title: H3K36 methylation maintains cell identity by regulating opposing lineage programs [RNA-seq II]

status: Public on Feb 21 2023

city: Boston

first: Michael

last: Hoetker

state: Massachusetts

address: Simches Building, Mail code CPZN 4200

department: Department of Molecular Biology

institute: Massachusetts General Hospital

summary: While epigenetic regulation in early development and differentiation is relatively well-characterized, the precise mechanisms that subsequently maintain specialized cell states remain largely unexplored. Here, we employed histone H3.3 mutants to uncover a crucial role for H3K36 methylation in the maintenance of cell identities across diverse developmental contexts. Focusing on the experimentally induced conversion of fibroblasts to pluripotent stem cells, we show that H3K36M-mediated disruption of H3K36 methylation endowed reprogramming intermediates with a plastic state poised to acquire pluripotency in virtually every cell. At a cellular level, H3K36M rendered mesenchymal cells insensitive to TGF signals and thus facilitated epithelial plasticity. At a molecular level, H3K36M led to the downregulation of mesenchymal genes by depleting H3K36me2 and H3K27ac at associated enhancers. In parallel, H3K36M led to the upregulation of epithelial and stem cell genes by enabling enhancer accessibility and hypomethylation. Mechanistically, we found that Tet-dependent demethylation uncouples pluripotency enhancer activation from somatic enhancer decommissioning in K36M cells. This dynamic switch of enhancer activities redirects Sox2 binding from promiscuous somatic targets to bona fide stem cell targets crucial for the establishment of the pluripotency network. Together, our findings reveal a dual role for H3K36 methylation in the maintenance of cell identity, by integrating a key developmental pathway into sustained expression of cell type-specific programs, and by opposing the expression of alternative lineage programs through continual enhancer methylation. Our results provide crucial insight into the impact of dynamic H3K36 methylation patterns on physiological and pathological cell fate transitions, including development, tissue regeneration and cancer.

overall_design: Reprogramming for sequencing samples was performed in AGi conditions. RNA-seq over reprogramming timecourse d0 (MEF), d2, d4, d6, d8, passaged iPSCs (S/L), MEFs without OKSM. ATAC-seq for d0 (MEF), d4, passaged iPSCs (S/L). CUT&Tag samples are reprogramming intermediates of d4. All reads aligned to mm9 genome.


title: Transcriptome profiling reveals potential core genes involved in metabolic detoxification of malathion in Asian tiger mosquito, Aedes albopictus

status: Public on Feb 28 2023

city: College Station

first: Xinyue

last: Huang

state: TX

address: 300 Spruce street, Apt 303

department: Entomology

country: USA

institute: Texas A&M University

type: Expression profiling by high throughput sequencing

summary: To compare different differential expression profile between malathion resistant and susceptible Ae. albopictus in Harris County and to identify candidate genes involved in matabolic detoxification of malathion

overall_design: We compared different gene expression patterns in both comparisons between malathion resistant (MR) versus malathion susceptible (MS) group, and between field collected Ae. albopictus that were not exposed to malathion (WI) versus a laboratory-maintained susceptible Sebring strain (CO)


title: H3K36 methylation maintains cell identity by regulating opposing lineage programs [ATAC-seq]

type: Genome binding/occupancy profiling by high throughput sequencing


title: Verson’s glands contribute to molting  and antimicrobial response in the Fall armyworm

