title: CD8+ T cells induce interferon-responsive oligodendrocytes during white matter aging

status: Public on Sep 13 2022

city: Bonn

first: Ozgun

last: Gokce

address: Venusberg-Campus 1/99

institute: UKB-DZNE

summary: A hallmark of nervous system aging is a decline of white matter volume and function, but the underlying mechanisms leading to white matter pathology are unknown. Here, we found age-related alterations of oligodendrocytes with a reduction of total oligodendrocyte density in the aging murine white matter. Using single-cell RNA sequencing, we identify interferon-responsive oligodendrocytes, which localize in proximity of CD8+ T cells in the aging white matter. Absence of functional lymphocytes decreased oligodendrocyte reactivity and rescued oligodendrocyte loss, while T-cell checkpoint inhibition worsened the aging effect. In addition, we identified a subpopulation of immune cell dependent interferon-responsive microglia in the aging white matter, and co-culture experiments revealed that interferon- activated microglia triggered oligodendrocytes cell death. In summary, we provide evidence that T cells induced interferon-responsive oligodendrocytes and microglia are important modifiers of white matter aging.

overall_design: Study of oligodendrocytes and microglia in aging in a tissue-specific manner (white and gray matter) using the 10X single-cell RNA-sequencing platform. We also analyzed Rag1-deficient mice to study how the lack of mature T cells affect the age-dependent glial alterations that occur in the white matter.

first: Tugberk

last: Kaya

first: Lu

last: Liu

first: Hao

last: Ji

first: Simon

last: Besson-Girard

first: Mikael

last: Simons


title: Genome-wide maps of H3K9me3 upon Mphosph8 or Morc2a loss in sorted neuronal nuclei of adult mouse brains.

city: Vienna

first: Maria

last: Novatchkova

address: Dr Bohrgasse

country: Austria

institute: IMP/IMBA

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report that murine MPP8 and MORC2A are highly expressed in the brain and exclusively found in neurons. We show that genetic inactivation of Mphosph8 (coding for MPP8) or Morc2a in the nervous system of mice leads to alterations in brain architecture, behavioral impairments and reduction of life span. By doing RNA-seq and ChIP-seq experiments, we found that MPP8 and MORC2A suppress the repetitive-like protocadherin gene cluster on mouse chromosome 18 in a H3K9me3-dependent manner.

overall_design: Examination of consequences of Nestin-Cre-mediated nervous system-specific knock-out of Mphosph8 and Morc2a in FACS-sorted neuronal nuclei (from at least 2 brains per genotype).

first: Astrid

last: Hagelkruys


title: Single cell RNA-seq and TCR-seq of T cell responses against DNAJB1-PRKACA

status: Public on Sep 12 2022

city: Freiburg

first: Severin

last: Dicks

address: Breisacherstr. 153

department: Institute of Medical Bioinformatics and Systems Medicine

country: Germany

institute: University Freiburg Medical Center

type: Expression profiling by high throughput sequencing

summary: The DNAJB1-PRKACA fusion transcript is the oncogenic driver in fibrolamellar hepatocellular carcinoma (FL-HCC), a lethal disease lacking specific therapies. Here, we report on the identification, characterization and first immunotherapeutic application of HLA-presented neoantigens specific for the DNAJB1-PRKACA fusion transcript in FL-HCC. To characterize the T cell response against DNAJB1-PRKACA-derived HLA class I and HLA class II ligands, single cell RNA sequencing (scRNA-seq) and single cell TCR profiling from CD4+ and CD8+ T cells were performed using 10x Genomics single cell immune profiling.

overall_design: In this study, we analyzed the expressional profile and T cell receptor (TCR) repertoire of CD4+ T cells from a patient with FL-HCC after vaccination with a personalized DNAJB1-PRKACA-derived peptide vaccine. Furthermore we analyzed flow cytometry-sorted PA*24-specific CD8+ T cells from two healthy volunteers (P3 and P4) after in vitro aAPC priming. Single cell RNA sequencing (scRNA-seq) and single cell TCR profiling were performed using 10x Genomics single cell immune profiling.

first: Melanie

last: Boerries

first: Melissa

last: Zwick

first: Natalie

last: Köhler

first: Jens

last: Bauer

first: Juliane

middle: S

last: Walz


title: Tissue-wide Genetic and Cellular Landscape Instructs the Execution of Sequential PRC2 Functions in Neural Stem Cell Lineage Progression [neurons]

city: Klosterneuburg

first: Florian

middle: M

last: Pauler

address: Am Campus 1

institute: Institute of Science and Technology Austria (IST Austria)

summary: The generation of a correctly-sized cerebral cortex with all-embracing neuronal and glial cell-type diversity critically depends on faithful radial glial progenitor (RGP) cell proliferation/differentiation programs. Temporal RGP lineage progression is regulated by Polycomb Repressive Complex 2 (PRC2) and loss of PRC2 activity results in severe neurogenesis defects and microcephaly. How PRC2-dependent gene expression instructs RGP lineage progression is unknown. Here we utilize Mosaic Analysis with Double Markers (MADM)-based single cell technology and demonstrate that PRC2 is not cell-autonomously required in neurogenic RGPs but rather acts at the global tissue-wide level. Conversely, cortical astrocyte production and maturation is cell-autonomously controlled by PRC2-dependent transcriptional regulation. We thus reveal highly distinct and sequential PRC2 functions in RGP lineage progression that are dependent on complex interplays between intrinsic and tissue-wide mechanisms. In a broader context our results imply a critical role for the genetic and cellular niche environment in neural stem cell behavior.

overall_design: RNA-Seq of Emx1 expessing cells from control, sparse and conditional tissue-wide deletion of Eed in mouse neocortex using a MADM system

first: Nicole

last: Amberg

last: Hippenmeyer


title: Transcriptome sequencing of transgenic Nicotiana benthamiana producing moth pheromones

status: Public on Sep 26 2022

city: Ljubljana

first: Mojca

last: Juteršek

address: Večna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

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

overall_design: Refer to individual Series


title: A non-coding single nucleotide polymorphism at 8q24 drives IDH1-mutant glioma formation

city: Toronto

first: Daniel

last: Schramek

state: ON

address: 600 University Ave, Room 1080

country: Canada

institute: Lunenfeld- Tanenbaum Research Institute

summary: Establishing causal links between inherited polymorphisms and cancer risk is challenging. Here, we focus on the single nucleotide polymorphism rs55705857 (A>G), which confers a 6-fold increased risk of IDH-mutant low-grade glioma (LGG) and is amongst the highest genetic associations with cancer. By fine-mapping the locus, we reveal that rs55705857 itself is the causal variant and is associated with molecular pathways that drive LGG. Mechanistically, we show that rs55705857 resides within a brain-specific enhancer, where the risk allele disrupts OCT2/4 binding, allowing increased interaction with the Myc promoter and increased Myc expression. To functionally test rs55705857, we generated an IDH1R132H-driven LGG mouse model and show that mutating the highly conserved, orthologous mouse rs55705857 locus dramatically accelerated tumor development from 463 to 172 days and increased penetrance from 30% to 75%. Overall, our work generates new LGG models and reveals mechanisms of the heritable predisposition to lethal glioma in ~40% of LGG-patients.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA Seq, ChIP seq, Genomic interactions

first: Connor

last: Yanchus

first: Ahmad

last: Malik


title: Array46 750k test is an in-depht analysis to detect chromosomal alterations, CNVs and SNPs

status: Public on Sep 10 2022

city: CDMX

first: consuelo

last: salas

state: CDMX

address: INSURGENTES SUR 3700C

country: Mexico

institute: Instituto Nacional de Pediatria

summary:
The array46 750k study was performed in the DNA sample for mosaicism aneuploidy detection and loss or absence of heterozygosity. Samples include patients with phenotype associated with pigmentary mosaicism
The array46 750k study was performed in the DNA sample to discard uniparental disomy (UPD)

overall_design: To detect chromosomal alterations, CNVs and SNPs

first: C

last: Salas-Labadia


title: Genome-wide H3k27ac levels following FOXA1 KO in UMUC-1 human bladder cancer cells [scRNA-Seq]

status: Public on Sep 08 2022

city: NEW YORK

first: WENHUO

last: HU

email: huwenhuo@gmail.com, huw@mskcc.org

state: NEW YORK

address: 1275 YORK AVENUE

department: HOPP

country: USA

institute: MEMORIAL SLOAN KETTERING CANCER CENTER

summary: 10x scRNA-Seq results of a bladder cancer case with extensive squamous cell differentation

overall_design: Fresh tumor tissue were digesteThe tumor sample analyzed by single cell (sc)-RNASeq was dissociated (Miltenyi biotec) at 37 °C for 30 min. A single cell suspension was then analyzed using the 10x genomics platform.

first: Kwagnhee

last: Kim

first: Wenhuo

last: Hu

first: Hikmat

last: Al-Ahmadie

first: David

middle: B

last: Solit


title: C/EBPβ regulates lipid metabolism and Pparg isoform 2 expression in alveolar macrophages

status: Public on Sep 16 2022

city: Turku

first: alexander

last: mildner

address: Tykistökatu 6A

department: Biomedicine

country: Finland

institute: University of Turku / Medicity

summary: Pulmonary alveolar proteinosis (PAP) is a syndrome characterized by accumulation of surfactant lipoproteins within the lung alveoli. Alveolar macrophages (AMs) are crucial for surfactant clearance and their differentiation depends on colony-stimulating factor 2 (CSF2) and the establishment of an AM-characteristic gene regulatory network. Here we report that the transcription factor C/EBPβ is essential for the development of the AM identity, as demonstrated by transcriptome and chromatin accessibility analysis. Furthermore, C/EBPβ-deficient AMs showed severe defects in proliferation, phagocytosis and lipid metabolism, collectively resulting in a PAP-like syndrome. Mechanistically, the long C/EBPβ protein variants LAP* and LAP together with CSF2 signaling induced expression of Pparg isoform2, but not isoform1, a molecular regulation that was also observed in other CSF2-primed macrophages. These results uncover C/EBPβ as a key regulator of AM cell fate and as the missing link between CSF2 and Pparg isoform 2 expression, thereby regulating lipid turnover in AMs.

overall_design: Comparison of transcriptome and chromatin assesibility of different mouse Cebpb mutant alveolar macrophages against respective controls

first: Alexander

last: Mildner

first: Benedikt

last: Obermayer

first: January

last: Weiner

first: Dorothea

last: Dörr


title: Functional E3 ligase hotspots and resistance mechanisms to small-molecule degraders via chemical genetics

status: Public on Sep 09 2022

first: Hana

last: Imrichova

address: Lazarettgasse 14, AKH BT 25.3

institute: CeMM, Vienna


title: sciDLO Hi-C of Thp1-mono, Thp1-macro, and Thp1-M.tb

status: Public on Sep 06 2022

city: ShangHai

first: Da

last: Lin

address: No. 650 Songjiang Road

country: China

institute: Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China

summary: Raw date of sciDLO Hi-C libraries

overall_design: We developed a single-cell-indexed DLO Hi-C (sciDLO Hi-C) to capture the chromatin conformation of individual cells based on DLO Hi-C and two rounds of molecular barcoding to capture the chromatin conformation of individual cells

first: Weize

last: Xu


title: ATAC-seq of Thp1-mono, Thp1-macro, and Thp1-M.tb

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

first: Ping

last: Hong


title: Transcriptomic analysis of edited human hematopoietic stem/progenitor cells

city: Padova

first: Oriana

last: Romano

address: Via U. Bassi 58/B

department: Molecular Medicine

country: Italy

institute: University of Padova

summary: We have developed a therapeutic strategy for beta-hemoglobinopathies aimed at reactivating fetal hemoglobin expression in red blood cells derived from human hematopoietic stem/progenitor cells edited with CRISPR/Cas9 nucleases, cytidine or adenine base editors targeting the fetal gamma-globin promoters. Here, we report the transcriptomic changes occurring in human hematopoietic stem/progenitor cells  (obtained from healthy donors) 48 h after transfection with CRISPR/Cas9 nucleases, cytidine or adenine base editors.

