AML and identified specific genes with promoter hyper-methylation. Additionally, pyrosequencing was used to quantify the methylation in 24 samples. We confirmed that the promoters of the genes MEST and GATA5, both previously reported as tumour suppressors, were specifically hyper-methylated in rt-AML in comparison to control and other subtypes of t-AML. These may represent the epigenetic contribution to rt-AML development at the molecular level and be potential drug targets in rt-AML.

overall_design: Illumina Infinium Human Methylation 450 K array for 12 patients: 5 de novo AMLs, 4 ct-AMLs and 3 rt-AMLs and Illumina Infinium Human Methylation EPIC Array in two batches: 3 de novo AML patients, 3 ct-AML patients and 2 rt-AML patients in the first batch, and 5 healthy donors, 2 de novo AML patients and 1 combined radio- and chemotherapy patient in the second batch.

first: Gráinne

last: O'Brien

first: Kalliopi

middle: N

last: Manola

first: Maria

last: Pagoni

first: Joanna

last: Polanska

first: Christophe

last: Badie


first: Paul

last: Meltzer

address: 9100 Rockville Pike

institute: NCI/NIH

type: Methylation profiling by genome tiling array

summary:
DNA methylation profiles from saliva collected from 89 mothers and 179 adolescent children who received or did not receive perinatal folic acid supplementation
Periconceptional folic acid supplementation and DNA methylation patterns in adolescents

overall_design: Illumina 450K methylation array study

first: Yonghong

last: Wang

first: Joseph

last: Su


title: Epithelial cell diversity in small intestine of pigs

city: Columbia

first: Sathesh

middle: K

last: Sivasankaran

state: MO

address: Bond Life Sciences Center Suite 106, 1201 Rollins Street

institute: University of Missouri

summary: To establish better understanding of specific epithelial cells found across different regions of the small intestine in pigs, we utilized single-cell RNA sequencing (scRNA-seq) to recover and analyze epithelial cells from duodenum, jejunum, and ileum. Cells identified included crypt cells, enterocytes, BEST4 enterocytes, goblet cells, and enteroendocrine (EE) cells. Overall, results provide new information on regional localization and transcriptional profiles of epithelial cells in the pig small intestine.

overall_design: Tissues were collected from 7.5 week old pigs and dissected into sample types: (1) Ileum collected 2-12 inches proximal to the ileocecal valve and divided into areas with Peyer's patches (IPP), (2) Ileum collected 2-12 inches proximal to the ileocecal valve and divided into areas without Peyer's patches (NoPP), (3) Duodenum collected immediately following pylorus (DUOD) and (4) Jejunum collected ~3 feet distal to pylorus (JEJ). Cells were extracted using 10X chrommium protocol, libraries were prepared using Illumina library prep and sequencing using Illumina HiSeq 3000. Sequences used in this study were deposited to the NCBI SRA and can be fount using the identifier PRJNA802582.

first: Jayne

middle: E

last: Wiarda

first: Sage

middle: R

last: Becker

first: Crystal

middle: L

last: Loving


title: Postnatal lung development under the influence of pulmonary hypoperfusion

city: Shanghai

first: Debao

last: Li

address: No. 1678 Dongfang Road, Tangqiao Street

country: China

institute: Shanghai Children's Medical Center

summary: We reported the RNAseq analyses of lungs tissues in neonatal SD rats with or without reduced pulmonary blood flow. Lung hypoperfution was induced by causing the supravalvular pulmonary stenosis through performing pulmonary artery banding surgery within 24 hours postnatally (P1). RNAseq analyses of the upper lobe of the right lung tissues was generated at P7 from 5 sham-operated rats and 4 pulmonary artery banding rats (1 rat dead before sample collection). The results revealed that there were 2666 differentially expressed genes between PAB and sham group at P7, among which 1255 were upregulated and 1411 were downregulated.

overall_design: RNAseq analyses of the upper lobe of the right lungs tissues in PAB and sham-operated neonatal rats.

first: Lijun

last: Chen

first: Lincai

last: Ye

first: Qi

last: Sun


title: Simplifying adipogenic differentiation – a step towards a food compatible media

city: Maastricht

first: Christoph

middle: S

last: Börlin

address: Watermolen 28

country: Netherlands

institute: Mosa Meat

summary: Cultivated meat is a promising technology with the potential to mitigate the ethical and environmental problems associated with traditional meat. Fat plays a key role in meat flavour and texture, however little academic research has focused on fat production resulting in a paucity of adequate adipogenesis protocols for most livestock-derived cells. The development of a suitable protocol is essential to pave the way for cultivated fat as an ingredient, as the traditional cocktail of IBMX, dexamethasone, insulin and rosiglitazone is not food-compatible. Here, we investigate the necessity of these four classic adipogenesis inducers in a serum-containing and an in-house developed serum-free medium (DMAD). Using a full-factorial design, we show that only two of these four inducers, insulin and rosiglitazone, are necessary for adipogenic differentiation, as measured by gene expression changes and lipid accumulation. Additionally, two glucocorticoid receptor binding molecules, progesterone and hydrocortisone, found in DMAD and FBS, are also required. Importantly, this protocol also leads to mature adipocytes in 3D, edible hydrogels. This was demonstrated in both media types and in four species; ruminant and monogastric. We therefore propose this as an alternative protocol for adipogenesis, which, given the replacement of rosiglitazone by a food-compatible PPARγ agonist, can be suitable for human consumption.

overall_design: 3 different MSC isolations from Bos Taurus were differentiated in media where each reduced inducer was taken out or when all of them were present (rDM), after 12 days cells were harvested for sequencing.

first: Rada

last: Mitic

first: Federica

last: Cantoni

first: Mark

last: Post

first: Laura

last: Jackisch


title: Gut microbiota analysis in poorly controlled diabetes patients with latent TB infection (LTBI) and nonLTBI [16S rRNA]

city: Hsinchu

first: Jinn-Moon

last: Yang

address: 75 Po-Ai Street

country: Taiwan

institute: National Chiao Tung University

summary: In previous study, patients with Diabetes Mellitus (DM) have high risk of active TB and LTBI. Here we report and compare 16S rRNA data of DM-LTBI and DM-nonLTBI in gut microbiota to identify differential candidates between the two groups. The results showed the differential genera have potential to predict the LTBI status in patients.

overall_design: Microbial DNA from fecal samples including two groups, DM with LTBI (n=43) and non-LTBI (n=87), were amplified by PCR using V3-V4 primers of bacteria.

first: Hung

last: Huang

first: Yong

middle: C

last: Luo

first: Po

last: Lu

first: Cheng

middle: H

first: Kun

middle: D

last: Lin

first: Meng

last: Lee

last: Cheng

first: Yao

middle: T

last: Yeh

first: Jann

middle: Y

first: Jinn

first: Inn

middle: W

last: Chong


title: DNA-methylation profiling of melanoma metastases

city: Dresden

first: Michael

last: Seifert

address: Fetscherstr. 74

country: Germany

institute: TU Dresden

summary: Genome-wide DNA-methylation profiling of intra- and extracranial melanoma metastases. The goal of the study was to identify differences between methylomes of intra- and extracranial metastases. For each metastasis, FFPE material was used to extract genomic DNA from a punch biopsy of a marked metastasis area. The Illumina Infinium MethylationEPIC array was used for hybridization.

overall_design: The cohort comprises 18 melanoma patients (P[id]). In total, 41 melanoma metastases samples were analyzed: 20 brain metastases samples (B), 8 lung metastases samples (Lun), 6 lymph node metastases samples (Lym), 3 skin metastases samples (Ski), 3 soft tissue metastases samples (Sof), and 1 liver metastasis sample (Liv). In some cases, multiple regions of a metastasis were analyzed, because they showed differences in histology. Such cases are denoted by an additional number at the end of the sample name.

first: Dana

last: Westphal

first: Matthias

last: Meinhardt

first: Christian

last: Kölsche

last: Muders

first: Friedegund

last: Meier

first: Theresa

last: Kraft


title: Mouse BM ILC progenitor subsets

city: Ann Arbor

first: Chang

last: Kim

address: 109 Zina Pitcher

institute: University of Michigan

summary: Scrna-Seq was performed on BM Lin- CD127+ cells

overall_design: Parenchyma and Sinusoid bone marrow Lin- CD127+ cells were stained with Mouse Immune  Single-Cell Multiplexing Kit and loaded onto a BD Rhapsody cartridge. cDNA synthesis was performed using the BD Rhapsody Express Single-Cell Analysis System, and gene expression libraries were prepared using Whole Transcriptome Analysis Amplification Kit (all from BD Biosciences).

