title: Loss of the cleaved-protamine 2 domain leads to incomplete histone-to-protamine exchange and infertility in mice [cPRM2]

first: Lena

last: Arévalo

summary: Protamines are unique sperm-specific proteins that package and protect paternal chromatin until fertilization. A subset of mammalian species expresses two protamines (PRM1 and PRM2), while in others PRM1 is sufficient for sperm chromatin packaging. Alterations of the species-specific ratio between PRM1 and PRM2 are associated with infertility. Unlike PRM1, PRM2 is generated as a precursor protein consisting of a highly conserved N-terminal domain, termed cleaved PRM2 (cP2), which is consecutively trimmed off during chromatin condensation. The carboxyterminal part, called mature PRM2 (mP2), interacts with DNA and together with PRM1, mediates chromatin-hypercondensation. The removal of the cP2 domain is believed to be imperative for proper chromatin condensation, yet, the role of cP2 is not yet understood. We generated mice lacking the cP2 domain while the mP2 is still expressed. We show that the cP2 domain is indispensable for complete sperm chromatin protamination and male mouse fertility. cP2 deficient sperm show incomplete PRM2 incorporation, resulting in a severely altered protamine ratio, retention of transition proteins and aberrant retention of the testis specific histone variant H2A.L.2. During epididymal transit, cP2 deficient sperm seem to undergo ROS mediated degradation leading to complete DNA fragmentation. The cP2 domain therefore seems to be a key aspect in the complex crosstalk between histones, transition proteins and protamines during sperm chromatin condensation. Overall, we present the first step towards understanding the role of the cP2 domain in paternal chromatin packaging and open up avenues for further research.

overall_design: Comparative testis gene expression profiling of cleaved-PRM2 deficient mice compared to WT

first: Gina

last: rMerges

first: Simon

last: Schneider

first: Franka

last: Oben

first: Isabelle

last: Neumann


status: Public on Apr 06 2022

city: Boston

first: Jonathan

middle: M

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

country: USA

institute: Joslin Diabetes Center

type: Expression profiling by high throughput sequencing

summary: RNA-seq of genetically engineered mouse microglia sorted into populations.

overall_design: Six samples of mouse microglia with three replicates each for a total of 18 samples

first: Al

last: Charest


title: Transcriptome profiling of DDX3X/DDX3Y dependency after DDX3X gRNA targeting in KNS-42 parental cell lines, and rescue experiments with DDX3X or DDX3Y overexpressing cells (PACT).

city: Vienna

first: Alexandra

last: Popa

state: Austria

address: Doktor-Boehringer-Gasse 5-11

country: Austria

institute: Boehringer Ingelheim

summary: Paralog dependency analysis of the DDX3X/DDX3Y genes through RNA-seq. Three types of KNS-42 cell lines are used in this experiment: one parental, one with a DDX3X over-expression (codon optimized) and one with DDX3Y over-expression (codon optimized). Targeting of the DDX3X gene is performed with guide RNAs 395 (TGGTACATGCGTATCCTTCA). The negative control is targeting AAVS1/PPP1R12C (AAVS1, GGGGCCACTAGGGACAGGAT). Samples were processed at 7 days after transduction. 3 independent repeats of the experiment were performed.

overall_design: KNS-42 cell line: parental, DDX3X codon optimized over expression, DDX3Y codon optimized over expression. Guide RNAs: 395 (targeting endogenous DDX3X) and AAVS1 (negative control).

first: Anna

last: Köferle

first: Ralph

last: Neumüller

last: Hörmann


title: RNA-seq of genetically engineered mouse EGFR positive glioblastoma tumors with PDGFRA and GAL-1 positive and negative populations

summary: RNA-seq of genetically engineered mouse EGFR positive glioblastoma tumors flow cytometry sorted into PDGFRA and GAL-1 positive and negative populations.

overall_design: There are 12 samples, where each of three tumors were flow cytometry sorted into 4 populations: PDGFR positive, PDGFR negative, GAL-1 positive, GAL-1 negative.


title: The binding sites of Foxp4 on genome in the  early stage of  SVF cells differentiating to beige adipocytes

city: Shanghai

first: Fuhua

last: Wang

address: 800 Dongchuan RD. Minhang District

country: China

institute: SJTU

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We found deletion of Foxp4 in SVF cells would inhibit beige adipocyte differentiation and thermogenesis.In order to investage the binding sites of Foxp4 on  genome of SVF cells, we isolated SVF cells from  ingunal adipose tissues and did Foxp4 and H3K27ac ChIP-Seqs after two days' browning differentiaion.

overall_design: Looking for binding sites of Foxp4 in the early stage of SVF cells differentiating to beige adipocytes

first: Xizhi

last: Guo


title: Effects of pan-UPF1 knockdown on RNA abundance

status: Public on Apr 07 2022

city: Bethesda

first: J. Robert

last: Hogg

state: MD

address: 50 South Drive, Room 2341

department: Biochemistry and Biophysics Center

institute: National Heart, Lung, and Blood Institute

summary: Flp-In T-REx-293 cells transfected with non-targeting control siRNA or UPF1-specific siRNA as indicated and used for total RNA-seq.

overall_design: Paired-end high-throughput RNA sequencing of total RNA from triplicate biological replicate treatments of Flp-In T-REx-293 cells.

first: Sarah

middle: E

last: Fritz

first: J

middle: R


title: SETD2 haploinsufficiency enhances germinal center-associated AICDA somatic hypermutation to drive B-cell lymphomagenesis

city: New York

first: Matt

last: Teater

state: NY

address: 445 E 69th St

institute: Weill Cornell Medical College

summary: SETD2 is the sole chromatin modifier responsible for H3K36me3, a histone mark linked to splicing, transcription initiation and DNA damage response. Homozygous disruption of SETD2 yields a tumor suppressor effect in various cancers. However, SETD2 mutation is virtually always heterozygous in diffuse large B-cell lymphomas (DLBCL). Here we show that heterozygous SETD2 deficiency results in germinal center (GC) hyperplasia and accelerated lymphomagenesis. SETD2 haploinsufficient GC B-cells exhibit increased competitive fitness and reduced DNA damage checkpoint activity, resulting in decreased apoptosis.  SETD2 haploinsufficient GCB and lymphoma cells featured increased off- and on-target AICDA induced somatic hypermutation (SHM), complex structural variants such as rygma, and increased translocations including those activating MYC.   DNA damage was selectively increased on the non-template strand and H3K36me3 loss was associated with greater RNA Pol II processivity and mutational burden, suggesting that SETD2-mediated H3K36me3 is required for proper sensing of cytosine deamination during transcription. Hence, SETD2 haploinsufficiency delineates a novel GC B-cell context specific oncogenic pathway involving defective epigenetic surveillance of AICDA mediated somatic hypermutation induced off target effects on transcribed genes.

overall_design: RNAseq ATAC-Seq and Cut&Run in murine cells with SETD2 haploinsufficiency

first: Leung

last: Wilfred

first: Ari

last: Melnick


title: Affymetrix OncoScan SNP arrays for profiling somatic copy-number alterations in blastic plasmacytoid dendritic cell neoplasm

status: Public on Apr 05 2022

city: Lübeck

first: Axel

last: Künstner

address: Ratzeburger Allee 160

department: LIED

country: Germany

institute: University of Lübeck

type:
Genome variation profiling by array
Genome variation profiling by SNP array

summary: Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is an aggressive malignancy assumed to originate from plasmacytoid dendritic cells (pDCs), which affects the skin and bone marrow and sequentially other organ systems. Here, we used Affymetrix OncoScan CNV arrays to characterize somatic copy number variations in 45 BPDCN cases.

overall_design: Total DNA was extracted and prepared for OncoSan CNV arrays from 45 FFPE BPDC cases following the manufacturer protocol.

first: Niklas

last: Gebauer

first: Hauke

last: Busch


title: Enhanced recovery of single-cell RNA-sequencing reads for missing gene expression data

city: Dallas

first: Allan-Hermann

last: Pool

state: TX

address: 6000 Harry Hines Blvd

department: Department of Neuroscience, Peter O'Donnell Brain Institute, Department of Anesthesia and Pain Management

institute: University of Texas Southwestern Medical Center

summary: Droplet based 3’ single-cell RNA-sequencing (scRNA-seq) methods have proved transformational in characterizing cellular diversity and generating valuable hypotheses throughout biology1,2. Here we outline a common problem with 3’ scRNA-seq datasets where genes that have been documented to be expressed with other methods, are either completely missing or are dramatically under-represented thereby compromising discovery of cell types, states and genetic mechanisms. We show that this problem stems from three main sources of sequencing read loss: (1) reads mapping immediately 3’ to known gene boundaries due to poor 3’ UTR annotation; (2) intronic reads stemming from unannotated exons or pre-mRNA; (3) discarded reads due to gene overlaps3. Each of these issues impacts detection of thousands of genes even in well characterized mouse and human genomes rendering downstream analysis either partially or fully blind to their expression. We outline a simple three step solution to recover the missing gene expression data that entails compiling a basic pre-mRNA reference to retrieve intronic reads4, resolving gene collision derived read loss through removal of readthrough and premature start transcripts, and redefining 3’ gene boundaries to capture false intergenic reads. We demonstrate with mouse brain and human peripheral blood datasets that this approach dramatically increases the amount of sequencing data included in downstream analysis revealing 20 - 50% more genes per cell and incorporates 15-20% more sequencing reads than with standard solutions5. These improvements reveal previously missing biologically relevant cell types, states and marker genes in the mouse brain and human blood profiling data. Finally, we provide simple algorithmic implementation of these solutions that can be deployed to both thoroughly as well as poorly annotated genomes. Our results demonstrate that optimizing the sequencing read mapping step can significantly improve the analysis resolution as well as biological insight from scRNA-seq. Moreover, this approach warrants a fresh look at preceding analyses of this popular and scalable cellular profiling technology.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Dissociated single cell suspension from mouse MnPO and human PBMCs

first: Yuki

last: Oka

first: Sisi

last: Chen

first: Matthew

last: Thomson


title: Expression data from non-infected and HAstV-1 infected Caco-2 cells

status: Public on Apr 08 2022

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary:
Human astrovirus infection is known to disrupt intestinal barrier function by increasing barrier permeabilty. However, the exact cellular mechanism(s) involved is unknown.
We used microarrays to detail the global gene expression changes occuring during astrovirus infection and identify necessary cellular pathways for astrovirus pathogenesis.

overall_design: Total RNA was extracted from human astrovirus HAstV-1 infected (24 hours post-infection) and non-infected Caco-2 cells and gene expression profiles were analyzed using Affymetrix Human Gene 2.0 sense transcript (ST) GeneChip microarrays. In order to determine genes modulated by infection and those required for infection we compared infected to non-infected Caco-2 cells as well as Cac0-2 cells that are permissive to infection (over-confluent) and non-permissive (sub-confluent) to infection. To perform this analysis, we harvested RNA from HAstV-1 infected (MOI of 10) and non-infected Caco-2 cells at 24 hours post-infection. Additionally, RNA was extracted from Caco-2 cells grown to differentiation which are permissive to HAstV-1 infection and cells grown only to sub-confluency which are non-permissive to HAstV-1 infection.