overall_design: Analysis of human hematopoietic stem/progenitors obtained from 3 dfferent healthy donors and treated with  CRISPR/Cas9 nucleases, cytidine or adenine base editors.

first: Annarita

last: Miccio

first: Panagiotis

last: Antoniou


title: ChIP-seq of Thp1-mono, Thp1-macro, and Thp1-M.tb

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


title: RNA seq of mouse low grade glioma tumors

first: Daniel

last: Schramek

summary: RNA sequencing was performed on paraffin embedded mouse low grade glioma tumor tissue

overall_design: RNA-seq of mouse low grade glioma tumors

first: Connor

last: Yanchus

first: Ahmad

last: Malik


title: Genome-wide H3k27ac levels following FOXA1 KO in UMUC-1 human bladder cancer cells [RNA-seq]

first: WENHUO

last: HU

summary: We report areas of H3K27ac modification in both wild-type (parental) UMUC-1 and UMUC-1 FOXA1 KO bladder cancer cells.

overall_design: RNA-seq of parental and FOXA1 KO UMUC-1 cells.

middle: J

last: DeGraff

first: Hikmat

last: Al-Ahmadie

first: Wenhuo

last: Hu

first: Joshua

last: Warrick


title: Single-Cell Sequencing Reveals the Overall Changes in Tumor Microenvironment Mediated by CD39i

city: Wu Han

first: Junyi

address: No. 1277 Liberation Avenue

department: Urology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Here we identified the ecto-enzyme, CD39 (encoded by ENTPD1), as a potential therapeutic target for BC via single-cell transcriptome analysis of BC and para-cancer tissues. In a subcutaneous model, inhibition of CD39 (CD39i) is able to limit the growth of BC and improve overall survival of tumor-bearing mice. Via single-cell sequencing of tumor infiltrated immune cells, we found that CD39i with POM-1 increased the intratumor NK cells, conventional type 1 dendritic cells (cDC1) and CD8+ T cells, along with decreased Treg abundance. The anti-tumor effect and reprogram of tumor microenvironment are blockade in a cDC1-deficient Batf3−/− model.

overall_design: Comparing changes in TME caused by CD39i.

first: Lilong

last: Liu

first: Yaxin

last: Hou


title: Single-cell RNA sequencing of peripheral blood mononuclear cells reveals immune signaling dysregulations in people living with HIV and atherosclerosis

city: Rochester

first: Juilee

last: Thakar

state: New York

address: 601 Elmwood Ave

department: Microbiology and Immunology

institute: University of Rochester

summary:
Background: Atherosclerosis (AS)-associated cardiovascular disease is an important cause of mortality in an aging population of people living with HIV (PLWH). This elevated risk of atherosclerosis has been attributed to viral infection, prolonged usage of anti-retroviral therapy, and subsequent chronic inflammation.
Methods: To investigate dysregulated immune signaling in PLWH with and without AS, we sequenced 9368 peripheral blood mononuclear cells (PBMCs) from 8 PLWH, 4 of whom also had atherosclerosis (AS+).  To develop executable models of signaling pathways that drive cellular states in HIV-associated atherosclerosis, we developed the single-cell Boolean Omics Network Invariant Time Analysis (scBONITA) algorithm. ScBONITA (a) uses single-cell RNA sequencing data to infer Boolean rules for topologically characterized networks, (b) prioritizes genes based on their impact on signaling, (c) performs pathway analysis, and (d) maps sequenced cells to characteristic signaling states. We used scBONITA to identify dysregulated pathways in different cell-types from AS+ PLWH and AS- PLWH. To compare our findings with pathways associated with HIV infection, we used scBONITA to analyze a publicly available dataset of PBMCs from subjects before and after HIV infection. Additionally, the executable Boolean models characterized by scBONITA were used to analyze observed cellular states corresponding to the steady states of signaling pathways
Results: We identified an increased subpopulation of CD8+ T cells and a decreased subpopulation of monocytes in AS+ PLWH. Dynamic modeling of signaling pathways and pathway analysis with scBONITA provided a new perspective on the mechanisms of HIV-associated atherosclerosis. Lipid metabolism and cell migration pathways are induced by AS rather than by HIV infection. These pathways included AGE-RAGE and PI3K-AKT signaling in CD8+ T cells, and glucagon and cAMP signaling pathways in monocytes. Further analysis of other cell subpopulations suggests that the highly interconnected PI3K-AKT signaling pathway drives cell migratory state in response to dyslipidemia. scBONITA attractor analysis mapped cells to pathway-specific signaling states that correspond to distinct cellular states.
Conclusions: Dynamic network modeling and pathway analysis with scBONITA indicates that dysregulated lipid signaling regulates cell migration into the vascular endothelium in AS+ PLWH. Attractor analysis with scBONITA facilitated pathway-based characterization of cellular states that are not apparent in gene expression analyses.

overall_design:
scRNA sequencing data for peripheral blood mononuclear cell samples from male HIV+ donors with and without atherosclerosis
***Raw data not available due to patient privacy concerns***

first: Mukta

middle: G

last: Palshikar

first: Rohith

last: Palli

first: Alicia

last: Tyrell

first: Sanjay

last: Maggirwar

first: Giovanni

last: Schifitto

first: Meera

middle: V

last: Singh


title: Tissue-wide Genetic and Cellular Landscape Instructs the Execution of Sequential PRC2 Functions in Neural Stem Cell Lineage Progression [astro]

first: Florian

last: Pauler

overall_design: RNA-Seq of enriched astrocytes from control and sparse deletion of Eed in mouse neocortex using a MADM system

first: Nicole

last: Amberg

first: Simon

last: Hippenmeyer


title: Genome-wide H3k27ac levels following FOXA1 KO in UMUC-1 human bladder cancer cells

first: WENHUO

last: HU


title: Transcriptomic profiles of OASL knockdown HUVECs under basal or activated condition

city: Seoul

first: GooTaeg

last: Oh

address: 52, Ewhayeodae-gil

department: Department of Life Sciences

country: South Korea

institute: Ewha Womans University

summary:
Purpose: The goal of this study is to compare endothelial transcriptome affected by OASL knockdown under basal or stimulated conditions by utilizing RNA-seq.
Methods: Endothelial mRNA profilies of siCTL or siOASL transfected HUVECs were generated by illumina sequencing method, in duplicate. Following an optimized data analysis workflow, RNA sequence reads were counted using StringTie-2.1.3b and used to identify genes differentially expressed between siCTL- and siOASL-transfected HUVECs treated with or without TNFα and IFNγ.
Results: DESeq2 was used to identify genes differentially expressed between siCTL- and siOASL-transfected HUVECs under basal or stimulated conditions. Genes showing <10 read counts total were pre-filtered.
Conclusions: Our study represents the first analysis of endothelial mRNA affected by OASL knockdown with biologic replicates, generated by RNA-seq.

overall_design: HUVECs were cultured in EGM-2 BulletKit medium containing 10% FBS, 2mM L-glutamine, and penicillin/streptomycin and used at passage 7-10 for experiments. Two replicates of siRNA-transfected HUVECs per group were treated with or without TNFα and IFNγ added in serum-free EGM-2 for 3hours. Endothelial mRNA profiles of siCTL- and siOASL-transfected HUVECs were generated by RNA-seq.

first: Tae-Kyeong

last: Kim

first: Seonjun

last: Park

first: Sung-Ho

first: Goo-Taeg


title: Transcriptional changes upon Mphosph8 loss in mouse brains on postnatal day 14.

first: Maria

last: Novatchkova

overall_design: Examination of consequences of Nestin-Cre mediated nervous system specific knock-out of Mphosph8 in whole brains at postnatal day 14 (from 3 mice per genotype).

first: Astrid

last: Hagelkruys


title: Tissue-wide Genetic and Cellular Landscape Instructs the Execution of Sequential PRC2 Functions in Neural Stem Cell Lineage Progression


title: Histone H1 regulates non-coding RNA turnover on chromatin in a m6A-dependent manner

city: Madrid

last: Gomez

address: Nicolas Cabrera, 1

country: Spain

institute: CBMSO(CSIC/UAM)

summary: Linker histones are highly abundant chromatin-associated proteins with well-established structural roles in chromatin and as general transcriptional repressors. In addition, it has been long proposed that histone H1 exerts context-specific effects on gene expression. Here, we have identified a new function of histone H1 in chromatin structure and transcription using a range of genomic approaches. We show that histone H1-depleted cells accumulate nascent non-coding RNAs on chromatin, suggesting that histone H1 prevents non-coding RNA transcription and regulates non-coding transcript turnover on chromatin. Accumulated non-coding transcripts have reduced levels of m6A modification causing replication-transcription conflicts. Accordingly, altering the m6A RNA methylation pathway rescues the replicative phenotype of H1 loss. This work unveils unexpected regulatory roles of histone H1 on non-coding RNA turnover and m6A deposition, highlighting the intimate relationship between chromatin conformation, RNA metabolism and DNA replication to maintain genome performance.

overall_design: We compare H1-TKO cells with their WT counterpart using a wide range of genomic approaches: RNAPII-ChIP-seq, MNase-seq, cheRNA-seq, TT-seq and MapR

first: Jose

last: Fernandez-Justel

first: Cristina

last: Santa-Maria

first: Sara

last: Martín-Vírgala

first: Shreya

last: Ramesh

first: Alberto

last: Ferrera-Lagoa

first: Mónica

last: Salinas-Pena

first: Javier

last: Isoler-Alcaraz

first: Magdalena

last: Maslon

first: Albert

last: Jordan

middle: F

last: Caceres


title: Analysis of de novo methylation in mouse embryonic stem cells mediated by Dnmt3a2 PWWP domain variants

status: Public on Sep 05 2022

city: Cambridge

first: Brian

last: Liau

state: MA

address: 12 Oxford St.

department: Department of Chemistry and Chemical Biology

institute: Harvard University

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is critical for regulating gene expression, necessitating its accurate placement by enzymes such as the DNA methyltransferase DNMT3A. Dysregulating this process is known to cause aberrant development and oncogenesis, yet how DNMT3A function is shaped holistically by its three domains remains challenging to study. Through in situ mutational scanning, we found mutations in the PWWP domain, a histone reader, that modulate enzyme activity by affecting DNA binding, despite preserving histone recognition and protein stability. To investigate the consequences of these mutations on DNMT3A function in cells, we expressed ectopic Dnmt3a2 variants in embryonic stem cells and used reduced representation bisulfite sequencing and histone modification ChIP-seq to study the resulting patterns of de novo DNA methylation. Our data show that PWWP domain DNA affinity is required for full activity in cells and constitutes a noncanonical function of the PWWP domain.

overall_design: Reduced representation bisulfite sequencing was performed to characterize DNA methylation gain in Dnmt1/Dnmt3a/Dnmt3b triple-knockout (TKO) mouse embryonic stem cells (ESCs) reconstituted with ectopic Dnmt3a2 in biological duplicate (separate transfections). As a negative control, we included the E752K variant, which is catalytically dead. Additionally, ChIP-seq was performed for the H3K4me3, H3K27me3, and H3K36me2 histone modifications in the parent TKO ESC line, each in singlicate (including an Input control).

first: Nicholas

middle: Z

last: Lue

first: Emma

last: Garcia


title: Quantitative analysis of transcriptomes of MKN1 control/LRRFIP2 variant 3 exon 7 knockout cell lines

first: Jihee

last: Lee

address: 92 Myeongdal-ro, Seocho-gu

institute: GILO Institute

summary: We performed RNA sequencing analysis of wild-type and LRRFIP2 variant 3(LRRFIP2, NM_001134369) exon 7-deleted MKN1 cell lines to validate differentially expressed genes in the absence of the exon.