first: Qingyang

last: Liu


title: RNAseq profiling of recirculating thymic Tregs in Aire-KO and WT mice

city: Nantes

first: Matthieu

last: Giraud

address: 30 bd Jean Monnet

department: CRTI

country: France

institute: INSERM _ Université de Nantes

summary: Impact of Aire on CCR6+ Treg suppressive properties

overall_design: Total RNA was extracted from CCR6+ Tregs (CCR6+CD4+CD8-CD25+) isolated from thymi of 6 week-old Aire-KO or WT mice. The extracted RNA was used to generate transcriptome libraries using the TruSeq Stranded mRNA kit following the manufacturer's protocols. Single-end (50 bp) sequencing was performed using the Illumina HISeq 2000 machine.

first: Magali

last: Irla


title: The expression patterns of piRNAs in the CA1 region of the transient Global Cerebral Ischemia rats hippocampus

city: Guangzhou

first: Astrame

last: Chen

address: Xinzao town, Panyu district

institute: Guangzhou Medical University

summary:
Purpose:To evaluate the effect of transient Global Cerebral Ischemia(tGCI) with Hypoxic Postconditioning (HPC) on piRNA expression profiles, piRNAs sequencing was performed.
Methods: Total RNA of each sample (n=3 in each group) was prepared using Trizol reagent (Invitrogen), and the RNA quality and integrity were confirmed. 5’- and 3’-Adaptors were ligated to the obtained small RNA. Reverse transcription followed by PCR was used to create cDNA constructs. Subsequently, an about 150 bp fraction corresponding to approximate the adaptor-ligated constructs derived from the 30 nts piRNA fragment was excised and purified. The purified libraries were sequenced on Illumina HiSeq 2000 apparatus. The raw data were refined using cutadapt software (v1.9.1). After filtering out low quality reads and short reads (<15 nts), trimmed reads from all samples were pooled, and piano software was used to predict novel piRNAs. The trimmed reads were aligned to the merged rat piRNA databases (known piRNA from piRNABank plus the newly predicted piRNAs) using Novoalign software (v3.02.12) with at most one mismatch. PiRNA-binding transposon and targets were predicted by miranda software (v3.3a). piRNA-targets networks were plotted by cytoscape software (v2.8.0).
Results:   After tGCI, a total of 5574 piRNAs in CA1 was detected after 26 h of reperfusion. Of those, 12 were significantly upregulated compared with Sham rats (≥1.5-fold change, p<0.05), including 6 novel piRNAs. Of the 12 piRNAs, 4 showed ≥2-fold change. In comparison to tGCI group, 6 piRNAs in CA1 were significantly downregulated after HPC. Interestingly, the piRNAs rno_piR_000618, rno_piR_017990 and rno_piR_014971 were significantly changed in both tGCI and HPC groups
Conclusions: In our study, we identified a cohort of piRNAs in CA1 of rats. Furthermore, we demonstrated directly contrast changes of piRNAs interacted with Piwil2 in CA1 after tGCI, as compared to those in HPC rats. Therefore, this study revealed that PIWI/piRNAs respond to ischemic brain damage and neuroprotection mediated by HPC. To the best of our knowledge, this is the first study ever on piRNAs associated with Piwil2 in cerebral ischemic tolerance.

overall_design: Brain hippocampal piRNA profiles in CA1 region of 7-8 weeks-old adult male Wistar rats（Sham,tGCI and HPC group, three replicates for each group.  ）

first: Lixuan

last: Zhan

first: Meiyan

first: Taoyan

last: Pang

first: Xinyu

last: Li

first: Long

last: Long

first: Donghai

last: Liang

first: Linhui

last: Peng

first: Weiwen

last: Sun

first: En

last: Xu


title: The piRNAs bounding to Piwil2 in the CA1 region of the transient Global Cerebral Ischemia rats hippocampus

summary:
Purpose：To identify piRNAs bound to Piwil2 in Sham,transient Global Cerebral Ischemia(tGCI) and transient Global Cerebral Ischemia(tGCI) with Hypoxic Postconditioning (HPC).
Methods: Samples from CA1 subregion were lysed in 500 μl lysis buffer and centrifuged. After centrifugation, supernatant was incubated with monoclonal mouse antibody against Piwil2 (Santa Cruz, California, CA, USA), preincubated with Protein A/G Agarose. The beads were washed twice with lysis buffer. After quality check by Western blot, the RNA was extracted from the magnetic beads using Trizol reagent (Invitrogen). Then, the immunoprecipitated RNA was analyzed with piRNAs sequencing.
Results: After tGCI, a total of 423 piRNAs interacted with Piwil2 in CA1 was upregulated after 26 h of reperfusion. Of the 423 piRNAs, 317 were significantly upregulated by more than 1.5-fold. Of the 317 piRNAs, 258 showed ≥2-fold change.  Comparison between tGCI and HPC groups revealed that 401 piRNAs interacted with Piwil2 in CA1 were significantly downregulated after HPC, whereas only 7 piRNAs were found to be altered in all 3 groups studied (≥1.5-fold change).
Conclusions: In our study, we identified a cohort of piRNAs in CA1 of rats. We demonstrated directly contrast changes of piRNAs interacted with Piwil2 in CA1 after tGCI, as compared to those in HPC rats. The results of the prediction showed that DNMT3A may be a potential common target of the 7 differentially expressed piRNAs interacted with Piwil2. Therefore, we focused on the expression of DNMT3A in CA1 after tGCI with or without HPC.


title: EKLF/Klf1 regulates erythroid transcription by its pioneering activity and selective control of RNA Pol II pause-release

city: New York

first: Kaustav

last: Mukherjee

state: NY

address: 1 Gustave Levy Place

department: Cell, Developmental and Regenerative Biology

institute: Icahn School of Medicine at Mount Sinai

type: Genome binding/occupancy profiling by high throughput sequencing

summary: EKLF/Klf1 is a Zinc-finger transcription activator essential for erythroid lineage commitment and terminal differentiation. Using ChIP-Seq, we investigate EKLF DNA binding and transcription activation mechanisms during mouse embryonic erythropoiesis. Our study focuses on global EKLF binding dynamics during embryonic erythropoiesis in primary WT and Nan/+ mouse fetal liver, and its correlation with chromatin accessibility, CBP occupancy, histone acetylation, and finally its effect on RNA Polymerase II pausing and elongation. Our goal is to elucidate the mechanisms of transcription activation by EKLF/Klf1 during embryonic erythropoiesis in vivo and in the context of RNA pol II pause-release control. Additionally, we aim to understand the unusually severe effects of conservative E to D change in Nan-EKLF and the molecular mechanisms leading to dominant anemia through global gene dysregulation.

overall_design: Chromatin Immunoprecipitation and NGS (ChIP-seq) for EKLF/Klf1, CBP, H3K27ac, RNA Polymerase II C-terminal domain phospho-Serine5, RNA Polymerase II C-terminal domain phospho-Serine2, ATAC-Seq in mouse E13.5 fetal liver from WT and Nan/+ embryos. All ChIPs except RNA Pol II are biological triplicates from littermate fetal livers. RNA Pol II was performed in duplicate for each experiment. ATAC-Seq was performed in biological duplicates

first: James

last: Bieker


title: RBM4 regulates lung cancer progression

city: Dalian

first: Wang

last: Yang

address: 9 Lvshun South Rd West Section, Lüshunkou District, Dalian, Liaoning, China

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

summary: In order to profile the transcription events that were regulated by RBM4, mRNA-seq was performed on A549_shRBM4 and A549_ctl which based on A549 cells , H1299_shRBM4 and H1299_ctl  which based on H1299 cells

overall_design: This study includes a total of 4 profiling samples, A549_shRBM4 and H1299_shRBM4 were generated as  RBM4 knocked down lung cancer cells . A549_ctl and H1299_ctl was generated as a control lung cancer cells .

first: Zhang

last: Wenjing


title: Multi-stage expression in BBN mouse model reveals progression-associated molecular changes in basal/squamous and sarcomatoid bladder carcinogenesis

city: paris

first: Elodie

last: chapeaublanc

address: 26 rue d'ulm

department: UMR 144

institute: Institut Curie

summary: RNA-seq data of microdissected lesions occurring in C57BL/6 male mice treated with N-butyl-N-(4-hydroxybutyl)-nitrosamine (BBN) and normal control urothelium from untreated mice.

overall_design: RNA-sequencing of 37 microdissected samples, including 29 lesions from 27 BBN-exposed mice representative of all stages of carcinogenesis - hyperplasia (n=4), dysplasia (n=5), CIS (n=3), pTa (n=5), pT1 (n=7), MIBC (n=5) - as well as 3 BBN-exposed urothelia of normal morphology (adjacent to hyperplasia) and 5 unexposed control urothelia.