first: Virginia

last: Hargest

first: Stacey

last: Schultz-Cherry


title: Metabolic stress and therapeutic response in heart failure associated with congenital heart disease

city: Pittsburgh

first: Cecilia

middle: Wenya

last: Lo

state: United States

address: 530 45th St. 8120 Rangos Research Center

department: Developmental Biology

institute: University of Pittsburgh

summary: Heart failure in congenital heart disease (CHD) has no effective treatment besides heart transplantation. While hemodynamic etiology is suggested, here we show hypoplastic left heart syndrome (HLHS), a severe CHD is a mitochondrial disease from analysis of HLHS mice and patient derived induced pluripotent stem cell cardiomyocytes (iPSC-CM). The iPSC-CM from patients suffering heart failure or death, but not those with long-term survival, showed reduced cell proliferation with increased apoptosis, mitochondrial hyperfusion with respiration defect and redox stress. Single cell sequencing showed protein synthesis overload with unfolded protein response. Drugs targeting the mitochondria restored metabolic function and rescued cell proliferation and apoptosis, suggesting new stragegies for heart failure therapy in CHD.

overall_design: induced pluripotent stem cell derived cardiomyocytes (iPSC-CM) from 1 healthy control and 3 HLHS patients.

first: Xinxiu

last: Xu

first: Abha

middle: S

last: Bais

middle: W


title: Th17 cell plasticity towards a T-bet-dependent Th1 phenotype is required for bacterial  control in Staphylococcus aureus infection

city: Hamburg

first: Yu

last: Zhao

address: Falkenried 94

department: Institute of Medical Systems Biology

institute: University Medical Center Hamburg-Eppendorf

summary: Th17 cells are involved in controlling systemic S. aureus infections especially in the kidney and T-bet expression during transdifferentiation by Th17 cells is required for bacterial clearance.

overall_design: Single cell sequencing of 6-8 week Il17aCre x R26eYFP and Il17aCre x R26eYFP x Tbx21-flox mice

first: Patricia

last: Bartsch

first: Christoph

last: Kilian

first: Malte

last: Hellmig

first: Hans-Joachim

last: Paust

first: Alina

last: Borchers

first: Amirrtavarshni

last: Sivayoganathan

first: Leon

last: Enk

first: Nikhat

last: Shaik

first: Henning

last: Büttner

first: Milagros

middle: N

last: Wong

first: Victor

middle: G

last: Puelles

first: Thorsten

last: Wiech

first: Richard

last: Flavell

first: Tobias

middle: B

last: Huber

first: Jan-Eric

last: Turner

first: Stefan

last: Bonn

first: Samuel

first: Nicola

last: Gagliani

first: Hans-Willi

last: Mittrücker

first: Holger

last: Rohde

first: Ulf

last: Panzer

first: Christian

middle: F

last: Krebs


title: rDNA Array Length is a Major Determinant of Replicative Lifespan in Budding Yeast - ATACseq

city: South San Francisco

first: Nathaniel

middle: H

last: Thayer

state: CA

address: 1130 Veteran's Blvd

institute: Calico Life Sciences LLC

summary: In this study we perform ATAC-seq of budding yeast strains with variable copy number of the rRNA genes (rDNA CN). We aim to better understand the relationship between DNA accessibility and replicative lifespan in strains with variable rDNA CN.

overall_design: Examination of ATAC-seq profile of strains with variable rDNA array lengths.

first: Manuel

last: Hotz

first: David

last: Hendrickson

first: Elisabeth

middle: L

last: Schinski

first: Jun

last: Xu

first: Daniel

last: Gottschling


title: A single-cell/nucleus atlas of pediatric rhabdomyosarcoma

first: Michael

last: Dyer

address: 262 Danny Thomas Pl MS 324

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

summary: Rhabdomyosarcoma (RMS) is the most soft tissue sarcoma of childhood and histologically mimics developing skeletal muscle. To better understand RMS, we performed single-cell RNA-seq of one embryonal subtype RMS (ERMS) and one alveolar subtype RMS (ARMS). We expanded our observations by performing single-nucleus RNA-seq of 18 patient tumors (12 ERMS, 6 ARMS). All 18 of these tumors were used to generate orthotopic patient-derived xenografts, and we performed single-cell RNA-seq of all 18 O-PDXs to compare heterogeneity between the original tumor and the patient-derived model. 15 of the O-PDXs underwent lentiviral barcoding, and lineage could be tracked using a separate dial-out PCR step during the single-cell RNA-seq workflow. We performed single-cell RNA-seq of an ex vivo organoid, showing that we can preserve heterogeneity in this model. We expanded our study to the epigenetic level by using single-cell ATAC-sequencing of 7 O-PDXs. Finally, we longitudinally tracked shifts in heterogeneity in an O-PDX model treated with chemotherapy.

overall_design: We performed single-cell RNA-seq from 2 patient RMS tumors, 18 O-PDXs, and 1 organoid. Additionally, we performed single-nucleus RNA-seq from 18 patient RMS tumors and single-cell ATAC-seq from 7 O-PDXs. We also provide dialout PCR data from 15 RMS O-PDX that were used for lentiviral barcode experiments to track clonal lineages within O-PDXs.

first: Anand

last: Patel


title: rDNA Array Length is a Major Determinant of Replicative Lifespan in Budding Yeast - RNAseq

summary: In this study we perform RNA-seq of budding yeast strains with variable copy number of the rRNA genes (rDNA CN) to assess the relationship between rDNA CN and gene expression. RNA-seq was performed on samples both with and without polyA selection (for all transcripts and for rRNA transcripts, respectively).

overall_design: Examination of RNA-seq profile of strains with variable rDNA array lengths.


title: Screening thousands of transcribed coding and non-coding regions reveals sequence determinants of RNA polymerase II elongation potential.

first: Hanneke

last: Vlaming

address: 45 Shattuck St

department: Department of Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

summary: Organismal growth and development rely on RNA Polymerase II (RNAPII) synthesizing the appropriate repertoire of messenger RNAs (mRNAs) from protein-coding genes. Productive elongation of full-length transcripts is essential for mRNA function, however what determines whether an engaged RNAPII molecule will terminate prematurely or transcribe processively remains poorly understood. Notably, despite a common process for transcription initiation across RNAPII-synthesized RNAs1, RNAPII is highly susceptible to termination when transcribing non-coding RNAs such as upstream antisense RNAs (uaRNAs) and enhancers RNAs (eRNAs)2, suggesting that differences arise during RNAPII elongation. To investigate the impact of transcribed sequence on elongation potential, we developed a method to screen the effects of thousands of INtegrated Sequences on Expression of RNA and Translation using high-throughput sequencing (INSERT-seq). We found that higher AT content in uaRNAs and eRNAs, rather than specific sequence motifs, underlies the propensity for RNAPII termination on these transcripts. Further, we demonstrate that 5’ splice sites exert both splicing-dependent and autonomous, splicing-independent stimulation of processive transcription, even in the absence of polyadenylation signals. Together, our results reveal a potent role for transcribed sequence in dictating gene output at mRNA and non-coding RNA loci, and demonstrate the power of INSERT-seq towards illuminating these contributions.

overall_design:
6 groups of INSERT-seq experiments were performed:
- 4 replicates of total-RNA (steady-state) experiment with library at Pou5f1 reporter locus
- 2 replicates of sort-seq experiment with library at Pou5f1 reporter locus
- 2 replicates of run-on RNA (nascent) experiment with library at Pou5f1 reporter locus
- 2 replicates of chromatin-associated RNA experiment with library at Pou5f1 reporter locus
- 3 replicates of total-RNA (steady-state) experiment with library at 4930461G14Rik lincRNA locus
- 3 replicates each of total-RNA (steady-state) experiment with siNT- and siRRP40-treated cells with library at Pou5f1 reporter locus

H3K4me3 ChIP and 20min TT-seq in wild-type F121-9 mESCs were performed in duplicate, four replicates of PRO-seq in wild-type F121-9 mESCs were performed.

first: Claudia

middle: A

last: Mimoso

first: Benjamin

middle: J

last: Martin

first: Andrew

last: Field

first: Karen

last: Adelman


title: PBAF complex deficiency in melanoma mediates BAF occupancy and transcription factor dynamics (RNA-Seq)

first: Emily

last: Bernstein

address: 1470 Madison Avenue, 6th floor Rm 302

department: Oncological Sciences

institute: Mount Sinai School of Medicine

summary: ARID2 is an essential subunit of the SWI/SNF PBAF chromatin remodeler and is highly mutate in melanoma. To elucidate the role of ARID2 in melanoma biology and chromatin structure we utilized CRISPR Cas9 methodology to generate isogenic ARID2 WT and KO melanoma clonal cell lines. We further map the genomic localization of several SWI/SNF subunits, open and repressed chromatin markers, and multiple transcription factors to characterize how loss of the PBAF subcomplex alters chromatin accessibility and the melanoma transcription factor network. Finally, we characterized the transcriptional changes produced by PBAF depletion.

overall_design: Gene expression analysis of ARID2 KO cell lines

first: Saul

last: Carcamo

first: Elena

last: Grossi

first: Christie

last: Nguyen

first: Dan

last: Hasson


title: Longitudinal blood transcriptome analysis of two patients with cyclic thrombocytopenia

city: Palo Alto

first: Haiyu

last: Zhang

address: 300 Pasteur Dr.

institute: Stanford University

summary: Cyclic thrombocytopenia (CTP) is a rare disease of characterized by periodic platelet count oscillations of uncertain etiology. As part of a study that applied systems biology approaches to investigate two patients with CTP, we performed whole blood transcriptome analyses on semi-weekly collected sequential samples covering two platelet cycles. This blood transcriptome analysis revealed cyclical gene expression changes of platelet-specific genes that are in parallel with, and leading platelet count oscillations in both patients. In addition, erythrocyte-specific genes and neutrophil-specific genes also exhibited cyclic patterns which preceded platelet-specific genes. These findings revealed cyclical trilineage hematopoiesis, most pronounced in megakaryopoiesis in both patients with CTP.

overall_design: This study was approved by the Stanford University Institutional Review Board. Two patients with CTP were consented and enrolled in the study. 24 consecutive blood samples from patient 1 (CT1), and 15 samples from patient 2 (CT2) were collected in EDTA blood tubes every 3-4 days covering two platelet cycles. Total RNAs were extracted after red blood cell lysis. 3SEQ (3’-end sequencing for expression quantification) analyses were performed on blood RNA samples. HiSeq 2000 system and NextSeq 500 (Illumina) were used to generate sequencing data for CT1 and CT2, respectively. 3SEQ data were filtered and mapped to human transcriptome hg19, and read counts for each gene were generated. Quantitative analysis of the Significance Analysis of Microarrays-Seq (SAMseq) algorithm was used to obtain genes that are quantitatively associated with platelet count.

first: Yu

last: Hou

first: Panpan

last: Han

first: May

last: Chien

first: Xiangqian

last: Guo

first: Jason

last: Gotlib

first: James

last: Zehnder


title: rDNA Array Length is a Major Determinant of Replicative Lifespan in Budding Yeast.