status: Public on Mar 01 2023

city: Lexington

first: Jin mo

last: Koo

state: Kentucky

address: 100 South Limestone Street

institute: University of Kentucky

summary: Verson’s glands are segmental pairs of dermal glands attached to the epidermis in lepidopteran larvae. They produce macromolecules during intermolt period and empty them during each molt. Morphological, histochemical, developmental, and protein analysis studies have been conducted to determine the functions of Verson’s glands. However, the exact role of Verson’s glands remains unclear. In our previous study, a strain of transgenic fall armyworm, Spdoptera frugiperda expressing green fluorescence protein (GFP) and Systemic RNA interference defective protein 1 (SID-1) from Caenorhabditis elegans was established to improve RNA interference (RNAi) efficiency. Unexpectedly, we found that GFP fluorescence was significantly brighter in Verson’s glands than in other tissues. Also, RNAi efficiency improved more in Verson’s glands than in other tissues. We took advantage of improved RNAi efficiency to explore the function of Verson’s glands. RNA-seq analysis revealed that genes highly expressed in Verson’s glands code for cuticular proteins, molting fluid proteins, hemolymph proteins, and antimicrobial peptides. Injection of dsRNA targeting essential genes interfered with Verson’s glands growth. These studies revealed that Verson’s glands contribute to hemolymph, cuticle, molting fluid, and immune response during molting.  These studies also provide useful tools for future research in identifying the physiological role of Verson’s glands in lepidopteran insects.

overall_design: Comparative gene expression analysis of RNA-seq data for Spodoptera frugiperda Verson's glands and other tissues (fat body, midgut, epidermis from bioproject PRJNA646922)

first: Jinmo

first: Xien

last: Chen

first: Subba

middle: R

last: Palli


title: H3K36 methylation maintains cell identity by regulating opposing lineage programs

status: Public on Feb 20 2023

city: Berlin

first: Helene

last: Kretzmer

address: Ihnestraße 63

department: Genome Regulation

country: Germany

institute: Max Planck Institute for Molecular Genetics

type: Methylation profiling by high throughput sequencing

overall_design: Reprogramming for sequencing samples was performed in AGi conditions. RRBS was performed for d0 samples (MEFs), d4 and d8 reprogramming intermediates, and passaged iPSCs of both backgrounds (S/L, no dox). All reads aligned to mm9 genome.


title: H3K36 methylation maintains cell identity by regulating opposing lineage programs [RNA-seq]


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

overall_design: Refer to individual Series


title: Extracellular vesicle long RNA markers of early-stage lung adenocarcinoma

city: Shanghai

first: Wei

last: Liu

state: Shanghai

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

country: China

institute: Chinese Academy of Sciences

summary: The serum EV genes has great diagnostic value for lung adenocarcinoma patients with tumor size smaller than 2cm, which may serve as an important supplement to lung cancer screening.

overall_design: Extracellular vesicle long RNA profiles of human serum by next generation sequencing

first: Hongdao

last: Zhang

first: Ligang

last: Wu


title: Analysis of nucleus and cytoplasm-specific HNRNPK binding on SINEUP RNA by seCLIP

status: Public on Mar 16 2023

city: Yokohama

first: Harshita

last: Sharma

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Division of Genomic Medicine

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

summary: To check the subcellular location-specific HNRNPK binding sites on mouse SINEB2 repeat element, we prepared seCLIP (single-end enhanced crosslinking and immunoprecipitation assay) libraries from SINEUP-GFP transfected nuclear and cytoplasmic fractions from HEK293T/17 cells.

overall_design:
HEK293T/17 cells were co-transfected with SINEUP-GFP and pEGFP-C2 plasmids, crosslinked by UV, and separated into nuclear and cytoplasmic fractions. Both fractions were immunoprecipitated with anti-hnRNPK antibody (IP sample) and corresponding samples without immunoprecipitation were used as input control and seCLIP libraries were prepared. Two biological replicates each for cytoplasmic IP/input, and nuclear IP/input.

Update: [09-15-2023] Read strand information corrected in the cyt.e.peaks.norm.bed, cyt.e.peaks.norm.full.bed, nuc.e.peaks.norm.bed, and nuc.e.peaks.norm.full.bed files.

first: Matthew

middle: N

last: Valentine

first: Naoko

last: Toki

first: Hazuki

last: Takahashi

first: Piero

last: Carninci


title: Transcriptional Analysis of the Effect of Cholinergic Receptor Muscarinic 1 (CHRM1) on Docetaxel Resistance in Human Prostate Cancer Cells

status: Public on Apr 01 2023

city: Spokane

first: Boyang

state: Washington

address: 412 E. Spokane Falls Blvd

institute: Washington State University

summary: The overall goal of this study was to investigate the role of CHRM1 in contributing to DTX resistance in human prostate cancer cells.