first: Jacqueline

last: Fontugne

first: Yves

last: Allory

first: François

last: Radvanyi

first: Isabelle

last: Bernard-Pierrot

last: Chapeaublanc


title: Dynamic 3D Genome and Epigenetic Landscapes of Macrophage Cells Reprogramming Gene Expression during Differentiation and Infection (ATAC-Seq)

city: Wuhan

first: Ping

last: Hong

state: Hubei

address: No.1,Shizishan Street

department: college of informatics

institute: Huazhong Agricultural University

summary: Next Generation Sequencing data of ATAC-Seq library of Thp1-mono, Thp1-macro, and Thp1-M.tb

overall_design: We constructed ATAC-Seq library of 3 samples (Thp1-mono, Thp1-macro, and Thp1-M.tb), and for each sample we did 2 replicates

first: Da

last: Lin


title: Dynamic 3D Genome and Epigenetic Landscapes of Macrophage Cells Reprogramming Gene Expression during Differentiation and Infection


title: Dynamic 3D Genome and Epigenetic Landscapes of Macrophage Cells Reprogramming Gene Expression during Differentiation and Infection (RNA-Seq)

summary: Next Generation Sequencing data of RNA-seq library of Thp1-mono, Thp1-macro, and Thp1-M.tb

overall_design: We constructed RNA-seq library of 3 samples (Thp1-mono, Thp1-macro, and Thp1-M.tb), and for each sample we did 2 replicates


title: Dynamic 3D Genome and Epigenetic Landscapes of Macrophage Cells Reprogramming Gene Expression during Differentiation and Infection (ChIP-Seq)

summary: Next Generation Sequencing data of ChIP-seq library of Thp1-mono, Thp1-macro, and Thp1-M.tb

overall_design: We constructed ChIP-seq library of 3 samples (Thp1-mono, Thp1-macro, and Thp1-M.tb), and for each sample we did 2 replicates


title: Noncoding RNA and mRNA expression data from human colorectal cancer tissues and adjacent non-cancerous tissues

city: Zhengzhou

first: Zhenqiang

address: No 1, Jianshe Road

institute: The First Affiliated Hospital of Zhengzhou University

summary: Total RNA from 6 pairs colorectal cancer tissues and its matched adjacent non-cancerous tissues was extracted and sequenced by high throughput sequencing. Then, differentially expressed circRNAs, long noncoding RNAs, and mRNAs were showed in colorectal cancer.

overall_design: Tumors from 6 pairs colorectal cancer tissues and its matched adjacent non-cancerous tissues were used. We aimed to study the noncoding RNA role in colorectal cancer progression using high-throughput sequencing

first: Chen

last: Chen


title: In vivo CRISPR screening unveils RNA binding protein dependencies for leukemic stem cells and identifies ELAVL1 as a potential therapeutic target [eCLIPseq]

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: RNA binding protein (RBP)-directed post-transcriptional control of stem cell fate represents an underexplored mechanism driving hematopoietic stemness and transformation. We show that a unique set of RBPs are specifically enriched in leukemic stem cells (LSCs) of human primary acute myeloid leukemia (AML) but repressed in normal hematopoietic stem cells. Using an in vivo CRISPR-Cas9-mediated screening approach, we identify 33 key RBPs specifically essential for LSC-mediated MLL-AF9/NrasG12D AML. Knock-down/genetic ablation of the hit RBP Elavl1 in genetically distinct leukemias significantly reduced LSC numbers, and hampered leukemic engraftment. In human AML we show impairment of LSC-driven in vivo leukemic reconstitution and selective depletion of AML progenitors upon ELAVL1 targeting, highlighting the potential clinical importance of our findings. Profiling of the leukemic ELAVL1-mRNA interactome revealed hematopoietic differentiation, RNA splicing and mitochondrial metabolism as major pathways impacted by ELAVL1. Altogether, this work demonstrates that Elavl1 and other RBPs are critical regulators of LSC-survival and self-renewal.

overall_design: 2x IP, 2x input control

first: Laura

middle: P

last: de Rooij

first: Ana

last: Vujovic

first: Sampath

last: Loganathan

first: Brian

last: Yee

first: Ava

last: Chahi

first: Derek

last: Chan

first: Amanda

last: Tajik

first: Sasan

last: Zandi

first: Nicholas

last: Wong

first: Stefan

last: Aigner

first: John

last: Dick

first: Mark

last: Minden

first: Daniel

last: Schramek

first: Kristin

last: Hope


title: A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung [ST]

status: Public on Jan 17 2023

city: Solna

first: Paulo

last: Czarnewski

address: Tomtebodavägen 23b

country: Sweden

institute: KTH

summary: The lung contains numerous specialized cell-types with distinct roles in tissue function and integrity. To clarify the origins and mechanisms generating cell heterogeneity, we created a comprehensive topographic atlas of early human lung development. Here, we report 83 cell states, several spatially-resolved developmental trajectories and predict cell interactions within defined tissue niches. We integrated scRNA-Seq and spatially resolved transcriptomics into a web-based, open platform for interactive exploration. We show distinct gene expression programs, accompanying sequential events of cell differentiation and maturation of the secretory and neuroendocrine cell-types in proximal epithelium. We define the origin of airway fibroblasts associated with airway smooth muscle in bronchovascular bundles and describe a trajectory of Schwann cell progenitors to intrinsic parasympathetic neurons controlling bronchoconstriction. Our atlas provides a rich resource for further research and a reference for defining deviations from homeostatic and repair mechanisms leading to pulmonary diseases.

overall_design:
One of the two lungs (preferentially the left), from each donor, was snap frozen in cryomatrix and further used for histological analyses. We cut 10-12μm-thick tissue sections with a cryostat (Leica CM3050S or analogue) and collected them onto poly-lysine coated slides (VWR Cat No. 631-0107)
NOTE FROM SUBMITTER: raw reads from our cohort are considered sensate and protected by GDPR regulations, and will therefore be uploaded to Swedish federated EGA.

first: Marco

last: Sergio

first: Sountoulidis

last: Alexandros

first: Czarnewski

last: Paulo

first: Samakovlis

last: Christos


title: TGFβ1-Induced EMT in the MCF10A Mammary Epithelial Cell Line Model Is Executed Independently of SNAIL1 and ZEB1 but Relies on JUNB-Coordinated Transcriptional Regulation

city: Freiburg

first: Andreas

last: Hecht

address: Stefan-Meier-Str. 17

institute: Albert-Ludwigs-Universität Freiburg

summary: Epithelial-mesenchymal transition (EMT) fosters cancer cell invasion and metastasis, the main cause of cancer-related mortality. Growing evidence that SNAIL and ZEB transcription factors, typically portrayed as master regulators of EMT, may be dispensable for this process, led us to re-investigate its mechanistic underpinnings. For this, we used an unbiased computational ap-proach that integrated time-resolved analyses of chromatin structure and differential gene ex-pression, to predict transcriptional regulators of TGFβ1-inducible EMT in the MCF10A mam-mary epithelial cell line model. Bioinformatic analyses indicated comparatively minor contri-butions of SNAIL proteins and ZEB1 to TGFβ1-induced EMT, whereas the AP-1 subunit JUNB was anticipated to have a much larger impact. CRISPR/Cas9-mediated loss-of-function studies confirmed that TGFβ1-induced EMT proceeded independently of SNAIL proteins and ZEB1. In contrast, JUNB was necessary and sufficient for EMT in MCF10A cells, but not in A549 lung can-cer cells, indicating cell-type-specificity of JUNB EMT-regulatory capacity. Nonetheless, the JUNB-dependence of EMT-associated transcriptional reprogramming in MCF10A cells allowed to define a gene expression signature which was regulated by TGFβ1 in diverse cellular back-grounds, showed positively correlated expression with TGFβ signaling in multiple cancer tran-scriptomes, and was predictive of patient survival in several cancer types. Altogether, our find-ings provide novel mechanistic insights into the context-dependent control of TGFβ1-driven EMT and thereby may lead to improved diagnostic and therapeutic options.