overall_design: mRNA profiles of MKN1 Control/LRRFIP2 variant 3(LRRFIP2, NM_001134369)-exon7-KO cell lines

first: Seong-Jin

last: Kim


title: Integrated analysis of cancer-related pathways affected by genetic and epigenetic alterations in gastric cancer

city: Shinagawa-ku

first: Hideyuki

last: Takeshima

state: Tokyo

department: Institute for Advanced Life Sciences

country: Japan

institute: Hoshi University

type: Methylation profiling by genome tiling array

overall_design:
DNA methylation was analyzed in human gastric cancers, and methylation status of cancer-related genes was analyzed.
Genome-wide DNA methylation analysis was conducted by an Infinium HumanMethylation450 BeadChip array.

first: Yukie

last: Yoda

first: Satoshi

last: Yamashita

first: Toshikazu

last: Ushijima


title: Genome-wide H3k27ac levels following FOXA1 KO in UMUC-1 human bladder cancer cells [ChIP-seq]

first: WENHUO

last: HU

overall_design: Examination of one histone modification in parental and FOXA1 KO UMUC-1 cells.

first: David

last: DeGraff

first: Hikmat

last: Al-Ahmadie

first: Wenhuo

last: Hu

first: Joshua

last: Warrick


title: Decoding the 3D genome of macrophage cells during differentiation and Immune activation [HiC]

first: Da

last: Lin

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

overall_design: In situ DLO Hi-C library construction strategies refer to previously published articles: “Lin, D. et al. Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture. Nature genetics 50, 754 (2018).”

first: Ping

last: Hong


title: Transcriptional profiling of organoid glomeruli isolated from human kidney organoids modelling congenital nephrotic syndrome

status: Public on Sep 07 2022

city: Parkville

first: Michael

last: See

state: VIC

address: Royal Children's Hospital, 50 Flemington Rd

country: Australia

institute: MCRI

summary:
To investigate the impact of various NPHS2 homozygous point mutations on podocyte biology in induced pluripotent stem cell (iPSC)-derived human kidney organoids, an iPSC allelic series was generated from a control fibroblast line  and two iPSC lines were derived from patient blood samples (one homozygous R168H and one unaffected relative)
iPSCs were differentiated into kidney organoids, organoids glomeruli were harvested and we performed gene expression profiling using data obtained from RNA-seq of 3 sets of 4 organoids for each genotype at D7+14 of our differentiation protocol (Takasato et al, Nature 2016)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for organoid glomeruli isolated at D7+14 from human kidney organoids with various NPHS2 homozygous point mutations.

first: Aude

last: Dorison

first: Irene

last: Ghobrial

first: Sara

middle: E

last: Howden

first: Alison

last: Graham

first: Mirana

last: Ramialison

first: Melissa

middle: H

last: Little


title: Quantitative profiling of differentially expressed miRNAs in siCTL- and siOASL-transfected HUVECs

first: GooTaeg

last: Oh

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: The goal of this study is to compare endothelial small RNA transcriptome to identify the target of OASL under basal or stimulated conditions by utilizing miRNA-seq.
Methods: Endothelial miRNA profilies of siCTL or siOASL transfected HUVECs were generated by illumina sequencing method, in duplicate. After sequencing, the raw sequence reads are filtered based on quality. The adapter sequences are also trimmed off the raw sequence reads. rRNA removed reads are sequentially aligned to reference genome (GRCh38) and miRNA prediction is performed by miRDeep2.
Results: We identified known miRNA in species (miRDeep2) in the HUVECs transfected with siCTL or siOASL. The expression profile of mature miRNA is used to analyze differentially expressed miRNA(DE miRNA).
Conclusions: Our study represents the first analysis of endothelial miRNA profiles affected by OASL knockdown with biologic replicates.

overall_design: HUVECs were cultured in EGM-2 BulletKit medium containing 10% FBS, 2mM L-glutamine, and penicillin/streptomycin and used at passage 7-10 for experiments. Two replicates of siRNA-transfected HUVECs per group were treated with or without TNFα and IFNγ added in serum-free EGM-2 for 3hours. Endothelial micro-RNA profiles of siCTL- and siOASL-transfected HUVECs were generated by miRNA-seq.

first: Tae-Kyeong

last: Kim

first: Seonjun

last: Park

first: Sung-Ho

first: Goo-Taeg


title: Single cell RNA sequencing analysis for atherosclerotic aortas in Oasl1/Apoe WT and Oasl1/Apoe DKO mice

summary: We have applied 10X single-cell RNA sequencing (scRNA-seq) technique to examine the cell type specific transcriptomes of heterogeneous cell populations in atherosclerotic aortas isolated from Oasl1+/+Apoe-/- and Oasl1-/-Apoe-/- mice.

overall_design: Single cell RNA sequencing analysis of the mouse atherosclerotic aortas. Aortic single cells were isolated from atherosclerotic aortic arch of Oasl1+/+Apoe-/- or Oasl1-/-Apoe-/- mice and were pooled (n=6, normal chow diet for 28 weeks). Total live aortic single cells were sorted by DAPI staining and subjected to characterization and further analysis of differentially expressed genes between two groups.

first: Sejin

last: Jeon

first: Nayoung

first: Hae-Ock

last: Lee


title: A pilot study of microRNA assessment as a means to identify novel biomarkers of spontaneous osteoarthritis in dogs

status: Public on Sep 04 2022

city: Fujisawa

first: Atsushi

last: Yamazaki

department: Department of Veterinary Medicine, College of Bioresource and Sciences

institute: Nihon University

summary: To investigate miRNA expression levels, RNA sequencing analysis (RNA-seq) was performed in synovial tissue and compared between the two groups.

overall_design: Differential expression analysis of RNA-seq data in synovial tissue of canine OA.

first: Yuma

last: Tomo

first: Hinano

last: Eto

first: Koji

last: Tanegashima

first: Kazuya

last: Edamura


title: Hoxa9/meis1-transgenic zebrafish develops acute myeloid leukemia-like disease with rapid onset and high-penetrance

status: Public on Sep 01 2022

city: Shanghai

first: Hongji

last: Li

state: Shanghai

address: Building 6, School of Pharmacy, Shanghai Jiao Tong University, No.800 Dongchuan Road, Minhang District, Shanghai

department: School of Pharmacy

institute: Shanghai Jiao Tong University

summary: HOXA9/MEIS1 plays a synergistic causative role and overexpresses frequently in acute myeloid leukemia (AML). Hoxa9/Meis1 transgenic murine results in rapid leukemic transformation of primary bone marrow cells. However, murine model is not suitable to perform a high-throughput phenotypic screen in vivo and identify compounds for AML therapy. A transgenic zebrafish overexpresses hoxa9/meis1 need to generate. We have engineered an inducible transgenic line Tg (drl:hoxa9;hsp70:meis1) harboring hoxa9/meis1 under the draculin (drl) promoter. The downregulation of runx1, c-myb, mpx, mfap4, and gata1 in Tg (drl:hoxa9;hsp70:meis1) embryos indicated enforced hoxa9/meis1 perturbs embryonic hematopoiesis. Importantly, adult Tg (drl:hoxa9;hsp70:meis1) develops malignant myeloid disease with an abundance of myeloid precursor cells, anemia, and high mortality after a latency period (~5-months-aged) with comparable to murine model and human AML patients. Genome-wide transcription changes analysis indicated arrested differentiation genes such as gata2b, notch1b, and gfi1ab are upregulated. Leflunomide, inhibitor of enzyme dihydroorotate dehydrogenase (DHODH) which is a potential option for differentiation therapy of AML, relieves defective hematopoiesis in transgenic embryos and larvae. Collectively, we have identified an inducible malignant myeloid disease transgenic zebrafish model similar to AML and provided a unique opportunity for high-throughput in vivo chemical screening for AML therapy and study the related mechanisms.

overall_design: To evaluate genome wide gene expression changes, the blood cells from kidneys were harvested from adult WT(AB strain) or Tg (drl:hoxa9;hsp70:meis1) zebrafish (~5-months-aged). The blood cells from three kidneys were mixed into one sample and lysed by Trizol.

first: Wei

last: Wang

first: Lili

last: Jing

first: Li

last: Hongji

first: Mengling

last: Huang


title: Gene expression levels of macrophage cells during differentiation and Immune activation

first: Da

last: Lin

summary: We then performed gene expression profiling analysis using data obtained from RNA-seq of Thp1-mono, Thp1-macro, Thp1-M.tb,  hMDMs-control, and hMDMs-M.tb

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Thp1-mono, Thp1-macro, Thp1-M.tb,  hMDMs-control, and hMDMs-M.tb.

first: Ping

last: Hong


title: Cell-type identity of the avian utricle

city: South San Francisco

first: Daniel

middle: C

last: Ellwanger

state: CA

address: 1120 Veterans Blvd

department: Genome Analysis Unit

institute: Amgen Inc

summary: The avian utricle, a vestibular organ of the inner ear, displays turnover of sensory hair cells throughout life. This is in sharp contrast to the mammalian utricle, which shows limited regenerative capacity. Here, we use single-cell RNA-sequencing to identify distinct marker genes for the different sensory hair cell subtypes of the chicken utricle, which we validated in situ . We provide markers for spatially distinct supporting cell populations, and identified two transitional cell populations of dedifferentiating supporting cells and developing hair cells. Trajectory reconstruction resulted in an inventory of gene expression dynamics of natural hair cell generation in the avian utricle.

overall_design: Utricles were dissected, single cells were deposited into individual wells of 96-well plates using flow cytometry and processed for single-cell RNA-sequencing

first: Mirko

last: Scheibinger

first: Stefan

last: Heller


title: Saliva methylome analysis of ART children that underwent embryo culture in G3 or K-SICM medium

city: Maastricht

first: Rebekka

middle: Maria

last: Koeck

address: Maastricht UMC+

department: Clinical Genetics

country: Netherlands

institute: Maastricht University Medical Centre

summary:
Follow-up study of 9 year old IVF children who underwent embryo culture in G3 (Vitrolife) or K-SICM (Cook) medium.
Genome-wide DNA methylation profiling of 9 year old IVF children (saliva samples) who had undergone embryo culture in G3 medium (Vitrolife) or K-SICM medium (Lonza). The EPIC array was used to profile the methylome at approximately 850,000 CpG sites across the human genome.

overall_design: Bisulphite converted DNA from umbilical cord blood samples from IVF 9-year-olds that had undergone embryo culture in G3 (n = 57 ) or HTF (n = 49) culture medium, were hybridised to the Illumina EPIC array. Data processing was conducted in R using the RnBeads package. Processing consisted of SWAN normalisation, and site/sample removal based on greedycut (detection p-value threshold 0.05), SNP proximity, position on the sex chromosomes, missing values in >5% of samples and sites not in a CpG context.

first: Florence

last: Busato

first: Jorg

last: Tost

first: Heleen

last: Zandstra

first: Sylvie

last: Remy

first: Sabine

last: Langie

first: Marij

last: Gielen

first: Ron

middle: T

last: van Golde

first: John

last: Dumoulin

first: Han

last: Brunner

first: Masoud

last: Zamani Esteki

first: Aafke

middle: A

last: van Montfoort


title: Single cell RNA and TCR profiling of tetramer sorted mouse mLN and IELs.

first: Damian

last: Plichta

address: 415 Main Street

institute: Broad Institute

summary: We utilized H2-I-Ab tetramers to isolate CD4 T cells from mice to characterize the functional characteristics of ileal intraepithelial T cells and their lymphoid counterparts in the corresponding draining lymph nodes (mLN). Non-CD4 T cells (B220+, CD11b+, CD11c+, F4/80+, CD8a+) were excluded before FACS-sorting of CD45+CD3+CD4+ tetramer-specific T cells discriminated by double-positive staining with dual-labeled tetramer fluorophores. We recovered tetramer+ and tetramer- IELs and mLN T cells, and profiled them by single-cell RNA and TCR sequencing.

