title: Targeting RTN4/NoGo-Receptor reduces levels of ALS protein ataxin-2

status: Public on Oct 18 2022

first: Caitlin

last: Rodriguez

address: 279 Campus Dr.

department: Genetics

country: USA

summary: Gene-based therapeutic strategies to lower ataxin-2 levels are emerging for neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and spinocerebellar ataxia type 2 (SCA2). To identify additional ways of reducing ataxin-2 levels, we performed a genome-wide screen in human cells for regulators of ataxin-2 and identified RTN4R, the gene encoding the RTN4/NoGo-Receptor, as a top hit. This dataset contains the RNA-sequencing data used to support the conclusions from this study.

overall_design: Transcriptional changes in RTN4R shRNA knockdown compared to non-targeting shRNA condition in iPSC-derived neurons (iNs). Differential gene expressoin derived from RNA-sequencing data, analyzed using DESeq2.

first: Garam

last: Kim

first: Aaron

last: Gitler


title: Genome-wide CRISPR screen reveals v-ATPase as a drug target to lower levels of ALS protein ataxin-2

city: Stanford

state: CA

address: 279 Campus Dr

institute: Stanford University

type: Expression profiling by high throughput sequencing

summary: ATXN2 has emerged as an exciting therapeutic target for neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and spinocerebellar ataxia type 2 (SCA2), as lowering its levels via genomic knockout or anti-sense oligonucleotide (ASO) treatment has been shown to mitigate disease phenotypes and led to a current clinical trial of ATXN2 ASOs for treatment of ALS in humans. To identify additional ways to lower ataxin‑2 protein levels, we performed a genome-wide fluorescence activated cell sorting (FACS)-based CRISPR screen in human cells and identified multiple components of the lysosomal vacuolar ATPase (v‑ATPase) as modifiers of ataxin‑2 levels. This dataset contains the RNA-sequencing data and CRISPR screen data used to support the conclusions from this study.

overall_design: Transcriptional changes in ATP6V1A siRNA knockdown compared to non-targeting siRNA condition in HeLa cells. Differential gene expressoin derived from RNA-sequencing data, analyzed using DESeq2. Additionally, results of FACS-based CRISPR genome-wide knockout screen data (gene knockouts that increase or decrease ataxin-2 protein levels).

first: Julien

last: Couthouis


title: HDAC7 regulates genes essential for the function of FoxP3+ regulatory T cells

status: Public on Oct 17 2022

city: Toulouse

first: Pierre-Paul

last: Axisa

address: 2 avenue Hubert Curien

department: CRCT

country: France

institute: INSERM

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Bulk RNAseq of human Tregs transduced with a lentivirus encoding a shRNA targeting the HDAC7 gene or a scrambled control

summary: Genome-wide association studies identifying hundreds of susceptibility loci for autoimmune diseases indicate that genes active in immune cells predominantly mediate risk. Identification and functional characterization of causal variants remains challenging. Here, we focused on the immunomodulatory role of a protective variant in HDAC7 (rs148755202, HDAC7.p.R166H), identified in a study of low-frequency coding variation in multiple sclerosis (MS). Through transcriptomic analysis, we demonstrate that HDAC7 regulates genes essential for the function of FoxP3+ regulatory T cells (Tregs), an immunosuppressive subset of CD4 T cells that is dysfunctional in patients with MS. Moreover, Treg cell-specific conditional hemizygous deletion of HDAC7 increases severity of experimental autoimmune encephalitis (EAE), a mouse model of MS. Strikingly, Tregs transduced with the protective HDAC7 R166H variant exhibit higher suppressive capacity in an in vitro functional assay, mirroring functional defects previously observed in patients. In vivo modelling of the human HDAC7 R166H variant, by generation of a knock-in mouse model bearing the orthologous R150H substitution, showed decreased EAE severity linked to transcriptomic alterations of brain infiltrating Tregs as assessed by single cell RNA-seq. Our data suggest that dysregulation of epigenetic modifiers, a novel molecular class associated with disease risk, can influence disease onset. Finally, our approach provides a template for translation of genetic susceptibility loci to detailed functional characterization, using human in vitro and mouse in vivo modelling.

overall_design: CD4+CD25hiCD127lo–neg Tregs are FACS-sorted and stimulated with aCD3/aCD28. On day 1, they are infected with lentiviral pseudoparticles containing HDAC7 or scrambled control shRNAs. After 5 days, GFP+ cells are sorted for transcriptomic analysis

first: Liliana

last: Lucca

first: David

last: Hafler

first: Tomokazu

last: Sumida


title: Bulk RNAseq of human Tregs transduced with a wild type HDAC7 or a version carrying the MS-protective R166H variant

overall_design: CD4+CD25hiCD127lo–neg Tregs are FACS-sorted and stimulated with aCD3/aCD28 in the presence of IL-2 for 7 days. On day 1, they are infected with lentiviral pseudoparticles containing WT or R166H mutated constructs. After 7 days, GFP+ cells are sorted for transcriptomic analysis


title: scRNAseq of CNS-infiltrating T cells from EAE-affected wt C57BL6 mice or littermate controls heterozygous or homozygous for a gene variant orthologous for the human polymorphism HDAC7 R166H

overall_design: wt, HDAC7 ki/wt or HDAC7 ki/ki littermate controls were immunized with MOG35-55 to induce experimental autoimmune encephalomyelitis (EAE). After 14 days, mice were sacrificed and brains and spinal cords were harvested. CNS-infiltrating T cells were FACS-sorted and used for t single-cell transcriptomic analysis.


title: transcriptional landscape of Germ cell differentiation at single cell resolution

status: Public on Oct 15 2022

city: CB2 0RE

first: Giorgia

last: Battistoni

address: Robinson Way

department: CRUK-CI

country: United Kingdom

institute: University of Cambridge

summary: Single cell sequencing technologies are powerful tools for the dissection of large regulatory networks and their role in directing developmental trajectories. The goal of this project is to profile the transcriptional landscape of germ cell development in the mouse male embryo at single cell resolution, and to examine the dynamic regulation of the molecular networks directing epigenetic reprogramming in these cells.

overall_design: Single cell RNAseq profiling (10x Genomics) of Primordial Germ Cells isolated via Fluorescence Actvated Cell Sorting, using a germ cell specific Oct4-EGFP fluorescent reporter. One replicate per time point (E10.5 and E13.5)

first: Gregory

middle: J

last: Hannon


title: The role of aD in sepsis

city: Boston

first: Koichi

last: Yuki

state: MA

address: 300 Longwood Avenue

institute: Boston Children's Hospital

summary: aD is one of the b2 integrin family members. The role of aD in sepsis has not been examined yet. aD is previously reported to be expressed on neutrophils. We performed cecal ligation and puncture sepsis model in wild type and aD knockout and examined the role of aD in neutrophils.

overall_design: We performed cecal ligation and puncture model and obtained blood and lung at 12 hours after the surgery. Neutrophils were sorted out as CD11b+Ly6G+CD45+ population, and then subjected to RNA sequencing.

first: Sophia

last: Koutsogiannaki


title: IFN-λ treatment accelerates SARS-CoV-2 clearance despite age-related delays in the induction of T cell immunity

status: Public on Oct 14 2022

city: Toronto

first: Adam

last: Gehring

state: ON

address: 101 College St

country: Canada

institute: UHN

summary: Interferons (IFNs) induced early after SARS-CoV-2 infection are crucial for shaping immunity and preventing severe COVID-19. We previously demonstrated that injection of pegylated interferon-lambda1 (PEG-IFN-λ) accelerated viral clearance in COVID-19 patients. To determine if the viral decline was mediated by enhanced immunity, we assessed in vivo responses to PEG-IFN-λ by single cell RNA sequencing and measured SARS-CoV-2-specific T cell and antibody responses between placebo and PEG-IFN-λ-treated patients. PEG-IFN-λ treatment induced interferon stimulated genes in peripheral immune cells expressing IFNLR1, including plasmacytoid dendritic cells and B cells. PEG-IFN-λ did not affect SARS-CoV-2-specific antibody levels or the magnitude of virus-specific T cells. However, we identified delayed T cell responses in older adults, suggesting that PEG-IFN-λ can overcome delays in adaptive immunity to accelerate viral clearance in high-risk patients. Altogether, PEG-IFN-λ offers an early COVID-19 treatment option for outpatients to boost innate antiviral defenses without dampening peripheral adaptive immunity.

overall_design:
PBMCs were isolated from COVID-19 patients treated with placebo or pegylated-IFN-lambda1 and analyzed by scRNA seq at 3 time points before or after treatment (n=9 subjects).
Submitter declares: "Due to patient privacy concerns, we are unable to submit raw sequences."

first: Deanna

middle: M

last: Santer

first: Daniel

last: Li

first: Yanal

last: Ghosheh

first: Muhammad

middle: A

last: Zahoor

first: Dhanvi

last: Prajapati

first: Bettina

middle: E

last: Hansen

first: Lorne

last: Tyrrell

first: Jordan

last: Feld


title: Dietary Linseed Oil Affects the Polyunsaturated Fatty Acid and Transcriptome Profiles in the Livers and Breast Muscles of Ducks

city: Yangzhou

first: Wang

last: Laidi

state: Jiangsu

address: East Wenhui Road

country: China

institute: Yangzhou University

summary:
To investigate the dietary linseed oil in the regulation of PUFA synthesis, we detected the genes in the livers and breast muscles of ducks.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 10 livers and 10 breast muscles from 10 individual ducks at two group.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for livers and breast muscles of ducks from the high linseed oil group and the control group.

first: Guobin

last: Chang

first: Guohong

last: Chen

first: Yang

last: Zhang

first: Laidi

last: Wang


title: Role of Setd2 on regulatory T cells [RNA-seq SP Treg]

city: Shanghai

first: Ju

last: Qiu

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary: To determine the mechanism of regulation of Tregs by Setd2, SPTregs (CD3+CD4+Foxp3-YFP+) from Setd2-deficient and control Tregs were subjected to RNA-seq analysis.

overall_design: About 1 × 10^6 sorted splenic Tregs (CD3+CD4+YFP+ cells) were pooled from littermate Foxp3Cre-YFPSetd2f/+ or Foxp3Cre-YFPSetd2f/f mice. Each biological replicate was pooled from 2 mice.

first: Zhaoyun

last: Ding

first: Ting

last: Cai


title: Systematic characterization of seed overlap microRNA cotargeting associated with lupus pathogenesis (small RNA-seq)

city: Nagoya

first: Hiroshi

middle: I.

last: Suzuki

address: 65 Tsurumai-cho, Showa-ku

department: DIvision of Molecular Oncology, Graduate School of Medicine

country: Japan

institute: Nagoya University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background:
Combinatorial gene regulation by multiple microRNAs (miRNAs) is widespread, and closely spaced target sites often act cooperatively to achieve stronger repression (“neighborhood” miRNA cotargeting). While miRNA cotarget sites are suggested to be more conserved and implicated in developmental control, the pathological significance of miRNA cotargeting remains elusive.
Results:
Here, we report pathogenic impacts of combinatorial miRNA regulation on inflammation in systemic lupus erythematosus (SLE). In the SLE mouse model, we identified downregulation of two miRNAs, miR-128 and miR-148a, by TLR7 stimulation in plasmacytoid dendritic cells. Functional analyses using human cell lines demonstrated that miR-128 and miR-148a additively target KLF4 via extensively overlapping target sites (“seed overlap” miRNA cotargeting) and suppress the inflammatory responses. At the transcriptome level, “seed overlap” miRNA cotargeting increases susceptibility to downregulation by two miRNAs, consistent with additive but not cooperative recruitment of two miRNAs. Systematic characterization further revealed that extensive “seed overlap” is a prevalent feature among broadly conserved miRNAs. Highly conserved target sites of broadly conserved miRNAs are largely divided into two classes—those conserved among eutherian mammals and from human to Coelacanth, and the latter, including KLF4-cotargeting sites, has a stronger association with both “seed overlap” and “neighborhood” miRNA cotargeting. Furthermore, a deeply conserved miRNA target class has a higher probability of haplo-insufficient genes.
Conclusions:
Our study collectively suggests the complexity of distinct modes of miRNA cotargeting and importance of their perturbations in human diseases.