overall_design: Assay for transposase-accessible chromatin using sequencing (ATAC-seq) performed on MCF10A cells treated with TGF-beta1 or solvent for different time periods

first: Pablo

last: Antón-García

first: Elham

middle: B

last: Haghighi

first: Katja

last: Rose

first: Georg

last: Vladimirov

first: Melanie

last: Boerries


title: Dynamic 3D Genome and Epigenetic Landscapes of Macrophage Cells Reprogramming Gene Expression during Differentiation and Infection (DLO Hi-C)

first: Ping

last: Hong

summary: Next generation sequencing data of in situ DLO Hi-C library of Thp1-mono, Thp1-macro, and Thp1-M.tb

overall_design: We constructed in situ DLO Hi-C library of 3 samples (Thp1-mono, Thp1-macro, and Thp1-M.tb), and for each sample we did 4 replicates

first: Da

last: Lin


title: In vivo CRISPR screening unveils RNA binding protein dependencies for leukemic stem cells and identifies ELAVL1 as a potential therapeutic target [RNA-seq]

first: Gene

last: Yeo

overall_design: 2x sgNTC, 2x sgELAVL1; Cells were transduced with lentiviral-packaged sgRNA targeting Elavl1 and, as control, Ano9. 72 hours following transduction live 7AAD- GFP+ cells were isolated.

first: Laura

last: de Rooij

first: Ana

last: Vujovic

first: Sampath

last: Loganathan

first: Brian

middle: A

last: Yee

first: Ava

last: Chahi

first: Derek

last: Chan

first: Amanda

last: Tajik

first: Sasan

last: Zandi

first: Nicholas

last: Wong

first: Stefan

last: Aigner

first: John

last: Dick


title: A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung

first: Paulo

last: Czarnewski

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

overall_design: Refer to individual Series


title: Bulk RNA-seq libraries of WT and Batf2KO HSCs with 1-mon M.avium infection

city: Houston

first: Duy

middle: Tri

last: Le

state: Texas

address: 1102 Bates Ave

department: Pediatrics

institute: Baylor College of Medicine

summary:
Purpose: To define the mechanism underlying BAFT2-driven HSC depletion during chronic infection, we performed RNA sequencing (RNA-seq) analysis of WT and Batf2 KO HSCs in the presence and absence of M. avium infection
Methods: 10,000-50,000 HSCs (CD45.1/CD45.2 KL CD150+ CD48- CD34-) into HBSS from naive or 1-month infected WT abd Batf2KO mice (n=10-12 per group). DNA and RNA were isolated with the RNeasy Kit (Qiagen, Cat#74004). RNA-seq libraries were prepared using SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara Bio Usa). Illumina NovaSeq SP was used for sequencing with a paired-end sequencing length of 10bp. Samples were sequenced at Admera Health using an Illumina HiSeq 2x150 at sequencing depth of ~40 million reads. FASTQ files were preprocessed using HTS stream (https://github.com/ibest/HTStream) and the clean FASTQ file were aligned using STAR. Differential expression (DE) analysis of gene expression was performed using Limma-Voom. False discovery rate (FDR)<0.05 was considered statistically significant. Further analysis was completed using Illumina Basespace packages and programs (deSeq2) We performed gene ontology analysis for differentially expressed genes with q value of <0.05. Gene set enrichment analysis (GSEA, Broad Institute and UC San Diego) was completed using normalized gene counts as previously described ((Subramanian et al., 2005). Results were visualized using Tidyverse packages in R. Comparison of differentially expressed gene lists and generation of Venn diagrams were generated using the GeneVenn webtool. Biological process and molecular function gene ontology analysis of differentially expressed genes found in bulk RNA-seq datasets were completed using GENEONTOLOGY of the Mus musculus database (Ashburner et al., 2000; Gene Ontology, 2021).
Results: Infection significantly stimulated the expression of inflammatory response pathways (Figure 6A-C) as well as similar induction of common IFNγ-regulated genes such as Stat1 and Stat2 (Figure 6D). Interestingly, we found an increased number of IFN response genes were upregulated during M. avium infection in WT but not Batf2 KO HSC, including Stat3, Mx2, Bst2, Ifi35, and Ifngr2 (Figure 6D and S5C), and the overall degree of induction of all IFN response genes was higher in the WT compared to Batf2 KO.
Conclusion: BATF2 amplifies pro-inflammatory signaling pathways in HSCs during chronic infection

overall_design: Comparison of transcriptomic profiles of WT and Batf2KO HSCs in chronic bacterial infection to further understand the role of BATF2 in HSCs function

first: Bailee

last: Kain

first: Pawel

last: Kus

first: Katherine

last: King


title: Single-cell Transcriptome Analyses Reveal Unique Microglia Types Associated with Retinal Pathological Angiogenesis

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

summary: We used single cell RNA-seq to comprehensively map all retinal microglia populations in a mouse model of oxygen-induced PR. We unveiled several unique types of PR-associated microglia (PRAM) and identified markers, signaling pathways, and regulons associated with these cells. Among these microglial subpopulations, we found a highly proliferative subset of cells with a high self-renewal capacity and a subset of cells with hypermetabolism that expresses high levels of activating microglia markers, glycolytic enzymes, and pro-angiogenic insulin-like growth factor 1. Immunohistochemical staining shows that PRAMs were spatially located within neovascular tufts. These unique microglial subtypes have the potential to promote retinal angiogenesis, which may have important implications for the future treatment of PR and other ocular diseases characterized by pathological angiogenesis.

overall_design: The objective of this study was to investigate heterogeneity of mononuclear phagocytes (MPs) recruited to areas of neovascularization that drive aberrant retinal angiogenesis in proliferative retinopathies (PRs). We first generated a mouse model of oxygen-induced retinopathy (OIR). We collected retinas from OIR mice and control room air (RA) mice. We sorted out F4/80 and CD11b positive cells and performed scRNAseq of these cells. We identified two unique PR-associated microglia (PRAM) subtypes. We analyzed detailed gene signatures, signaling pathways, transcription factor regulons, transcriptional dynamics, and metabolic characteristics in PRAM. Further we unraveled the spatial location of PRAM adjacent to pathological neovascularization tufts by immunostaining mouse whole mounts of retinas with fluorescent antibodies. Collectively, our study provides a comprehensive perspective that defines the contributions of retinal microglia to PR at the single-cell level.

first: Zhiping

last: Liu

first: Yuqing

last: Huo


title: Transcriptional and Epigenetic profiling of Batf2 -/- mice in chronic infection


title: Single-Cell RNA-Seq analysis of diabetic wound CD45+ cells in STZ-induced mice

city: Jinan

first: Yibing

last: Wang

address: Jingshi road

institute: The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital

summary: The crucial role of immune cells in the healing of chronic diabetic wounds is widely known, but previous in vitro classification and marker genes of immune cells may not be fully applicable to cells in the microenvironment of chronic wounds. The heterogeneity of immune cells was studied and classified at the single-cell level in a chronic wound model. We performed single-cell sequencing of CD45+ immune cells within the wound edge and obtained 17 clusters of cells, including 4 clusters of macrophages. This project has provided an important reference for the study of immune-related mechanisms in diabetic chronic wounds.

overall_design: STZ-induced C57Bl6j mice diabetic wound and control wound CD45+ cells.Single cell RNA sequencing was performed with 10XGenomics.


title: Investigation of the effects of Dsi-RNA-loaded lipid nanoparticles on whole liver tissue

city: Aachen

first: Matthias

last: Bartneck

address: Pauwelsstraße 30

department: Internal medicine III

institute: University Hospital Aachen

summary: The response of the liver tissue towards the injection of the lipid nanoparticles with Dsi-RNA was studied.

overall_design: Injection of an inhibitor (where indicated), after 24 hours injection of lipid nanoparticles and after another 24 hours mice were killed for final analysis.

first: Cheng

last: Lin


title: Epigenomics of metabolic organs from in vitro or in vivo-produced dairy male calves

city: Utrecht

first: Maria

middle: Belen

last: Rabaglino

address: Yalelaan 7

department: Population Health Science

institute: Utrecht University

type: Methylation profiling by high throughput sequencing

summary: In cattle, two of the most common technologies for embryo production are “in vivo”, after multiple ovulation and embryo transfer (MOET), or “in vitro” (IVP). IVP can sometimes impact fetal growth, resulting in large offspring, although most IVP calves are born apparently healthy. However, gene regulation changes in the organs involved in the developmental process in phenotypically normal postnatal calves are unknown and could indicate physiological programming. The objective was to compare the epigenomic and transcriptomic modifications in the liver, muscle, and organs of the hypothalamus-pituitary-gonadal and adrenal (HPGA) axes between IVP and MOET male calves of three months of age. Pregnancies were monitored until delivery. Male calves were maintained in similar conditions during the postnatal period until euthanasia at around 100 days of age. There were no differences regarding body weight at birth and growth rate among the animals in both groups at this age.

overall_design: Samples were obtained from the liver, muscle, hypothalamus, pituitary, testicle and adrenal from three-month-old IVP calves (n=4) and control MOET calves (n=4).