first: Nathaniel

last: Thayer

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

overall_design: Refer to individual Series


title: PHF6 drives satellite DNA chromatin remodeling for resolution of replicative stress-induced DNA damage

first: Robert

last: Albero

address: 1130 St Nicholas Ave

institute: Columbia University

summary: The Plant Homeodomain 6 gene (PHF6) encodes a nucleolar and chromatin-associated factor with proposed roles in chromatin remodeling and transcription regulation. Germline mutations in PHF6 are causative of Börjesson-Forsmann-Lehman syndrome, while somatic loss-of-function genetic alterations support a tumor suppressor role in leukemia. Yet, the specific molecular function and mechanisms of PHF6 remain poorly understood. Here we show that PHF6 associates with chromatin remodeling and DNA repair factors in multiprotein complexes at satellite repeat heterochromatin regions and facilitates double strand break repair in the context of replicative stress-induced DNA damage. Mechanistically, PHF6 localizes to sites of DNA damage and its inactivation impairs the resolution of DNA breaks promoting the accumulation of single and double-stranded DNA lesions. In addition, PHF6 associates with difficult to replicate Histone H3 lysine 9 trimethylation (H3K9me3)-marked heterochromatin at satellite DNA regions, prevents accelerated replication fork dynamics and is required to maintain genomic integrity at fragile sites. In all, these results demonstrate a critical role for PHF6-containing chromatin-remodeling complexes in homologous recombination DNA-repair and in the resolution of satellite DNA-associated replicative stress.

overall_design: Examination of PHF6 chromatin binding in T-acute lymphoblastic leukemia cells

first: Silvia

last: Alvarez

first: Ana

middle: C

last: da Silva Almeida

first: Mayukh

last: Biswas


title: An endogenously activated antiviral state restricts SARS-CoV-2 infection in differentiated primary airway epithelial cells

city: Belfast

first: Guillermo

last: López-Campos

state: Northern Ireland

address: 97 Lisburn road

department: Centre for Experimental Medicine

country: United Kingdom

institute: Queen's University of Belfast

summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of the coronavirus disease-19 (COVID-19) pandemic, was identified in late 2019 and went on to cause over 3.3 million deaths in 15 months. To date, targeted antiviral interventions against COVID-19 are limited. The spectrum of SARS-CoV-2 infection ranges from asymptomatic to fatal disease. However, the reasons for varying outcomes to SARS-CoV-2 infection are yet to be elucidated. Here we show that an endogenously activated interferon lambda (IFNλ) pathway leads to resistance against SARS-CoV-2 infection. Using a well-differentiated primary nasal epithelial cell (WD-PNEC) model from multiple adult donors, we discovered that susceptibility to SARS-CoV-2 infection, but not respiratory syncytial virus (RSV) infection, varied. One of four donors was resistant to SARS-CoV-2 infection. High baseline IFNλ expression levels and associated interferon stimulated genes correlated with resistance to SARS-CoV-2 infection. Inhibition of the JAK/STAT pathway in WD-PNECs with high endogenous IFNλ secretion resulted in higher SARS-CoV-2 titres. Conversely, prophylactic IFNλ treatment of WD-PNECs susceptible to infection resulted in reduced viral titres. An endogenously activated IFNλ response, possibly due to genetic differences, may be one explanation for the differences in susceptibility to SARS-CoV-2 infection in humans.

overall_design: Well-differentiated primary nasal epithelial cells from different human healthy donors were mock-infected and infected with SARS-CoV-2 and gene expression was measured and compared at 48 hours and 96 hours post infection

first: Lindsay

last: Broadbent

first: Connor

last: Bamford

last: Lopez Campos

first: Sheerien

last: Manzoor

first: David

last: Courtney

first: Ahlam

last: Ali

first: Olivier

last: Touzelet

first: Conall

last: McCaughey

first: Ken

last: Mills

first: Ultan

last: Power


title: CTCF Functions as an Insulator for Somatic Genes and a Structural Regulator for Pluripotent Genes during Reprogramming [BL-Hi-C]

city: Guangzhou

first: ya

middle: wei

last: song

state: Guangdong

address: 190 Kai Yuan Avenue, Science Park

department: South China Institute for Stem Cell Biology and Regenerative Medicine

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

summary: CCCTC binding factor (CTCF) has been implicated in mediating chromatin insulation and long-distance interactions between enhancer and promoter. In this study, to study the roles of CTCF in somatic cell reprogramming, we performed RNA-seq, Hi-C, ChIP-seq and ATAC-seq at the specific stage of reprogramming. Through bioinformatics analysis, our data indicated that CTCF promotes enhancer-promoter interactions and chromatin accessibility to regulate the expression of key pluripotency genes; meanwhile, it serves as an insulator to suppress the expression of key somatic genes. Smarca5 loss inhibits CTCF-promoted reprogramming by reversing CTCF insulator activity on MEF-specific genes and leading to incorrect nucleosome positioning adjacent to CTCF binding sites. These findings reveal the dual functions of CTCF as both a structural regulator and insulator in conjunction with a key chromatin remodeler to drive cellular reprogramming towards pluripotency.

overall_design: Examination of chromatin interactions in mouse embryonic fibroblast (MEF) and OSKM reprogrammed cells on day 10. Examination of chromatin interactions in reprogramming cells with OSKM plus control, OSKM plus Ctcf overexpression and OSKM with Ctcf overexpression plus Smarca5 knockdown, reprogramming cells with OSKM plus control or Ctcf shRNA on day 10. Examination of chromatin interactions in sorted reprogramming intermediate cells in the TetOn lentivirus OSKM reprogramming system with both control shRNA and Ctcf knockdown by BL-Hi-C deep sequencing.

first: Andrew

middle: P

last: Hutchins

first: Zhengyu

last: Liang

first: Gongcheng

last: Hu

first: Yawei

last: Song


title: Profiling H3K4me3, H3K4me1, H3K9ac and H3K27ac in OCI-AML3 cells

status: Public on Apr 04 2022

city: Paris

first: Camille

last: Lobry

address: 16 rue de la Grange aux Belles

department: IRSL Inserm U944 / CNRS UMR7212

country: France

institute: Inserm

summary: OCI-AML3 Acute myeloid leukemia cell line was used for ChIP-sequencing profiling of H3K4me3, H3K4me1, H3K9ac and H3K27ac histone post-translational modifications to identify active promoter and enhancer regions.

overall_design: ChIPseq for H3K4me3, H3K4me1, H3K9ac and H3K27ac in OCI-AML3 cells.


title: CTCF Functions as an Insulator for Somatic Genes and a Structural Regulator for Pluripotent Genes during Reprogramming [RNA-seq]

overall_design: Gene expression profiling of reprogramming cells with OSKM plus control, OSKM plus Ctcf overexpression, OSKM with Ctcf overexpression plus Smarca5 knockdown on day 10. Gene expression profiling of reprogramming cells with OSKM plus control or Ctcf shRNA on day 10. Gene expression profiling of mouse embryonic fibroblast (MEF) cells, iPSCs, sorted reprogramming intermediate cells in the TetOn lentivirus OSKM reprogramming system with both control shRNA and Ctcf knockdown.


title: Sequencing and Quantitative Analysis of Skin Transcriptomes from Rats with EGFR Inhibitors Induced Rash

first: Shiyi

last: Zhang

address: 800 Dongchuan Rd

institute: Shanghai Jiao Tong University

summary: Skin mRNA profiles of wild-type (WT) and EGFR Inhibitors (Gefitinib and Afatinib) induced rash rats were generated by deep sequencing, in triplicate, using Illumina GAIIx. Raw sequences were mapped to the rat reference sequence by Hisat2 v2.0.5. FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis was performed using the DESeq2 R package (1.16.1).

first: Xin

last: Liu

first: Xinran

last: Xie

first: Leying

last: Chen


title: VAP-A and its binding partner CERT drive biogenesis of RNA-containing extracellular vesicles at ER membrane contact sites

city: NASHVILLE

first: Marisol

last: Ramirez

state: TENNESSEE

address: 2220 Pierce Avenue, 571 Preston Research Building

department: Center for Quantitative Sciences, Department of Biostatisticss

institute: Vanderbilt University Medical Center

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA transfer via extracellular vesicles (EVs) influences cell phenotypes; however, lack of information regarding biogenesis of RNA-containing EVs has limited progress in the field. Here, we identify endoplasmic reticulum membrane contact sites (ER MCS) as platforms for generation of RNA-containing EVs. We identify a subpopulation of small EVs that is highly enriched in RNA and regulated by the ER MCS linker protein VAP-A. Functionally, VAP-A-regulated EVs are critical for miR-100 transfer between cells and in vivo tumor formation. Lipid analysis of VAP-A-knockdown EVs revealed reductions in the EV biogenesis lipid ceramide. Knockdown of the VAP-A-binding ceramide transfer protein CERT led to similar defects in EV RNA content. Imaging experiments revealed that VAP-A promotes lumenal filling of multivesicular bodies (MVBs). CERT localizes to MVBs, and the ceramide-generating enzyme neutral sphingomyelinase 2 colocalizes with VAP-A-positive ER. We propose that ceramide transfer via VAP-A-CERT linkages drives biogenesis of a select RNA-containing population.

overall_design: Small RNA profiles in control (Sc) and VAP-A knockdown (KD1 & KD2) DKs-8 cells and in extracellular vesicles (small and large EVs) purified from their respective parental cells.

first: Bahnisikha

last: Barman

first: Bong

last: Sung

first: Evan

last: Krystofiak

first: Jie

last: Ping

first: Bryan

last: Millis

first: Ryan

last: Allen

first: Nripesh

last: Prasad

first: Sergei

last: Chetyrkin

first: Wade

last: Calcutt

first: Kasey

last: Vickers

first: James

last: Patton

first: Qi

first: Alissa

middle: M

last: Weaver


title: CTCF Functions as an Insulator for Somatic Genes and a Structural Regulator for Pluripotent Genes during Reprogramming [ChIP-seq]

first: ya

last: song

overall_design: Analysis of CTCF binding sites in reprogramming cells with OSKM plus control, OSKM plus Ctcf overexpression, OSKM with Ctcf overexpression plus Smarca5 knockdown on day 10. Analysis of CTCF binding sites in wild type (WT) and Smarca5 knockout mESCs, sorted reprogramming intermediate cells in the TetOn lentivirus OSKM reprogramming system with both control shRNA and Ctcf knockdown. Analysis of SMARCA5 binding sites in mESCs.

first: Andrew

last: Hutchins

first: Zhengyu

last: Liang

first: Gongcheng

last: Hu

first: Yawei

last: Song


title: Fig3_CARo2RvsCARo9R-invitro

city: Stanford

first: Anusha

last: Kalbasi

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford

summary: nCounter reads (RCC files)

overall_design: Mouse CAR T cells transduced with orthogonal cytokine receptors o2R and o9R and treated with wild-type or orthogonal IL-2 cytokines

first: Mikko

last: Siurala


title: RNA-seq Fig2_Exp-010_o2Rvo9R-invitro

summary: RNAseq of pmel T cells transduced with orthogonal cytokine receptors o2R and o9R

overall_design: pmel T cells are transduced with orthogonal cytokine receptors o2R or o9R and treated with wildtype or orthogonal IL-2.