overall_design: First, we compare gene expression profiles in DTX-resistant versus DTX-sensitive 22Rv1 cells. We then performed gene expression profiling analysis using data obtained from DTX-resistant 22Rv1 cells treated with or without 25 µM Dic for 72 hrs, with each group of duplicates.


title: CUT&RUN analysis of TWIST1 binding chromatin profile in human tumor endothelial cells

status: Public on Feb 15 2023

city: Philadelphia

first: Yi

last: Fan

state: PA

address: 3400 Civic Center Blvd, SCTR 8-168

department: Radiation Oncology

institute: University of Pennsylvania

summary: The global chromatin binding profile of TWIST1 was assayed on human glioblastoma-derived tumor endothelial cells (ECs).

overall_design: GBM tumor-derived ECs were were lyzed and incubated with control IgG or anti-TWIST1 antibody, followed by cleavage under targets & release using nuclease (CUT&RUN) assay. Isolated DNA was enriched for library preparation and sequenced.

first: Yang

first: Zhang

last: Duo

first: Fan

last: Yi


title: Transcriptome analysis of Arabidopsis thaliana and Lotus japonicus exposed to arbuscular mycorrhizae

status: Public on Feb 13 2023

city: Raleigh

first: Heike

last: Sederoff

state: NC

address: 851 Main Campus Dr

department: Plant & Microbial Biology

institute: North Carolina State University

summary: Key genes involved in symbiosis have been lost in nonmycorrhizal plants such as Arabidopsis thaliana. We studied the effects on gene expression in A. thaliana expressing an abbreviated, functional version of one of genes, the transcription factor Interacting Protein of DMI3 (IPD3-min), under low nutrient conditions in the presence and absence of a mycorrhizal fungi, Rhizophagus. We conducted the same transcriptome analysis  with a cyclops-4 knockout mutant in Lotus japonicus to compare with the expression profile of a mycorrhizal host model lacking IPD3.

sample_organism:
Arabidopsis thaliana
Lotus japonicus

platform_organism:
Arabidopsis thaliana
Lotus japonicus

overall_design: Total RNA was extracted from six-week-old root tissue of A. thaliana wildtype and IPD3-min transgenic plants as well as L. japonicus wildtype and cyclops-4 knockout mutants. Differential gene expression was studied in plants grown with and without the presence of Rhizophagus arbuscular mycorrhizae (AM) on 1/2 MS and low-nutrient media.

first: Eli

middle: D

last: Hornstein

first: Melodi

last: Charles

first: Megan

last: Franklin


title: MeDIP-seq in human lung cancer tissues

city: 上海

first: Yani

last: Kang

address: 东川路800号

institute: Shanghai Jiaotong University

summary: we used methylated DNA immunoprecipitation sequencing (MeDIP-Seq) to detect DNA methylation levels and lncRNA-seq to detect lncRNA expression levels in 3 lung cancer samples and 3 matched normal samples. Then 255 differentially methylated genes (DMGs) and 246 differentially expressed lncRNAs (DELs) were identified. Finally, LINC01354 was founded to be differentially methylated and predictive of transcription. Besides, the prognostic value of differential methylation related DELs was analyzed.

overall_design: MeDIP-seq combined with lncRNA-seq analysis to find the regulation network in lung cancer

first: Mengju

last: He

first: Baiqing

last: Wen

first: Hui

last: Zhao

first: Fei


title: Discovery of factors that improve the effectiveness of radiation therapy by inducing reoxygenation of lung cancer cells through aerobic exercise

city: Busan

first: Jaewan

last: Jeon

address: 875, Haeun-daero, Haeundae-gu, Busan, Republic of Korea

country: South Korea

institute: Jaewan Jeon

summary: We performed transcriptomic analysis to discover the key factors that aerobic exercise induces reoxygenation.

overall_design: Four xenograft animal models were established to confirm the level of oxygenation in cancer cells through aerobic exercise.