overall_design: Small RNA sequencing (small RNA-seq) in pDCs from the IMQ-induced SLE mouse model.

first: Hiroki

last: Kitai

first: Noritoshi

last: Kato

first: Koichi

last: Ogami

first: Shintaro

last: Komatsu

first: Yu

last: Watanabe

first: Seiko

last: Yoshino

first: Eri

last: Koshi

first: Shoma

last: Tsubota

first: Yoshio

last: Funahashi

first: Takahiro

last: Maeda

first: Kazuhiro

last: Furuhashi

first: Takuji

last: Ishimoto

first: Tomoki

last: Kosugi

first: Shoichi

last: Maruyama

first: Kenji

last: Kadomatsu

middle: I


title: Muscle injury induces a transient senescence-like state that is required for myofiber growth during muscle regeneration [Spatial Transcriptomics]

city: Halifax

first: Adam

last: Johnston

state: NS

address: 1344 Summer Street

department: Medical Neuroscience

institute: Dalhousie University

summary: Cellular senescence is the irreversible arrest of normally dividing cells and is driven by the cell cycle inhibitors Cdkn2a, Cdkn1a, and Trp53. Senescent cells are implicated in chronic diseases and tissue repair through their increased secretion of proinflammatory factors known as the senescence-associated secretory phenotype (SASP). Here, we use spatial transcriptomics and single-cell RNA sequencing (scRNAseq) to demonstrate that cells displaying senescent characteristics are “transiently" present within regenerating skeletal muscle and within the muscles of D2-mdx mice, a model of Muscular Dystrophy. Following injury, multiple cell types including macrophages and fibro-adipogenic progenitors (FAPs) upregulate senescent features such as senescence pathway genes, SASP factors, and senescence-associated beta-gal (SA-β-gal) activity. Importantly, when these cells  were removed with ABT-263, a senolytic compound, satellite cells are reduced, and muscle fibers were impaired in growth and myonuclear accretion. These results highlight that an “acute” senescent phenotype facilitates regeneration similar to skin and neonatal myocardium.

overall_design: 10x Genomics Visium platform was used to assay the spatial distribution of skeletal muscle transcriptome in situ in D2-Mdx mouse, a model of muscular dystrophy. Gastrocnemius muscle of 8-week old D2-Mdx mouse was dissected and frozen in OCT compound using liquid nitrogen-cooled 2-methylbutane. We performed spatial transcriptomics on a 10µm section of this tissue. To identify spatially-correlated genes expressed preferentially within areas of focal regeneration in the dystrophic muscle, we used SpatialDE2 (Kats et al., 2021) (all spatially-variable genes provided in metadata).

first: Laura

middle: V

last: Young

first: Griffen

last: Wakelin

middle: P


title: scRNA-seq of in vitro differentiated D6 mPGCLCs

first: Giorgia

last: Battistoni

summary: Germ cell specification is an elusive biological event, as it occurs in a small group of cells in the very early embryo (E6.5). In vitro differentiation of naive mouse Embryonic Stem Cells (mESCs) to mouse Primordial Germ Cell like cells (mPGCLCs) allows the mechanistic investigation of germ cell specification. The goal of this study is to profile of gene expression via single cell RNA sequencing throughout the differentiation protocol. In particular, this project aims at examining the transcriptional activation of the molecular networks that direct the epigenetic reprogramming of mPGCLCs.

overall_design: Single cell RNAseq profiling (10x Genomics) of mESc during in vitro differentiation to mPGCLCs. One replicate for the bulk cell cultures (mESCs and mEPILCs), three biologial replicates for the Embryoid bodies at day 6 (EBd6) each derived from one individual dissociated EB

first: Gregory

last: Hannon


title: Small RNA Sequencing of GOF mPGCs and SGET mPGCLCs

city: Cambridge

first: Navin

middle: B

last: Ramakrishna

address: Tennis Court Rd

institute: Gurdon Institute

summary: Mouse Primordial Germ Cells (mPGCs) are the precursors of gametes specified around E6.25 in the developing mouse embryo. This process can be modelled in vitro using the mPGC-Like Cell (mPGCLC) differentiation protocol. The aim of this study is the detection and profiling of mouse small RNAs via small RNA sequencing of male E12.5 to E15.5 mPGCs and Day 6 SGET mPGCLCs. In particular, this study is aimed at the detection of small RNA length and first nucleotide biases, covering the time window for in vivo piRNA emergence.

overall_design: Examination of all small RNA-mapping profiles in biological duplicates of male primordial germ cell development from E12.5 to E15.5 in comparison with biological duplicates of Day 6 in vitro SGET mPGCLCs

first: Eric

last: Miska

first: M

last: Surani


title: Systematic characterization of seed overlap microRNA cotargeting associated with lupus pathogenesis (miRNA microarray)

first: Hiroshi

last: Suzuki

overall_design: miRNA expression profiling (miRNA microarray) in pDCs in the IMQ-induced SLE mouse model.

first: Hiroki

last: Kitai

first: Noritoshi

last: Kato

first: Koichi

last: Ogami

first: Shintaro

last: Komatsu

first: Yu

last: Watanabe

first: Seiko

last: Yoshino

first: Eri

last: Koshi


title: Small RNA Sequencing of in vitro Day 6 mPGCLCs

summary: Mouse Primordial Germ Cell Like Cells (mPGCLCs) are an in vitro model of the specification of mPGCs which happen around E6.25 in the developing mouse embryo. The aim of this study is the detection and profiling of mouse small RNAs via small RNA sequencing of E14-mESC-derived and Blimp1-GFP (BG5)-mESC-derived Day 6 mPGCLCs, each from diffent mouse strain backgrounds, alongside Day 6 non-PGCLC cells from E14, BG5 and Stella-GFP/Esg1-tdTomato (SGET) Embryoid Bodies. In particular, this study is aimed at the detection of small RNA length and first nucleotide biases.

overall_design: Examination of all small RNA-mapping profiles in biological duplicates of of Day 6 in vitro E14 and BG5 mPGCLCs, alongside E14, BG5 and SGET non-PGCLCs.


title: Systematic characterization of seed overlap microRNA cotargeting associated with lupus pathogenesis


title: Analysis of the liver transcriptome from wild-type and Gpr151 knock-out mice

city: Palo Alto

first: Ewa

last: Bielczyk-Maczynska

address: Falk Cardiovascular Research Center, 870 Quarry Rd

department: Division of Cardiovascular Medicine

summary:
Purpose: The goal of this study is to identify genes and molecular pathways whose expression is altered in the livers of Gpr151 knock-out (KO) mice compared to Gpr151 wild-type (WT).
Methods: Total RNA was isolated from livers of fasted (5h) 16-week-old male mice. Deep sequencing of RNA from three wild-type and three knock-out mice was done using the mRNA-Seq pipeline at Novogene. The sequence reads that passed quality filters were aligned to the mouse GRCm38.p6 genome using STAR 2.6.1d. Differential expression testing was conducted using DESeq2.
Results: Using an optimized data analysis workflow, we mapped about 40 million sequence reads per sample to the mouse genome (build mm10) and identified 54,532 transcripts in the livers of Gpr151 WT and KO mice. RNA-seq data identified 79 transcripts which were significantly upregulated in KO (p-adj < 0.05, log2FoldChange>1) and 338 transcripts which were significantly downregulated (p-adj<0.05, log2FoldChange<-1) in KO.
Conclusions: Our study represents the first detailed analysis of the liver transcriptome of Gpr151 KO mice.

overall_design: Hepatic mRNA profiles of 16-week-old Gpr151 WT and KO mice which were fed high-fast diet from 4 weeks of age.

first: Joshua

middle: W

last: Knowles


title: Role of Setd2 in regulatory T cells [Pol II CUT&Tag]

first: Ju

last: Qiu

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To determine the molecular regulation of Tregs by Setd2, spleen Tregs (CD3+CD4+Foxp3-YFP+) from Setd2-deficient and control Tregs were subjected to polII CUT&Tag analysis

overall_design: IL-2/anti-IL-2 complexes (IL-2c) were prepared by mixing 1 ug recombinant mouse IL-2 (Peprotech) with 5 ug anti-IL-2 (bioxcell, clone JES6-1) and incubated at 37°C for 30 min.  Foxp3Cre-YFPSetd2f/+ or Foxp3Cre-YFPSetd2f/f mice (n=2) were injected intraperitoneally (i.p.) with IL-2c for three consecutive days and sacrificed for analysis 48 h later. Splenic Tregs (CD3+CD4+Foxp3-YFP+) were sorted by flow cytometry and nuclei were extracted. Biological replicates of 80000 nuclei from each group were subjected to RNA polymerase II  (Pol II ) CUT&Tag analysis.

first: Zhaoyun

last: Ding

first: Ting

last: Cai


title: Role of Setd2 in regulatory T cells

summary:
This SuperSeries is composed of the SubSeries listed below.
To determine the molecular regulation of Tregs by Setd2, Spleen or large intestine Tregs (CD3+CD4+Foxp3-YFP+) were purified from littermate Foxp3Cre-YFPSetd2f/+ and Foxp3Cre-YFPSetd2f/f mice. Setd2-deficient and control Tregs were subjected to RNA-seq, RNA Polymerase II CUT&Tag or H3K27ac CUT&Tag analyses.

overall_design: Refer to individual Series


title: Profiling the transcription alteration and R-loop formation in Suv420h1 mutant muscle stem cell

status: Public on Oct 13 2022

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research


title: Role of Setd2 in regulatory T cells [RNAseqTreg]

summary: To determine the mechanism of regulation of Tregs by Setd2, LI Tregs (CD3+CD4+Foxp3-YFP+) from Setd2-deficient and control Tregs were subjected to RNA-seq analysis.

overall_design: About 2 × 10^5 sorted large intestinal Tregs (CD3+CD4+YFP+ cells) were pooled from littermate Foxp3Cre-YFPSetd2f/+ or Foxp3Cre-YFPSetd2f/f mice. Each biological replicate was pooled from 2-3 mice.


title: Role of Setd2 in regulatory T cells [H3K36me3 ChIP-seq]

summary: ChIP-sequencing for H3K36me3 analysis was performed on Tregs purified from the spleen and large intestine of naïve mice.

overall_design: Tregs (CD3+CD4+Foxp3-YFP+) sorted by flow cytometry from the spleen and large intestine of adult Foxp3Cre-YFP mice (cells were pooled from 7 male and 7 female mice) were subjected to H3K36me3 CHIP-seq analysis.