first: Jan

last: Bojsen-Møller Secher

first: Marc-Andre

last: Sirad

first: Poul

last: Hyttel

first: Haja

last: Kadarmideen


first: Andreas

last: Hecht

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MCF10A cells treated with TGF-beta1 or solvent for different time periods.

first: Pablo

last: Antón-García

first: Elham

last: Bavafaye Haghighi

first: Katja

last: Rose

first: Georg

last: Vladimirov

first: Melanie

last: Boerries


overall_design: Comparative gene expression profiling analysis of RNA-seq data for MCF10A cells with wild-type or inactivated JUNB genes and treated with TGF-beta1 or solvent for different time periods.


title: The effect of signal inhibitors on human induced pluripotent stem cells in suspension culture conditions

city: Tsukuba

first: Yohei

last: Hayashi

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Research Center

country: Japan

institute: RIKEN

summary:
To examine the effect of the effects of PKCbeta and Wnt inhibitors on global gene expression of iPSCs in suspension conditions, RNA-seq experiments were performed.
Total RNA was extracted with a FastGene RNA premium kit (Nippon Genetics, Co., Ltd, Tokyo, Japan) and strand-specific library preparation was performed. The prepared library was sequenced by a NovaSeq6000 (Illumina, Inc, CA, USA). Sequencing was performed in a 150 bp x2 paired-end configuration with a data output of about 6 Gb per sample (equivalent to about 20 million paired reads). Library preparation and its sequencing were performed in GENEWIZ (Azenta, MA, USA). The sequencing data were analyzed with a CLC Genomics Workbench (QIAGEN, Hulsterweg, the Neterlands) and the R package edgeR (v3.30.3) to identify differentially regulated genes.

overall_design: RNA-seq data from each conditions (n=3)


title: Single-cell atlas of mouse limb development reveals that the skeleton forms nonconsecutively by progressive differentiation of Msx1+ naïve progenitors

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Limb development has long served as a model system for studying how a pool of progenitor cells undergoes coordinated spatial patterning and differentiation to produce complex and well-organized structures. Here, we identify a population of naïve-state limb progenitors and show that they differentiate progressively to form the skeleton in a complex nonconsecutive three-dimensional pattern.   First, by performing single-cell RNA sequencing of the developing mouse forelimb we created an atlas of cellular compositions and transcriptional states. This atlas revealed three progenitor states: naïve, proximal and autopodial, as well as Msx1 as a marker for the naïve progenitors. In vivo lineage tracing analysis firmly established this role of Msx1 and localized the naïve progenitors to the outer margin of the developing limb, along the anterior-posterior axis. Sequential pulse-chase experiments showed that Msx1 naïve progenitors undergo progressive and simultaneous transition into both proximal and autopodial progenitors and then to Sox9+ chondroprogenitors.   Interestingly, the progressive differentiation to chondroprogenitors occurred along all the skeletal segments concurrently, suggesting that skeleton form in a nonconsecutive way. Indeed, by tracking the spatiotemporal sequence of naïve progenitor differentiation, we found that the skeleton forms in a complex nonconsecutive three-dimensional pattern. Overall, these findings propose a new model for limb skeleton development.   Limb development has long served as a model system for studying how a pool of progenitor cells undergoes coordinated spatial patterning and differentiation to produce complex and well-organized structures. Here, we identify a population of naïve-state limb progenitors and show that they differentiate progressively to form the skeleton in a complex nonconsecutive three-dimensional pattern.   First, by performing single-cell RNA sequencing of the developing mouse forelimb we created an atlas of cellular compositions and transcriptional states. This atlas revealed three progenitor states: naïve, proximal and autopodial, as well as Msx1 as a marker for the naïve progenitors. In vivo lineage tracing analysis firmly established this role of Msx1 and localized the naïve progenitors to the outer margin of the developing limb, along the anterior-posterior axis. Sequential pulse-chase experiments showed that Msx1 naïve progenitors undergo progressive and simultaneous transition into both proximal and autopodial progenitors and then to Sox9+ chondroprogenitors.   Interestingly, the progressive differentiation to chondroprogenitors occurred along all the skeletal segments concurrently, suggesting that skeleton form in a nonconsecutive way. Indeed, by tracking the spatiotemporal sequence of naïve progenitor differentiation, we found that the skeleton forms in a complex nonconsecutive three-dimensional pattern. Overall, these findings propose a new model for limb skeleton development.   Limb development has long served as a model system for studying how a pool of progenitor cells undergoes coordinated spatial patterning and differentiation to produce complex and well-organized structures. Here, we identify a population of naïve-state limb progenitors and show that they differentiate progressively to form the skeleton in a complex nonconsecutive three-dimensional pattern.   First, by performing single-cell RNA sequencing of the developing mouse forelimb we created an atlas of cellular compositions and transcriptional states. This atlas revealed three progenitor states: naïve, proximal and autopodial, as well as Msx1 as a marker for the naïve progenitors. In vivo lineage tracing analysis firmly established this role of Msx1 and localized the naïve progenitors to the outer margin of the developing limb, along the anterior-posterior axis. Sequential pulse-chase experiments showed that Msx1 naïve progenitors undergo progressive and simultaneous transition into both proximal and autopodial progenitors and then to Sox9+ chondroprogenitors.   Interestingly, the progressive differentiation to chondroprogenitors occurred along all the skeletal segments concurrently, suggesting that skeleton form in a nonconsecutive way. Indeed, by tracking the spatiotemporal sequence of naïve progenitor differentiation, we found that the skeleton forms in a complex nonconsecutive three-dimensional pattern. Overall, these findings propose a new model for limb skeleton development.

overall_design: For each biological replicate, forelimbs of embryos from the same litter were pooled together (six forelimbs at E10.5 and E11.5, four forelimbs at E12.5 and E13.5, and two forelimbs from one E14.5 embryo. For collection of  E10.5:  Sox9-GFP 3  biol. replicates  and  2 biol. replicate of E10.5 Sox9-CreER; tdTomato;Scx-GFP ( Cre activation). For E11.5 and E12.5  4 biological replicated,  For E13.5-E14.5 5 biological replicated, in which Sox9+ cells were labeled by tamoxifen administration 48 h before harvesting and sorted into tdTomato+GFP-, tdTomato-GFP+, double-positive and double-negative cells. Sorting gates and fluorescence compensation were defined based on ScxGFP, tdTomato single-stained and unstained control cells.

first: Svetlana

last: Markman

first: Mor

last: Zada

first: Eyal

last: David

first: Amir

last: Giladi

first: Elazar

last: Zelzer


title: Single-cell RNA sequencing of sstr2 knockout mice

city: Daejeon

first: Byoung-Ha

last: Yoon

address: Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea

country: South Korea

institute: KRIBB

summary: single-cell Gene expression signatures in gastric tissues of sstr2 knockout and wild type mice using Chromium’s 10x single-cell RNA-seq platform

overall_design: single-cell RNA sequencing of sstr2 knockout mouse and wild type mouse was generated by Chromium’s 10x single-cell RNA-seq platform.

first: Yong

last: Kim


title: A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung [SC]

first: Paulo

last: Czarnewski

overall_design:
For tissue dissociation, tracheas were removed and lungs were finely minced. For later timepoints, lobes were first dissected into smaller pieces. Then, they were digested in 4U/ml Elastase (Worthington, cat no. LS002292), 1 mg/ml of DNase (Worthington, cat no. LK003170) in HBSS (Gibco, cat no. 14170) at 37°C ranging between 30 min to 3 h depending on the age (older timepoints require longer digestion times). HBSS supplemented with 2 % FCS (Gibco, cat no. 10500064) was used for the whole procedure. The tissues were triturated with fire polished glass Pasteur pipettes every 15-20 min for the tissue to fall apart more easily and enhance the dissociation. After digestion, the cell suspension was filtered (twice if needed) in a 15ml Falcon tube using a 30μm cell strainer (CellTrics, Sysmex), to remove remaining undissociated clumps and debris. The filtered cell suspension was kept ice cold and was diluted (roughly 1:2) with ice cold HBSS to prevent further digestion by the enzyme.. The filtered cell suspension wascells were pelleted through centrifugation at 200g for 5 min at 4 °C, the supernatant was removed and the pellet resuspended in a small volume of calcium- and magnesium-free HBSS (Gibco, cat no.14170) and transferred to 1.5ml Eppendorf tubes precoated with 30% BSA (A9576, Sigma-Aldrich). A Bürker chamber was used for cell counting.
NOTE FROM SUBMITTER: raw reads from our cohort are considered sensate and protected by GDPR regulations, and will therefore be uploaded to Swedish federated EGA.

first: Marco

last: Sergio

first: Sountoulidis

last: Alexandros

first: Czarnewski

last: Paulo

first: Samakovlis

last: Christos


title: Renal transcriptome changes in testosterone deficient-pigs fed a high-fat diet

city: Hangzhou

first: zhaowei

last: cai

state: Zhejiang

address: Binwen road 548

department: Laboratory Animal Research Center

institute: zhejiang chinese medical university

summary:
Purpose: Obesity and dyslipidemia are associated with increased risk of renal disease.Testosterone deficiency aggravated high-fat diet-induced obesity and hypercholeterolemia. However,whether testosterone deficiency or testosterone deficiency-induced dyslipidemia aggravate the progression of renal disease is not clear. To gain insight into the role of testosterone in modulating renal lipid metabolism, we profiled renal gene expression by RNA-Seq in HFC-fed intact male pigs (IM), castrated male pigs (CM), and castrated male pigs with testosterone replacement (CMT).