first: Sunmi

last: Jo


title: Single-cell transcriptomics reveals natural product Shi-Bi-Man promotes hair regeneration

status: Public on Feb 14 2023

city: Nanjing

first: zhang

last: zhang chenyang

address: 163 Xianlin Avenue

institute: Nanjing University

summary:
Purpose: This study aimed to explore the mechanism of SBM to promote hair regeneration through single-cell transcriptomics
Methods: Supplementation with intragastric administration or smear administration of SBM in artificially shaved C57BL/6 mice to observe its hair growth.  Single-cell RNA sequencing were performed to explore the role of SBM for hair regeneration.
Results: SBM significantly induced hair growth compared with control treatment.The results of single-cell sequencing revealed that after SBM treatment, the number of hair follicle stem cells (HFSCs) and dermal papilla cells (DPCs) increased significantly. Cell interactions and volcano maps show that interaction of FGF signaling pathway was significantly enhanced, in which FGF7 expression was especially upregulated in DPCs. In addition, Wnt signaling pathway also had a partially enhanced effect on the interactions between various cells in the skin. Network pharmacology study showed that the promotion of FGF and Wnt pathways by SBM was also enriched in alopecia diseases.
Conclusion: We report that SBM has a potential effect on the promotion of hair growth by mainly activating FGF signaling pathway. The use of SBM may be a novel therapeutic option for hair loss.

overall_design: Molecular mechanism of  natural product Shi-Bi-Man  promoting hair growth

last: Sun

first: Chenyang

last: Zhang

first: Qianqian

last: Liu

first: Mingrui

last: Han


title: Transcriptome analysis of TWIST1 sgRNA-treated human tumor endothelial cells

first: Yi

last: Fan

summary: The global RNA expression was assayed on human glioblastoma-derived tumor endothelial cells (ECs) treated with CRISPR/sgRNA targeting Twist1 or control sequence.

overall_design: GBM tumor-derived ECs were treated with CRISPR/sgRNA targeting Twist1 or control sequence. RNA was isolated and analyzed by RNAseq.

first: Yang

first: Zhang

last: Duo


title: H3K36 methylation maintains cell identity by regulating opposing lineage programs [CUT&Tag]

first: Michael

last: Hoetker

overall_design: Reprogramming for sequencing samples was performed in AGi conditions. RNA-seq over reprogramming timecourse d0 (MEF), d2, d4, d6, d8, passaged iPSCs (S/L), MEFs without OKSM. ATAC-seq for d0 (MEF), d4, passaged iPSCs (S/L). CUT&Tag samples are reprogramming intermediates of d4 if not otherwise specified. Samples labeled with DMOG are treated with Tet inhibitor DMOG. CUT&Tag samples labeled iPSC are from passaged iPSCs of WT and K36M background as indicated (without doxycycline). All reads aligned to mm9 genome.


title: Single-cell deconvolution of a specific malignant cell population as a poor prognostic biomarker in low-risk clear cell renal cell carcinoma patients

status: Public on Feb 09 2023

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

summary: BACKGROUND: Intra-tumor heterogeneity (ITH) is a key feature in clear-cell renal cell carcinomas (ccRCCs) which impacts outcomes such as aggressiveness, response to treatments or recurrence. In particular, it may explain tumor relapse after surgery in clinically low-risk patients who did not benefit from adjuvant therapy. Recently, single-cell RNA-seq (scRNA-seq) has emerged as a powerful tool to unravel expression intra-tumor heterogeneity (eITH) and might enable better assessment of clinical outcomes in ccRCC.  OBJECTIVE: To explore eITH in ccRCC with a focus on malignant cells (MCs), and assess its relevance to improve prognosis for low-risk patients.  RESULTS AND LIMITATIONS: We analyzed 54,812 cells and identified 35 cell subpopulations. The eITH analysis revealed that each tumor contained various degrees of clonal diversity. The transcriptomic signatures of MCs in one particularly heterogeneous sample were used to design a deconvolution-based strategy which allowed to risk-stratify 310 low-risk ccRCC patients.