first: Xinyi

last: Qi


title: Genome-wide maps of nascent transcriptions in proliferating Ctrl and Suv420h1 mutant muscle stem cells

summary: To profile the nascent transcription activity including coding genes and eRNAs, we performed precision nuclear run-on sequencing (PRO-Seq) in control and Suv420h1 mutant MuSC

overall_design: PRO-seq in control and Suv420h1 mutant MuSC

last: Zhang

first: Stefan

last: Günter


title: Cut & Run mapping the alteration of H4K20me1 and transcription activity in cultured MuSC upon Suv420h1 depletion.

summary: H4K20me1/2/3 is dynamically regulated during cell cycle to maintain the genomic stability. Here, we found that depletion of H4K20 di-methyltransferase Suv420h1 in mouse adult MuSCs leads to strong accumulation of H4K20me1 specifically in S phase. In response to it, the transcription activity is increased upon Suv420h1 depletion. To investigate which genomic regions and how the transcription are regulated by Suv420h1 in MuSC, we performed Cut&Run of H4K20me1 and RNA polymerase II Ser2P in control and Suv420h1 inactivated MuSCs.

overall_design: Cut & Run of H4K20me1 and RNA polymerase II Ser2P in MuSC upon Suv420h1 depletion.

first: Dong


title: DRIP-seq mapping the R-loop formation in cultured Ctrl and Suv420h1 mutant MuSC

summary: Inactivation of Suv420h1 in MuSC lead to increased transcription and replication collision thereby caused accumulation of RNA:DNA hybrids. This study profiles the R-loops in Ctrl and Suv420h1m mutant MuSCs.

overall_design: DRIP-seq in Ctrl and Suv420h1 mutant MuSC


title: Systematic characterization of seed overlap microRNA cotargeting associated with lupus pathogenesis (RNA-seq)

first: Hiroshi

last: Suzuki

overall_design: RNA sequencing (RNA-seq) to study the effects of miR-128 and miR-148a overexpression on transcriptome.

first: Shoma

last: Tsubota

first: Yoshio

last: Funahashi

first: Takahiro

last: Maeda

first: Kazuhiro

last: Furuhashi

first: Takuji

last: Ishimoto

first: Tomoki

last: Kosugi

first: Shoichi

last: Maruyama

first: Kenji

last: Kadomatsu


title: Deep learning based transcriptome model robustly predicts survival in T-cell acute lymphoblastic leukemia

status: Public on Oct 12 2022

city: Guangzhou

first: Lenghe

address: No. 106, Zhongshan Second Road

institute: Guangdong Provincial People's Hospital

summary: Identifying subgroups of T-cell acute lymphoblastic leukemia (T-ALL) with poorer survival will significantly influence patient treatment options and improve patient survival expectations. Current efforts to unambiguously predict T-ALL survival expectations in multiple patient cohorts are lacking. A deep learning (DL)-based model was developed in order to reliably determine the prognostic staging of T-ALL patients. We used transcriptome sequencing data from TARGET to build a DL-based survival model on 265 T-ALL patients, we found that patients could be divided into two subgroups (K0 and K1) with significant differences (P < 0.0001) in survival rates. The more malignant subgroup was significantly associated with some tumor-related pathways, such as PI3K-Akt, cGMP-PKG and TGF-beta signaling pathway. DL-based model also showed good performance in a cohort of patients from our clinical center (P = 0.0248). T-ALL patients survival was successfully predicted using a DL-based model, and we hope to apply it to our clinical practice in the future.

overall_design: Analysis of 20 samples from patients with T-ALL.

first: Lijuan

last: Zhou

first: Chao

last: Li

first: Yulian

last: Wang

first: Pengjun

last: Liao

first: Liye

last: Zhong

first: Suxia

last: Geng

first: Peilong

last: Lai

first: Xin

last: Du

first: Jianyu

last: Weng


title: Role of Setd2 in regulatory T cells [H3K27ac CUT&Tag]

first: Ju

last: Qiu

summary: To determine the molecular regulation of Tregs by Setd2, large intestine Tregs (CD3+CD4+Foxp3-YFP+) from Setd2-deficient and control Tregs were subjected to H3K27ac CUT&Tag analysis.

overall_design: Biological replicates of 60000 Tregs (CD3+CD4+Foxp3-YFP+) sorted by flow cytometry from the large intestine of 2 week old Foxp3Cre-YFPSetd2f/+ or Foxp3Cre-YFPSetd2f/f mice （n=3-5） were subjected to H3K27ac CUT&Tag analysis.

first: Zhaoyun

last: Ding

first: Ting

last: Cai


title: Transgenerational transmission of aspartame induced anxiety and changes in glutamate-GABA signaling and gene expression in the amygdala

city: Tallahassee

first: Cynthia

last: Vied

state: Florida

address: 1115 W. Call St

department: Translational Science Laboratory

institute: Florida State University

summary: We show that daily exposure of mice to aspartame, an artificial sweetener found in over 5,000 diet foods and drinks at doses equivalent to only 15% of the FDA recommended maximum daily intake for humans produces anxiety. The anxiety is alleviated by diazepam, a drug used in the treatment of generalized anxiety disorder. We completed RNA sequencing of the amygdala of male mice that were exposed to aspartame or plain drinking water (control), as this brain region regulates anxiety and fear. The aspartame exposure produces changes in the expression of genes regulating excitation-inhibition balance in the amygdala. The anxiety, its response to diazepam and the changes in amygdala gene expression are not limited to the aspartame-exposed individuals but also appear in up to two generations descending from the aspartame-exposed males. Thus, aspartame’s neurobehavioral effects are not limited to those who consume it but also impact generations of descendants, a finding that highlights the need for a re-evaluation of current policies on artificial sweetener use.

overall_design: Amygdala mRNA from adult C57BL/6 males exposed to either 0.03% aspartame or plain drinking water were analyzed by RNA sequencing of 4 biological replicates using an Illumina NovaSeq 6000

first: Sara

middle: K

last: Jones

first: Deirdre

last: McCarthy

first: Pradeep

middle: G

last: Bhide


title: SERPINB9 is commonly amplified and high expression in cancer cells correlates with poor immune checkpoint blockade response

city: Amsterdam

first: Alex

last: van Vliet

address: Plesmanlaan 121

department: Molecular Oncology & Immunology

country: Netherlands

institute: Netherlands Cancer Institute

summary: After exposing a panel of non-small cell lung cancer (NSCLC) cell lines to cytotoxic CD8+ T-cells, we found SERPINB9 to be the most differentially expressed gene between the cell lines most and least resistant to T-cell killing.

overall_design: Gene expression profiling (RNAseq) of a NSCLC cell line panel pre- and post-T-cell exposure as well as concordant pre- and post-cytotoxic T-cell samples.

first: Sofía

last: Ibañez Molero


title: Effect of knockdown of DIO3OS and PTBP1 on gene expression of MCF-7 LTED cells [cellseq]

status: Public on Oct 11 2022

first: Xueman

last: Chen

state: Guangdong

address: 107 Yanjiang West Road

institute: Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University

summary: To investigate the function of DIO3OS and PTBP1 in the metabolic regulation, we used LNA and siRNA to silence DIO3OS and PTBP1, respectively, in established MCF-7 LTED cell lines. We then performed gene expression profiling analysis using data obtained from RNA-seq of six different cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MCF-7 LTED cell controls (LTnc and PTBnc) and their KD derivatives (LTlna1, LTlna2, PTBsi1, PTBsi2).

first: Man-Li

last: Luo

first: Erwei

last: Song


title: DNA sequeencing for pHLA-B27 yeast display library selection for AS related TCRs

status: Public on Oct 09 2022

first: Xinbo

last: Yang

address: 279 Campus Drive

department: MCP

summary: AS TCR related antibody Fab fragment was selected on a HLA-A2 peptide library displayed on yeast for cross-reactivity check

first: K

middle: C

last: Garcia


title: Effect of aromatase inhibitor (AI) treatment on gene expression of breast cancer [tissueseq]

summary: To investigate the expression profiling of estrogen receptor positive breast cancer after AI treatment, we obtained tumor samples from breast cancer patients receiving adjuvant AI treatment, then performed RNA sequencing and gene expression profiling analysis for 14 different breast tumor samples.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for AI-sensitive (S1-S7) and AI-resistant (R1-R7) tumor samples obtained from breast cancer patients


title: Transcriptomic analysis of the effect of Kap120 deletion

status: Public on Oct 10 2022

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

summary: The effect of Kap120 deletion at transcriptional level was investigated by GRO analysis of the transcription rates (TR) and mRNA levels (RA) genome-wide. mRNA stabilities can be calculated as RA /TR for each gene in all samples.

overall_design: Cells were grown in YPD at 30ºC to 0.4-0.5 OD600. Cells were spun-down and collected. Note that each sample record represents three replicates.

first: José

last: Pérez-Ortín

last: García-Martínez


title: Gene expression profile at single cell level of cultured Myb-68 GFP+ Ly6C- GMP cells

city: Singapore

first: Takayoshi

last: Matsumura

address: 14 Medical Drive #12-01

country: Singapore

institute: National University of Singapore

summary: A novel Myb-68 enhancer is predominant in basohil and mast cell lineages. To analyze their differentiation trajectories, we conducted scRNA-seq of Myb-68 GFP+ bone marrow cells.

overall_design: Bone marrow cells were harvested from Myb-68 GFP cells. GFP+ Ly6C- GMP cells were sorted and cultured with IL3 for 3 days.

first: Toshio

last: Suda


title: RNA sequencing on the PyMt cell line after culture with test versus control CD4+ T supernatants

status: Public on Oct 08 2022

city: Charleston

first: Heehwa

last: Son

address: 149 13 street

institute: MASSACHUSETTS GENERAL HOSPITAL

summary: The antitumor immunity mediated by TSLP-stimulated CD4+ T cells in advanced breast cancer is mediated by the induction of a senescent-like phenotype in cancer cells.

overall_design: Analysis of differentially regulated genes in test group versus control

first: Margherita

last: Boieri

first: Shadmehr

last: Demehri

first: Emanuela

last: Marchese


title: Ethanol and its nonoxidative metabolites promote acute liver injury by inducing ER stress, adipocyte death and lipolysis

status: Public on Oct 07 2022

city: Rockville

first: Bryan

last: Mackowiak

state: MD

address: 5625 Fishers Lane, 2S12

institute: NIH

summary: We gave mice either a 5g/kg ethanol (EtOH) gavage, a 7g/kg EtOH gavage, or an isocaloric maltose gavage (equivalent to 5g/kg EtOH) in the morning and sacrificed mice 9h later. Microarray analyses were performed on liver tissue from these mice to determine genes and pathways contributing to acute ethanol-induced liver injury. Lipid metabolism-associated genes were found to be dysregulated in both the 5g/kg and 7g/kg groups, with the majority of changes occuring in the 7g/kg group. Genes related to fatty acid metabolism were most changed in the 7g/kg group compared to control and 5g/kg groups.