Methods: Sexually mature male miniature pigs were either surgical castrated or sham-operated, and castrated with testosterone replacement. We administrated to pigs a high-fat and high-cholesterol (HFC) diet for twelve weeks. RNA-Seq was employed to profile renal gene expression in pigs with different testosterone levels.

Conclusions: This study demonstrated that testosterone deficiency aggravated renal lipid accumulation in pigs fed an HFC diet and that these effects could be reversed by testosterone replacement therapy. Impaired metabolic processes, bile acid secretion,estrogen signaling pathway and enhanced triglyceride synthesis may contribute to the increased renal lipid accumulation induced by testosterone deficiency and an HFC diet.

overall_design: Renal mRNA profiles of intact male pigs fed a HFC diet (IM), castrated male pigs fed a HFC diet (CM) ,and castrated male pigs treated with testosterone (CMT) were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.

first: Zhaowei

last: Cai


title: Whole genome bisulfite sequencing of sstr2 knockout mice

summary: GC-specific methylation profiling in Sstr2 knockout and wild type mice using Whole genome bisulfite sequencing

overall_design: Whole genome bisulfite sequencing of Sstr2 knockout mie (n=3) and wild type mice (n=3) was generated by NGS using Illumina HiSeq 2000


title: RNA sequencing of sstr2 knockout mice

summary: Gene expression signatures in sstr2 knockout and wild type mice using RNA sequencing

overall_design: RNA sequencing of sstr2 knockout mie (n=18) and wild type mice (n=17) was generated by NGS using Illumina HiSeq 2000

first: Hee-Jin


title: Senescence rewires microenvironment sensing to facilitate anti-tumor immunity (bulk RNA-Seq)

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

summary: Cellular senescence involves a stable cell cycle arrest coupled to a secretory program that, in some instances, stimulates the immune clearance of senescent cells. Using an immune competent tumor model in which senescence triggers CD8 T cell-mediated tumor rejection, we show that senescence also remodels cell surface proteome to alter how they sense environmental factors, as exemplified by Type II interferon gamma (IFN-γ). Compared to proliferating cells, senescent cells upregulate IFN-γ receptor, become hypersensitized to microenvironmental IFN-γ, and more robustly induce antigen presenting machinery -effects also recapitulated in human tumor cells treated with senescence-inducing drugs. Disruption of the IFN-γ sensing by senescent cells blunts their immune-mediated clearance without disabling their characteristic secretory program or immune cell recruitment. Our results demonstrate that senescent cells have an enhanced ability to both send and receive environmental signals, and imply that each process is required for their effective immune surveillance.

sample_organism:
Mus
Mus musculus

platform_organism:
Mus
Mus musculus

overall_design: Transcriptomic characterization of in vitro proliferating (p53 suppressed) and senescent Nras mutant-p53 retorable (NSP) liver tumor cells:1) comparison between proliferating and senescent cells induced by different  triggers (p53 restoration, trametinib+palbociclib); 2) identification of BRD4-dependent transcriptional programs by JQ1 treatment upon proliferating and senescent (p53-restored) cells; 3) characterization of the effect of IFNg on proliferating or senescent (p53-restored) cells. For in vivo bulk tumor RNA-seq, proliferating tumor (p53 suppressed) was harvested 7-10 day after randomization point and senescent-induced tumor (p53 restored) was harvested 12 days after p53 restoration, allowing similar size of tumor at harvest.

first: Hsuan-An

last: Chen

first: Riccardo

last: Mezzadra

first: Jose

middle: M

last: Adrover

first: Ryan

last: Smolkin

first: Changyu

last: Zhu

first: Wei

last: Luan

first: Alexandra

last: Wuest

first: Sha

last: Tian

first: Xiang

last: Li

first: Ronald

last: Hendrickson

first: Mikala

last: Egeblad

first: Direna

last: Alonso-Curbelo

first: Scott

last: Lowe


title: RNA-binding protein complex AMG-1/SLRP-1 mediates germline development and spermatogenesis by maintaining mitochondrial homeostasis in Caenorhabditis elegans [RNA-seq]

status: Public on Jan 16 2023

city: Beijing

first: Hailian

last: Zhao

state: Beijing

address: 15 Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: The mechanisms of RNA-binding proteins (RBPs)-mediated post-transcriptional regulation of pre-existing mRNAs, which is essential for spermatogenesis, remains poorly understood. Here, we identify a germline-specific mitochondrial RBP AMG-1, a homolog of mammalian LRPPRC, required for spermatogenesis in C. elegans.  amg-1 mutation hinders germline development without affecting somatic development and leads to the aberrant mitochondrial morphology and structure associated with mitochondrial dysfunctions specifically in germline. We demonstrate that AMG-1 is most frequently bound to mtDNA-encoded 12S and 16S ribosomal RNA, the essential components of mitochondrial ribosome, and that 12S rRNA expression mediated by AMG-1 is crucial for germline mitochondrial protein homeostasis. Besides, mitochondrial dysfunction by AMG-1 mutation triggers sperm apoptosis in C. elegans. Furthermore, SLRP-1, the homolog of mammalian SLIRP in C. elegans, interacts with AMG-1 genetically to regulate germline development and reproductive success in C. elegans. Taken together, these findings reveal the novel function of mtRBP in specifically regulating germline development.

overall_design: Germline of L4-stage him-5 and amg-1;him-5 hermaphrodites were dissected out, flash frozen on dry ice, and RNA was collected using Trizol reagent.

first: Long

last: Miao

first: Peng

last: Wang


title: RNA-binding protein complex AMG-1/SLRP-1 mediates germline development and spermatogenesis by maintaining mitochondrial homeostasis in Caenorhabditis elegans

overall_design: Refer to individual Series


title: RNA-binding protein complex AMG-1/SLRP-1 mediates germline development and spermatogenesis by maintaining mitochondrial homeostasis in Caenorhabditis elegans [LACE-seq]

overall_design: LACE-seq reads of  N2 and amg-1::gfp hermaphrodite in L4 stage


title: DNMT3A-coordinated splicing governs the stem state switch toward differentiation in embryonic and hematopoietic stem cells.

first: Margaret

last: Goodell

state: TX

address: One Baylor Plaza, N1030


title: Pre-implantation alcohol exposure induces lasting sex-specific DNA methylation programming errors in the developing forebrain

city: Montreal

first: Serge

last: McGraw

state: Qc

address: 3175 Côte Sainte-Catherine, office 5.17.005

country: Canada

institute: CHU Ste-Justine Research Center/Université de Montréal

summary: Prenatal alcohol exposure is recognized to alter DNA methylation profiles of brain cells during development, and as being part of the molecular basis underpinning Fetal Alcohol Spectrum Disorder (FASD) etiology. However, we have negligible information on the effects of alcohol during the initial embryonic stages, a window marked with dynamic DNA methylation reprogramming, and on how this may rework  the brain developmental program. Using a pre-clinical in vivo mouse model, we show that pre-implantation alcohol exposure leads to adverse developmental outcomes that replicate clinical facets observed in children with FASD. Genome-wide DNA methylation analyses of fetal forebrains uncovered sex-specific alterations, including partial loss of DNA methylation maintenance at imprinted control regions, and abnormal re-establishment of de novo DNA methylation profiles in various biological pathways (e.g, neural/brain development). These findings support the contribution of alcohol-induced DNA methylation programming deviations during pre-implantation to the manifestations of neurodevelopmental phenotypes associated with FASD.