overall_design:
We performed scRNA-seq on tumor samples from five untreated ccRCC patients ranging from pT1a to pT3b. Data was complemented with a published dataset composed of pairs of matched normal and ccRCC samples.
Submitter states that the raw data files (fastq files) have been submitted to the EGA repository

first: Judikael

last: Saout

first: Gwendoline

last: Lecuyer

first: Bertrand

last: Evrard

first: Nathalie

last: Rioux-Leclercq

first: Aurélie

last: Lardenois


title: sRNA participates in hyperosmotic stress response regulation in Sphingomonas melonis TY

status: Public on Feb 07 2023

city: Hangzhou

first: Xiaoyu

last: Wang

state: Zhejiang

address: Yuhangtang Road

department: College of Life Sciences

institute: Zhejiang University

summary: Drought and salinity are most ubiquitous environmental factors that causing hyperosmotic threats to Sphingomonas and impairs their efficiency of performing environmental functions. However, bacteria have developed various responses and regulation systems to coping with these abiotic challenges. Among which post-transcriptional regulation plays vital roles in regulating gene expression and cellular homeostasis, as hyperosmotic stress conditions could lead to induction of specific small RNA (sRNA) that participates in stress response regulation. Here, we report a candidate functional sRNAs landscape of S. melonis which could help for comprehensive analyses of sRNA regulation in Sphingomonas species. WGCNA analysis revealed a 263 nt sRNA SNC251 which transcribed from its own promoter and shew the most dramatic correlation coefficient with hyperosmotic factors was characterized. An in vivo translation-reporter system constructed in this study revealed positive regulation and feedback mechanisms between the SNC251 and nicotine degradation genes. Deletion of snc251 affected multiple cellular processes and nicotine degradation capacity of S. melonis TY, while overexpression of SNC251 facilitated the biofilm formation capability of TY under hyperosmotic stress. Two genes of TonB system were further verified could be activated by SNC251, which also means SNC251 is a trans-acting small RNA. Briefly, this research reported a summary of sRNAs which participate in hyperosmotic stress response in S. melonis TY and revealed a novel sRNA SNC251 which is necessary for hyperosmotic stress response.

overall_design: The wild type (WT) of S. melonis TY and snc251 deleted cells carrying either a plasmid overexpressing SNC251 (Δsnc251 comp.), or an empty control vector (Δsnc251) were grown in Luria-Bertani (LB) culture to an OD600 of 0.6.

first: Lvjing

first: Haixia

first: Zhenmei

last: Lu


title: OmpC and bile tolerance are important for Escherichia coli colonization of the mammalian intestine

city: STILLWATER

first: Tyrrell

last: Conway

state: OKLAHOMA

address: 307 Life sciences east, OKLAHOMA STATE UNIVERSITY

department: Microbiology and Molecular Genetics

institute: Oklahoma state university

summary: Our focus of this study is to determine the gene expression changes in E. coli colonizing the mouse intestine as compared to E. coli grown in minimal medium in vitro. We colonized CD-1 male mice with E. coli MG1655 StrR  wild type and extracted the total RNA from mouse cecal mucus. We also extracted E. coli MG1655 StrR  RNA from in vitro culture and sequenced and compared to determine the genes important for E. coli colonization of the mammalian intestine. Our results indicate that OmpC is important for E. coli to colonize the mouse intestine as it is upregulated as compared to in vitro culture. OmpF is not important; it is detrimental for E. coli colonization of the mouse intestine and is highly downregulated in the colonized E. coli

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: E. coli MG1655 StrR  was fed to CD-1 male mice and on the 9th day, the mice were euthanized, mucus from the cecum was obtained and total RNA was extracted and sequenced. E. coli MG1655 StrR  was cultured in MOPS minimal glucose medium, and the total transcriptome of exponential phase culture was sequenced

first: Sudhir

last: Doranga


title: RNA-RNA interaction analysis of functional SINE repeat elements-derived transcripts

status: Public on Feb 06 2023

first: Harshita

last: Sharma

summary: We studied functional and structural features of mouse and human SINE repeat elements-derived RNAs in SINEUP long non-coding RNAs which upregulate the translation of the target protein coding gene. To check the interaction of functional SINE RNAs with ribosomal RNAs, we created PARIS2 (psoralen analysis of RNA interactions and structures) libraries from SINEUP (with embedded mouse SINEB2 or human FRAM repeat) and the target sense GFP plasmids co-transfected human cells.