title: RNAseq transcriptome analysis of Streptococcus pyogenes HKU16 and an isogenic gshT mutant. Manuscript title: Streptococcus pyogenes hijacks host glutathione for growth and innate immune evasion

city: Parkville

first: Magnus

middle: Ganer

last: Jespersen

state: Victoria

address: 792 Elizabeth street

country: Australia

institute: The University of Melbourne

summary: The nasopharynx and the skin are the major oxygen-rich anatomical sites for colonization by the human pathogen Streptococcus pyogenes (group A Streptococcus, GAS). To establish infection, GAS must survive oxidative stress generated during aerobic metabolism and the release of reactive oxygen species (ROS) by host innate immune cells. Glutathione is the major host antioxidant molecule while GAS is glutathione-auxotrophic. Here we report the molecular characterization of the ABC transporter substrate binding protein GshT in the GAS glutathione salvage pathway. We demonstrate that glutathione uptake is critical for aerobic growth of GAS and that impaired import of glutathione induces oxidative stress that triggers enhanced production of the reducing equivalent NADPH. Our results highlight the interrelationship between glutathione assimilation, carbohydrate metabolism, virulence factor production and innate immune evasion. Together, these findings suggest an adaptive strategy employed by extracellular bacterial pathogens to exploit host glutathione stores for their own benefit.

overall_design: Bacteria were grown to late-logarithmic growth phase in Todd Hewitt broth supplemented with 1% yeast extract (THY). 3 biological replicates for each strain, HKU16 wildtype and gshT mutant.

first: Stephan

last: Brouwer

first: Cheryl-lynn

middle: Y

last: Ong

first: David

last: De Oliveira

first: Bernhard

last: Keller

first: Amanda

last: Cork

first: Karrera

last: Djoko

first: Mark

last: Davies

last: Walker


title: Cardiac miRNA profiling during pressure overload-induced hypertrophy in PTP1B-deficient mice

city: Albany

first: Ben

last: Boivin

address: 257 Fuller road

institute: SUNY Polytechnic Institute

summary: The switch from the faster α-MHC to the slower β-MHC isoform that occurs in cardiac hypertrophy is generally thought to reduce contractile performance and to contribute to functional maladaptation. This MHC switch is regulated by miRNAs and thyroid hormones in development and hypertrophy. Since exacerbated hypertrophy is observed in absence of β-MHC expression in PTP1B cKO mice, we speculated that PTP1B inactivation associated with pressure-overload hypertrophy could disrupt miRNAs homeostasis. In this dataset, expression status of 1908 mouse miRNAs was investigated and reveal that PTP1B contribute to gene silencing by mediating miRNA loading onto the RISC complex.

overall_design: Cardiac miRNA populations were extracted from sham and TAC PTP1B floxed and PTP1B cKO mice 4 weeks post-surgery. The RNAs were then analyzed on an Affimetrix 4.0 miRNA Array. Intensity values were transformed into log2 scale, and the heat map shows log2 fold change values for each data set

first: Benoit

first: Gerald

last: Coulis


title: Bulk RNA sequencing of mouse embryonic fibroblasts in autophagy processes

city: Dongjak-Gu

first: Junil

last: Kim

state: Seoul

address: 369 Sangdo-Ro

department: Department of Bioinformatics

country: South Korea

institute: SOONGSIL UNIVERSITY

summary: Autophagy, a catabolic process to remove unnecessary or dysfunctional cells, is triggered by various signals including nutrient starvation. Depending on the type of the nutrient deficiency, diverse sensing mechanisms and pathways are used for autophagy, suggesting subsequent nutrient dependent transcriptional regulation. Still, however, our knowledge about nutrient specific transcriptional regulation during autophagy is limited.    To understand nutrient type dependent transcriptional mechanisms during autophagy, we performed single cell RNA sequencing (scRNAseq) for the mouse embryonic fibroblasts (MEFs) before and after applying glucose- (GS) as well as amino acid starvation (AAS). Trajectory analysis using scRNAseq identified sequential induction of potential transcriptional regulators for each deficiency condition. Gene regulatory rules inferred using TENET newly identified CCAAT/enhancer binding protein γ (C/EBPγ) regulates autophagy processes specifically to AAS condition. Strikingly, knockdown of C/EBPγ attenuated the autophagic process only in the AAS condition.  Cell biological and biochemical studies validated that C/EBPγ plays a switching role for ATF4 to activate autophagy genes under AAS, but not under GS. Together, our data identified C/EBPγ as a previously unidentified key regulator under amino acid starvation-induced autophagy.

overall_design: MEF cells (MEFs) were cultured at 37 °C in Dulbecco’s modified Eagle’s medium (DMEM) containing 10 % fetal bovine serum (FBS) and antibiotics in a humidified incubator with 5 % CO2. MEFs used in the study was regularly tested for mycoplasma contamination. For glucose/amino acid starvation, cells were washed with PBS, then incubated with glucose/amino acid-free DMEM supplemented with 10 % dialyzed FBS. Transfection was performed with Lipofectamine 3000 (Invitrogen). 500000 of MEFs were plated on culture dish containing high glucose DMEM (Cat. SH30243.01) with FBS and were stabilized for one day. After stabilization, the cells were washed with either glucose starvation media (Cat. LM001-56) or amino acid starvation media (Cat. LM001-90) containing dialyzed FBS. Subsequently, the normal media was changed with appropriate starvation media and cells were incubated in the cell incubator for different duration of time according to starvation signal (amino acid starvation and glucose starvation 3, 6 and 12 hours). At the end of starvation, MEFs were collected using trypsin EDTA and resuspended in freezing media (10% DMSO + 90% dialyzed FBS). The control sample (0 hour starvation) was collected and resuspended in freezing media composed of 90% FBS instead of dialyzed FBS. Vials containing each sample were stored in a deep freezer before proceeding to sequencing.

first: Dongha


title: The ubiquitous human skin commensal Staphylococcus hominis protects against opportunistic pathogens

city: Aurora

first: Morgan

last: Severn

state: CO

institute: University of Colorado Anschutz Medical Campus

summary: Staphylococcus hominis is frequently isolated from human skin and we hypothesize that it may protect the cutaneous barrier from opportunistic pathogens. We determined that S. hominis makes six unique auto inducing peptide (AIP) signals that inhibit the major virulence factor accessory gene regulator (agr) quorum sensing system of Staphylococcus aureus. We solved and confirmed the structures of three novel AIP signals in conditioned media by mass spectrometry, then validated synthetic AIP activity against all S. aureus agr classes. Synthetic AIPs also inhibited the conserved agr system in a related species, Staphylococcus epidermidis. We determined the distribution of S. hominis agr types on healthy human skin and found S. hominis agr-I and agr-II were highly represented across subjects. Further, synthetic AIP-II was protective in vivo against S. aureus-associated dermonecrotic or epicutaneous injury. Together, these findings demonstrate that a ubiquitous colonizer of human skin has a fundamentally protective role against opportunistic damage.

overall_design: We analyzed bacterial RNA from Staphylococcus hominis (strain C5) treated for 8 hours with DMSO (vehicle) or the AgrA inhibitor Apicidin (Parlet. Et al. Cell Rep. 2019) to determine genes under the transcriptional regulation of AgrA. Each group (treatment or control) contains three biological replicates for a total of 6 samples.

first: Michael

middle: R

last: Williams

first: Ali

last: Shahbandi

first: Zoie

last: Bunch

first: Laurie

last: Lyon

first: Amber

last: Nguyen

first: Livia

last: Zaramela

first: Daniel

last: Todd

first: Karsten

last: Zengler

first: Nadja

last: Cech

first: Richard

last: Gallo

first: Alexander

last: Horswill


title: Feminization of mouse liver gene expression by constitutively active STAT5b

city: Boston

first: David

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary: This SuperSeries is composed of the SubSeries listed below. This SuperSeries is part of a study entitled 'Constitutively active STAT5b feminizes mouse liver gene expression', where delivery of constitutively active STAT5 (STAT5CA) to male mouse liver was shown to induce widespread feminization of the liver, with extensive induction of female-biased genes and repression of male-biased genes, largely mimicking results obtained when male mice are given GH as a continuous infusion. Many of the STAT5CA-responding genes were associated with nearby (< 50 kb) sites of STAT5 binding to liver chromatin, supporting the proposed direct role of persistently active STAT5 in continuous GH-induced liver feminization. The feminizing effects of STAT5CA were dose-dependent; moreover, at higher levels, STAT5CA overexpression resulted in some histopathology, including hepatocyte hyperplasia, and increased karyomegaly and multinuclear hepatocytes. Together, these findings establish that the persistent activation of STAT5 by GH that characterizes female liver is by itself sufficient to account for the sex-dependent expression of a majority of hepatic sex-biased genes.


title: Morphine  addiction-NAc_small RNA sequencing

city: shijiazhuang

first: xiaojie

last: li

address: 361 Zhongshan East Road, Chang'an District, Shijiazhuang, Hebei Province

institute: Hebei Medical University

summary: The current study aimed at addressing two questions: 1) How the expression of key miRNAs is altered in the NAc during the morphine-induced addiction? 2) Which is/are the target gene(s) and what is/are the regulatory mechanism(s) of gene(s) in response to the candidate miRNAs? To answer these two questions, the morphine addiction model was first established by using the conditioned place preference (CPP) paradigm. Then, the aberrant expression of miRNAs was identified in the NAc tissue by RNA-sequencing.

overall_design: The NAc tissues from C57BL/6N mice from the two groups that were subjected to morphine or saline training CPP model were harvested; three samples (6 mice) from each group were used for total RNA isolation. RNA-seq was performed by Novogene Co., LTD (Beijing, China). In short, following RNA quantification and qualification, RNA integrity was examined with the RNA Nano 6000 assay kit and Agilent Bioanalyzer 2100 library preparation for small RNA sequencing system (Agilent Technologies, CA, USA). Any library preparations in this study were sequenced on an Illumina HiSeq 2500 platform (Illumina, San Diego, CA, USA). We explored the occurrence of miRNA families identified from the samples in other species and used miFam.dat (http://www.mirbase.org/ftp.shtml) for known miRNAs to determine families. New miRNA precursors were submitted via the Rfam website (http://rfam.sanger.ac.uk/search/) for Rfam family identification.

first: Bing

last: Xie

first: Di

last: Wen

first: Chunling

last: Ma

first: Xiaojie

last: Li


title: Human iPS-derived-keratinocytes, a new useful model to identify and explore pathological phenotype of Epidermolysis Bullosa Simplex.

city: Corbeil-Essonnes

first: Hélène

last: Polvèche

address: 28, Rue Henri Desbruères

institute: I-Stem

summary: Epidermolysis Bullosa Simplex (EBS), an autosomal dominant skin disorder, is characterized by trauma-induced skin fragility. Genetically, majority of cases are related to missense mutations in two keratin genes, KRT5 or KRT14, leading to cytolysis of basal keratinocytes and intraepidermal blistering. Only symptomatic treatment exists for EBS patients so far. Progress towards identification of new treatments have been hampered by incomplete understanding of the mechanisms underlying this disease, and availability of relevant and reliable in vitro models recapitulating the physiopathological mechanisms. Recent advances in stem cell field have fueled the prospect that these limitations could be overcome thanks to the availability of disease-specific human induced pluripotent stem cells (hiPSC). Here we generated hiPSC-derived keratinocytes from EBS patients carrying KRT5 dominant mutations and compared them to non-affected hiPSC-derived keratinocytes as well as their primary counterparts. Our results demonstrated that EBS hiPSC-derived keratinocytes displayed proliferative defects, increased capacity to migrate, alteration of ERK signaling pathway and cytoplasmic keratin filament aggregates in response to osmotic-shock treatment in a pattern similar to primary EBS keratinocytes. Of interest, EBS hiPSC-derived keratinocytes exhibited a downregulation of hemidesmosomal proteins revealing the different effects of KRT5 mutations on keratin cytoskeletal organization. Combination of culture miniaturization and treatment with the chaperone molecule 4-Phenybutiric acid (4-PBA), our results demonstrated that hiPSC-derived keratinocytes represent a suitable model for identifying novel therapies for EBS.