overall_design: FACS sort of tetramer positive and tetramer negative cells in mLN and IELs.

middle: R

first: Eric

last: Brown

last: Graham

first: Thomas

middle: K

last: Pedersen


title: Dynamic control of metabolic zonation and liver repair by endothelial cell Wnt2 and Wnt9b revealed by single cell spatial transcriptomics using Molecular Cartography

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

summary: The conclusive identity of Wnt proteins regulating liver zonation (LZ) and regeneration (LR) remains unclear despite an undisputed role of beta-catenin. Using single-cell analysis of liver cells from various species, a conserved Wnt2 and Wnt9b expression in endothelial cells (ECs) in zone 3 shown to be the major Wnt cell source, was identified. Conditional EC-elimination of Wnt2 and Wnt9b led to perturbation of LZ with not only loss of beta-catenin targets in zone 3, but also re-appearance of zone 1 genes in zone 3, unraveling dynamicity as revealed by single-cell spatial transcriptomics using Molecular Cartography. Defective LR observed in the knockouts phenocopied other models of defective hepatic Wnt signaling. Administration of a tetravalent antibody to activate Wnt signaling rescued LZ and LR in the knockouts. Molecular Cartography on the livers of the agonist-treated animal revealed changes in LZ. Administration of the agonist also promoted LR in acetaminophen overdose acute liver failure (ALF) fulfilling an unmet clinical need. Overall, we report an unequivocal role of EC-Wnt2 and Wnt9b in LZ and LR and show the role of Wnt activators as regenerative therapy for ALF.

overall_design: Spatial single-cell gene quantification on three libraries. A1: Wildtype; A2: FL6.13 treatment and B2: Lyve1-Wnt2/9b

first: Shikai

last: Hu

first: Silvia

first: Yu

last: Bian

first: Minakshi

last: Poddar

first: Sucha

last: Singh

first: Catherine

last: Cao

first: Jackson

last: McGaughey

first: Aaron

last: Bell

first: Levi

middle: L

last: Blazer

first: Jarret

last: Adams

first: Sachdev

last: Sidhu

first: Stephane

last: Angers

first: Satdarshan

middle: P

last: Monga


title: Decoding the Spatial Chromatin Organization and Dynamic Epigenetic Landscapes of Macrophage Cells During Differentiation and Immune Activation

first: Da

last: Lin

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

overall_design: Refer to individual Series


title: bZIP17 regulates heat stress tolerance at reproductive stage in Arabidopsis [RNA-seq]

city: Hangzhou

first: Juan

last: Gao

address: 866 Yuhangtang Road, Xihu District, Hangzhou

department: College of Life Sciences

institute: Zhejiang University

summary: To understand the function of AtbZIP17 in heat stress responses at reproductive stage, we performed RNA-seq analysis of heat-stressed flowers (stage 1-12) in WT and bzip17 mutant (SALK_104326) plants with 38°C for 6 hours, and the control plants were kept at 22°C.

overall_design: There were 12 samples in RNA-seq analysis, wild-type and bzip17 mutant plants at flowering stage were treated at 22°C and 38°C for 6 hours. The unopened flower buds (stage 1-12) from 8 plants were collected and immediately frozen in liquid nitrogen with a total of 3 biological replicates for each treatment. The analysis was processed in according to standard protocols on Illumina Novaseq™ 6000.

first: Mei-Jing

last: Wang

first: Jing-Jing

first: Hai-Ping

last: Lu

first: Jian-Xiang


title: Bulk RNA-seq of FACS sorted astrocytes upon microglial depletion

first: Bo

last: Peng

address: 138 Yixueyuan Road

department: Institute for Translational Brain Research

institute: Fudan University

summary: As the professional phagocyte in the central nervous system (CNS), microglia are the primary scavenger removing cell corpses. The failure of microglia in debris clearance influences the normal CNS function. Meanwhile, microglia undergo turnover during the whole lifespan. If dead microglia are not timely removed, accumulated corpses may influence the CNS function. The microglial corpse clearance is hereby crucial for CNS homeostasis. However, the underlying mechanism remains obscure. In this study, we investigated how microglial corpses are removed. We found that microglial corpses are mainly phagocytosed by astrocytes, mediated by C4b opsonization. Then engulfed microglial fragments are degraded in astrocytes via the RUBICON-dependent LC3-associated phagocytosis (LAP), a form of non-canonical autophagy. The interference of the C4b-mediated engulfment and its subsequent LAP disrupt the microglial debris removal and degradation, respectively. Together, we elucidated cellular and molecular mechanisms of microglial debris removal, extending the knowledge on how the CNS homeostasis is maintained.

overall_design: Tamoxifen induced adult ALDH1L1-CreER::Ai14 mice. A group was fed PLX5622-formulated chow diet while the other group was fed control diet (CD)

first: Yanxia

last: Rao

first: Xiaoyu

last: Li

first: Yafei

first: Tian

last: Zhou


title: Global miRNA Expression of Bone Marrow Mesenchymal Stem/Stromal Cells in Fanconi Anemia Patients

city: Ankara

first: Ayşen

last: Özcan

address: Sihhiye

department: Department of Stem Cell Sciences

country: Turkey

institute: Hacettepe University


title: RNA-seq analysis of miR-2b-1 testes in Drosophila melanogaster

status: Public on Aug 31 2022

city: Gelugor

first: Ghows

last: Azzam

state: Penang

address: 1112 Jalan Persiaran Sains

department: School of Biological Sciences

country: Malaysia

institute: Universiti Sains Malaysia

summary: We have identified that miR-2b-1 of D. melanogaster causes testicular bulging (a tumour like phenotype) and hence have performed a transcriptomic analysis on these bulged testes. Adult flies overexpressing miR-2b-1 were used to perform transcriptomic analysis to identify the differentially expressed genes.

overall_design: Differential gene expression profiling analysis using RNA-seq data of Drosophila melanogaster miR-2b-1 overexpressing adult testes

first: Sharvin

last: Manickam

first: Shallinie

last: Thangadurai

first: Azali

last: Azlan

first: Mardani

last: Abdul Halim


title: Transient regulation of focal adhesion via Tensin3 is required for nascent oligodendrocyte differentiation

city: Paris

first: Carlos

last: Parras

address: 47 boulevard de l'hôpital

country: France

institute: Paris Brain Institute


title: Cue-specific remodeling of the neuronal transcriptome through intron retention programs

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary: We provide a comprehensive map of the subcellular localization of mRNAs in mature neurons and reveal that transcripts stably retaining introns are broadly targeted for nuclear retention. We systematically probed the fate of nuclear transcripts upon neuronal stimulation and found that sub-populations of transcripts are bi-directionally regulated in response to neuronal cues: some are targeted for degradation while others undergo splicing completion to generate fully mature mRNAs which are exported to the cytosol.

overall_design: Comparative intron retention profiling analysis of RNA-seq data for mouse primary cortical cells treated with bicuculline or BDNF.

first: Maxime

last: Mazille

first: Peter

last: Scheiffele

first: Oriane

last: Mauger


title: Transient regulation of focal adhesion via Tensin3 is required for nascent oligodendrocyte differentiation [ChIP-seq]

summary: The differentiation of oligodendroglia from oligodendrocyte precursor cells (OPCs) to complex and extensive myelinating oligodendrocytes (OLs) is a multistep process that involves largescale morphological changes with significant strain on the cytoskeleton. While key chromatin and transcriptional regulators of differentiation have been identified, their target genes responsible for the morphological changes occurring during OL myelination are still largely unknown. Here, we show that the regulator of focal adhesion, Tensin3 (Tns3), is a direct target gene of Olig2, Chd7, and Chd8, transcriptional regulators of OL differentiation. Tns3 is transiently upregulated and localized to cell processes of immature OLs, together with integrin-b1, a key mediator of survival at this transient stage. Constitutive Tns3 loss-of-function leads to reduced viability in mouse and humans, with surviving knockout mice still expressing Tns3 in oligodendroglia. Acute deletion of Tns3 in vivo, either in postnatal neural stem cells (NSCs) or in OPCs, leads to a two-fold reduction in OL numbers. We find that the transient upregulation of Tns3 is required to protect differentiating OPCs and immature OLs from cell death by preventing the upregulation of p53, a key regulator of apoptosis. Altogether, our findings reveal a specific time window during which transcriptional upregulation of Tns3 in immature OLs is required for OL differentiation likely by mediating integrin-b1 survival signaling to the actin cytoskeleton as OL undergo the large morphological changes required for their terminal differentiation.

overall_design: Olig2 and histone marks ChIP-seq from in vivo mouse O4+ cells

first: Emeric

last: Merour

first: Corentine

last: Marie


title: Loss of GPHR in the brain

city: Bunkyo-ku

first: Yu-shin

last: Sou

address: 2-1-1 Hongo

department: Department of Cell Biology and Neuroscience

institute: Juntendo University Graduate School of Medicine

summary: The Golgi apparatus plays a central role in the protein glycosylation where it is required for secretory trafficking. Abnormal morphology of the Golgi apparatus has been widely observed in neurodegenerative disease. Golgi pH regulator (GPHR) is an anion channel essential for acidification of the Golgi lumen and its essential for normal morphology and function of the Golgi apparatus. To address the Golgi dysfunction in neuronal cells, we established brain-specific GPHR knockout mice (GPHRf/f;Nes).

overall_design: The total RNA was prepared from GPHRf/f;Nes and control littermate mouse brain at P10.


title: bZIP17 regulates heat stress tolerance at reproductive stage in Arabidopsis

first: Juan

last: Gao


title: Systematic Single Cell Pathway Analysis (SCPA) reveals novel pathways engaged during early T cell activation

city: Bethesda

first: Jack

last: Bibby

address: 10 Center Drive

institute: National Institutes of Health

summary: Pathway analysis is a key analytical stage in the interpretation of omics data, providing a powerful method for detecting alterations in cellular processes. We recently developed a sensitive and distribution-free statistical framework for multisample distribution testing, which we implement here in the open-source R package Single Cell Pathway Analysis (SCPA). We demonstrate the effectiveness of SCPA over commonly used methods, generate a scRNA-seq T cell dataset, and characterize pathway activity over early cellular activation. This reveals regulatory pathways in T cells, including an intrinsic type I interferon system regulating T cell survival and a reliance on arachidonic acid metabolism throughout T cell activation. A systems-level characterization of pathway activity in T cells across multiple tissues also identifies alpha defensin expression as a hallmark of bone marrow derived T cells. Overall, this work provides a widely applicable tool for single-cell pathway analysis and highlights unexpected regulatory mechanisms of T cells.

overall_design:
CD4+ and CD8+ T cells were isolated from the peripheral blood of healthy donors via negative selection using the EasySep kits (Stemcell). These populations were then further sorted into naïve and memory populations by FACS, generating four populations in total: CD45RA+CD4+ cells (naive CD4), CD45RA+CD8+ cells (naive CD8), CD45RO+CD4+ (memory CD4), and CD45RO+CD8+ (memory CD8). Each cell population was then either left unstimulated, or stimulated for 12 or 24 hours with anti-CD3 and anti-CD28 before scRNA-sequencing.