overall_design: Three condition experiment - control (maltose), 5g/kg EtOH gavage, 7g/kg EtOH gavage

first: Mackowiak

last: Bryan

first: Xu

last: Ming-Jiang

first: Gao

last: Bin


title: Oncogenic RAS triggers stem cell: microenvironment crosstalk to drive malignant progression [ATAC-seq]

city: New York City

first: Katherine

last: Stewart

state: NY

address: 1230 York Avenue

department: Laboratory of Mammalian Cell Biology and Development

institute: The Rockefeller University

summary: Oncogenic RAS/MAPK signaling drives metastatic squamous cell carcinomas (SCCs). These cancers are typified by high mutational burden, often featuring activating mutations in phosphatidylinositol-3-kinase (PI3K). Here we show that early in skin HRASG12V-induced oncogenesis, transitions from benign to malignant states are also marked by PI3K, this time super-activated through a temporal cascade of non-genetic events. Coupling clonal skin SCC genetic models with bulk and single-cell transcriptomics, chromatin-landscaping, lentiviral reporters, and lineage-tracing, we trace its roots. We show that following HRASG12V activation, oncogenic stem cells rewire their gene expression program. Initially, they produce an array of angiogenic factors, triggering a striking influx of vasculature and TGFβ into the microenvironment. Sparked by TGFβ-signaling, the stem cells induce leptin receptor (LEPR), which through the angiogenic influx activates LEPR-signaling to launch downstream PI3K-AKT-mTOR signaling. Our findings show how dynamic temporal crosstalk with the microenvironment, orchestrated by the stem cells, can drive the path to malignancy.

overall_design: ATAC-seq was performed as described before in Buenrostro et al., 2013. Briefly, FACS sorted were lysed with ATAC lysis buffer on ice for 1 minute. Lysed cells were then tagmented with Tn5 transposase (Illumina) at 37C for 30min. Cleaned up fragments were PCR amplified (NEB) and size selected with 1.8X SPRI beads (Beckman Coulter). All libraries were sequenced on Illumina NextSeq 500 with 40-bp paired-end settings.

first: Shaopeng

last: Yuan

middle: S

first: Yihao

first: Elaine

last: Fuchs


title: Integration of single-cell transcriptomes and biological function reveals distinct behavioral patterns in bone marrow endothelial cells [scRNA-Seq]

city: Duarte

first: Denis

last: OMeally

state: California

address: 1500 E Duarte Rd

department: Arthur Riggs Diabetes & Metabolism Research Institute

institute: City of Hope

summary: Heterogeneity of endothelial cell populations reflects their diverse functions in maintaining tissue’s homeostasis. However, their phenotypic, molecular, and functional properties are not entirely mapped. We used a new Tie2-CreERT2;Rosa26-tdTomato reporter mouse to trace, profile, and cultivated primary ECs from different organs. As platform paradigm, we used this strategy to study bone marrow endothelial cells (BMEC). Single-cell mRNA sequencing of primary BMEC revealed that their diversity and native molecular signatures is transitorily preserved in an ex-vivo culture that conserves key cell-to-cell microenvironment interactions. Macrophages sustained primary BMEC cellular diversity and expansion and were critical to preserve sinusoidal-like BMEC ex-vivo. Expression of endomucin discriminated BMEC in populations exhibiting mutually exclusive properties and distinct tip and stalk signatures. In contrast to arterial-like, sinusoidal-like BMECs were short-lived, formed 2D-networks, contributed to in-vivo angiogenesis and supported hematopoietic stem/progenitor cells in-vitro. This platform can be extended to other organs’ ECs to decode mechanistic information and explore therapeutics.

overall_design: Single-cell mRNA sequencing of primary BMEC cultures and bulk sequencing of Emcn+ and Emcn- BMEC sorted from P0 WBM, cultured MSC and lung.

first: Young-Woong

last: Kim

first: Greta

last: Zara

first: Sergio

last: Branciamore

last: O'Meally

first: Yuxin

last: Feng

first: Chia-Yi

last: Kuan

first: Yingjun

last: Luo

first: Michael

last: Nelson

first: Alex

last: Brummer

first: Russell

last: Rockne

first: Zhen

last: Bouman Chen

first: Yi

last: Zheng

first: Angelo

last: Cardoso

first: Nadia

last: Carlesso


title: Programmatic building of a secretory acinus is driven by neuronal-epithelial NRG1-ERBB3-mTORC2 signaling.

city: San Francisco

first: Sarah

last: Knox

address: 513 Parnassus Ave

institute: UCSF

summary: Acinar cells are the principal secretory unit of multiple exocrine organs. A single cell layered, lumenized acinus forms from a large cohort of epithelial progenitors that must initiate and coordinate three cellular programs of acinar specification, namely, lineage progression, secretion, and polarization. Despite this well-known outcome, the mechanism(s) regulating these complex programs are unknown. Here, we demonstrate that neuronal-epithelial cross-talk drives acinar specification through neuregulin (NRG1)-ERBB3-mTORC2 signaling. Using single-cell and global RNA-sequencing of developing salivary glands, we identified NRG1-ERBB3 to precisely overlap with acinar specification during gland development. Genetic deletion of Erbb3 prevented cell lineage progression and the establishment of lumenized, secretory acini. Conversely, NRG1 treatment of isolated epithelia was sufficient to recapitulate the development of secretory acini. Mechanistically, we found NRG1-ERBB3 regulates each developmental program through an mTORC2 signaling pathway. Thus, we reveal a novel neuronal-epithelial (NRG1/ERBB3/mTORC2) mechanism to orchestrate the creation of functional acini.

overall_design: Comparative analysis of gene expression between 1) salivary glannds at different stages of development (E13-E18), 2) salivary epithelia treated with NRG1 for 4, 48, 72 or 96 hrs compared to corresponding controls and 3) wild type and Erbb3 deficient E16 salivary glands.

first: Alison

last: May

first: Aaron

last: Mattingly

first: Eliza

last: Gaylord

first: Nathan

last: Griffin

first: Sonia

last: Sudiwala

first: Noel

last: Cruz Pacheco

last: Emmerson

first: Seayar

last: Mohabbat

first: Sara

last: Nathan

first: Hanan

last: Sinada

first: Isabelle

last: Lombaert


title: Gene expression profile at single cell level of Myb-68 GFP+ bone marrow cells

first: Takayoshi

last: Matsumura

overall_design: Bone marrow cells were harvested from Myb-68 GFP cells, and GFP+ cells were sorted twice by FACS.

first: Toshio

last: Suda


title: Towards Optimization of Precision Oncology in Metastatic Uterine Tumors

status: Public on Oct 06 2022

city: Seville

first: Juan

last: Diaz-Martin

address: Av Manuel Siurot

institute: IBiS

summary: The incidence of new cancer cases is expected to increase significantly in the future, posing a worldwide problem. In this regard, precision oncology and its diagnostic tools are essential for developing personalized cancer treatments. Nowadays, it is almost impossible to separate technology and digitization from medicine and health sciences, and digital pathology (DP) is emerging as one of the most influential technologies in the transition towards the 4P of new medicine (preventive, participatory, personalized and predictive). DP is a particularly key strategy to study the interactions of tumor cells and the tumor microenvironment (TME), which play a crucial role in tumor initiation, progression and metastasis. The purpose of this study was to integrate data on the digital patterns of reticulin fiber scaffolding and the immune cell infiltrate, transcriptomic and epigenetic profiles in aggressive uterine adenocarcinoma (uADC), uterine leiomyosarcoma (uLMS) and their respective lung metastases, with the aim of obtaining key TME biomarkers that can help improve metastatic prediction and shed light on potential therapeutic targets. Automatized algorithms were used to analyze reticulin fiber architecture and immune infiltration in colocalized regions of interest (ROIs) of 133 invasive tumor front (ITF), 89 tumor niches and 70 target tissues in a total of six paired samples of uADC and nine of uLMS. Microdissected tissue from the ITF was employed for transcriptomic and epigenetic studies in primary and metastatic tumors. Reticulin fiber scaffolding was characterized by a large and loose reticular fiber network in uADC, while dense bundles were found in uLMS. Notably, more similarities between reticulin fibers were observed in paired uLMS then paired uADCs. Transcriptomic and multiplex immunofluorescence-based immune profiling showed a higher abundance of T and B cells in primary tumor and in metastatic uADC than uLMS. Moreover, the epigenetic signature of paired samples in uADCs showed more differences than paired samples in uLMS. Some epigenetic variation was also found between the ITF of metastatic uADC and uLMS. Altogether, our data suggest a correlation between morphological and molecular changes at the ITF and the degree of aggressiveness. The use of DP tools for characterizing reticulin scaffolding and immune cell infiltration at the ITF  in paired samples together with information provided by omics analyses in a large cohort will hopefully help validate novel biomarkers of tumor aggressiveness, develop new drugs and improve patient quality of life in a much more efficient way.

overall_design: Transcriptomic profiling of invasive tumor front of aggressive metastatic uterine adenocarcinomas (n=6) and leiomyosarcomas (n=7) using HTG EdgeSeq Precision Immuno-Oncology Panel, which interrogates 1,392 genes involved in tumor/immune interaction.

first: Carmen

last: Salguero-Aranda

first: Enrique

last: de Alava


title: Oncogenic RAS triggers stem cell: microenvironment crosstalk to drive malignant progression

first: Katherine

last: Stewart

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

overall_design: Refer to individual Series


title: Oncogenic RAS triggers stem cell: microenvironment crosstalk to drive malignant progression [RNA-seq]

overall_design: FACS-sorted tumor cells were directly sorted into TRI Reagent, and total RNA was purified using the Direct-zol RNA kit (Zymo Research) according to the kit protocol. RNA quality was determined by Agilent 2100 Bioanalyzer, and cDNA libraries were prepared using the Illumina TrueSeq mRNA sample preparation kit (non-stranded, poly-A selection) and sequenced on an Illumina HiSeq 4000 or NovaSeq.

first: Shaopeng

last: Yuan

first: Yihao

last: Yang

first: Elaine

last: Fuchs


title: Human blood monocytes scRNAseq

status: Public on Oct 05 2022

city: Paris

first: Javiera

last: Villar

address: 25 rue d'Ulm

institute: Institut Curie

summary: scRNAseq of human blood monocytes isolated with magnetic CD14+ beads from two healthy donors.

overall_design: We performed scRNA sequencing to understand the hetereogenity of the cell population we are culturing in vitro. We combined this technology to HASH-sequencing in order to measure these data simultaneously in two healthy human donors.

first: Elodie

last: Segura


title: Ascertaining cells' synaptic connections and RNA expression simultaneously with barcoded rabies virus libraries

city: Boston

first: Arpiar

last: Saunders

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

summary: We describe "SBARRO" a system in which synaptic networks of cells are reconstructed from scRNA-seq data using clonal infectivity paths of barcoded rabies virus RNAs

overall_design: single-cell RNA-seq libraries were collected from cell infected with barcoded rabies virus. Barcoded viral mRNAs were used to reconstruct inferred synaptic networks. Host cell RNAs were used to identify cell types and states as well as pre vs postsynaptic identity

first: Steve

last: McCarroll


title: Oncogenic RAS triggers stem cell: microenvironment crosstalk to drive malignant progression [scRNA-Seq]

overall_design: FACS sorted tumor cells were sorted directly into SMARTSeq2 lysis buffer in 96-well plates and snap frozen.


title: Gene expression profile at the singe-cell level on human induced pluripotent stem cell (hiPSC) derived midbrain dopaminergic neurons

city: London

first: Sonia

last: Gandhi

address: 1 Midland Road

institute: The Francis Crick Institute

summary: We optimised a new differentiation paradigm to produce midbrain dopaminergic neurons from hiPSCs. To characterise their identity, we performed scRNA-seq to investigate their gene expression and molecular identity.

overall_design: hiPSCs were differentiated using small molecule combination for 20 days to produce midbrain dopaminergic (mDA) precursor cells. These were then terminally differentiated into mDA neurons and grown for a further 28 days. The mDA monolayer was then dissociated into a single-cell suspension to perform scRNA-seq.