overall_design: Comparison of gene expression profiles of 3 hiPSC-derived WT keratinocytes and 3 hiPSC-derived EBS keratinoctyes (3 different KRT5 dominant mutations)

first: Julien

last: Coutier

first: Manon

last: Bonnette

first: Sabrina

last: Martineau

first: Aurélie

last: Mercadier

first: Sophie

last: Domingues

first: Margot

last: Jarrige

first: Helene

last: Polveche

first: Manoubia

last: Saidani

first: Annabelle

last: Darle

first: Nathalie

last: Holic

first: Smain

last: Hadj-Rabia

first: Christine

last: Bodemer

first: Gilles

last: Lemaitre

first: Cécile

last: Martinat

last: Baldeschi


title: RNA-seq gene expression profiling of livers from C57Bl/6 mice treated with adeno-associated virus encoding constitutively active STAT5b (AAV8-STAT5ca)

first: David

last: Waxman

summary: PolyA-selected total RNA isolated from livers of adult male mice administered AAV8-STAT5ca was analyzed by RNA-seq to determine the impact of constitutive STAT5 activation on the expression of sex-biased genes in male mouse liver. This is part of a study entitled 'Constitutively active STAT5b feminizes mouse liver gene expression', where delivery of constitutively active STAT5 (STAT5CA) to male mouse liver was shown to induce widespread feminization of the liver, with extensive induction of female-biased genes and repression of male-biased genes, largely mimicking results obtained when male mice are given GH as a continuous infusion. Many of the STAT5CA-responding genes were associated with nearby (< 50 kb) sites of STAT5 binding to liver chromatin, supporting the proposed direct role of persistently active STAT5 in continuous GH-induced liver feminization. The feminizing effects of STAT5CA were dose-dependent; moreover, at higher levels, STAT5CA overexpression resulted in some histopathology, including hepatocyte hyperplasia, and increased karyomegaly and multinuclear hepatocytes. Together, these findings establish that the persistent activation of STAT5 by GH that characterizes female liver is by itself sufficient to account for the sex-dependent expression of a majority of hepatic sex-biased genes.

overall_design: Total liver RNA, polyA-selected, was isolated from adult male mice. RNA-seq libraries were prepared and subject to Illumina sequencing.

first: Hong

last: Ma

first: Andrea

last: Sarmento-Cabral

first: Dana

last: Lau-Corona

first: Rhonda

middle: D

last: Kineman


title: CTCF Functions as an Insulator for Somatic Genes and a Structural Regulator for Pluripotent Genes during Reprogramming [ATAC-seq]

first: ya

last: song

overall_design: Examination of the chromatin accessibility in reprogramming cells with OSKM plus control, Ctcf overexpression or Ctcf overexpression plus Smarca5 knockdown on day 10, sorted reprogramming intermediate cells in the TetOn lentivirus OSKM reprogramming system with both control shRNA and Ctcf knockdown by ATAC-seq.

first: Andrew

last: Hutchins

first: Zhengyu

last: Liang

first: Gongcheng

last: Hu

first: Yawei

last: Song


title: Transcriptomic profile of FERONIA mutant treated with Aradopside

city: Ames

first: Natalie

last: Clark

state: IA

address: Advanced Teaching and Research Building 2213 Pammel Drive

department: Plant Pathology and Microbiology

institute: Iowa State University

summary: FERONIA (FER) receptor kinase has a versatile role in plant growth and development, biotic and abiotic stress responses, and reproduction. To gain new insights into the molecular interplay of these processes and to identify new functions of FER, we carried out quantitative transcriptome, proteome, and phosphoproteome profiling of wild type (WT) and a loss-of-function fer mutant in Arabidopsis plants. Gene Ontology terms for hormone signaling, abiotic stress, and biotic stress were significantly enriched among mis-expressed transcripts, proteins, and/or mis-phosphorylated proteins, in agreement with FER’s known roles in these processes. Analysis of multi-omics data and subsequent experimental evidence identified previously unknown functions of FER in ER (Endoplasmic Reticulum) body formation, glucosinolate biosynthesis. FER functions through transcription factor NAI1 to mediate ER body. FER also negatively regulates indole glucosinolates biosynthesis, partially through NAI1. Furthermore, we found that a group of abscisic acid (ABA)-induced transcription factors are hypo-phosphorylated in the fer mutant and demonstrated that FER acts through ABI5 to negatively regulate the ABA response during germination. Our integrated-omics study therefore reveals novel functions of FER and provides new insights into the underlying mechanisms of FER function.

overall_design: Four biological replicates each of Col-0 (WT) and fer-4 mutant seedlings were treated with Aradopside and compared to four biological replicates of untreated seedlings from each genotype.

first: Hongqing

last: Guo

first: Justin

middle: W

last: Walley

first: Yanhai

last: Yin


title: LGR5 expressing skin fibroblasts define a major hub perturbed in Systemic Sclerosis

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Systemic sclerosis (SSc) is an incurable autoimmune disease with high morbidity and mortality rates, with no effective treatment. Here, we conducted a population scale single-cell genomic analysis of skin and blood samples of 56 healthy controls, and 97 SSc patients at different stages of disease. We found immune compartment activation in only a subset of diffuse SSc patients, but global dysregulation of the stromal compartment, including a novel subset of LGR5+ scleroderma associated fibroblasts (ScAF). ScAF cells are mainly localized in the deep reticular dermis of healthy subjects and are dramatically perturbed morphologically and molecularly in SSc patients. Single-cell multiome profiling of the epigenetic and transcriptional landscapes of stromal cells in healthy subjects and SSc patients, revealed ScAF-specific markers, pathways, and transcription factors important in disease development. Systematic analysis combining the clinical metadata and molecular features of the patients, associates specific ScAF targets with disease pathogenesis and SSc clinical traits. Our study provides a high-resolution atlas of the entire spectrum of sclerodermatous skin, proposing a paradigm shift in the understanding of SSc disease and facilitating the development of new biomarkers and therapeutic strategies for SSc.

overall_design: Patients who were diagnosed with SSc based on the 2013 American College of Rheumatology/European League against Rheumatism revised criteria for SSc (Van Den Hoogen et al., 2013), were recruited to the study from rheumatology departments in two medical centers in Israel.  We excluded SSc patients under biological Disease-Modifying antirheumatic Drugs (DMARDs). After informed consent (in accordance with Helsinki declaration), skin samples were obtained through punch biopsy (4 mm), 10 cm distal to the elbow and placed in saline containing tubes on ice and then transferred to cold FACS buffer (EDTA pH8.0 2mM, BSA 0.5% in PBS). Whole blood samples were collected at the time of skin biopsy, were placed in EDTA-containing tubes (Beckton Dickenson) on ice and diluted 1:1 with ice cold FACS buffer. Skin and blood samples immediately transported to the lab. As a control, we also collected blood and skin samples from healthy patients following the same procedure.

first: Chamutal

last: Gur

first: Shuang-Yin

last: Wang


title: Transcriptomic profile of the FERONIA mutant

summary: The goal of this study was to determine transcriptional changes in the FERONIA mutant (fer) in Arabidopsis leaves

overall_design: Three biological replicates of WT and fer mutant rosette leaves were collected at 4 weeks and sequenced using QuantSeq.


title: A temporally controlled sequence of X-chromosome inactivation and reactivation defines female mouse in vitro germ cells with meiotic potential

city: Barcelona

first: Moritz

last: Bauer

address: C/ Dr. Aiguader, 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Centre for Genomic Regulation

summary: To investigate the interplay of X-chromosome status and meiosis during primordial germ cell (PGC) maturation, we differentiated mouse embryonic stem cells (ESCs) via epiblast-like cells (EpiLCs) into primordial germ cell like cells (PGCLCs) and further into meiotic germ cells. During the differentiation of PGCLCs, we assessed the kinetics of X-chromosome inactivation and reactivation. We generated allele-specific total RNA-seq datasets to assess gene inactivation and reactivation dynamics, as well as allele-specific single-cell RNA-seq using SMART-Seq v5 to investigate the interplay of meiosis and X-chromosome status in germ cells.

overall_design: Allele-specific total RNA-seq in ESC, EpiLCs and PGCLCs with distinct X-chromosome status. Allele-specific single-cell RNA-seq of ESCs and germ cells upon aggregation with gonadal somatic cells.

first: Bernhard

last: Payer

first: Jacqueline

last: Severino


title: mRNAseq and proteomic data set of one week old WT (Chop wt/wt CkmmCre wt/wt Dars2 fl/fl), Chop KO (Chop ko/ko CkmmCre wt/wt Dars2 fl/fl), Dars2 KO (Chop wt/wt CkmmCre tg/wt Dars2 fl/fl) and DKO (Chop ko/ko CkmmCre tg/wt Dars2 fl/fl) mice

city: Stockholm

first: Christian

last: Oertlin

address: Tomtebodavägen 23A

country: Sweden

institute: Karolinska Institutet

summary: Maintenance of mitochondrial homeostasis is essential for a broad spectrum of signalling, metabolic and energetic processes. Consequently, mitochondrial dysfunction is linked to the development of a wide range of myopathies and many common diseases including type 2 diabetes, Parkinson’s and Alzheimer’s diseases. In response to disturbed mitochondrial proteostasis, an organelle-specific stress response is initiated, which results in a global adaptive transcriptional response partially sharing the signature of the integrated stress response (ISR). However, the exact sequence of events of the signalling cascade resulting in the activation of the ISR remains elusive. CHOP was the first transcription factor (TF) proposed to play a role in this process, although - due to the lack of a trans-activating domain - it needs to heterodimerize with other TFs to activate or suppresses its target genes. Therefore, we decided to investigate the molecular aspects and in vivo functions of CHOP in a murine model of mitochondrial dysfunction triggered by the loss of mitochondrial translation. Disruption of mitochondrial translation by heart and skeletal muscle-specific knock-out of the mitochondrial aspartyl-tRNA synthetase DARS2 on its own results in death of the animals within 7-8 weeks. Additional deletion of CHOP even further reduces the lifespan to less than 3 weeks, suggesting an existential role of the TF within the initiated stress signalling pathway. Our recent data indicates that CHOP's impact arises from the regulation of another TF with detrimental effects when exceedingly activated under certain circumstances: ATF4.

overall_design: Comparison of mRNA expression with proteomic data sets at early (1 week) and late (2 weeks) stages of mitochondrial dysfunction

first: Sophie

last: Kaspar

first: Katharina

last: Senft

first: Alexandra

last: Kukat

first: Peter

last: Frommolt

first: Susanne

last: Bodesser

first: Ivan

last: Topisirovic

first: Ola

last: Larsson

first: Aleksandra

last: Trifunovic


title: A complex seeding of multiple metastases in clear cell renal cell carcinoma