overall_design: RRBS analyses of E10.5 mouse embryo forebrain

first: Lisa-Marie

last: Legault

first: Karine

last: Doiron

first: Mélanie

last: Breton-Larrivée

last: Langford-Avelar

first: Anthony

last: Lemieux

first: Maxime

last: Caron

first: Loydie

last: Jerome-Majewska

first: Daniel

last: Sinnett


title: Characterisation of VDR signaling in prostate cancer health disparities (RNA-Seq)

city: WEST HOLLYWOOD

first: Moray

last: Campbell

address: 8687 Melrose Avenue, Office B227.5G

institute: Cedars-Sinai Medical Center

summary: To investigate the effect of 1,25(OH)2D3 activation on RNA expression in prostate cell lines derived from European Americans and African Americans

overall_design:
RNA was extracted from cells in the presence of 1α,25(OH)2D3 (100nM, 8hr) or EtOH in biological triplicate samples and analyzed by RNA-Seq. Sequencing libraries prepared with the TruSeq Stranded Total RNA kit (Illumina Inc), from 1ug total RNA. Alignment of raw sequence reads to the human transcriptome (hg38) was performed via Rsubread (33) and transcript abundance estimates were normalized and differentially expressed genes (DEGs) identified using a standard edgeR pipeline.
Comparative RNA gene expression profiling analysis of RNA-seq data for prostate cell lines treated with 1α,25(OH)2D3 (100 nM, 8h)

first: Clayton

last: Yates


title: Characterisation of VDR signaling in prostate cancer health disparities (ATAC-Seq)

summary: To investigate the effect of 1,25(OH)2D3 activation on chromatin accessabilty in prostate cell lines derived from European Americans and African Americans

overall_design:
Cells were treated cells in the presence of 1α,25(OH)2D3 2D3 (100nM, 4hr) or EtOH in triplicate independent experiments. Briefly, 50x103 cells were resuspended in 50ul of ATAC-resuspension buffer (ATAC-RSB - 10mM Tris-HCl, 10mM NaCl, 3mM MgCl2) containing (0.1% NP-40, 0.1% tween-20, and 0.01% digitonin) and pipetted up and down 3 times. Further, 1ml of ATAC-wash-resuspension buffer (ATAC-RSB + 0.1% tween 20) was used to pellet down the nuclei. The nucleic were further resuspended in transposition mix (2X TD buffer, 1X PBS, Digitonin 0.01%, tween 20 0.1%, NFW 5ul, and Illumina transposase 2.5ul). Mixing, cleanup and library preparation, quantification and sequencing was performed using NovaSeq6000 S1 PE150bp Sequencing as per protocol51 (28846090). (ATAC-Seq data were separated into nucleosome free (NF), mono-, di- and tri-nucleosome compartments (ATACSeqQC)52.
Comparative chromatin accessability analsyes byATAC-seq analsyes of prostate cell lines treated with 1α,25(OH)2D3 (100 nM, 4h)


title: Characterisation of VDR signaling in prostate cancer health disparities (ChIP-Seq)

summary: To investigate the effect of 1,25(OH)2D3 activation on VDR genomic binding in prostate cell lines derived from European Americans and African Americans

overall_design:
Cells were treated cells in the presence of 1α,25(OH)2D3 2D3 (100nM, 6hr) or EtOH in triplicate independent experiments. Briefly, approximately 20x106 cells were crosslinked with 1% formaldehyde solution, quenched with glycine (0.125 M) and harvested in cold PBS. Sonication of crosslinked chromatin was performed using a Bioruptor® UCD-200TM Sonicator (Diagenode) with optimized cycles for each cell type. Immunoprecipitation of sonicated material was performed with antibodies against VDR (D2K6W) – Cell Signaling) or IgG (Rabbit IgG sc2729 – Santa Cruz) for 16 hours, and antibody/bead complexes isolated with Magna ChIPTM Protein A+G magnetic beads (Millipore). Complexes were washed, reverse crosslinked, and treated sequentially with RNase and proteinase K prior to DNA isolation.
Comparative VDR cistrome analsyes by ChIP-seq analsyes of prostate cell lines treated with 1α,25(OH)2D3 (100 nM, 6h)


title: Effect of HIV infection and antiretroviral therapy initiation on genome-wide DNA methylation patterns.

city: Madrid

first: Juan

middle: Carlos

last: Silla-Castro

address: Melchor Fernandez Almagro 3

department: Bioinformatics

country: Spain

institute: CNIC

summary:
Background. Previous epigenome-wide association studies have shown that HIV infection can disrupt the host DNA methylation landscape. However, it remains unclear how antiretroviral therapy (ART) affects the HIV-induced epigenetic modifications.
Methods. 184 individuals with HIV from the NEAT001/ANRS143 clinical trial (with pre-ART and post-ART samples [96 weeks of follow-up]) and 44 age-and-sex matched individuals without HIV were included. We compared genome-wide DNA methylation profiles in whole blood between groups adjusting for age, sex, batch effects, and leucocyte type heterogeneity.
Findings. We identified 430 differentially methylated positions (DMPs) between HIV+ pre-ART individuals and HIV-uninfected controls. In participants with HIV, ART initiation modified the DNA methylation levels at 845 CpG positions and restored 49.3% of the changes found between HIV+ pre-ART and HIV-uninfected individuals. We only found 15 DMPs when comparing DNA methylation profiles between HIV+ post-ART individuals and participants without HIV. The Gene Ontology enrichment analysis of DMPs associated with untreated HIV infection revealed an enrichment in biological processes regulating the immune system and antiviral responses. In participants with untreated HIV infection, DNA methylation levels at top HIV-related DMPs were associated with CD4/CD8 ratios and viral loads. Changes in DNA methylation levels after ART initiation were weakly correlated with changes in CD4+ cell counts and the CD4/CD8 ratio.
Interpretation. Control of HIV viraemia after 96 weeks of ART initiation restores most of the host DNA methylation changes that occurred before antiretroviral treatment of HIV infection.

overall_design: 185 individuals with HIV from the NEAT001/ANRS143 clinical trial (with pre-ART and post-ART samples [96 weeks of follow-up]) and 44 age-and-sex matched individuals without HIV were included

first: Andrés

last: Esteban-Cantos

first: Javier

last: Rodríguez-Centeno

first: Pilar

last: Barruz

first: Fátima

last: Sánchez-Cabo

first: Gabriel

last: Sáiz-Medrano

first: Julián

last: Nevado

first: Beatriz

last: Mena-Garay

first: María

last: Jiménez-González

first: Rosa

last: de Miguel

first: Jose

middle: I

last: Bernardino

first: Rocío

last: Montejano

first: Julen

last: Cadiñanos

first: Cristina

last: Marcelo

first: Lucía

last: Gutiérrez-García

first: Patricia

last: Martínez-Martín

first: Cédrick

last: Wallet

first: François

last: Raffi

first: Berta

last: Rodés

first: José

last: Arribas


title: Host cellular and immune responses in models of inflammatory skin conditions

city: Southampton

first: Francesca

last: Ciccarelli

address: Southampton General Hospital

institute: University of Southampton

summary: Skin colonisation of varied communities of commensal microorganisms, such as Staphylococcus aureus (SA), Staphylococcus epidermidis (SE) and Staphylococcus capitis (SC) form the microbiome; a necessity for healthy skin. The skin changes characteristic of atopic dermatitis, a common inflammatory skin disease, have been shown to provide a favourable niche for SA colonisation. We utilised a reconstructed human epidermal (RHE) model recapitulating the stratified anatomy of the epidermis on which to test host responses to bacterial colonisation. SA proliferation was significantly inhibited in contrast to that seen with SE at both high and low colonisation loads after 24 hours. These data strongly suggest species specific regulation of staphylococcal growth, which is partially mediated by interaction with the epidermis.

overall_design: Confluent monolayer primary keratinocyte cultures were used to seed and establish reconstituted human epideris models after 13-15 days of growth within cell culture inserts at the air-liquid interface. Approximate absolute numbers of 10^6 CFU of bacteria were used per model for the challenge protocol. Models were challeged with either S. aureus (ATCC 29213 or NCTC-8325-4), S. epidermidis (ATCC 12228) or S. capitis (ATCC 27840). The challenge protocol consisted of an intial three hour incubation, at which point the 3-hour samples were collected, the 24-hour samples were then treated by PBS washing and further incubation of 21 hours. Subsequently models underwent trypsinisation and lysis for RNA extraction and whole transcriptome profiline by microarray. S. aureus ATCC 29213 proved destructive to models at 24h so data are not avialble for this strain at this timepoint. All three and 24 hour time points were conducted in triplicate or quadruplicate, while only a single unchallenged baseline sample was used for comparisons.