Splenic CD4+ T cells from WT and Ifnar1-/- mice were stimulated with anti-CD3 and anti-CD28 (2ug/ml) for 24 hours then harvested for bulk RNA-sequencing

first: Claudia

last: Kemper


title: Purifying selection acting on the sequence of highly expressed proteins in the microevolution

city: Suita

first: Atsushi

last: Shibai

state: Osaka

address: 6-2-3 Furuedai

department: Center for Biosystems Dynamics Research

institute: RIKEN

summary: Constraints on the rate of protein sequence evolution have been a central question in evolutionary biology. Orthology analysis between closely related species has revealed that the evolutionary speed is constrained by the expression level, with highly expressed proteins evolving slowly. This negative correlation between expression levels and evolutionary rates (known as the E-R anticorrelation) has already been widely observed in past macroevolution between species, for example, between Escherichia coli and Salmonella. However, it remains unclear whether this seemingly general law also governs microevolution, including past and de novo, within a species. To explore the ubiquitous impact of expression level on molecular evolution in bacteria, we analysed genome sequences for 99 strains of E. coli for microevolution in nature. We also analysed genomic mutations accumulated under laboratory conditions as a model of de novo microevolution. Here, we show that the E-R anticorrelation is significant in both past microevolution and de novo evolution in E. coli. Our data also indicate that purifying selection acting on highly expressed genes contributes to the ubiquity of the E-R anticorrelation. This study confirmed ongoing purifying selection acting on highly expressed genes, and implied that expression level has a ubiquitous impact on the speed of molecular diversification evolution in bacteria.

overall_design: Transcriptomes of the 6 evolved strains and their ancestral strain of E. coli were compared by microarray analysis. Cells were grown on the modified M63 medium and total RNA was extracted from the cells in the exponential growth phase.

first: Hazuki

last: Kotani

first: Natsue

last: Sakata

first: Chikara

last: Furusawa

first: Saburo

last: Tsuru


title: Transient regulation of focal adhesion via Tensin3 is required for nascent oligodendrocyte differentiation [RNA-seq]


title: Parenchymal border macrophages regulate CSF flow dynamics [5xFAD]

city: Saint Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

department: Pathology and Immunology

institute: Washington University in Saint Louis

summary: Microglial cells are the resident macrophages of the brain. Perivascular macrophages (PVM) are also myeloid resident cells that are located at the interface between blood, CSF and brain in the perivascular space. Due to their strategic location and their ability to sample CSF content, we hypothesized that PVM might play a role in CSF flow. Using different fluorescent tracers injected either into the CSF (influx) or the brain parenchyma (efflux) we assessed their spatio-temporal distribution and found that ablation (using clodronate liposomes) or dysfunction (using genetic tools) of PVM alters CSF dynamics and patterns. Using single cell RNA sequencing, we found that PBMs can be divided in two sub-populations, and that one population of PBMs could interact with vascular smooth muscle cells, which allow arterial pulsations and subsequently CSF flow. Interestingly, aging results in altered PVM phenotype, and reversing this phenotype using macrophage specific grown factors reversed some of aging-associated dysfunctions of CSF flow. In summary, our results identify a new role of PVM in CSF flow and open new avenues for therapeutical applications targeting PVM in neurodegenerative diseases such as Alzheimer’s disease.

overall_design: Mice received a lethal intraperitoneal injection of euthasol (10% v/v in saline, 250ml), and transcardially perfused with PBS containing 10U/ml heparin. Cortex were gently dissected in PBS, digested and stained after myelin removal with CD13 (to stain for mural cells), CD31 (endothelial cells), and CD45 (immune cells). Stromal cells (i.e., endothelial+mural) and immune cells were then sorted and prepared for single cell sequencing.

first: Antoine

last: Drieu

first: Taitea

last: Dykstra


title: The proneural transcription factor ASCL1 regulates cell proliferation and primes for differentiation in neuroblastoma

first: Sarah

last: Gillen

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

country: United Kingdom

institute: Wellcome - MRC Cambridge Stem Cell Institute


title: A single cell transcriptional roadmap of human pacemaker cell differentiation

city: Amsterdam

first: Alexandra

last: Wiesinger

state: Amsterdam

address: Meibergdreef 9

institute: Amsterdam UMC

summary: Each heartbeat is triggered by the sinoatrial node (SAN), the primary pacemaker of the heart. Studies in animal models have revealed that pacemaker cells share a common progenitor with the (pro)epicardium, and that the pacemaker cardiomyocytes further diversify into “transitional”, “tail” and “head” subtypes. However, the underlying molecular mechanisms, especially of human pacemaker cell development are poorly understood. Here, we performed single cell RNA sequencing (scRNA-seq) and trajectory inference on human induced pluripotent stem cells (hiPSCs) differentiating to SAN-like cardiomyocytes (SANCM) to construct a roadmap of transcriptional changes and lineage decisions. In differentiated SANCM, we identified distinct clusters that closely resemble different subpopulations of the in vivo SAN. Moreover, the presence of a side population of proepicardial cells suggested their shared ontogeny with SANCM, as also reported in vivo. Our results demonstrate that the divergence of SANCM and proepicardial lineages is determined by WNT signaling. Furthermore, we uncovered roles for TGFβ and WNT signaling in the branching of transitional and head SANCM subtypes, respectively. These findings provide new insights into the molecular processes involved in human pacemaker cell differentiation, opening new avenues for complex disease modeling in vitro and inform approaches for cell-therapy based regeneration of the SAN.

overall_design: single cell RNA sequencing of human induced PSC-derived sinoatrial node-like cells. Single cell collection was performed at several stages during differentiation: hiPSC (day 0), cardiac mesoderm stage (day 4), 24 hrs after treatment (day 5), 48 hrs after treatment (day 6), early sinoatrial node cardiomyocytes (day 10) and late sinoatrial node cardiomyocytes (day 19). Additionally, hiPSC-derived ventricular (VCM), atrial (ACM) and TGFB2 induced SAN (TGFB2_SANCM) cardiomyocytes were collected on day 19.

first: Harsha

middle: D

last: Devalla


title: Adolescent bone sarcomas have distinct immune signatures and intercellular communication networks

first: Anthony

middle: Richard

last: Cillo

address: The Assembly, Room 4070C Bay 10, 5051 Centre Ave

department: Immunology

summary: Ewing and osteosarcoma are bone sarcomas that occur predominantly in adolescents. In the setting of metastatic or recurrent disease, overall prognosis is poor. While immunotherapy is effective for some adult soft tissue sarcoma, limited success has been achieved with immunotherapy for pediatric bone sarcomas. To better understand antitumor immunity in Ewing and osteosarcoma patients, we performed single-cell RNAseq on peripheral blood and tumor infiltrating immune populations using 10X Genomics droplet-based approach. We also included peripheral blood from healthy adolescent blood donors as a comparator. Utilizing these transcriptional profiles, we characterized tumor infiltrating CD8+ T cells and myeloid cells and identified intercellular communication networks in both primary and recurrent disease.

overall_design: In total, we generated single-cell transcriptional profiles from sorted live CD45+ immune cells from paired blood and tumor samples from 4 patients with Ewing sarcoma and 4 patients with osteosarcoma. Among these, 2 patients had primary disease and 2 patients had recurrent disease from both Ewing and osteosarcoma. We also generated single-cell transcriptional profiles from PBMC obtained from 4 healthy adolescent blood donors.

first: Kelly

middle: M

last: Bailey

first: Tullia

last: Bruno

first: Dario

last: Vignali


title: The proneural transcription factor ASCL1 regulates cell proliferation and primes for differentiation in neuroblastoma [RNA-Seq]

city: Cambridge

summary: To compare the function of endogenous ASCL1 in different neuroblastoma cell contexts, we have used CRISPR-mediated deletion to compare the effects of ASCL1 deletion in a MYCN-amplified and an ALK-driven neuroblastoma line and assessed the transcriptome wide impact of ASCL1 knockout using RNA-seq

overall_design: RNA-seq in parental, ASCL1 knockout lines and rescue lines where ASCL1 has been re-expressed in ASCL1 knockout lines

first: Lydia

last: Parkinson

first: Laura

last: Woods

first: Lewis

last: Chaytor

first: Daniel

last: Marcos

first: Fahad

last: Ali

first: Jason

middle: S

last: Carroll

first: Anna

last: Philpott


title: WDR5 promotes breast cancer growth and metastasis via KMT2-independent translation regulation

city: New Haven

first: Qin

last: Yan

email: qin.yan@yale.edu, craig.wilen@yale.edu

address: 310 Cedar St.

department: Pathology

institute: Yale University

summary:
Purpose: Metastatic breast cancer remains a major cause of cancer related deaths in women and there are few effective therapies against this advanced disease. Using an in vivo genetic screen, we identified WDR5 as an actionable epigenetic regulator that is required for metastatic progression in models of triple-negative breast cancer. Here we profile the transcriptome of metastatic breast cancer cells following WDR5 knockdown
Methods: RNA-Seq analysis of breast cancer cell lines MDA-MB-231 LM2, BoM, BrM3
Results: We identified that WDR5 directly controls the expression of ribosomal genes.
Conclusions: We found that WDR5 is a potential target in breast cancer metastasis

overall_design: RNA-seq analysis in human breast cancer cell lines

first: Wesley

last: Cai

first: Jocelyn

last: Chen


title: The proneural transcription factor ASCL1 regulates cell proliferation and primes for differentiation in neuroblastoma [ATAC-seq]

first: Sarah

last: Gillen

summary: To compare the function of endogenous ASCL1 in different neuroblastoma cell contexts, we have used CRISPR-mediated deletion to compare the effects of ASCL1 deletion in a MYCN-amplified and an ALK-driven neuroblastoma line and assessed the impact of ASCL1 knockout on chromatin accessiblity genome-wide using ATAC-seq

overall_design: ATAC-seq in parental and ASCL1 knockout lines


title: bZIP17 regulates heat stress tolerance at reproductive stage in Arabidopsis [ChIP-seq]

first: Juan

last: Gao

summary: To reveal genome-wide direct targets of AtbZIP17, we carried out Chromatin immuno-precipitation coupled with high-throughput sequencing (ChIP-seq) experiments with heat-stressed MYC-bZIP17 expressing seedling plants. For ChIP-seq, 13-day-old 35Spro::MYC-bZIP17 seedlings grown at 22°C were placed at 42°C for 2 h.

overall_design: There were 4 samples in ChIP-seq analysis, 13-day-old 35Spro::MYC-bZIP17 seedlings grown at 22°C were placed at 42°C for 2 h, lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. The ChIP-DNA and INPUT DNA libraries were constructed and sequenced by Genergy Bio (Shanghai, China) with Illumina Novaseq 6000.

first: Mei-Jing

last: Wang

first: Jing-Jing

first: Hai-Ping

last: Lu

first: Jian-Xiang

last: Liu


title: Gene expression in murine CD8+ T cells treated with leukemia extracellular vesicles

city: Luxembourg

first: Etienne

last: Moussay

address: 6 rue Nicolas-Ernest Barblé

department: Cancer Research

country: Luxembourg

institute: Luxembourg Institute of Health

summary: mRNA profiles of CD8+ T cells from 8-week-old wild-type (Foxp3 YFP/cre) mice treated with control or leukemic sEV were generated by 3'-sequencing, in triplicate.

overall_design: mRNA profiles from CD8+ T cells treated with control or leukemia extracellular vesicles

first: Jerome

last: Paggetti


title: Gene expression in murine leukemic B cells treated with leukemic extracellular vesicles

summary: mRNA profiles of murine leukemic B cells (Eu-TCL1 mice) treated with extracellular vesicles were generated by 3'-sequencing, in triplicate.

overall_design: mRNA profiles from leukemic B cells from Eu-TCL1-Rab27DKO mice treated with splenic extracellular vesicles from leukemic Eu-TCL1 or Eu-TCL1-Rab27DKO mice.


title: Gene expression in murine chronic lymphocytic leukemia B cells (Eu-TCL1 and Eu-TCL1-Rab27DKO)

summary: mRNA profiles of leukemic B cells from 8-week-old leukemic (Eu-TCL1 and Eu-TCL1-Rab27DKO) mice were generated by 3'-sequencing, in triplicate.