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

institute: Inserm U1085-Irset

type:
Expression profiling by array
Genome variation profiling by array

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

overall_design: Refer to individual Series


title: Laminar shear stress inhibits inflammation by activating autophagy in human aortic endothelial cells through HMGB1 nuclear translocation

status: Public on Apr 03 2022

city: Changchun

first: luya

last: pu

address: No. 126 Xinmin St, Changchun, Jilin

institute: Jilin University

summary: Laminar shear stress (LSS) plays a variety of biological roles, one of which is regulation of gene expression in vascular endothelial cells. Prevention and treatment of atherosclerosis by targeting the inflammatory response in vascular endothelial cells has attracted much attention in recent years. In this study, we found that LSS could specifically inhibit the increased expression of intercellular adhesion molecule-1 (ICAM-1), vascular cell adhesion molecule-1 (VCAM-1), cyclooxygenase-2 (COX-2), and matrix metallopeptidase-9 (MMP-9) caused by tumor necrosis factor-α (TNF-α) stimulation in an autophagy-dependent pathway in human aortic endothelial cells (HAECs) and human umbilical vein endothelial cells (HUVECs). Whole-transcriptome sequencing analysis revealed that erythropoietin-producing hepatocyte receptor B2 (EPHB2) was a key gene in response to LSS. Moreover, co-immunoprecipitation (co-IP) assay indicated that LSS could activate autophagy flux by enhancing the EPHB2-mediated nuclear translocation of high mobility group box-1 (HMGB1), which interacts with Beclin-1 (BECN1) and finally leads to autophagy in HAECs. We also found that overexpression of EPHB2 can activate autophagy and exert the same anti-inflammatory effect as LSS. Simultaneously, we identified a novel LSS-sensitive long non-coding RNA (lncRNA), LOC10798635, and constructed an LSS-related LOC107986345/miR-128-3p/EPHB2 regulatory axis. Further research revealed the inhibition of endothelial inflammatory by LSS depends on autophagy activation resulting from the nuclear translocation of HMGB1 via the LOC107986345/miR-128-3p/EPHB2 axis. In conclusion, our study demonstrates for the first time that LSS regulates the expression of EPHB2 in HAECs, and the LOC107986345/miR-128-3p/EPHB2 axis plays a vital role in atherosclerosis development.

overall_design: This study included 3 samples, each with 3 replicates, where HAEC_0dy_0h was the control group.

first: Qingyu

last: Meng

first: Luya

last: Pu

first: Mingran

last: Qi

first: Shuai

last: Li

first: Banghao

last: Sun

first: Yaru

first: Bin

last: Liu

first: Fan


title: A complex seeding of multiple metastases in clear cell renal cell carcinoma (expression)

summary:
Tumor heterogeneity resulting from clonal evolution is a frequent feature in clear cell renal cell carcinoma (ccRCC) and could play a role in metastatic dissemination. However, the dynamics of metastatic evolution is not completely elucidated and could follow a complex seeding process.
Using a unique experimental design with a rare matched primary-metastatic case prior to any medical treatment, we retraced the lineage of metastatic clones that showed a complex, multiple, polyphyletic seeding of two functionally interdependent subclonal populations originating from the primary tumor, in the direction of all metastatic sites.

overall_design: We used integrative omics approaches combining genomic and transcriptomic data, on fourteen specimens from different macroscopic areas of a primary kidney tumor and three non-primitive sites including a vein thrombus and two metastases. All sites were heterogeneous and polyclonal, each containing simultaneously two aggressive sub clonal populations, with differentially expressed genes implicated in distinct biological functions. Our hypothesis is a polyclonal seeding with interactions between each sub-population in every analyzed metastatic context.

first: Julien

last: Dagher

first: Angélique

last: Brunot

first: Nathalie

last: Rioux-Leclercq


title: A complex seeding of multiple metastases in clear cell renal cell carcinoma (CGH)

overall_design:
We used integrative omics approaches combining genomic and transcriptomic data, on fourteen specimens from different macroscopic areas of a primary kidney tumor and three non-primitive sites including a vein thrombus and two metastases. All sites were heterogeneous and polyclonal, each containing simultaneously two aggressive sub clonal populations, with differentially expressed genes implicated in distinct biological functions. Our hypothesis is a polyclonal seeding with interactions between each sub-population in every analyzed metastatic context.
Multiple interdependent lineages could be the source of metastatic heterogeneity in ccRCC and could affect clinical outcome. Combining similar sampling strategies with single-cell transcriptomic approaches would produce a clearer picture of the subclonal evolution in ccRCC.


title: Molecular mechanisms underlying plasticity in a thermally varying environment

city: Aarhus N

first: Paul

middle: Vinu

last: Salachan

state: Aarhus

address: Brendstrupgårdsvej 21A

country: Denmark

institute: Aarhus University

summary: To investigate the molecular basis of fluctuating temperature induced phenotypic plasticity, we ran genome-wide transcriptomic analysis on Drosophila melanogaster subjected to acclimation at constant (19 +/- 0 degree Celcius) and fluctuating (19 +/- 8 degree Celcius) temperatures and contrasted the induction of molecular mechanisms in adult males, adult females, and larvae. We investigated whether fluctuations act by permanently activating the involved mechanisms, or whether fluctuations repeatedly activate and repress mechanisms, during the hot (or heating) and the cold (or cooling) phase of thermal fluctuations. We show that adult flies acclimated to fluctuating temperatures tolerate high temperatures better than the constant temperature acclimated controls. Differential gene expression indicated that responses to thermal variability rely partly on life stage and sex specific mechanisms. Our results show that some of the involved mechanisms were permanently activated, while others tracked the thermal fluctuations. Further, for a number of genes, fluctuating temperature resulted in canalization of gene expression. Molecular mechanisms related to environmental sensing and chromatin reorganization seems to be important components of adaptive responses to thermal variability.

overall_design: A total of 80 samples were analysed across different timepoints for males, females and larvae, which includes 4 biological replicates per timepoint and sex/lifestage combination. Half of these samples were subjected to fluctating temperature (treatment) and the other half to constant temperature (control).

middle: V

first: Jesper

middle: G

last: Sørensen


title: Methylation array analysis of FACS-sorted, normal human mammary epithelial subtypes

status: Public on Apr 02 2022

city: Woolloongabba

first: Jodi

last: Saunus

state: Qld

address: 37 Kent St

department: Mater Research Institute

institute: The University of Queensland

type: Methylation profiling by genome tiling array

summary: The Illumina Infinium MethylationEPIC BeadChip was used to obtain DNA methylation profiles across >850,000 CpGs in mammary epithelial cell subsets isolated from two cosmetic breast reduction mammoplasty specimens.

overall_design: Bisulphite-converted DNA from the 8 samples was hybridised to the beadchips according to the manufacturer's instructions.

first: Xavier

last: De Luca

first: Peter

middle: T

last: Simpson


title: Spatiotemporal expression of HMGB2 regulates cell proliferation and hepatocyte size during liver regeneration

city: Miyazaki

first: Koichi

last: Yano

state: Miyazaki

address: 5200 Kihara, Kiyotake

department: Department of Anatomy, Histochemistry and Cell Biology, Faculty of Medicine

country: Japan

institute: University of Miyazaki

summary: Liver regeneration is an extraordinarily complex process involving a variety of factors; however, the role of chromatin protein in hepatocyte proliferation is largely unknown. In this study, we investigated the functional role of high-mobility group box 2 (HMGB2), a chromatin protein in liver regeneration using wild-type and HMGB2-knockout (KO) mice.   Liver tissues were sampled after 70% partial hepatectomy (PHx), and analyzed by immunohistochemistry using various markers of cell proliferation, including Ki-67, PCNA, cyclin D1, cyclin B1, EdU and pH3S10. In WT mice, hepatocyte proliferation was strongly correlated with the spatiotemporal expression of HMGB2; however, cell proliferation was significantly delayed in hepatocytes of HMGB2-KO mice. Quantitative PCR demonstrated that cyclin D1 and cyclin B1 mRNAs were significantly decreased in HMGB2-KO mice livers. Interestingly, hepatocyte size was significantly larger in HMGB2-KO mice at 36-72 h after PHx, and these results suggest that hepatocyte hypertrophy appeared in parallel with delayed cell proliferation. In vitro experiments demonstrated that cell proliferation was significantly decreased in HMGB2-KO cells. A significant delay in cell proliferation was also found in HMGB2-siRNA transfected cells. In summary, spatiotemporal expression of HMGB2 is important for regulation of hepatocyte proliferation and cell size during liver regeneration.

overall_design: Microarray analysis was used to screen for genes that are related to HMGB2 expression. RNA was isolated from WT and HMGB2-KO mouse livers (n = 3 each), and cRNA was prepared. cRNA from each sample was hybridized to a pre-equilibrated Clariom S mouse microarray chip, which was then washed, stained, and scanned in an HP ChipScanner (Affymetrix Inc., Santa Clara, USA).

first: Narantsog

last: Choijookhuu


title: Immune memory after respiratory infection with Streptococcus pneumoniae is revealed by in vitro stimulation of murine splenocytes with inactivated pneumococcal whole cells: evidence of early recall responses by transcriptomic analysis

city: Siena

first: Francesco

last: Santoro

state: SI

address: Viale Bracci, 16, V lotto, I piano

department: Department of Medical Biotechnologies

country: Italy

institute: University of Siena

summary: In the present study, we used RNA sequencing on mouse splenocytes to describe the immune recall in the days following pneumococcal lung infection. Mice were sacrificed at days 1, 2, 4, and 7 after Streptococcus pneumoniae (TIGR4 serotype 4) intranasal infection and splenocytes were cultured in the presence or absence of the same inactivated bacterial strain to access the transcriptomic profile.

overall_design: RNA sequencing on splenocytes of intranasally infected mice sacrificed at 1, 2, 4, or 7 days after infection. Splenocytes were stimulated with inactivated whole pneumococcal cells or not.

first: Isabelle

middle: F

last: Moscardini

first: Monica

last: Carraro

first: Alice

last: Gerlini

first: Fabio

last: Fiorino

first: Chiara

last: Germoni

first: Samaneh

last: Gholami

first: Elena

last: Pettini

first: Donata

last: Medaglini

last: Iannelli

first: Gianni

last: Pozzi


title: A nuclear receptor facilitates differentiation of human PSCs into more mature hepatocytes

city: Cambridge

first: Haiting

last: Ma

state: MA

address: 455 Main Street

institute: Whitehead Institute


title: A nuclear receptor facilitates differentiation of human PSCs into more mature hepatocytes [ChIP-seq]

summary: The capacity to generate functional hepatocytes from renewable human pluripotent stem cells (hPSCs) could address limited supplies of primary human hepatocytes. However, hepatocytes differentiated from hPSCs in vitro are functionally immature. To understand mechanisms regulating maturation of in vitro derived hepatocytes, we developed a 3D spheroid differentiation system and compared gene regulatory elements in uncultured human primary hepatocytes with those in hepatocytes that were differentiated in 2D or 3D conditions from human PSCs by RNA-seq, ATAC-seq, and H3K27Ac ChIP-seq. Three-dimensional differentiation improved enhancer activity and expression of transcription factor ONECUT1, but was insufficient to upregulate human-specific mature hepatocytes marker gene CYP3A4 or super-enhancer regulated transcription factor gene NFIC. Regulome comparisons showed reduced enrichment of thyroid receptor THRB motifs in accessible chromatin and in active enhancers without reduced transcription of THRB, suggesting the regulation at the level of THRB ligands in PSC-differentiated hepatocytes. Addition of thyroid hormone T3 to the PSC-differentiated hepatocytes increased CYP3A4 expression. T3 increased binding of THRB to the CYP3A4 proximal enhancer and restored the super-enhancer status and gene expression of NFIC and reduced expression of AFP. The resultant hPSC-hepatocytes showed gene expression, epigenetic status and super-enhancer landscape closer to primary hepatocytes and activated regulatory regions including non-coding SNPs associated with liver-related diseases. Transplanting the 3D PSC-hepatocytes into immunocompromised mice resulted in engraftment of human hepatocytes in the mouse liver parenchyma without disrupting normal liver histology at 6 months after transplantation. This work provides insights into the functions of nuclear receptor THRB and highlights the importance of the environmental factors-nuclear receptors axis in regulating maturation of human PSC-differentiated cell types.