overall_design: HEK293T/17 cells were co-transfected with sense EGFP and SINEUP-GFP (with SINEB2) or miniSINEUP-GFP FRAM plasmids. After 24h of transfection, cells were crosslinked by Amotosalen and UV treatment, total RNA was extracted for PARIS2 library preparation. Two biological replicates, each for SINEUP-GFP and miniSINEUP-GFP FRAM were prepared.

first: Hiromi

last: Sueki Nishiyori

first: Matthew

last: Valentine

first: Hazuki

last: Takahashi

first: Piero

last: Carninci


title: Long noncoding RNA and messenger RNA profiling in epicardial adipose tissue of patients with new-onset postoperative atrial fibrillation after coronary artery bypass grafting

city: beijing

first: yuanshu

last: peng

state: 北京

address: 8 Beijing Workers stadium South Road, Chaoyang District, Beijing

department: heart center, beijing chaoyang hospital

institute: Beijing Chaoyang Hospital, Capital Medical University

summary: This study intended to explore the core genes that might be involved in the occurrence and development of POAF after CABG by RNA sequencing (RNA-seq) of EAT

overall_design: This study aimed to explore the association between POAF and EAT at the gene level by analyzing the EAT gene expression profile of postoperative and non-postoperative atrial fibrillation groups

first: Yuanshu

last: Peng

first: Pixiong

last: Su

first: Lei

last: Zhao


title: In-cell RNA secondary structure analysis of functional SINE transcripts

summary: SINEUPs are long non-coding RNAs which contain a functionally crucial SINE repeat element and positively regulate target mRNA translation at post-transcription level. To study secondary (2D) structure of these functional SINE-derived RNAs, various SINEUP-GFP plasmids containing different mouse SINEB2 repeat elements or human SINE FRAM repeat were transfected along with sense EGFP plasmid in HEK293T/17 cells. Total RNA in transfected cells were probed at flexible regions with NAI-N3 reagent and icSHAPE (in-vivo click selective hydroxyl acylation and profiling experiment) libraries were prepared. To further understand the structure dynamics of SINE transcripts in subcellular locations, cells were fractionated in nuclear and cytoplasmic fractions after 24 h of transfection and fraction-specific icSHAPE libraries were constructed.

overall_design: In-vivo icSHAPE libraries for mouse (SINEB2) and human (FRAM) SINE-derived transcripts from whole cell lysate. Two biological replicates (rep) of each NAI-N3 and DMSO (mock) treated samples. For RNA structure study in cellular compartments, mouse SINEB2 and human FRAM containing functional SINEUP-GFPs were transfected in HEK293T/17 cells and pooled together (SINE) to treat with either NAI-N3 or DMSO and then separated in nuclear (Nuc) and cytoplasmic (Cyto) fractions followed by standard icSHAPE library preparation.


title: A neutrophil response linked to tumor control in immunotherapy II

first: Nicolas

middle: Alejandro

last: Gort-Freitas

state: MA

address: 200 Longwood Ave

department: Systems Biology

institute: Harvard Medical School

summary: Neutrophils accumulate in solid tumors and their abundance correlates with poor prognosis. Neutrophils are not homogenous, however, and could play different roles in cancer therapy. Here, we investigated the role of neutrophils in immunotherapy leading to tumor control. We show that successful therapies acutely expanded tumor neutrophil numbers. This expansion could be attributed to a Sell-hi state, rather than to other neutrophils that accelerate tumor progression. Therapy-elicited neutrophils acquired an interferon gene signature, also seen in human patients, and appeared essential for successful therapy, as loss of the interferon-responsive transcription factor IRF1 in neutrophils led to failure of immunotherapy. The neutrophil response depended on key components of antitumor immunity, including BATF3-dependent DCs, IL12 and IFNγ. In addition, we found that a therapy-elicited systemic neutrophil response positively correlated with disease outcome in lung cancer patients. Thus, we establish a crucial role of a neutrophil state in mediating effective cancer therapy.