overall_design: mRNA profiles from leukemic B cells from leukemic (Eu-TCL1 and Eu-TCL1-Rab27DKO) mice


title: Parenchymal border macrophages regulate CSF flow dynamics [leptomeningeal macs]

first: Jonathan

last: Kipnis

overall_design: Fifteen mice (3-month-old males; C57BL6/J) received an i.c.m. injection of 5ml (23mg/ml) of Dil-liposomes (Liposoma, I-005). Mice were perfused with heparinized PBS and tissues were harvested the next day. Subdural meninges were gently collected from the brains and were dissected in FACS buffer and digested in a digestion solution containing 1:50 Collagenase-VIII – 1:500 DNase – 1:50 FBS in FACS buffer for 15 minutes. Tissues were then mashed through 70mm strainers in 50ml tubes containing FACS buffer and 10% FBS to stop enzymatic digestion. After centrifugation, the supernatant was removed and cells were resuspended in FACS buffer and transferred to a V-bottom plate. Cells were sorted and only Dil-positive cells were used for sequencing.

first: Antoine

last: Drieu

first: Taitea

last: Dykstra


title: Parenchymal border macrophages regulate CSF flow dynamics [CLO depletion]

overall_design: To deplete parenchymal border macrophages (PBMs), mice received an i.c.m. injection of clodronate-loaded liposomes (CLO; 5ul; 5mg/ml; Fisher Scientific; CLD-8901). The control group consisted of mice that received an i.c.m. injection of PBS-loaded liposomes (PBS). One week later, mice received a lethal intraperitoneal injection of euthasol (10% v/v in saline, 250ml), and transcardially perfused with PBS containing 10U/ml heparin. Lateral choroid plexuses were gently removed, then whole brains were digested, myelin was removed, and brain were stained with CD13 (to stain for mural cells), CD31 (endothelial cells), and CD45 (immune cells). Stromal cells (i.e., endothelial+mural) were then sorted and prepared for single cell sequencing.


title: Parenchymal border macrophages regulate CSF flow dynamics

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

overall_design: Refer to individual Series


title: Parenchymal border macrophages regulate CSF flow dynamics [brain]

overall_design: Four mice (4-month-old males; Aldh1l1Cre-ERT2/RosaCAG-tdTomato (C57BL6/J background)) received three injections of tamoxifen to induce expression of tdTomato in astrocytes. Mice were then perfused with heparinized PBS. Brains were gently dissected using scissors and incubated in digestion solution 3 times 20 minutes each (brains were also mechanically grinded using descending diameter glass pipettes between incubations). Tissues were then mashed through 70mm strainers in 50ml tubes containing FACS buffer and 10% FBS to stop enzymatic digestion. Myelin was removed by transferring samples into 3ml FACS buffer containing 22% BSA and centrifuged (1000g; 9 accelerations; 2 decelerations; 10min at 4°C). The remaining supernatant containing myelin was carefully removed, the pellet resuspended in FACS buffer and transferred to a V-bottom plate. Fifty ml of FcBlock solution (1:50) were added to the wells and after 20min, antibodies (CD13, CD31 and CD45; 1:200) were added (total volume = 200ml). Cells were then sorted in three different categories: CD45+ CD13- CD31- (immune), CD45- CD13+ CD31- (mural) and CD45- CD13- CD31+ (endothelial).


title: Expression profile of BAT from TAC-operated mice

city: Niigata

first: Yohko

last: Yoshida

address: 1-757, Asahimachi-dori, Chuo-ku

institute: Niigata University

summary: To analyze the gene expression profile of BAT in heart failure mice model, we performed whole genome microarray expression profiling using brown adipose tissue (BAT) from mice at 2 weeks after Sham or TAC operation.

overall_design: Gene expression profile of mice BAT was analyzed at 2 weeks after Sham or TAC operation.  Four independent samples were subjected to the microarray analysis.

first: Ippei

last: Shimizu


title: The transcriptional response to MESH1 silencing

city: Durham

first: Jen-Tsan

last: Chi

state: NC

address: 101 Science Drive, DUMC 3382

department: Molecular Genetics and Microbiology

institute: Duke University

summary: All organisms are exposed to various stresses, necessitating adaptive strategies for survival and homeostasis. In bacteria, the main stress-coping mechanism is stringent response triggered by the accumulation of the “alarmone” (p)ppGpp to trigger proliferation arrest and transcriptional reprogramming. Mammalian genomes encode MESH1  —the homologue of the (p)ppGpp hydrolase SpoT, with unknown function.  Therefore, we used microarrays to determine the transcriptional response to MESH1 silencing.

overall_design: H1975 cells were transfected with either siRNAs or one of three MESH1 siRNAs

first: Tianai

last: Sun

first: Chien-Kuang

last: Ding


title: A Preliminary Study for Identifying Genes Associated with Pellicle Development in Xinjiang Walnut (Juglans regia L.)

status: Public on Aug 30 2022

city: Alar

first: Qiang

last: Jin

email: jqzky@163.com, qiangjin@taru.edu.cn

address: Alar 843300, China

institute: College of Horticulture and Forestry，Tarim University

summary: Walnut (Juglans regia L.) is an important nut fruit crop mainly grown for its high nutritional and medicinal value. In walnut fruit, the pellicle is the main source of polyphenols (such as proanthocyanidins), which are natural bioactive compounds but also cause astringency and bitterness for walnut fruit consumption. However, the gene regulatory networks of phenolic biosynthetic pathways remain largely unknown in walnut pellicles. Here, we performed RNA sequencing (RNA-seq) to identify differentially expressed genes (DEGs) associated with pellicle development in walnut. In this study, seven developmental stages (8-, 9-, 11-, 13-, 15-, 17-, and 19-week after pollination) of ‘Xinwen179’ pellicle tissues were harvested to conduct further transcriptome-wide profiles. Via RNA-seq, we explored several key DEGs involved in the phenolic biosynthetic pathway, such as dihydroflavonol-4-reductase (DFR), leucoanthocyanidin reductase (LAR), anthocyanidin synthase (ANS) and anthocyanidin reductase (ANR), which are dynamically expressed at developmental stages of the walnut pellicle. Taken together, our preliminary investigation on DEGs associated with pellicle development will not only elucidate the gene regulatory networks of the phenolic biosynthetic pathway for pellicle development, but also contribute to the broad spectrum of RNA-seq data resources for further genetic improvement of walnut.

overall_design: Seven developmental stages of pellicle tissue in 'Xinwen179' was performed RNA-seq with three replicates.

first: Shan

first: Rongli

last: Mo

first: Fang

last: Sheng

first: Qinglin

last: Zhang

first: Cuiyun

last: Wu

first: Rui

first: Zhengrong

last: Luo


title: Transcriptional characterization of phagocytic vs. non-phagocytic cells during Staphylococcus aureus craniotomy infection

city: OMAHA

first: Meng

last: Niu

state: NE

address: 42nd and Emile

department: Department of Neurological sciences

institute: University of Nebraska Medical Center

summary: scRNA-seq of phagocytic vs. non phagocytic immune cells during acute S. aureus craniotomy infection

overall_design: Mice were infected with a dsRed expressing strain of S. aureus (S. aureus-dsRed) using an established model of craniotomy infection. Animals were sacrificed at day 3 post-infection, whereupon CD45+ cells were purified by fluorescent-activated cell sorting (FACS) into phagocytic (dsRed+) and non-phagocytic (dsRed-) populations from the brain and galea and subjected to scRNA-seq using the 10X Genomics platform.

first: Joseph

last: Menousek

first: Christopher

last: Horn

first: Cortney

last: Heim

first: Lee

last: Korshoj

first: Tammy

last: Kielian


title: Differentiation-related epigenomic changes define clinically distinct keratinocyte cancer subclasses [Multiome]

city: Heidelberg

first: Llorenç

last: Solé Boldo

address: Im Neuenheimer Feld, 580

country: Germany

institute: DKFZ

summary: Keratinocyte cancers (KC) are the most prevalent malignancies in fair-skinned populations, posing a significant medical and economic burden to health systems. KC originate in the epidermis and mainly comprise basal cell carcinoma (BCC) and cutaneous squamous cell carcinoma (cSCC). Here, we combined single-cell transcriptomics, methylomics and multi-omics to investigate the epigenomic dynamics during epidermal differentiation. We identified ~4,000 differentially accessible regions between undifferentiated and differentiated keratinocytes, corresponding to regulatory regions associated with key transcription factors. DNA methylation at these regions defined AK/cSCC subtypes with epidermal stem cell- or keratinocyte-like features. Using cell type deconvolution tools and integration of bulk and single-cell methylomes, we demonstrate that these subclasses are consistent with distinct cells-of-origin. Further characterization of the subclasses with an epigenetic mitotic-like clock, and the study of other unstratified KC entities uncovered distinct phenotypic and clinical features for the subclasses, linking invasive and metastatic KC cases with undifferentiated cells-of-origin. Our study provides a thorough characterization of the epigenomic dynamics underlying human keratinocyte differentiation and uncovers novel links between KC cells-of-origin and their prognosis

overall_design: Two healthy sun-protected epidermis from the inguinoiliac region were analysed using the 10X Genomics Multiome kit (S1 = 72 y/o, S2 = 55 y/o)

first: F

last: Lyko

first: M

last: Rodríguez-Paredes


title: HMGN5 escorts oncogenic STAT3 signaling by regulating chromatin landscape in tumorigenesis of breast cancer

city: Haining

first: Chaochen

last: Wang

address: 718 East Haizhou Rd

department: ZJU-UoE Institute

institute: Zhejiang University

summary: Epigenetic alterations are widely linked with carcinogenesis, therefore becoming emerging therapeutic targets in the treatment of cancers, including breast cancer. HMGNs are nucleosome binding proteins, which regulate chromatin structures in a cell type- and disease-specific manner. However, the roles of HMGNs in the tumorigenesis of breast cancer are less known. In this study, we report that HMGNs are highly expressed in 3D-cultured breast cancer cells. HMGN5, a member of HMGNs, controls the proliferation, invasion and metastasis of breast cancer cells in vitro and in vivo. Clinically, HMGN5 is an unfavorable prognostic marker in patients. Mechanistically, HMGN5 is governed by active STAT3 transcriptionally and further escorts STAT3 to shape oncogenic chromatin landscape and transcriptional program. Lastly, we provide evidence that interference of HMGN5 by nanoparticle-packaged siRNA is potentially an effective approach in breast cancer treatment. Taken together, our findings reveal a novel feed-forward circuit between HMGN5 and STAT3 in promoting breast cancer tumorigenesis and suggest HMGN5 as a novel epigenetic therapeutic target in STAT3-hyperactive breast cancer.

overall_design: MDA-MB-231 cells are transfected with control siRNA (NC) or siRNA targeting STAT3 (siSTAT3) or HMGN5 (siHMGN5) to examine the transcriptome and genomic histone H3K27ac alteration upon STAT3 or HMGN5 depletion. In the second experiment, siSTAT3 cells are further infected with lentiviral vector or HMGN5 to detect the effect of ectopic HMGN5 on the transcriptome in siSTAT3 cells

first: Mou

last: Jiahui

first: Huang

last: Meijun

first: Xie

last: Hanqi

first: Wang

last: Chaochen


title: Single Cell Characterization of Myeloma and its Precursor Conditions Reveals Transcriptional Signatures of Early Tumorigenesis

city: Boston

first: Irene

last: Ghobrial

address: 4 Blackfan Circle, 2nd Floor, Suite 240

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Multiple myeloma is a plasma cell malignancy almost always preceded by precursor conditions, but low tumor burden of these early stages has hindered the study of their molecular programs through bulk sequencing technologies. Here, we generated and analyzed single cell RNA-sequencing of plasma cells from 26 patients at varying disease stages and 9 healthy donors. In silico dissection and comparison of normal and transformed plasma cells from the same bone marrow biopsy enabled discovery of novel, patient-specific transcriptional changes. Using Bayesian Non-Negative Matrix Factorization, we discovered 15 gene expression signatures which represent transcriptional modules relevant to myeloma biology, and identified a signature that is uniformly lost in neoplastic cells across disease stages. Finally, we demonstrated that tumors contain heterogeneous subpopulations expressing distinct transcriptional patterns. Our findings characterize transcriptomic alterations present at the earliest stages of myeloma, paving the way for exploration of personalized treatment approaches prior to malignant disease.

overall_design:
This study includes single cell RNA-sequencing data from 29,387 plasma cells representing 26 samples from patients with MGUS, SMM, or MM as well as 9 normal bone marrow donors (NBM). One patient was biopsied both at the SMM stage and after progression to MM (SMM-1 and MM-8).