overall_design: Examination of gene expression of primary human non-cultured hepatocytes, human pluripostent stem cells differentiated hepatocyte-like cells under 2D condition, 3D spheroid condition, and 3D spheroid condition with T3 and without OSM.

first: Rudolf

last: Jaenisch


title: RNA-seq gene expression profiling of livers from CD1 mice treated with adeno-associated virus encoding constitutively active STAT5b (AAV8-STAT5ca)

first: David

last: Waxman

summary: PolyA-selected nuclear RNA isolated from livers of adult male mice administered AAV8-STAT5ca was analyzed by RNA-seq to determine the impact of constitutive STAT5 activation on the expression of sex-biased genes in male mouse liver. This is part of a study entitled 'Constitutively active STAT5b feminizes mouse liver gene expression', where delivery of constitutively active STAT5 (STAT5CA) to male mouse liver was shown to induce widespread feminization of the liver, with extensive induction of female-biased genes and repression of male-biased genes, largely mimicking results obtained when male mice are given GH as a continuous infusion. Many of the STAT5CA-responding genes were associated with nearby (< 50 kb) sites of STAT5 binding to liver chromatin, supporting the proposed direct role of persistently active STAT5 in continuous GH-induced liver feminization. The feminizing effects of STAT5CA were dose-dependent; moreover, at higher levels, STAT5CA overexpression resulted in some histopathology, including hepatocyte hyperplasia, and increased karyomegaly and multinuclear hepatocytes. Together, these findings establish that the persistent activation of STAT5 by GH that characterizes female liver is by itself sufficient to account for the sex-dependent expression of a majority of hepatic sex-biased genes.

overall_design: Liver nuclear RNA, polyA-selected, was isolated from adult male mice, with and without AAV8-STAT5ca treatment. RNA-seq libraries were prepared and subject to Illumina sequencing.

first: Hong

first: Dana

last: Lau-Corona


title: A nuclear receptor facilitates differentiation of human PSCs into more mature hepatocytes [ATAC-seq]


title: Systems-wide analysis of the GATC-binding nucleoid-associated protein Gbn and its impact on Streptomyces development

city: Ledien

first: Gilles

middle: P.

last: van Wezel

address: Sylviusweg 72

department: Institute of Biology Leiden

country: Netherlands

institute: Leiden University

summary: We report the regulatory effect of a novel family of nucleoid-associated protein in Streptomyces coelicolor

overall_design: To investigate the regulatory effect of Gbn (SCO1839), the knockout mutant  and its parient were investigated at two different growth stages: vegetative growth (24 h) and sporulation stage (45 h).

first: Chao

last: Du


title: Specification of fetal liver endothelial progenitors to functional zonated adult sinusoids requires c-Maf induction [c-Maf KO]

city: New York

first: Franco

last: Izzo

state: NY

address: 1470 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

summary: Endothelial cell heterogeneity shapes the unique attributes of organ-specific blood vessels; however, how intra-organ vascular cell diversity is established remains unsolved. Liver vascular network is patterned by sinusoidal and hepatocyte co-zonation, however how intra-liver vessels acquire their hierarchical specialized functions is unknown. Here, we resolve the heterogeneity of hepatic vascular cells during development through functional and single-cell RNA sequencing. We show that acquisition of sinusoidal endothelial cell identity is initiated during early development and is completed postnatally, originating from a pool of undifferentiated vascular progenitors at E12. Notably, we identify the peri-natal induction of the transcription factor c-Maf as a critical switch for sinusoidal identity determination. Endothelium-restricted deletion of c-Maf disrupts liver sinusoidal development, aberrantly expands postnatal liver hematopoiesis, promotes excessive postnatal sinusoidal proliferation, and aggravates liver pro-fibrotic sensitivity to chemical insult. Notably, c-Maf overexpression in generic differentiated endothelial cells switches on a liver sinusoidal transcriptional zonation program that maintains hepatocyte function. Therefore, c-Maf represents an inducible intra-organotypic and niche-responsive molecular determinant of sinusoidal cell identity and lays the foundation for designing strategies to initiate vasculature-driven liver repair.

overall_design: Single cell RNA sequencing of controls and c-Maf KO endothelial cells at P15.

first: Jesus

last: Salinero

first: Shahin

last: Rafii


summary: We report the DNA binding profile of a novel family of nucleoid-associated protein in Streptomyces coelicolor

overall_design: Two different growth stages were investigated, specifically vegetative growth and sporulation stage.


title: Fracture callus from young and aged mice

status: Public on Apr 01 2022

city: Rochester

first: Andrew

last: McDavid

address: 265 Crittenden Boulevard, CU 420630

institute: University of Rochester

summary: Skeletal stem/progenitor cells are critical for fracture repair by providing osteochondro precursors in the callus, which is impaired in aging. However, the molecular signatures of callus skeletan progenitor cells during aging is not known. We performed single-cell RNA sequencing on  CD45-CD31-Ter119- skeletan progenitor cells isolated from young and aged mouse calluses.

overall_design: C57BL/6J mice were housed in micro-isolator rodent rooms.  Open tibial fractures were performed on one 4-month-old mouse and one 21-month-old mouse.  Callus tissues were harvested on day 10.

first: Xi

last: Lin

first: Hengwei

last: Zhang

first: Jiatong

last: Liu

first: Chia-Lung

last: Wu

first: Andrea

last: Baran

first: Brendan

last: Boyce

first: Lianping

last: Xing


title: Nucleosome organization dynamics during fertilization reveals regulation factors of zygotic gene activation in mouse

city: Shanghai

first: Shaorong

last: Gao

state: Shanghai

address: 1239 Siping Road, Yangpu District

department: School of life science and technology

institute: Tongji University


title: Single-cell chromatin and gene-regulatory dynamics of mouse nephron progenitors [ChIP-seq]

city: New Orleans

first: Samir

middle: S

last: El-Dahr

state: Louisiana

address: 1430 Tulane Avenue

department: Pediatric Nephrology

institute: Tulane University

summary:
Background: We reasoned that unraveling the dynamic changes in accessibility of genomic regulatory elements and gene expression at single-cell resolution will inform the basic mechanisms of nephrogenesis.
Methods: We performed single-cell ATAC-seq and RNA-seq both individually (Singleomes; Six2GFP cells) and jointly in the same cells (Multiomes; kidneys) to generate integrated chromatin and transcriptional maps in mouse embryonic and neonatal nephron progenitor cells (NPCs).
Results: We demonstrate that singleomes and multiomes are comparable in assigning most cell states, identification of new cell type markers, and defining the transcription factors driving cell identity. However, multiomes are more precise in defining the progenitor population. Multiomes identified a “pioneer” bHLH/Fox motif signature in NPCs. Moreover, we identified a subset of Fox factors exhibiting high chromatin activity in podocytes. One of these Fox factors, Foxp1, is important for nephrogenesis. Key nephrogenic factors are distinguished by strong correlation between linked gene-regulatory elements and gene expression.
Conclusion: Mapping the regulatory landscape at single-cell resolution informs the regulatory hierarchy of nephrogenesis. Paired single-cell epigenomes and transcriptomes of nephron progenitors should provide a foundation to understand prenatal programming, regeneration following injury, and ex vivo nephrogenesis.

overall_design:
Chip-seq from E13.5 and P0 Nephron Progenitor Cells with H3K4me1, H3K27me3 and H3K27ac.
Nephron Progenitor cells (NPCs) were isolated by Magnetic Activated Cell Sorting (MACS) from  E13.5 and P0 CD1 mouse kidneys. The NPCs were cultured in nephron progenitor expansion medium (NPEM) and passaged twice before the cells were subjected to ChIP-seq for H3K4me1, H3K27me3, and H3K27ac.


title: Expression data from  Green cells (BT-GC) -treated HFDPCs

city: Tsukuba,

first: Meriem

last: Bejaoui

state: Ibaraki

address: 1 Chome-1-1 Tennodai

institute: University of Tsukuba

summary:
Gene expression profiling reveals a potential role of Green cells (BT-GC) in stimulating hair growth in dermal papilla cells.
HFDPCs were human primary cells line, treated with 1:2000 Green cells (BT-GC) for 48 h. Microarray gene expression profiling was conducted for three biological replicates

overall_design: RNA was extracted using Isogen (Nippon Gene Co. Ltd., Toyama, Japan). The integrity of RNA was quantified using NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). RNA samples were prepared for gene expression profiling analysis with GeneChip® 3' Expression Arrays using 3' IVT PLUS Reagent Kit (Affymetrix Inc., Santa Clara, CA, USA). Two hundred and fifty ng of total RNA from each sample was used to generate amplified and biotinylated complementary RNA (cRNA) from poly (A) RNA in a total RNA sample according to the user manual. IVT Incubation time was 16 hour. GeneAtlas® Hybridization, Wash and Stain Kit was used for hybridizing 3' IVT Array Strips according to the user manual (P/N 08-0306). Human genome array strips (HG-U219) were hybridized for 16 hours in a 45oC incubator, washed and stained and finally imaging was done with the GeneAtlas Fluidics and Imaging Station.


title: Transcriptomic analyses of co-treatment of AFB1 and curcumin in chicken liver

city: Harbin

first: Sihong

last: Li

address: 600 Changjiang Road

institute: Northeast Agricultural University

summary:
Purpose:In order to assess the toxicity of AFB1 in chicken liver and the mechanism of curcumin alleviating AFB1-induced liver toxicity in chicken, we established a co-administered model to investigate LncRNA and mRNA profiles of chicken liver.
Methods: RNA extracted by Total RNA Extractor (Trizol) was utilized to construct the final library. Libraries were pooled and sequenced on a 150-bp paired-end Illumina HiSeq™ 2000 run.  The sequencing data obtained from Illumina Hiseq™ was filtered to get clean reads using Trimmomatic. The reads themselves and their matching reads which length was less than 35nt were removed. Clean reads were aligned to the reference sequence (Gallus_gallus-5.0, NCBI) using HISAT2.
Results: Sampling directly from the liver yielded sufficient quantities of RNA to assess transcripts from each chicken and mapped to 24,883 Gallus gallus genes.
Conclusions: We used the method of RNA-seq to find the target genes and related signaling pathways involved in the co-administered (AFB1 and curcumin) and their underlying mechanisms.

overall_design: RNA-seq of livers from chickens treated with AFB1, or AFB1 and curcumin or no treatment control.

first: Xiuying

first: Ruimeng

first: Hongxiao

last: Yu


title: Expression data from  Orange cells (BT-OC) -treated HFDPCs

summary:
Gene expression profiling reveals a potential role of Orange cells (BT-OC) in stimulating hair growth in dermal papilla cells.
HFDPCs were human primary cells line, treated with 1:2000  Orange cells (BT-OC) for 48 h. Microarray gene expression profiling was conducted for three biological replicates


title: Time-dependent alteration of gene expression after induced knockout of Trex1 in bone marrow derived macrophages.