first: Daniel

middle: J

last: Holbrook

first: Fei-Ling

last: Lim

first: Marta

middle: E

last: Polak

first: Michael

middle: R

last: Ardern-Jones


city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

institute: University of Torino

summary: Background: Gain and/or amplification of chromosome 1q are frequently found in Multiple Myeloma (MM). The number of 1q copies correlates with a poor prognosis. The aim of this work is to study the impact on the clinical outcome and the trascriptomic changes induced by Gain1q (3 copies of 1q, 3X) and amplification 1q (Amp1q, ≥4 copies of 1q, 4X) in MM patients enrolled in the CoMMpass study (NCT145429). Methods: Fluorescence in situ hybridization (FISH) in CD138+ purified bone marrow plasma cells was centralized and performed at baseline. The cut-off level for Gain1q was 10% of nuclei with ≥3 copies of 1q (3X), while Amp1q was defined as ≥ 20% of nuclei with ≥4 copies of 1q (4X). Transcriptome data from patients were used to find differentially expressed genes (DEGs) in gain (3X) and amp1q (4X) patients.

overall_design: 24 samples, 8 with two copies of 1q (2X), 8 with three copies of 1q (3X) and 8 with four copies of 1q (4X)

first: Mattia

last: D'Agostino

last: Gay


title: Skin programming of inflammatory responses to Staphylococcus aureus is compartmentalised within epidermal keratinocytes differentiation status.

summary: During acute cutaneous inflammation in diseases such as atopic eczema there are alterations in the microbiome as well as histological and ultrastructural changes to the stratified epidermis, but the precise interaction between the keratinocyte proliferation and differentiation status and the skin microbiome has not been fully explored. We hypothesised that the skin microbiome contributes to regulation of keratinocyte differentiation and can modify antimicrobial responses.  Therefore, we examined the effect of exposure to topical commensal or pathogenic Staphylococcal challenge on skin models. To further explore the cell types regulating inhibition specifically targeting SA, single-cell DropSeq analysis of unchallenged naïve, SE challenged, and SA challenged epidermis models was undertaken. Transcriptomic analysis distinguished cells from basal, spinous, and granular layers which could then be interrogated individually in relation to model exposure. In contrast to SE, SA specifically induced a sub-population of spinous cells which highly expressed transcripts related to epidermal inflammation and antimicrobial response such as IL36G, IVL, IL1RN, KLK7, PI3, MMP1, S100A7, S100A8, S100A9, SERPINB1, SERPINB2, SERPINB3, and SLPI. Furthermore, SA, but not SE, specifically induced a basal population which highly expressed IL-1-alpha and IL-1-beta.

overall_design: Confluent monolayer primary keratinocyte cultures were used to seed and establish reconstituted human epideris models after 13-15 days of growth within cell culture inserts at the air-liquid interface. Approximate absolute numbers of 10^6 CFU of bacteria were used per model for the challenge protocol. Models were challeged with either S. aureus (ATCC 29213 or NCTC-8325-4), S. epidermidis (ATCC 12228) or S. capitis (ATCC 27840). The challenge protocol consisted of an intial three hour incubation, then treated by PBS washing and further incubation of 21 hours. Subsequently models underwent trypsinisation to prepare for single-cell sequencing by DropSeq. Models were challenged over three batches (0110, 1811, 2011), with n=3-5 models challenged per condition that were pooled to reduced model variation. Per batch, challenge conditions were then multiplexed using cell hashtag antibodies for control (GTCAACTCTTTAGCG), S. aureus (TGATGGCCTATTGGG) and S. epidermidis (TTCCGCCTCTCTTTG).

first: Kalum

last: Clayton

first: Andres

last: Vallejo


title: The cis-Regulatory Landscape of Cardiac Rhythm

city: Dallas

first: Nikhil

middle: V

last: Munshi

address: 6000 Harry Hines Blvd.

department: Internal Medicine-Cardiology

institute: UT Southwestern Medical Center

summary: Genome-wide identification of gene regulatory networks for murine cardiac conduction system

overall_design: Focusing on the primary pacemaker (Sino-Atrial Node(SAN)) of the heart, we used Shox2-KI-Cre mouse line to perform cellular analysis of SAN tissue. Utilizing this SAN-specific mouse model, we performed Single cell RNA sequencing (scRNA-Seq) on neonatal (P4) Shox2-Cre/+; R26 tdTomato/+ mice to guide our single-cell atlas of the SAN.

first: Samadrita

last: Bhattacharyya

first: Sean

last: Goetsch

first: Jialei

last: Duan

first: Boxun

last: Li


title: Epigenome analysis in several cohorts of HIV progession and in uninfected individuals

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

institute: Josep Carreras Leukaemia Research Institute (IJC)

summary: Genome wide DNA methylation profiling of CD4 T cells from uninfected and HIV-infected individuals (viremic, ART-suppressed and elite controllers [EC]) The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 485,577 CpGs in DNA from peripheral CD4 T cells samples. Samples included: 22 from HIV-uninfected individuals (uninfected group), 42 from HIV-infected individuals (21 from HIV-infected viremic (viremic group) and 21 from the same participants after viral suppression (viral load< 50 copies HIV-1 RNA/plasma) by antiretroviral therapy administrarion (ART group), and 21 from elite controllers (EC group)

overall_design:
Bisulphite converted DNA from the 85 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip v1.2.
Table "correspondence_paired_samples.csv" shows correspondence between 21 individuals from HIV-infected viremic (viremic group) and the same 21 individuals after viral suppression.

first: Javier

last: Martinez-Picado


title: Transcriptional Response of Multi-stress Tolerant Saccharomyces cerevisiae to Sequential Stress

city: Hershey

first: James

last: Broach

state: PA

address: 700 HMC Crescent Rd

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University College of Medicine

summary: To better understand how yeast adapt and respond to sequential stressors, an industrial yeast strain, URM 6670 (also known as BT0510), which is highly flocculent, tolerant to ethanol, osmotic and heat shock stresses, was subjected to three different treatments: 1. osmotic stress followed by ethanol stress, 2. oxidative stress followed by ethanol stress, 3. glucose withdrawal followed by ethanol stress. Samples were collected before the first stress (control), after the first stress and after the second stress (ethanol).  RNA was extracted and analyzed by RNAseq.

overall_design: Comparison of the transcriptional responses, relative to untreated samples, of yeast strain BT0510 subjected to oxidative stress, osmotic stress and glucose deprivation stress, followed in all cases by ethonal exposure

first: Ane

middle: C

last: Costa

first: Mariano

last: Russo


title: Gene expression analysis of nasal Ly6G+SiglecF+ double positive cells

city: Yokohama

first: Hidehiro

last: FUKUYAMA

state: Kanagawa

address: 1-7-22, Suehirocho, Tsurumi-ku

department: IMS

summary: mRNA expression profiles among nasal double positive cells nasal and peripheral blood neutrophils from LPS-treated mice were analyzed by RNA-sequencing

overall_design: mRNA profiles of nasal double positive cells, nasal neutrophils, and peripheral blood neutrophils from C57BL/6J mice were generated by deep sequencing, using [an NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (NEB)].

first: Kei

last: Ogawa

first: Kenichi

last: Asano

first: Masato

last: Tanaka


title: Zebrafish chemical compound screen uncovers inducers of skeletal muscle engraftment across species

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

summary: Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle, but the application of this approach has been limited due to the deleterious effects of cell expansion in vitro and poor engraftment efficiency. In an effort to overcome this hurdle, we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here, we report the development and application of a cross-species small molecule screening platform employing zebrafish and mouse, which enables rapid, direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system, we screened a library of bioactive lipids to identify those that could increase myogenic engraftment in zebrafish and mice. These efforts identified two lipids, lysophosphatidic acid (LPA) and niflumic acid (NFA), both linked to activation of intracellular calcium ion flux, which showed conserved, dose-dependent and synergistic effects in promoting muscle engraftment across these vertebrate species.

sample_organism:
Danio rerio
Mus musculus

platform_organism:
Danio rerio
Mus musculus

overall_design: To analyze the effect of LPA and NFA on gene expression of mice and zebrafsh muscle cells, we treated freshly isolated mice muscle stem cells and cultured zebrafish myogenic progenitor cells and the  with 5uM LPA and 10 uM NFA for 2 hrs. Control treatment was done with DMSO.

first: Song

last: Yang


title: lncRNA and circular RNAs in orbital adipose/connective tissue from patients with thyroid-associated ophthalmopathy

city: Shanghai

first: Lian-Qun

last: Wu

address: 83 Fenyang Road

institute: Fudan University

summary: Our study aimed to investigate the differentially expressed lncRNA and circRNAs and their potential roles in orbital adipose/connective tissue from patients with thyroid-associated ophthalmopathy (TAO).

overall_design: The orbital adipose/connective tissue samples from three TAO patients and three control individuals were collected for RNA sequencing after depletion of ribosomal RNA.

first: Lianqun