***Please note that the raw data files have been uploaded to dbGaP (phs001323.v3.p1) since this is patient data****

first: Gad

last: Getz

first: David

last: Sontag


title: Differentiation-related epigenomic changes define clinically distinct keratinocyte cancer subclasses [scRNA-seq]

overall_design: One healthy sun-protected epidermis from the inguinoiliac region from a 30y/o male donor was analysed using the Chromium Single Cell 3’ Reagent Kit, v2 chemistry (10X Genomics).


title: Loss of hsf-1 initiates intracellular lipid surveillance

city: Dallas

first: Peter

last: Douglas

state: Texas

address: 6000 Harry Hines Blvd

department: Department of Molecular Biology

institute: University of Texas Southwestern Medical Center at Dallas

summary: To identify genes transcriptionally regulated by the nuclear hormone receptor, NHR-49, we performed RNA sequencing of wild-type and nhr-49(nr2041) loss-of-function mutant C. elegans. This transcriptomic dataset is utilized in the respective study to compare differentially regulated genes in nhr-49(nr2041) mutant worms to those treated with hsf-1 RNAi.

overall_design: mRNA profiling from whole wild-type and nhr-49(nr2041) mutant worms cultured on empty vector RNAi.

first: Abigail

last: Watterson


title: Dynamic landscapes of H3K27ac in mouse preimplantation embryos

first: Yi

last: Zhang

address: 200 Longwood Avenue WAB 149

department: PCMM

institute: Boston Children's Hospital / Harvard Medical School

summary: Histone acetylation H3K27ac is a well-established chromatin marker for active enhancers and promoters. However, reprogramming dynamics of H3K27ac during maternal-to-zygotic transition (MZT) in mammalian embryos has not been well studied. By profiling the allelic landscape of H3K27ac during mouse MZT, here we show that H3K27ac undergoes three waves of rapid global transitions from oocyte to 2-cell stages. Notably, germinal vesicle (GV) oocyte and zygote are globally hyperacetylated by forming noncanonical broad H3K27ac domains that correlate with broad H3K4me3 and open chromatin. H3K27ac also marks genomic regions primed for activation including ZGA gene promoters, retrotransposons, and active alleles of imprinted genes. Importantly, both CBP/p300 and HDAC activities play important roles in regulating the H3K27ac dynamics and are essential for pre-implantation development. Specifically, CBP/p300 deposits broad H3K27ac domains in zygotes and open condensed chromatin at putative enhancers to ensure proper ZGA. In contrast, HDACs mediate the broad to canonical H3K27ac transition to safeguard ZGA by preventing premature expression of developmental genes and promoting ZGA gene activation. Our study demonstrates that coordinated activities of CBP/p300 and HDACs during mouse MZT are essential for ZGA and mouse pre-implantation development.

overall_design: We profiled the allelic landscape of H3K27ac in mouse early embryos using low-input CUT&RUN, by crossing B6D2F1/J female mice and PWK/PhJ male mice. The role of CBP/p300 and HDACs activities in regulating H3K27ac dynamics and ZGA in mouse early preimplantation embryos were studied using A485 and TSA treatment followed by RNA-seq and ATAC-seq comparisons.

first: Meng

first: Zhiyuan

last: Chen


title: A spatio-temporally resolved single cell atlas of the Plasmodium liver stage

city: Modiin

first: Amichay

last: Afriat

state: non-US Resident

address: Nehar Hayarden Modiin

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

summary: To study the liver stage of the rodent malaria parasite Plasmodium berghei, we molecularly characterized thousands of infected and uninfected hepatocytes in different time points and inferred their spatial coordinates. Thus enabling us to characterize the host’s and parasite’s temporal expression programs in a zonally-controlled manner.

overall_design: Mice infected with GFP expressing Plasmodium berghaei ANKA (clone 259cl2), either via injection or mosquito-bite,  were sacraficed at different time points;  FACS sorted infected and uninfected hepatocytes; mRNA profiles from single cells,  sequenced in an Illumina NextSeq/NovaSeq.

first: Vanessa

last: Zuzarte-Luís

first: Keren

last: Bahar Halpern

first: Lisa

last: Buchauer

first: Sofia

last: Marques

first: Aparajita

last: Lahree

first: Ido

last: Amit

first: Maria

last: Manuel Mota

first: Shalev

last: Itzkovitz


title: Gene expression analysis in murine lymphocyte subsets incubated with control or leukemia-derived extracellular vesicles

first: Etienne

last: Moussay

summary: mRNA profiles of Treg, CD4+, CD8+, CD19+ splenic cells from 8-week-old Foxp3 YFP/cre mice incubated with control (WT) or leukemic (TCL1) extracellular vesicles (EV) were analyzed in triplicate.

overall_design: mRNA profiles from splenic lymphocyte subsets isolated from Foxp3 YFP/cre mice incubated with control (WT) or leukemic (TCL1) extracellular vesicles (EV)

first: Jerome

last: Paggetti


title: Single-cell RNAseq analysis of wildtype and CaMKK2 KO immune infiltrate of CT2a preclinical murine glioma

city: DURHAM

first: William

last: Tomaszewski

address: 303 Research Dr.

summary: CaMKK2 promotes a more pro-tumor and checkpoint blockade-resistance associated immune tumor microenvironment in glioblastoma.

overall_design: Tumors were disaggregated, sorted on the basis of CD45+ and Live/Dead-, and profiled using 10x Chromium 3' v3.1 chemistry on day 14 post-implantation of CT2a.Tumor-infiltrating cells were encapsulated into droplets and libraries were prepared using a Chromium Single Cell 3’ Kit using the v3.1 chemistry with feature barcoding (10X Genomics). Cell-hashing (https://doi.org/10.1186/s13059-018-1603-1) was utilized and for each 10X channel, 4 samples were equally combined: n = 4 WT, and n = 4 CaMKK2-/-. 7,000 cells per genotype were targeted with 1,750 cells per biological replicate contributing to each genotype. The generated scRNA-seq and hashtag libraries were pooled at a 25:1 ratio and sequenced on a Novaseq S Prime Flow Cell to an average depth of 61,286 and 59,013 reads per cell for WT and CaMKK2 KO samples, respectively.


title: RB-N phosphorylation promotes BRD4-mediated CREB signaling hyperactivation and BET inhibitor resistance

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

summary: The combination of CREB inhibitor and JQ1 could overcome the resistance to BET inhibitors in RB loss prostate cancer. Our study firstly showed that GNB1L-CREB pathway was activated after RB loss and considered as the potential target for the prostate cancer therapy

overall_design: To find the candidate genes which are regulated by RB, endogenous RB in C4-2 cells were knocked down by shRNA and cells were collected for ChIP-seq after puromycin selection.

first: Haojie

last: Huang

first: Liguo

last: Wang

first: Donglin

last: Ding

first: Yundong

last: He


title: RBM45 is an m6A-binding protein that affects neuronal differentiation and the splicing of a subset of pre-mRNAs II

city: D

first: Kate

last: Meyer

address: 307 Research Drive Box 3711

department: Biochemistry

institute: Duke University School of Medicine

summary: Here, we identify RNA-binding motif containing protein 45 (RBM45) as a novel m⁶A reader, enriched in the brain, and highly expressed during embryonic neurodevelopment. We demonstrate that RBM45 recognizes intronic m⁶A and that its primary role is as a direct regulator of pre-mRNA splicing for its target genes, many of which are associated with neurodevelopment. Furthermore, we show that RBM45 is absolutely required for proper differentiation in cultured SH-SY5Y neuroblastoma cells, and that RBM45 regulates splicing of neurodevelopmental target genes central to the activation of gene expression programs that regulate differentiation in vitro.

overall_design: Transcriptomic profiling of RBM45 binding sites and target genes (CLIP-seq) in wild-type (WT) and m6A-depleted (Mettl3 KO) mHippoE2 cells expressing FLAG-HA-Rbm45

first: Seung

last: Choi


title: Temperature-sensitive sterility in rice determined by the dual role of AGO1d in phasiRNA biogenesis and function

city: Shenzhen

first: Chuanlin

last: Shi

address: Dapeng

institute: Chinese Academy of Agricultural Sciences

summary: Phased secondary siRNAs (phasiRNAs) are broadly present in the reproductive tissues of flowering plants. Monocots generate 21- and 24-nt phasiRNAs by miR2118 and miR2275 respectively from noncoding RNAs with spatial-temporal specificity during anther development. However, which ARGONAUTES (AGOs) associate with these two miRNAs remains elusive. Here we show that rice AGO1d, specifically expressed in anther wall cells before and during meiosis, associates with both miR2118 and miR2275 to mediate phasiRNA biogenesis. Furthermore, AGO1d also binds to miR2118-triggered 21-nt phasiRNAs preferentially with a 5’-terminal uridine, suggesting a dual role in phasiRNA biogenesis and function. Depletion of AGO1d causes reduction of 21- and 24-nt phasiRNAs and temperature-sensitive sterility. Anthers of the ago1d mutants at lower temperatures mainly display defects in tapetal cells and vacuolation during pollen formation. These results uncover an essential role of AGO1d in rice anther development at lower temperatures and demonstrate coordinative roles of AGO proteins during reproductive phasiRNA biogenesis and function

overall_design: For RNA-seq, rice anthers at stages of 4-6, 7-8, and 9 from both wild-type and ago1d mutant grown at 28 °C and 22°C were collected with three biological replicates. Total RNA was isolated from each sample and then used for poly(A) RNA isolation with oligo(dT) beads. Poly(A) RNA samples were then used for RNA-seq library construction using NEBNext UltraTM RNA Library Prep Kit for Illumina (New England Biolabs, USA) following manufacturer’s recommendations. RNA-seq libraries were sequenced on an Illumina NovaSeq 6000 platform at Novogene. For small RNA-seq, anthers at stages of 4-6, 7-8, and 9 from both wild-type and ago1d mutant grown at 28 °C and 22°C were collected with three biological replicates. The small RNA libraries were prepared from a total of 2 μg total RNA isolated from each sample using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. All the small RNA libraries were sequenced on an Illumina novaseq 6000 platform at Novogene.For the AGO1d-FLAG RIP-seq, three biological replicates of rice spikelets at developmental stages of 4-6, 7-8, and 9 from AGO1d::AGO1d-FLAG transgenic plants were collected,  and grounded in liquid nitrogen into fine powder. The grounded powder was homogenized in 4 uL extraction buffer [50 mM Tris–HCl pH 7.5, 150 mM NaCl, 0.1% NP-40, 4 mM MgCl2, 5 mM DTT, EDTA-free protease inhibitor cocktail (Roche), and 400 U RNasin Ribonuclease Inhibitor (Promega)] and centrifuged at 12,000 g for 10 min at 4°C. 200 μL of the supernatant was aliquoted for RNA extraction using TRIzol reagent and used as input for RIP-seq. The rest of supernatant was precleared with Protein A/G magnetic beads (MedChemExpress, USA) at 4 °C for 1 h and then incubated with the anti-FLAG antibody (Cat. M185-3L, MBL, Japan) at 4°C for 2 h. Thereafter, 50 μL Protein A/G magnetic beads were added in and incubated at 4°C for 1 h. After 3 times of wash with the extraction buffer containing 2 mM DTT at 4°C, magnetic beads were extracted using TRIzol reagent for RNA isolation. Precipitated RNA was then used for small RNA library construction using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, USA). For the RIP-seq input library construction, total RNA was loaded on a 15% urea PAGE gel for electrophoresis with the small-RNA Ladders (New England Biolabs, USA). Small RNA in ~15- to 30-nt was extracted from gel slices and used for input library construction. All the small RNA libraries were sequenced on an Illumina novaseq 6000 platform at Novogene, China.