overall_design: Single cell RNA sequencing (scRNAseq) of CD45-sorted cells from tumors of mice that were treated or not with agonist anti-CD40 immunotherapy. CD45+ cells were sorted from untreated (n=1) and anti-CD40-treated (n=2) tumors.

first: Marie

last: Siwicki

middle: A

first: Marius

last: Messemaker

first: Camilla

last: Engblom

first: Rapolas

last: Zilionis

first: Allon

middle: M

last: Klein

first: Mikael

middle: J

last: Pittet


title: A neutrophil response linked to tumor control in immunotherapy I

overall_design: KP tumors were induced in C57BL6/J mice, and allowed to grow for 31 days before treating, or not, with aCD40. Two days after aCD40 treatment, the lungs of these mice were perfused, and tumor nodules were macroscopically dissected from the lungs and digested as above to generate single cell suspensions. Cells were then stained with a combination of DNA-tagged TotalSeq-A antibodies and Hashtag antibodies (listed in table S2), stained with a fluorochrome-labelled CD11b antibody for sorting, and labelled with 7AAD to identify live cells. CD11b+ cells were sorted, using a BD FACSAria sorter, into PBS (no Ca or Mg) with 0.04% BSA, at a concentration of 1000-1500 cells/µL. After this, cells were processed with Chromium Next GEM Single Cell 3’ Kit v3.1, 4 rxns (PN-1000269) before loading on a Chromium Next GEM Chip G Single Cell Kit, 16 rxns (PN-1000127). In collaboration with the Single Cell Core Facility at Harvard Medical School, standard steps were followed for library preparation, quality control and amplification. Sequencing was performed in collaboration with the Biopolymers Facility at Harvard Medical School, using the NovaSeqSP platform (1,600,000,000 reads, 20k reads/cell).

first: Jeremy

last: Gungabeesoon

first: Ruben

last: Bill


title: Detection of SINEUP RNA modification by Oxford Nanopore direct-RNA sequencing

status: Public on Feb 04 2023

first: Harshita

last: Sharma

institute: RIKEN IMS

summary: To detect the modifed bases in SINEUP RNA, we compared chemically modified in vitro transcribed (IVT) SINEUP-GFP RNA and in-cell transcribed (ICT) SINEUP RNA from SINEUP-GFP and sense EGFP co-transfected HEK293T/17 cells. Comparative study of Nanopore direct RNA sequencing data from non-modified and modified IVT samples against the data from ICT SINEUP RNA sample revealed modified k-mers positions in SINEUP RNA in the cell.

overall_design: We used in vitro transcribed (IVT) SINEUP-GFP RNA with 0 % (no modification) and 20% Ψ modification conditions. In parallel, we captured and enriched in-cell transcribed (ICT) SINEUP RNA from SINEUP-GFP and sense EGFP co-transfected HEK293T/17 cells by SINEUP-specific biotinylated oligos. Both in vitro and in-cell transcribed samples were sequenced by Nanopore direct RNA sequencing.

first: Naoko

last: Toki


title: H3K36 methylation maintains cell identity by regulating opposing lineage programs

first: Simona

last: Cristea

address: 450 Brookline Ave.

department: Biostatistics and Computational Biology

institute: Dana-Farber Cancer Institute

summary: While epigenetic regulation in early development and differentiation is relatively well-characterized, the precise mechanisms that subsequently maintain specialized cell states remain largely unexplored. Here, we employed histone H3.3 mutants to uncover a crucial role for H3K36 methylation in the maintenance of cell identities across diverse developmental contexts. Focusing on the experimentally induced conversion of fibroblasts to pluripotent stem cells, we show that H3K36M-mediated disruption of H3K36 methylation endowed reprogramming intermediates with a plastic state poised to acquire pluripotency in nearly all cells. At a cellular level, H3K36M rendered mesenchymal cells insensitive to TGF signals and thus facilitated epithelial plasticity. At a molecular level, H3K36M led to the downregulation of mesenchymal genes by depleting H3K36me2 and H3K27ac at associated enhancers. In parallel, H3K36M led to the upregulation of epithelial and stem cell genes by enabling enhancer accessibility and hypomethylation. Mechanistically, we found that Tet-dependent demethylation uncouples pluripotency enhancer activation from somatic enhancer decommissioning in K36M cells. This dynamic switch of enhancer activities redirects Sox2 binding from promiscuous somatic targets to bona fide stem cell targets crucial for the establishment of the pluripotency network. Together, our findings reveal a dual role for H3K36 methylation in the maintenance of cell identity by integrating a key developmental pathway into sustained expression of cell type-specific programs, and by opposing the expression of alternative lineage programs through continual enhancer methylation. Our results provide crucial insight into the impact of dynamic H3K36 methylation patterns on physiological and pathological cell fate transitions, including development, tissue regeneration and cancer.