first: Gurvir

last: Virdi

first: Stephanie

last: Strohbuecker


title: Invasive tumor front (ITF) of uterine adenocarcinomas and leiomyosarcomas. Primary and metastatic specimens

status: Public on Oct 04 2022


title: RNA-seq analysis of human monocytes exposed to lentivirus expressing shRNA against ETV3 or ETV6 during differentiation

summary: Human monocytes exposed to lentivirus expressing shRNA against ETV3 or ETV6 during differentiation

overall_design: Human monocytes treated with shRNA against ETV3 or ETV6 during differentiation


title: ChIP-seq analysis of ETV3 and ETV6 in monocyte-derived cells

summary: We analyzed by ChIPseq the genes bound by ETV3 or ETV6 in differentiating monocytes.

overall_design: Immuno-precitipation of ETV3 or ETV6 was performed in monocytes cultured with cytokines for 3 days. We sequenced DNA of inmuno-precipitated material from two independent donors and the corresponding input.

last: Vilar


title: Postnatal expansion of the lymph node stromal cell pool towards reticular and CD34+ stromal cell subsets [ATAC-seq]

city: Lausanne

first: Joern

last: Pezoldt

address: Station 19, SV 3818.A

department: SV

country: Switzerland

institute: EPFL

summary: Gut-draining mesenteric lymph nodes (mLN) provide the framework and microenvironment to shape intestinal adaptive immune responses. We previously delineated transcriptional signatures in LN stromal cells (SC), pointing to tissue-specific variability in composition and immuno-modulatory function of SCs. Here, we dissect the tissue-specific epigenomic DNA accessibility and CpG methylation landscape of LN non-endothelial SCs and identify a microbiota-independent core epigenomic signature of LN SCs. By combined analysis of transcription factor (TF) binding sites together with the gene expression profiles of non-endothelial SCs, we delineated TFs poising skin-draining peripheral LN (pLN) SCs for pro-inflammatory responses. Furthermore, using scRNA-seq, we dissected the developmental trajectory of mLN SCs derived from postnatal to aged mice, identifying two distinct putative progenitors, namely CD34+ SC and fibroblastic reticular stromal cell (FRC) progenitors, which both feed the rapid postnatal LN expansion. Finally, we identified Irf3 as a key differentiation TF inferred from the epigenomic signature of mLN SCs that is dynamically expressed along the differentiation trajectories of FRCs, and validated Irf3 as a regulator of Cxcl9+ FRC differentiation. Together, our data constitute a comprehensive transcriptional and epigenomic map of mLN development and dissect location-specific, microbiota-independent properties of mLN non-endothelial SCs. As such, our findings represent a valuable resource to identify core transcriptional regulators that impinge on the developing mLN early in life, thereby shaping long-lasting intestinal adaptive immune responses.

overall_design: ATAC-seq on FACS-isolated CD45-CD24-CD31-Pdpn+ cells from skin- or gut-draining lymph nodes of SPF or GF housed mice

first: Carolin

last: Wiechers

first: Maria

last: Litovchenko

first: Bart

last: Deplancke

first: Jochen

last: Huehn


title: Integration of single-cell transcriptomes and biological function reveals distinct behavioral patterns in bone marrow endothelial cells [bulk RNA-seq]

first: Denis

last: OMeally

first: Young-Woong

last: Kim

first: Greta

last: Zara

first: Sergio

last: Branciamore

last: O'Meally

first: Yuxin

last: Feng

first: Chia-Yi

last: Kuan

first: Yingjun

last: Luo

first: Michael

last: Nelson

first: Alex

last: Brummer

first: Russell

last: Rockne

first: Zhen

last: Bouman Chen

first: Yi

last: Zheng

first: Angelo

last: Cardoso

first: Nadia

last: Carlesso


title: I536T variant of RBM20 affects splicing of cardiac structural proteins that are causative for developing dilated cardiomyopathy

city: Nishinomiya

first: Takuma

last: Yamamoto

address: 1-1 Mukogawa-Cho

institute: Hyogo Medical University

summary: Background: RBM20 gene is one of the genetic predispositions for dilated cardiomyopathy (DCM). Variants in RS domain has been reported in many DCM patients, while the pathogenicity of variants within the RNA-recognition motif remains unknown.  Methods and results: We detected two human patients of I536T-RBM20 variant without DCM phenotype in sudden death cohorts. We performed splicing reporter assay and generated I538T knock-in (KI) mouse model (Rbm20I538T) in order to reveal the significance of this variant. The reporter assay revealed that human I536T variant affected TTN splicing pattern compared to wild-type. In the mouse experiments, Rbm20I538T mice presented a different splicing pattern in Ttn, Ldb3, Camk2d and Ryr2. The expression of Casq1, Mybpc2 and Myot were upregulated in Rbm20I538T mice. Whereas, Rbm20I538T mice did show neither DCM nor cardiac dysfunction by histopathological examination and ultrasound echocardiography.  Conclusion: I536T-RBM20 (I538T-Rbm20) variant does not cause DCM phenotype, but changes the gene splicing and expression effect. The splicing and expression changes in Ttn and Ca handling genes such as Casq1, Camk2d and Ryr2 may be contributory to sudden arrhythmogenic death.

overall_design: Using the CRISPR/Cas system, we generated KI mice harboring the c.T1613C (p.I538T) point mutation in the mouse Rbm20 gene, which corresponded to human c.T1607C (p.I536T).


title: Transcriptome analysis of Pectobacterium atrosepticum

city: Seoul

first: JIEUN

last: KANG

country: South Korea

institute: Korea university

summary: The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of Pectobacterium upon treatment of polyphenol compound.

overall_design: mRNA from Pectobacterium incubated in Pel inducing medium

first: Jieun

last: Kang

first: Eui-Hwan

last: Chung

first: Sungmin

last: Hwang


title: Integration of single-cell transcriptomes and biological function reveals distinct behavioral patterns in bone marrow endothelial cells

first: Denis

last: OMeally


title: Single-cell sequencing and second-generation RNA sequencing-based screening of macrophage-associated marker genes for recurrent miscarriage diagnosis

city: Nanning

first: Peiru

last: Wei

address: Shuangyong Road, 22

institute: Guangxi Medical University

summary: We profiled the transcriptomes of about 110000 single cells from 16 human first-trimester decidual and villi samples from 5 normal samples and 3 recurrent miscarriage (RM) samples. Each decidual and villi samples was collected from the same patient. The cellular composition revealed five major subsets of immune cells including NK, T cell, macrophage, monocytes and B cell in the maternal fetal interface. We used the marker gene of macrophages to establish the diagnosis and treatment model of unexplained recurrent abortion, in order to explore the relationship between immune cells and unexplained recurrent abortion.

overall_design: Profiling the transcriptomes of about 110000 single cells from 16 human first-trimester decidual and villi samples from 5 normal samples and 3 recurrent miscarriage (RM) samples. Each decidual and villi samples was collected from the same patient using single-cell RNA Seq. Decidua and villi samples with the same number (such as NC_D6-1 and NC_V6-1, RM_D6 and RM_V6) were collected from the same patient.

first: Yihua

last: Yang

first: Xiaoqian

last: Fu

first: Mingyou

last: Dong

first: Yin

last: Bi

first: Saiqiong

last: Chen

first: Weiyu

last: Huang

first: Ting

last: Li

first: Bo

last: Liu


title: Active DNA damage response signaling initiates and maintains meiotic sex chromosome inactivation

city: Davis

first: Satoshi

middle: H

last: Namekawa

address: One Shields Avenue

department: Department of Molecular and Cellular Biology

institute: University of California, Davis

summary: Meiotic sex chromosome inactivation (MSCI) is an essential process in the male germline. While genetic experiments have established that the DNA damage response (DDR) pathway directs MSCI, due to limitations to the experimental systems available, mechanisms underlying MSCI remain largely unknown. Here we establish a system to study MSCI ex vivo, based on a short-term culture method, and demonstrate that active DDR signaling is required both to initiate and maintain MSCI via a dynamic and reversible process. DDR-directed MSCI follows two layers of modifications: active DDR-dependent reversible processes and irreversible histone post-translational modifications. Further, the DDR initiates MSCI independent of the downstream repressive histone mark H3K9 trimethylation (H3K9me3), thereby demonstrating that active DDR signaling is the primary mechanism of silencing in MSCI. By unveiling the dynamic nature of MSCI, and its governance by active DDR signals, our study highlights the sex chromosomes as an active signaling hub in meiosis.

overall_design: The isolated pachytene spermatocytes were cultured with DMSO or 10 µM AZ20 for 24 h at 34 C at 5% CO2.RNA-seq analysis using cultured spermatocytes for 24 h.

first: Hironori

last: Abe

first: Yasuhisa

last: Munakata


title: SHARE-seqV2 for single-cell epigenomic and transcriptomic mapping of human hematopoiesis at scale

city: New York

first: Sai

last: Ma

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: A growing body of single-cell multi-omic tools enables a better understanding of gene regulation underlying development and disease. Tools mapping chromatin and gene expression (such as SHARE-seq) are limited in sensitivity and scalability. Here, we describe SHARE-seqV2 and its associated cloud-computing resource, enabling single-cell analysis at improved quality, robustness, and scale. We apply SHARE-seqV2 across various cell lines, primary tissues, and immune cells, demonstrating a generalizable platform for single-cell multi-omics.

overall_design: SHARE-seqV2 to profile chromatin accessibility and gene expression in the same cell from cell lines (HEK and 3T3), mouse colon, cultured HSC, and primey BMMC.

first: Jason

last: Buenrostro


title: Gene expression profiles of MLL-AF9 leukemia cells treated with FF-10501-01

status: Public on Oct 01 2022

city: Tokyo

first: Susumu

last: Goyama

address: 4-6-1 Shirokanedai, Minato-ku

department: Graduate School of Frontier Sciences

institute: The University of Tokyo

summary: To assess the molecular changes induced by IMPDH inhibition in MLL-AF9 leukemia, we examined gene expression profiles of vehicle- or FF-10501-01-treated MLL-AF9 cells by RNA-seq.

overall_design: FF-10501-01 was orally administered to leukemic mice for two consecutive days.  48 hours after first treatment, GFP+ leukemia cells were collected from bone marrow and isolated using cell sorter before RNA extraction.

first: Xiaoxiao

last: Yamasaki

first: Tatsuhiro

last: Shibata


title: Transcriptional instability prevents dispersion of functional vomeronasal receptor genes [scRNA-seq]

status: Public on Oct 02 2022

city: Geneva

first: Ivan

last: Rodriguez

address: 30 quai Ernest Anrsermet

department: Genetics and Evolution

institute: University of Geneva

summary: Rodents perceive pheromones via vomeronasal receptors encoded by the Vr and Fpr gene superfamilies. The evolution of these latter is exceptionally dynamic. We report here that high numbers of V1r pseudogenes are scattered in mammalian genomes, contrasting with the clustered organization of functional V1r and Fpr genes. We also found that V1r pseudogenes are more likely to be expressed when located in a functional V1r gene cluster than when isolated. To explore the potential regulatory role played by the association of functional vomeronasal receptor genes with their clusters, we dissociated the mouse Fpr-rs3 from its native cluster via transgenesis. Singular and specific transgenic Fpr-rs3 transcription was observed in young vomeronasal neurons, but was only transient. Our data point to the existence of transcription stabilizing elements not coupled to vomeronasal gene units but rather associated with vomeronasal gene clusters, and thus explain the evolutionary conserved clustered organization of functional vomeronasal genes.