first: Qili

last: Fei


title: Transcriptional analysis of DENV-elicited inflammation following experimental human DENV-1 challenge

city: Syracuse

first: Adam

middle: Tully

last: Waickman

address: 766 Irving Avenue

institute: SUNY Upstate Medical University

summary: The objective of this analysis was to determine the transcriptional signature associated with experimental DENV-1 infection in human volunteers. Nine flavivirus naive volunteers were challenged with an attenuated DENV-1 strain - 45AZ5 - and blood collected for RNA extraction and transcriptional analysis on days 0, 8, 10, 14, and 28 post challenge using PAXgene collection tubes. Total RNA was isolated from the collection tubes and subjected to RNAseq analysis to identify genes and gene sets that were differentially expressed across the infection time course.

overall_design: Whole blood was collected at days 0, 8, 10, 14, and 28 post DENV-1 infection 9 subjects using Paxgene tubes.

first: Stephen

last: Thomas


title: RBM45 is an m6A-binding protein that affects neuronal differentiation and the splicing of a subset of pre-mRNAs I

overall_design: Transcriptomic profiling of RBM45 binding sites and target genes (CLIP-seq) in wild-type (WT) and m6A-depleted (METTL3 KO) HEK293T cells expressing FLAG-HA-RBM45


title: Human lung AT2 cell organoids infected with CoV-2, treated with inhibitors

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

institute: University Münster

summary:
RNAseq analysis of human lung AT2 cell organoids infected with CoV-2, treated with inhibitors
Results: Differentially expressed genes after infection and treatment with inhibitors.

overall_design: Infection with SARS-CoV-2 and treatment with inhibitors PH-797804, VX-702

first: Linda

last: Brunotte


title: Gene expression analysis in lymphocyte subsets from mice injected with control- or leukemia-derived extracellular vesicles

address: 6 rue Nicolas-Ernest Barblé

summary: mRNA profiles of Treg, CD4+, CD8+, CD19+ splenic cells from 8-week-old Foxp3 YFP/cre mice injected with control (WT) or leukemic (TCL1) extracellular vesicles (EV) were analyzed in triplicate.

overall_design: mRNA profiles from splenic lymphocyte subsets isolated from Foxp3 YFP/cre mice treated in vivo for 7 days with control (WT) or leukemic (TCL1) extracellular vesicles (EV)


title: Effect of microRNA-27b-3p mimic treatment on human osteoarthritis fibroblast-like synoviocyte gene expression profiles

city: Toronto

first: Mohit

last: Kapoor

state: Ontario

address: 60 Leonard Ave

country: Canada

institute: Schroeder Arthritis Institute

summary: OBJECTIVE: To identify the changes in gene expression elicited by miR-27b-3p mimic transfection of human osteoarthritis (OA) primary fibroblast-like synoviocytes (FLS) obtained from patients undergoing knee arthroplasty. Cells were cultured, and treated for 48 h with miR-27b-3p mimic or Cel-miR-39-3p control mimic. Total RNA was then extracted, and mRNA libraries were prepared using Illumina's TruSEQ stranded total RNA library preparation kit, pooled together, and sequenced on Illumina's NextSeq550.

overall_design: Differential expression analysis was performed on the RNA-SEQ data obtained from 6 prepared libraries, where 3 were treated with the miR-27b-3p mimic and 3 with Cel-miR-39-3p control mimic. Subsequent pathway analysis identified the upregulation of ECM-related genes and pathways suggesting that miR-27b-3p is involved in the modulation of synovial ECM production.

first: Ghazaleh

last: Tavallaee

first: Starlee

last: Lively

first: S

last: Ali

first: Michelle

last: Im

first: Clementine

last: Sarda

first: Evgeny

last: Rossomacha

first: Sayaka

last: Nakamura

first: Pratibha

last: Potla

first: Konstantin

last: Shestopaloff

first: John

last: Matelski

first: Anusha

last: Ratneswaran

first: Kim

last: Perry

first: Greniqueca

last: Mitchell

first: Rajiv

last: Ghandhi

first: Jason

last: Rockel

first: Boris

last: Hinz

first: Igor

last: Jurisica


title: Boron homeostasis functions in meristem maintenance in maize by regulating knotted1, cell cycle, and hormone signaling pathways

first: Michaela

middle: Sylvia

last: Matthes

state: Bonn

address: Friedrich Ebert Allee 144

department: INRES-Crop Functional Genomics

institute: University of Bonn

summary: Here we report, that levels of the micronutrient boron are instrumental for meristem maintenance by integration into specific meristem maintenance pathways. We used RNA-seq analysis of the boron deficient maize mutant tassel-less1 to identify early molecular defects induced by boron deficiency in maize reproductive (tassel) meristems. RNA-seq results were independently verified through downstream in silico, double mutant, microscopy, proteomic, and molecular analyses.

overall_design: 1 mm tassel meristems prior morphologic defects of the maize tassel-less1 (tls1) mutant and B73 (three replicates each)

first: Paula

last: McSteen


title: Transcriptional changes upon Mphosph8 or Morc2a loss in sorted neuronal nuclei of adult mouse brains.

city: Vienna

first: Maria

last: Novatchkova

address: Dr Bohrgasse

country: Austria

institute: IMP/IMBA

summary: We report that murine MPP8 and MORC2A are highly expressed in the brain and exclusively found in neurons. We show that genetic inactivation of Mphosph8 (coding for MPP8) or Morc2a in the nervous system of mice leads to alterations in brain architecture, behavioral impairments and reduction of life span. By doing RNA-seq and ChIP-seq experiments, we found that MPP8 and MORC2A suppress the repetitive-like protocadherin gene cluster on mouse chromosome 18 in a H3K9me3-dependent manner.

overall_design: Examination of consequences of Nestin-Cre-mediated nervous system-specific knock-out of Mphosph8 and Morc2a in FACS-sorted neuronal nuclei (from at least 2 brains per genotype).

first: Astrid

last: Hagelkruys


title: PfSRPK1 regulates asexual blood stage schizogony and is essential for male gamete formation

status: Public on Aug 29 2022

city: Seattle

first: Alison

last: Paquette

state: Washington

address: 1900 Ninth Ave.

department: Center for Developmental Biology and Regenerative Medicine

country: USA

institute: Seattle Childrens

summary: Serine/arginine-rich protein kinases (SRPK) are cell cycle-regulated serine/threonine protein kinases and are important regulators of splicing factors. In this study, we functionally characterize SRPK1 of the human malaria parasite Plasmodium falciparum (Pf). PfSRPK1 was expressed in asexual blood stages and sexual stage gametocytes. Pfsrpk1¯ parasites formed asexual schizonts that generated far fewer merozoites when compared to wildtype parasites, causing reduced replication rates. Pfsrpk1¯parasites also showed a severe defect in the differentiation of male gametes, causing a complete block in parasite transmission to mosquitoes. RNA-seq analysis of wildtype PfNF54 and Pfsrpk1¯ stage V gametocytes suggested a role for PfSRPK1 in regulating transcript splicing and transcript abundance of genes coding for (i) microtubule/cilium morphogenesis related proteins, (ii) proteins involved in cyclic nucleotide metabolic processes, (iii) proteins involved in signaling such as PfMAP2, (iv) lipid metabolism enzymes, (v) proteins of the osmophilic bodies and (vi) crystalloid components. Our study reveals an essential role for PfSRPK1 in parasite cell morphogenesis and suggests this kinase as a target to prevent malaria transmission from man to mosquito.

overall_design: Stage V gametocyte samples from WT (control) and SRPK1-KO (KO) parasites were analyzed for transcriptional perturbations.

first: Sudhir

last: Kumar

first: Stefan

last: Kappe


title: The time-dependent effects of ONC201 on transcriptome in MDA-MB-231 cells

city: Bethesda

first: Jonathan

last: Hernandez

state: MD

address: Building 37

institute: NCI/NIH

summary: Goal of this study was to investigate the time-dependent impact of ONC201 on gene expression changes in MDA-MB231, a triple negative breast cancer cell line

overall_design: RNA-seq of MDA-MB 231 cells treated with ONC201 (5uM) for 0h, 6h, 12h, 24h. Each time point had 3 biological replicates.

first: Yoshimi

last: Greer

first: Vishal

last: Koparde

first: Maggie

last: Cam

first: Stan

last: Lipkowitz


title: A balancing act: Interactions within NuA4/TIP60 regulate picNuA4 function in Saccharomyces cerevisiae and humans

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

summary: The NuA4 lysine acetyltransferase complex acetylates histone and non-histone proteins and functions in transcription regulation, cell cycle progression, and DNA repair. NuA4 harbors an interesting duality in that its catalytic module can function independently and distinctly as picNuA4. At the molecular level, picNuA4 anchors to its bigger brother via physical interactions between the C-terminus of Epl1 and the HSA domain of Eaf1, the NuA4 central scaffolding subunit. This is reflected at the regulatory level, as picNuA4 can be liberated genetically from NuA4 by disrupting the Epl1-Eaf1 interaction. As such, removal of either Eaf1 or the Epl1 C-terminus offers a unique opportunity to elucidate the contributions of Eaf1 and Epl1 to NuA4 biology and in turn their roles in balancing picNuA4 and NuA4 activities. Using high-throughput genetic and gene expression profiling, and targeted functional assays to compare eaf1∆ and epl1-C∆ mutants, we found that EAF1 and EPL1 had both overlapping and distinct roles. Strikingly, loss of EAF1 or its HSA domain led to a significant decrease in the amount of picNuA4, while loss of the Epl1 C-terminus increased picNuA4 levels, suggesting starkly opposing effects on picNuA4 regulation. The eaf1∆ epl1-C∆ double mutants resembled the epl1-C∆ single mutants, indicating that Eaf1’s role in picNuA4 regulation depended on the Epl1 C-terminus. Key aspects of this regulation were evolutionary conserved, as truncating an Epl1 homolog in human cells increased the levels of other picNuA4 subunits. Our findings suggested a model in which distinct aspects of the Epl1-Eaf1 interaction regulated picNuA4 amount and activity.

overall_design:
Microarray expression profiling was performed in duplicate. Cultures were grown in a 24-well plate incubator/reader to mid-log phase, with spiked-in RNA controls to monitor global changes in mRNA levels. Since no global changes in mRNA levels were detected, expression values were normalized to total mRNA levels. Fold changes were determined by comparing mutant to wild type profiles, with differentially expressed genes having a p-value <0.01 and absolute fold change >1.7 .
Please note that the protocol_details.txt contains all protocol description.

first: Phoebe

middle: Y

last: Lu

first: Alyssa

last: Kirlin

middle: J

last: Aristizabal

first: Nancy

last: Lévesque

first: Dheva

last: Setiaputra

first: Joris

last: Benschop

first: Frank

last: Holstege

first: Nevan

last: Krogan

first: Calvin

last: Yip

first: Jacques

last: Côté

first: Michael

last: Kobor

first: Hilary

last: Brewis

first: Nikita

last: Avvakumov