city: Heidelberg

first: Axel

last: Roers

address: Im Neuenheimer Feld 305

department: Institute of Immunology

institute: Heidelberg University Hospital

summary: Defects in three prime repair exonuclease (TREX1) cause the type I interferonopathy Aicardi Goutières syndrome. In absence of TREX1 some unknown DNA is accumulating in the cytosol which triggers cGAS/STING activation and type I interferon production. This analysis was designed to understand the kinetics of accumulation of the pathogenic cGAS ligand and the resulting altered gene expression upon induced loss of TREX1.

overall_design: Trex1 ko was induced in bone marrow derived macrophages from Trex1FL/FL Cre-ERT2WT/KI mice and Trex1WT/FL controls by 4-Hydroxytamoxifen treatment. Cells were harvested from day 1 to day 4 after 4-OHT treatment. Total RNA was isolated using NucleoSpin RNA Kit (Macherey-Nagel). RNA was sequenced on Illumina NovaSeq 6000.

first: Nadja

last: Schubert


title: GENE EXPRESION PROFILE OF HEPATIC PROGENITOR CELLS FROM Ptpn1+/+ AND Ptpn1-/- MICE AFTER PALMITIC ACID TREATMENT

city: MADRID

last: VALDECANTOS

state: MADRID

address: C/ARTURO DUPERIER, 4

institute: IIB ALBERTO SOLS

summary: We report the role of PTP1B deficiency in hepatic progenitor cells in the protection against lipotoxic injury

overall_design: RNAseq analysis of Ptpn1+/+ abd Ptpn1-/- HPCs (oval cells) treated with or without palmitic acid during 8 h

first: I

last: Barahona

first: P

last: Rada

first: M

last: Valdecantos

first: A

last: Valverde


title: RNA-seq analysis to examine the effect of KDM2B knockdown or overexpression on transcriptional responses in ECs during VEGF-signaling

city: Tokyo

first: Yoshiki

last: Higashijima

address: 1-5-45 Yushima, Bunkyo

department: Medical Research Institute

institute: Tokyo Medical and Dental University

summary: Vascular endothelial growth factor (VEGF) signaling serves a central role in vascular development as well as maintaining vascular homeostasis. In endothelial cells (ECs), VEGF activates gene expression of angiogenic transcription factors (TFs) followed by downstream induction of angiogenic responsive genes. Recent findings support histone modification dynamics contribute to transcriptional control of genes important for EC functions. Lysine demethylase 2B (KDM2B) demethylates histone H3K4me3 and H3K36me2/3 and also mediates monoubiquitylation of histone H2A119K. KDM2B functions as a transcriptional repressor in somatic cell reprograming and tumor development. However, the role of KDM2B during VEGF-signaling remains to be elucidated. Here, we show in cultured human ECs that knockdown of KDM2B enhances VEGF-induced angiogenesis via increased abilities of migration and proliferation. In contrast, ectopic expression of KDM2B has inhibitory effects on angiogenesis. The function of KDM2B is possibly dependent on its catalytic Jumondi C domain. Genome-wide analysis further reveal that KDM2B selectively controls transcription of VEGF-induced angiogenic TFs where increased H3K4me3/H3K36me3 and decreased of H2A119Kub are associated. These findings suggest an essential role of KDM2B during VEGF-signaling in ECs. Because dysregulation of VEGF signaling in ECs is involved in various diseases including cancer, KDM2B may be a potential therapeutic target in VEGF-mediated vasculopathic diseases.

overall_design: Total 15 samples were derived from VEGF-stimulated human cultured endothelial cells in [1] KDM2B knockdown experiments  and [2] KDM2B overexpression experiments.

first: Yuji

last: Sasaki

first: Yasuharu

last: Kanki


title: Transcriptome and epigenetic characterization of ECs during VEGF-signaling

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

overall_design: Refer to individual Series


title: Mouse embryonic fibroblasts in autophagy processes

city: Dongjak-Gu

first: Junil

last: Kim

address: 369 Sangdo-Ro

institute: SOONGSIL UNIVERSITY


title: Transcriptomic analysis in airway epithelial cells in HDM-sensitized STAT3-WT and STAT3-cKO mice

city: Chiba

first: Masaya

last: Yokota

address: 1-8-1 Inohana

department: Department of Allergy and Clinical Immunology

institute: Graduate school of Medicine, Chiba University

summary: Purpose: To elucidate the roles of airway epithelial STAT3 in allergic airway inflammation.  Method: Doxycycline-induced airway epithelial cells-specific STAT3-deficient mice (STAT3-cKO) and their genetic control mice (STAT3-WT) were sensitized intratracheally twice with house dust mite (HDM) extract or PBS at a 7-day interval. Airway epithelial cells were isolated by a cell sorter 48 h after the last senstization. N=2 each.  Results: Using an optimized data analysis workflow, 206 transcripts showed differential expression between HDM-treated STAT3-WT and STAT3-cKO with adjusted p value <0.05.

overall_design: mRNA profiles of airway epithelial cells isolated from the lung of STAT3-WT and STAT3-cKO mice after HDM sensitization.

first: Nozomi

last: Nishimura

first: Arifumi

last: Iwata


title: Transcriptomic analysis in airway epithelial cells in HDM-sensitized mice


title: Effects of paternal nicotine taking on gene expression in dorsal hippocampus of drug naïve male offspring

city: Philadelphia

first: Heath

last: Schmidt

address: 125 South 31st Street

institute: University of Pennsylvania

summary:
Nicotine intake, whether through tobacco smoking or e-cigarettes, remains a global health concern. An emerging preclinical literature indicates that parental nicotine exposure produces behavioral, physiological, and molecular changes in subsequent generations. However, the heritable effects of voluntary parental nicotine taking are unknown. Here, we show increased acquisition of nicotine taking in male and female offspring of sires that self-administered nicotine. In contrast, self-administration of sucrose and cocaine were unaltered in male and female offspring suggesting that the intergenerational effects of paternal nicotine taking may be reinforcer specific. Further characterization revealed memory deficits and increased anxiety-like behaviors in drug-naïve male, but not female, offspring of nicotine-experienced sires. Using an unbiased, genome-wide approach, we discovered that these phenotypes were associated with decreased expression of Satb2, a transcription factor known to play important roles in synaptic plasticity and memory formation, in the hippocampus of nicotine-sired male offspring. This effect was sex-specific as no changes in Satb2 expression were found in nicotine-sired female offspring. Finally, increasing Satb2 levels in the hippocampus prevented the escalation of nicotine intake and rescued the memory deficits associated with paternal nicotine taking in male offspring. Collectively, these findings indicate that paternal nicotine taking produces heritable sex-specific molecular changes that promote addiction-like phenotypes and memory impairments in male offspring.
To characterize the molecular changes associated with the heritable effects of paternal nicotine taking, an unbiased, whole-genome analysis was used to characterize the hippocampal transcriptome of drug-naïve F1 males

overall_design: Dorsal hippocampi were dissected from young adult male offspring of sires that self-administered nicotine. Saline-sired male offspring served as controls.

first: John

middle: J

last: Maurer


title: IL-17RA blockade by brodalumab hidradenitis suppurativa

first: James

last: Krueger

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

summary: The goal of this study is to characterize the molecular response of HS patients to brodalumab therapy in skin and serum, and to identify biomarkers of treatment response. Ten participants that received 210 mg/1.5mL brodalumab subcutaneously at week 0, 1, 2, 4 and every 2 weeks after were included in this molecular profiling study (NCT03960268). RNA-sequencing of nonlesional, perilesional and lesional HS skin biopsies was assessed.

overall_design: Punch biopsies of nonlesional, perilesional and lesional HS skin were collected under ultrasound guidance as part of NCT03960268. Biopsies were collected prior to treatment (baseline) and at week 12, with an optional week 4 biopsy.

first: Kristina

last: Navrazhina

last: Frew

first: Samuel

middle: C

last: Williams

first: David

last: Grand

first: Juana

last: Gonzalez

first: Sandra

last: Garcet


title: Transcriptomic analysis in airway epithelial cells in HDM-sensitized and SCD1 inhibitor-treated or vehicle-treated mice

summary: Purpose: To elucidate the effects of SCD1 inhibitor in allergic airway inflammation.  Method: Wild-type mice were sensitized intratracheally twice with house dust mite (HDM) extract at a 7-day interval. Along with that, an SCD-1 inhibitor, A939572 was also administered intraperitoneally daily. Airway epithelial cells were isolated by a cell sorter 48 h after the last senstization. N=2 each.  Results: Using an optimized data analysis workflow, 385 transcripts showed differential expression between SCD1 inhibitor-treated mice and DMSO (vehicle)-treated mice with adjusted p value <0.05.

overall_design: mRNA profiles of airway epithelial cells isolated from the lung of SCD1 inhibitor-treated mice and DMSO-treated mice after HDM sensitization.


title: Nucleosome organization dynamics during fertilization reveals regulation factors of zygotic gene activation in mouse (MNase-seq)

first: Shaorong

last: Gao

summary: Chromatin remodeling is essential for epigenome reprogramming after fertilization. However, the underlying mechanisms of chromatin remodeling remain to be explored. Here, we investigated the dynamic changes in nucleosome occupancy and positioning in pronucleus-stage zygotes using low-input MNase-seq. We observed distinct features of inheritance and reconstruction of nucleosome position in both male and female genomes. Genome-wide de novo nucleosome occupancy in the paternal genome was observed as early as 1 hour after the injection of sperm. The nucleosome positioning pattern was continually rebuilt to form nucleosome depletion regions (NDRs) at promoters and transcription factor (TF) binding sites. NDRs formed more quickly on the promoters of genes involved in zygotic genome activation (ZGA), and their formation is closely connected with histone acetylation, but not transcription elongation or DNA replication. Importantly, we found that NDR establishment on the binding motifs of specific TFs might be associated with their potential pioneer functions in ZGA. Further investigations suggested that the predicted factors MLX and RFX1 played important roles in regulating minor and major ZGA, respectively. Our data not only elucidate the nucleosome positioning dynamics in both male and female pronuclei following fertilization, but also provide an efficient method for identifying key transcription regulators during development.

overall_design: We generated the nucleosome profiles using ultra-low input MNase-seq in mouse gametes and pronucleus. For mouse gametes, we generated sperm, oocyte and round spermatid (RS) MNase-seq profiles. For sperm fertilized pronucleus, we separated them into male pronucleus and female pronucleus, collected the samples at 0.5h, 1h, 1.5h, 2h, 3h, 4h, 6h, 8h, 12h after fertilization. For RS fertilized pronucleus, we generated the samples at 0.5h, 1h, 2h and 3h after fertilization. To investigate whether block transcription, DNA replication or histone acetylation affect the nucleosome positioning, we generated MNase-seq profiles for pronucleus samples at 6h treated with a-amantin, aphicolin, Hdac1/2 and JQ1. To explore the function of potential ZGA factors on nucleosome positioning, we generated MNase-seq profiles for pronucleus samples at 8h treated with siMlx, siRfx1 treatment.

first: Chenfei

last: Wang

first: Chuan

last: Chen

first: Xiaoyu

last: Liu

first: Chong

last: Li

first: Qiu

last: Wu

first: Lingyue

last: Yang

first: Xiaolan

first: Xiaochen

last: Kou

first: Yanhong

last: Zhao

first: Hong

first: Yong

last: Zhang

first: Yawei