overall_design: Vomeronasal receptor gene expression profiling in the mouse and the rat vomeronasal organ using whole tissue and single-cell RNA sequencing.

first: Quentin

last: Dietschi

first: Joel

last: Tuberosa

first: Leon

last: Fodoulian

first: Chenda

last: Kan

first: Julien

last: Codourey

first: Alan

last: Carleton


title: Transcriptional instability prevents dispersion of functional vomeronasal receptor genes

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus


title: Systematic transcriptome analysis associated with physiological and chronological aging in Caenorhabditis elegans

city: Daejeon

first: Seung-Jae

last: Lee

address: 291 Daehak-ro

department: Biological Sciences

institute: KAIST

summary: We analyzed transcriptomic features associated with physiological and chronological aging using Caenorhabditis elegans as a model.

overall_design: The investigation of gene expression changes during aging in wild-type and daf-2 mutant worms.

first: Sieun

last: Kim

first: Sangsoon

last: Park

first: Eun Ji

first: Sujeong

last: Kwon

first: Seokjin

last: Ham

first: Seung


title: Transcriptional instability prevents dispersion of functional vomeronasal receptor genes [mouse]

overall_design: Vomeronasal receptor gene expression profiling in the mouse vomeronasal organ using whole tissue and single-cell RNA sequencing.


title: Transcriptomic analysis of isolated human postmortem Purkinje neurons implicates developmental organization/connectivity, extracellular matrix organization, calcium ion response, immune function and signaling alterations in autism spectrum disorders

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

summary: At present, the underlying neuronal mechanisms leading to an autism spectrum disorder (ASD) diagnosis have not been identified.  However, studies from human postmortem ASD brains have consistently revealed disruptions in cerebellar circuitry, specifically with a reduction in Purkinje cell (PC) number and size.  Alterations in cerebellar circuitry would have important implications for information processing within the cerebellum and affect a wide range of human motor and non-motor behaviors.  Laser capture microdissection was performed to obtain pure PC populations from a cohort of postmortem control and ASD cases and transcriptional profiles were compared.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from postmortem ASD Purkinje neurons compared to controls.

first: Cheryl

last: Brandenburg


title: Gene expression profile at single cell level of colonic epithelial cells from the distal colon

first: Isaac

last: Chiu

institute: Harvard medical school

summary: The colon is densely innervated by nociceptor neurons. Single cell RNA sequencing (scRNA-seq) of colon epithelial cells was performed to analyze the role of nociceptor neurons and Ramp1 signaling in regulating colonic epithelial cells.

overall_design: Colonic epithelial cells were purified by Fluorescence-activated cell sorting (FACS) from nociceptor knockout (Nav1.8Cre_P_DTA) mice, epithelial specific Ramp1 knockout (VillinCre_P_Ramp1) mice and their littermate control mice. The purified cells were used for scRNAseq using 10X.

first: Daping

last: Yang


title: Omics analyses of a somatic Trp53R245W/+ breast cancer model identify cooperating driver events activating PI3K/Akt/mTOR signaling

city: Houston

first: Khandan

last: Keyomarsi

state: TX

address: 1515 Holcombe Blvd

department: Experimental Radiation Onc

institute: The University of Texas MD Anderson Cancer Center

summary: Alterations of the tumor suppressor TP53, one of the most common events in cancer, alone are insufficient for tumor development but serve as drivers of transformation. We sought to identify cooperating events through genomic analyses of a novel somatic Trp53R245W mouse model (equivalent to the TP53R248W hot spot mutation in human cancers) that recapitulates metastatic breast cancer development. We identified cooperating lesions similar to those found in human breast cancers. Moreover, we identified activation of the Pi3k/Akt/mTOR pathway in most tumors via mutations in Pten, Erbb2, Kras and/or a recurrent Pip5k1c mutation that stabilizes the Pip5k1c protein to activate Pi3k/Akt/mTOR signaling. Another PIP5K1C family member, PIP5K1A, is co-amplified with PI4KB in 18% of human breast cancer patients and both encode kinases that are responsible for production of the PI3K substrate, phosphatidylinositol 4,5-bisphosphate. Thus, the TP53R248W mutation and PI3K/Akt/mTOR signaling are major cooperative events driving breast cancer development. Additionally, we demonstrated that the upregulation of oxidative phosphorylation by Pi3k/Akt/mTOR signaling is a vulnerability in murine as well as human breast cancer cell lines. These findings advance our understanding of mutant p53-driven breast tumors and expand testable targets for breast cancer treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse breast tumors driven by somatic Trp53R245W and enriched epithelia isolated from mammary glands of mice in the same cohort

first: Xiaojie

last: Yu

first: Yun

last: Zhang

first: Shunbin

last: Xiong

first: Joy

last: McDaniel

first: Chang

last: Sun

first: Jovanka

last: Gencel-Augusto

first: Dhruv

last: Chachad

first: Rhiannon

last: Morrissey

first: Xiayu

last: Rao

first: Jing

last: Wang

first: Guillermina

last: Lozano


title: Transcriptional instability prevents dispersion of functional vomeronasal receptor genes [rat]

first: Ivan

last: Rodriguez

overall_design: Vomeronasal receptor gene expression profiling in the rat vomeronasal organ using whole tissue and single-cell RNA sequencing.

first: Quentin

last: Dietschi

first: Joel

last: Tuberosa

first: Leon

last: Fodoulian

first: Chenda

last: Kan

first: Julien

last: Codourey

first: Alan

last: Carleton


title: Gene expression profile at single cell level of small intestine epithelial cells from the distal ileum

first: Isaac

last: Chiu

summary: Small intestine is highly innervated by nociceptor neurons. Single cell RNA sequencing (scRNA-seq) of ileal epithelial cells was performed to analyze the role of nociceptor neurons in regulating small intestinal epithelial cells.

overall_design: Ileal epithelial cells were purified by Fluorescence-activated cell sorting (FACS) from both nociceptor knockout (Nav1.8Cre_P_DTA_P) mice and the control (Nav1.8Cre_M_DTA_P) mice. The purified cells were used for scRNAseq using inDrops.

first: Daping

last: Yang


title: tRNA abundance, modification and fragmentation as biomarkers for COVID-19 severity

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

summary: Respiratory viruses such as SARS-CoV-2 are pathogens that can reach pandemic proportions. The early human response to respiratory viruses are in the nasal cavity and nasopharyngeal regions. Defining biomarkers of disease trajectory at the time of a positive test is important for opting for treatment and monitoring decisions. We hypothesize that the nasopharyngeal tRNA profiles can be used to predict symptom severity resulting from SARS-CoV-2 infection. We carried out multiplex small RNA sequencing (MSR-seq) on nasopharyngeal swaps to measure the human tRNA response to SARS-CoV-2 infection. Our result simultaneously measured full-length tRNA abundance, tRNA modifications, and tRNA fragmentation among individuals that went on to develop no/mild or severe symptoms. We identified distinct tRNA signatures that can predict the clinical outcome of SARS-CoV-2 infected individual at the time of a positive test. These results highlight the utility of using host tRNA properties as biomarkers for clinical applications.

overall_design: Healthy, Influenza, and Covid Samples

first: Chris

last: Katanski

last: Watkins

first: Karen

last: Lolans

first: Sihao

last: Huang

first: Viviana

last: Simon


title: ETS1 is a novel transcriptional regulator of adult T-cell leukemia/lymphoma of North American descent

first: Rebecca

last: Luchtel

state: IL

address: 303 E Superior St

institute: Northwestern University

summary: Transcriptional analysis of patient-derived cell lines of adult T-cell leukemia/ lymphoma (ATLL).

overall_design: RNA-seq was performed on ATLL cell lines.


title: Genomics of sexual cell fate transdifferentiation in the mouse gonad

status: Public on Sep 30 2022

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

summary: Sex determination in mammals hinges on a cell fate decision in the fetal bipotential gonad between male Sertoli cells and female granulosa cells.  While this decision normally is permanent, loss of key cell fate regulators such as the transcription factors Dmrt1 and Foxl2 can cause postnatal transdifferentiation from Sertoli to granulosa-like or vice versa.  Here we examine the mechanism of transdifferentiation in mice carrying either a null mutation of Dmrt1 or a point mutation, R111G, that alters the DNA binding motif and causes human XY gonadal dysgenesis and sex reversal.  We first define genes misexpressed during transdifferentiation and then show that female transcriptional regulators driving transdifferentiation in the mutant XY gonad (ESR2, LRH1, FOXL2) bind chromatin sites related to those normally bound in the XX ovary.  We then define gene expression changes at the onset of transdifferentiation and abnormal chromatin compartments that may help destabilize cell fate and initiate transdifferentiation.  We model the R111G mutation in mice and show that it causes dominant gonadal dysgenesis, analogous to its human phenotype but less severe.  We show that R111G partially feminizes the testicular transcriptome and causes dominant disruption of DMRT1 binding specificity in vivo.  These data help illuminate how transdifferentiation occurs when sexual cell fate maintenance is disrupted and identify chromatin sites and transcripts that may play key roles in the transdifferentiation process.

overall_design: RNA-seq (30 samples), ChIP-seq (17 samples, and Hi-C (2 samples) on gonads and purified Sertoli cells.

first: David

last: Zarkower

middle: D


title: RNA-seq of human CD8low and CD8high cytotoxic T lymphocytes upon in vitro starvation

city: Frankfurt am Main

first: Tobias

last: Burkard

address: Theodor-Stern-Kai 7

department: Institute of General Pharmacology and Toxicology

institute: Goethe University Frankfurt

summary: The mechanistic target of rapamycin (mTOR) signaling, which is an essential metabolic pathway that influences T cell differentiation, can be limited under conditions of metabolic stress e.g. during the cell starvation. As we observed reduced CD8 expression upon cell starvation in vitro, we sorted human cytotoxic T lymphocytes derived from six donors into low CD8 expression and high CD8 expressing T lymphocytes using flow cytometry. Their transcriptome was analyzed in order to investigate the two CD8 subsets. Our data suggests a functional diversity of CD8low and CD8high T cells with regard to cytotoxic effector function that might be useful to study these cells also in tumor sections or under conditions when cytotoxic T cells need to adapt to a changing microenvironment.

overall_design: mRNA profiling of purified and FACS sorted human CD8low and CD8high cytotoxic T lymphocytes after 40h of in vitro starvation.

first: Andreas

last: Weigert

first: Heinfried

last: Radeke


title: High-resolution Ribosome Profiling Reveals Translational Selectivity in Bovine Preimplantation Embryo Development

city: Gainesville

first: Zongliang

last: Jiang

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

summary: High resolution polysome fractionation and low-input ribosome profiling of bovine oocytes and preimplantation embryos has enabled us to define the translational landscape of early embryo development at an unprecedented level. We systematically and comparatively analyzed the transcriptome, polysome- and nonpolysome-bound RNA profiles of bovine oocytes and early embryos at 2-, 8-cell, morula, and blastocyst stage, and defined four modes of translational selectivity in bovine preimplantation embryo development: i. selective translation of non-abundant mRNAs, ii. active translating highly expressed mRNAs, iii. Translationally suppressed abundant mRNAs, and iv. Monosomaly occupied mRNAs. A strong selection towards genes involved in mitochondrial function and metabolic pathways was found throughout bovine preimplantation development. We found translatome largely follows transcriptome at oocytes, followed by a marked translational control at 8-cell embryos, which is gradually synchronized at the morula and blastocyst stage. We identified important novel cellular/embryonic functional regulators that being utilized and prioritized for translation at each developmental stage, that accompanies little-known bovine embryonic developmental programming. Together, these data reveal a unique spatiotemporal translational regulation that accompanies bovine preimplantation development.

overall_design: First, 10 ribosome fractionations were collected from each of 200 bovine oocytes (GV and MII stage oocyte) or preimplantation embryos at 2-, 8-cell, morula, and blastocyst stages, followed by RNA-sequencing analysis. This experiment was performed in biological duplicates. In addition, the oocytes or embryos collected from the same batch in each developmental stage were used to profile their transcriptomes by mRNA-seq. This experiment was performed in biological triplicates.

first: Zongliagn

first: Linkai

last: Zhu

first: Tong

last: Zhou


title: Identification and characterization of repressive domains in Drosophila transcription factors

city: Wien

first: Bernardo

last: de Almeida

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

summary: All multicellular life relies on differential gene expression, determined by regulatory DNA elements and DNA-binding transcription factors that mediate activation and repression via cofactor recruitment. While activators have been extensively characterized, repressors are less well studied and their repressive domains (RDs) are typically unknown, as are the RDs’ properties and the co-repressors (CoRs) they recruit. Here, we develop the high-throughput next-generation-sequencing-based method Repressive-Domain (RD)-seq to systematically identify RDs in complex libraries. Screening more than 200,000 fragments covering the coding sequences of all transcription-related proteins in Drosophila melanogaster, we identify 195 RDs in known repressors and in proteins not previously associated with repression. Many RDs contain recurrent short peptide motifs that are required for RD function, as demonstrated by motif mutagenesis, and are conserved between fly and human. Moreover, we show that RDs which contain one of five distinct repressive motifs interact with and depend on different CoRs, including Groucho, CtBP, Sin3A or Smrter. Overall, our work constitutes an invaluable resource and advances our understanding of repressors, their sequences, and the functional impact of sequence-altering mutations.

overall_design: Examination of transcription factor's repressive domains activity between GFP-neg and GFP-pos cells through repressive domain sequencing (RD-seq). A Gal4-DBD-fused candidate library consisting of over 200,000 150 bp-long DNA fragments coding for 50 AA was generated. This library was tested in RD-seq screens with two different reporter cell lines in which GFP expression is driven by the zfh1-DSCP or the ent1-rps12 enhancer-promoter pair.

first: Loni

last: Klaus

first: Anna

last: Vlasova

first: Filip

last: Nemčko

first: Alexander

last: Schleiffer

first: Katharina

last: Bergauer

first: Lorena

last: Hofbauer

first: Martina

last: Rath

last: Stark


title: Group B Streptococcal Pathogenesis in Diabetic Wounds

city: Aurora

first: Kelly

last: Doran

state: Colorado

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

summary: Diabetic wound infections have poor healing outcomes due to the presence of numerous pathogens in addition to an impaired immune response. Group B Streptococcus (GBS) is one of the most commonly isolated bacteria from diabetic wound infections, but virulence mechanisms GBS uses during these infections have not been investigated. Here, we developed a new murine model of GBS diabetic wound infection to determine how GBS establishes infection and persists in the wound environment. Using dual RNA sequencing, we demonstrate that GBS infection of diabetic wounds triggers an inflammatory response, leading to increased transcript levels of inflammatory cytokines and chemokines as well as markers of neutrophil degranulation such as myeloperoxidase, calprotectin, and elastase. We then confirm that diabetic wounds infected with GBS have significantly higher abundance of Il-1b, KC (CXCL1), myeloperoxidase, calprotectin and elastase in wound tissues than uninfected controls . When examining how GBS adapts to this hyper-inflammatory environment we find that GBS upregulates numerous virulence factors including the surface plasminogen-binding protein pbsP, the nuclease nucA, the cyl operon which is responsible for hemolysin production and pigmentation as well as numerous effectors of type VII secretion. In addition, we recovered multiple hyper-pigmented/hemolytic GBS colonies from the murine diabetic wound environment which encode mutations in the two-component system covRS. We then go on to demonstrate that a mutant in cylE, which is repressed by CovR, is attenuated in diabetic wound infection. Finally, we examine the most highly upregulated gene pbsP in diabetic wound infection and find that PbsP is necessary for diabetic wound infection via adherence to the skin and promotion of inflammation.

sample_organism:
Streptococcus agalactiae
Mus musculus

platform_organism:
Streptococcus agalactiae
Mus musculus

overall_design: We performed RNA-sequencing of Group B Streptococcus in 3 different conditions as well as mus musculus in 4 different conditions.

first: Rebecca

last: Keogh

first: Amanda

last: Haeberle

first: Christophe

middle: L

last: Astrie

first: Eric

last: Schmidt

last: Horswill


title: Enhanced flavour profiles through radicicol induced genomic variation in S. pastorianus lager yeast

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

summary: We report the gene expression profile of two polypolid Saccharomyces pastorianus mutants obtained by random mutagenesis using radicicol. Mutants derived from the Group I strain CBS1538 and the Group II strain W34/70. Saccharomyces pastorianus is a hybrid of Saccharomuyces cerevisiaie and Saccharomyces eubayanus. We report changes in transcriptome of the mutants compared to their respective parental strain

overall_design: Mutant strains were generated using a mutagenesis approach that involved racicicol, an inhibitor of the chaperone Hsp90p. Amino acid analogues of phenylalanine were used as selection method. The strains were grown under fermentation conditions and samples were taken on Day 2 and Day 4 of the fermentation for RNAseq analysis. The strains were also grown in minimal medium without amino acids and with (NH4)2SO4 as a nitrogen source. The transcript patterns were compared in the three conditions.

first: Roberto

last: de la Cerda García-Caro

first: Georgia

last: Thompson

first: Penghan

last: Zhang

first: Fiona

last: Roche

first: Silvia

last: Carlin

first: Urska

last: Vrhovsek

first: Ursula

last: Bond


title: Human and rodent cell susceptibility and response to different orthohantaviruses uncovers various levels of cellular restriction

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

institute: Institut Pasteur

summary: This study highlighted the complexity of host/virus relationship, showed that viruses are restricted at different levels of the viral cycle, and provided multiple levels of analysis to understand how these viruses differ in their interactions with cells to escape innate immunity, depending on the tissue and host origin

overall_design: Total RNA was extracted from 4 independent biological replicates of bank vole cells upon infection with PUUV or PHVs and non infected (12 samples).

first: Myriam

last: Ermonval

first: Marc

last: Monot


title: Expression data from peripheral human T cells stimulated with an anti-CD96 mAb

city: Southampton

first: Aymen

last: Al-Shamkhani

address: Tremona Road

department: School of Cancer Sciences

institute: University of Southampton

summary: The role of CD96 in human T cells is ambiguous. We demonstrated that engagement of CD96 on human T cells by antibodies provides a strong activating signal dependent on antibody isotype and cross-linking by a subset of Fcγ receptors. Here we used RNASeq profiling to analyze the gene expression programme associated with anti-CD96 mAb treatment in purified T cells isolated from the blood of healthy donors. We showed that multiple hallmarks associated with an activated T-cell signature were significantly enriched in the anti-CD96 treatment group. These included gene signatures associated with cell cycle progression, metabolic reprogramming, effector differentiation, and sustained proliferation and survival. Using pathway analysis, we identified several candidate molecules that could mediate signaling downstream of CD96.

overall_design: RNASeq profiling of purified T cells isolated from peripheral blood mononuclear cells of 3 healthy donors, and stimulated for 6 hours with plate-bound anti-CD3 mAb and either plate-bound anti-CD96 mAb or a matching isotype control antibody.

first: Anne

last: Rogel

first: Stephen

middle: M

last: Thirdborough

first: Fathima

last: Ibrahim


title: Parallel single cell and bulk transcriptome analyses reveal key features of the gastric tumor microenvironment

city: Beijing

first: Zemin

address: 5 Yiheyuan Rd, Haidian

institute: Peking University

summary: We used single-cell RNA-sequencing from tumors and matched normal tissue of 24 treatment-naïve patients to generate a single cell landscape of gastric cancer tumor microenvironment.

overall_design:
48 samples from tumors and matched normal tissue of 24 treatment-naïve patients were sequenced using 10X single-cell RNA-seq platform and then analyzed.

***Please note that, due to Chinese regulations on human genetics information, the raw sequence files are deposited to the GSA Human database (ngdc.cncb.ac.cn), under Accession Number HRA002336***

first: Boxi

last: Kang

first: Jordi

last: Camps

first: Biao

last: Fan

first: Hongpeng

last: Jiang

first: Mahmoud

first: Xueda

last: Hu

first: Shishang

last: Qin

first: Dennis

last: Kirchhoff

first: Derek

middle: Y

last: Chiang

first: Shan

last: Wang

first: Yingjiang

last: Ye

first: Zhanlong

last: Shen

first: Zhaode

last: Bu

first: Helge

last: Roider


title: GWAS and tissue transcriptomics identify embryonic drivers for classic bladder exstrophy and provide clues to the associated susceptibility to bladder cancer

first: Phillip

last: Grote

state: Hessen

address: Paul-Ehrlich-Str. 42-44

department: Genome Regulation

institute: Georg-Speyer-Haus

summary: Developmental time course of bladder development in the mouse from the urogenital ridge to the developed bladder at E15.5.

overall_design: RNA profile of three different timepoints of embryonic bladder development

first: Tamer

last: Ali

first: Enrico

last: Mingardo

first: Heiko

last: Reutter


title: Exogenous artificial DNA forms chromatin structure with active transcription in yeast [ChIP-seq]

first: Ran

last: Wei

address: Haidian District, Beijing Summer Palace Road No. 5

summary: Chromosomes and plasmids are two forms of genetic carriers. Exogenous yeast artificial chromosomes are also considered as yeast centromeric plasmids in many cases. Here, we used state-of-the-art sequencing technologies to comprehensively profile the genetic, epigenetic, transcriptional and proteomic characteristics of an exogenous data-carrying chromosome. We found that the data-carrying DNA formed active chromatin with high chromatin accessibility and H3K4 tri-methylation levels. We also confirmed that the data-carrying chromosome had a circular shape in the nucleus and was arranged in the Rabl configuration, which may contribute to the self-replication and haploidy of the chromosome in vivo. The data-carrying chromosome displayed highly pervasive transcriptional ability and transcribed hundreds of non-coding RNAs. In summary, this work explores the chromatin epigenetic state, chromatin structure and transcriptional landscape of an exogenous artificial chromosome. The results demonstrated that the exogenous artificial chromosome did form a chromatin structure and was not a naked and incompact plasmid, which strengthen our understanding of artificial chromosomes.

overall_design: Examinations of histone modification (H3K4me3 ChIP-seq) in two different kinds of yeast cells. One kind of these yeast cells contains an artificial data-carrying chromosome (dChr), another only contains an empty plasmid as control group.

first: Jianting

last: Zhou

first: Chao

last: Zhang

first: Wei

last: Tao

first: Ying

middle: J

last: Yuan


title: Exogenous artificial DNA forms chromatin structure with active transcription in yeast [RNA-seq]

overall_design: RNA profile of two different kinds of yeast cells. One kind of these yeast cells contains an artificial data-carrying chromosome (dChr), another only contains an empty plasmid as control group.


title: Ezh2Y641F mutations co-operate with Stat3 to enhance MHC Class I antigen processing and alter the tumor immune response in melanoma

city: St. Louis

first: George

middle: P.

last: Souroullas

state: MO

address: 660 S. Euclid Av

department: Medicine

institute: Washington University School of Medicine

summary: Enhancer of Zeste Homolog 2 (EZH2) is the catalytic component of the Polycomb Repressive Complex 2, a chromatin modifying complex, which mediates methylation of lysine 27 on histone 3 (H3K27me3), a repressive chromatin mark.  Genetic alterations in EZH2 in melanoma include amplifications and activating point mutations at tyrosine 641 (Y641) whose underlying oncogenic mechanisms remain largely unknown.  Here, we found that expression of Ezh2Y641F causes upregulation of a subset of interferon-regulated genes in melanoma cells.  Upregulation of these genes was not a direct effect of changes in H3K27me3, but via a non-canonical interaction between Ezh2 and Signal Transducer and Activator of Transcription 3 (Stat3).  Ezh2 and Stat3 together function as transcriptional activators to mediate gene activation of numerous genes, including MHC-Ib antigen processing genes.  Furthermore, expression of Stat3 is required to maintain an anti-tumor immune response in Ezh2Y641F melanomas and to prevent melanoma progression and recurrence.

overall_design: Examine Ezh2 and Stat3 binding across the genome in Ezh2 WT vs Ezh2 Y641F mutant melanoma cells

first: Sarah

last: Zimmerman

first: Samantha

last: Nixon


title: Expression of candidate genes associated with congenital heart disease in adult human atrial and ventricular tissue

city: Munich

first: Harald

last: Lahm

address: 36, Lazarettstraße

department: INSURE

institute: German Heart Center Munich

summary: We have used single nuclei RNAseq technology to analyze the expression of four candidate genes (MACROD2, GOSR2, WNT3, MSX1) in right atria and interventicular samples of adult human hearts. We find a robust expression of MACROD2 in all adult cardiac cell types. In contrast, expression of GOSR2 could not be detected in any cell of the adult human heart. WNT3 was sporadically expresssed in fibroblasts, epi- and andocardial cells, smooth muscle cells and cardiomyocytes. MSX1 expression shows a similar isolated expression, except that it is not found in smooth muscle cells and cardiomyocytes.

overall_design: single nuclei mRNA profile of four candidate genes in adult human atrium and ventricle

first: Felix

last: Wirth

first: Martina

last: Dressen


title: Single-cell transcriptomic analysis of PB and BM NK cells from severe aplastic anemia patients

status: Public on Sep 29 2022

city: Tianjin

first: yingying

last: chen

state: Tianjin

address: 154 Anshan Street

institute: Department of Hemataology,Tianjin Medical University General Hospital

summary: NK cells are believed to be involved in the immune pathogenesis of SAA. We used single cell RNA sequencing (scRNA-seq) to analyze the differences of NK cells in BM and PB between SAA patients and healthy volunteers.

overall_design: NK cells from BM and PB of SAA patients and healthy volunteers were sorted by magnetic beads and analyzed by scRNA-seq.

first: Chunyan

last: Liu

first: Yingying

last: Chen

first: Rong

last: Fu


title: Exogenous artificial DNA forms chromatin structure with active transcription in yeast

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

overall_design: Refer to individual Series


title: Effect of disruption of tonB, exbB, exbD and MccY treatment  on gene expression in Salmonella enterica subsp. enterica serovar Typhimurium

city: Guangzhou

first: Saixiang

last: Feng

address: South China Agricultural University, No. 483, Wushan Road, Tianhe District

institute: South China Agricultural University

summary: To investigate the effects of MccY on Salmonella Typhimurium, Ton system genes mutants were constructed and RNA-seq analysis were performed.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for tonB, exbB, exbD mutants and MccY treatment group.

first: Yu

last: Han

first: Weisheng

last: Cao


title: A REF6-dependent H3K27me3-depleted state facilitates gene activation during germination in Arabidopsis

first: Jie

last: Pan

address: No.1 West Beichen Road,Chaoyang District

institute: Institute of Genetics and Developmental Biology


title: Integrated analysis reveals effects of bioactive ingredients from Limonium Sinense (Girard) Kuntze on hypoxia-inducible factor (HIF) activation

first: Yihua

last: Wang

address: University Road

summary: Limonium Sinense (Girard) Kuntze is a traditional Chinese medicinal herb, showing blood replenishment, anti-tumour, anti-hepatitis, and immunomodulation activities amongst others. However, the mechanism of its pharmacological activities remains largely unknown. Here, we investigated the effects of bioactive ingredients from Limonium Sinense using integrated analysis. Water extracts from Limonium Sinense (LSW) showed a strong growth inhibitory effect on multiple cells in both 2D and 3D cultures. Global transcriptomic profiling and further connectivity map (CMap) analysis identified several similarly acting therapeutic candidates, including Tubulin inhibitors and hypoxia-inducible factor (HIF) modulators. The effect of LSW on cell cycle was verified with flow cytometry showing a G2/M phase arrest. Integrated analysis suggested a role for gallic acid in mediating HIF activation. Taken together, this study provides novel insights into the bioactive ingredients in Limonium Sinense, highlighting the rich natural resource and therapeutic values of herbal plants.

overall_design: MDA-MB-468 cells were treated with Limonium Sinense Water extract (LSW) for 48 hours at 500 μg/mL, and untreated cells were used as control.

first: Hualong

last: Zhao

first: Yilu

last: Zhou

first: Jianlian


title: Evidence that direct inhibition of transcription factor binding is the prevailing mode of gene and repeat repression by DNA methylation [WGBS-Seq]

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

institute: Friedrich Miescher Institute for Biomedical Research

type: Methylation profiling by high throughput sequencing

summary: Cytosine methylation efficiently silences CpG-rich regulatory regions of genes and repeats in mammalian genomes. To what extent this entails direct inhibition of transcription factor (TF) binding versus indirect inhibition via recruitment of Methyl-CpG Binding Domain (MBD) proteins is unclear. Here we show that combinatorial genetic deletions of all four proteins with functional MBDs in mouse stem cells, derived neurons or a human cell line does not reactivate genes or repeats with methylated promoters. These do however become activated by methylation-restricted TFs if DNA methylation is removed. We identify several causal TFs in neurons, including ONECUT1, which is methylation-sensitive only at a motif variant. Rampantly upregulated retrotransposons in methylation-free neurons feature a CRE motif, which activates them in absence of DNA methylation via methylation-sensitive binding of CREB1. Our study reveals methylation-sensitive TFs in vivo and argues that direct inhibition, rather than indirect repression by the tested MBD proteins, is the prevailing mechanism of methylation-mediated repression at regulatory regions and repeats.

overall_design: WGBS-seq of WT or MBD-QKO HEK293 cells or mouse ES cells and derived neurons.

first: Sebastian

last: Kaluscha

first: Lukas

last: Burger

last: Schubeler

first: Silvia

last: Domcke


title: Evidence that direct inhibition of transcription factor binding is the prevailing mode of gene and repeat repression by DNA methylation [ChIP-Seq]

overall_design: ChIP-seq in WT or DNMT-TKO Ngn2 neurons with minimum two replicates per condition and factor with corresponding input samples.


title: Evidence that direct inhibition of transcription factor binding is the prevailing mode of gene and repeat repression by DNA methylation [ATAC-Seq]

overall_design: ATAC-seq in mouse ESCs and derived neurons. WT, MBD-QKO, DNMT-TKO and DNMT-TKO with CREB1-KO (neurons only). All conditions with minimum two replicates.


title: Evidence that direct inhibition of transcription factor binding is the prevailing mode of gene and repeat repression by DNA methylation


title: Evidence that direct inhibition of transcription factor binding is the prevailing mode of gene and repeat repression by DNA methylation [RNA-Seq]

overall_design:
RNA-seq in mouse ESCs and derived neurons. WT, MBD-QKO, DNMT-TKO and DNMT-TKO with CREB1-KO (neurons only). All conditions with minimum two replicates.
RNA-seq in MBD-TKO mouse ESC treated with siRNA or human HEK293 cells WT or MBD-QKO. All conditions in triplicates.


title: Macrophage-mediated abscopal effects of radiation therapy

city: Stanford

first: Yoko

last: Nishiga

state: CA

address: 265 Campus Drive

department: Departments of Pediatrics and Genetics

institute: Stanford University

summary: Radiation therapy is a mainstay of cancer treatment, with more than 50% of all cancer patients receiving radiation during the course of their disease. Tumor irradiation can activate both innate and adaptive immune responses, and these responses can be pro- or anti-tumor growth . These observations have led to the search for antitumor approaches combining radiotherapy and specific immunotherapies, most commonly strategies promoting the systemic activation of T cells. Thus far, however, many cancer patients still suffer from local recurrence and/or untreatable metastatic disease after radiotherapy. Here we combine radiotherapy with activation of macrophage-mediated phagocytosis via blockade of the ?don?t-eat-me? cell surface molecule CD47 in small-cell lung cancer (SCLC), a highly metastatic form of lung cancer for which treatment options remain limited. We found that irradiation of SCLC cells in culture results in the secretion of inflammatory cytokines that results in increased migration and phagocytosis by macrophages. In vivo, CD47 blockade potently enhances the local antitumor effects of radiation therapy in murine and human pre-clinical models of SCLC. Strikingly, CD47 blockade also stimulates abscopal antitumor effects inhibiting the growth of non-irradiated SCLC tumors in mice receiving radiation. Similar abscopal antitumor effects were observed in colon cancer and lymphoma models. Surprisingly, these abscopal effects are completely independent of T cells but require macrophages that migrate into the non-irradiated tumor sites in response to inflammatory signals mediated by radiation and are locally activated by CD47 blockade to eliminate cancer cells. The systemic activation of antitumor macrophages following radiotherapy and CD47 blockade may be particularly important in cancer patients who suffer from metastatic disease.

overall_design: Single-cell RNA sequencing (scRNA-seq) of CD45+ leukocytes at non-irradiated sites in mice treated either with radiotherapy alone  or radiotherapy and CD47

first: Alexandros

last: Drainas

first: Julien

last: Sage


title: Cap-binding complex assists RNA Polymerase II transcription in plant salt stress response

status: Public on Sep 28 2022

first: Zhang

last: Huairen

address: No. 1 West Beichen Road

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

summary: Adaptive response to stress involves an extensive reprogramming of gene expression. Under stressful conditions, the induction of efficient changes in mRNA production is crucial for maximized plant survival. Transcription and pre-mRNA processing are two closely related steps in mRNA biogenesis, yet how they are controlled in plant stress response remains elusive. Here, we show that the Arabidopsis nuclear cap-binding complex (CBC) component CBP20 directly interacts with ELF7, a subunit of the transcription elongation factor RNA Pol II-associated factor 1 complex (PAF1c) to promote RNA Pol II transcription in plant response to salt stress. CBP20 and ELF7 co-regulate the expression of a large number of genes including those crucial for salt tolerance. Both CBP20 and ELF7 are required for enhanced RNA Pol II elongation at salt-activated genes. Though CBP20 also regulates intron splicing, this function is largely independent of ELF7. Our study reveals the function of an RNA processing regulator CBC in assisting efficient RNA Pol II transcription and pinpoints the complex roles of CBC on mRNA production in plant salt stress resistance.

overall_design: Transcriptome profiles were examined by RNA-seq in WT (Col), elf7-3, cbp20 under control (no salt) and salt treatment conditions

first: Danhua

last: Jiang

first: Huairen

last: Zhang