overall_design: single cell RNA-seq was performed for 10 samples

first: Michael

last: Hoetker

first: Franziska

last: Michor

first: Konrad

last: Hochedlinger


title: Effects of pharmacological manipulations of the NA system on the transcriptional stress response in the mouse hippocampus

status: Public on Feb 02 2023

city: Zürich

first: Lukas

middle: Matthias

last: von Ziegler

address: Winterthurerstrasse 190

department: D-HESZ

country: Switzerland

institute: ETH Zürich

summary: Here, we extensively characterize noradrenaline (NA) mediated transcriptomic response during acute stress in the mouse hippocampus. Combining for the first time bulk mRNA-sequencing and selective pharmacological manipulations of the NA system. We show that the NA mediates robust stress associated transcriptomic alterations across the dorsal and ventral hippocampus via β-adrenergic receptors

overall_design:
This repository contains data from two experiments (STR2 and STR3). First experiment (STR2): animals were injected with saline or adrenergic receptor antagonists (propranolol = beta-adrenergic receptor antagonist, prazosin = alpha-adrenergic receptor antagonist). After 45 minutes animals were then subjected either to stress, pharmacologically induced stress (Yohimbine injection) or kept in their homecage as controls. Animals were dissected 45min after onset of stress (90min after the initial injection) and dorsal hippocampus (dHC) and ventral hippocampus (vHC) were sequenced (bulk mRNA sequencing). Second experiment (STR3): Repeat of the main findings of STR3 with a better experimental design (full model with all proper control groups) and with male and female mice. Animals were injected with Propranolol (systemic beta-adrenergic antagonist), Sotalol (beta adrenergic antagonist that is unable to cross the blood brain barrier) or saline. then 45min after initial injections animals were subjected to either stress or kept in their homecage as control. 45min after onset of stress (90min after the initial injections) animals were dissected and vHC was sequenced.

This repository addition contains additional data for the second experiment (STR3), adding data for a dHC for saline and propranolol injected animals

first: Mattia

last: Privitera

first: Pierre-Luc

last: Germain

first: Johannes

last: Bohacek


title: Effects of optogenetic and chemogenetic LC activation on the hippocampal transcriptome

summary: The locus coeruleus noradrenergic (LC-NA) system plays an important role in organizing a physiological response to acute stress. However, if and how the LC affects stress-mediated transcriptomic changes in the brain is still barely understood. Here, we extensively characterize LC mediated transcriptomic response during acute stress in the hippocampus. Combining for the first time bulk mRNA-sequencing and selective chemogenetic and optogenetic manipulations of the LC-NA system

overall_design: This repository contains data from 4 different experiments: First experiment: chemogenetic activation of the locus coeruleus (LC) followed by sequencing of the ventral hippocampus (vHC) and the dorsal hippocampus (dHC) 45min after activation. Two-group design (hM3Dq virus vs control virus). Second experiment: optogenetic activation of the LC followed by sequencing of the vHC 45 and 90min after stimulation. Three groups, control virus, Chr2 virus after 45min and ChR2 virus after 1h30min. Third experiment: Optogenetic stimulation of the LC at different stimulation frequencies (Sham stimulation, 3Hz, 5Hz, 15Hz) followed by sequencing of the vHC 45min after stimulation. Fourth experiment: Selective Retrograde optogenetic stimulation of hippocampus-projecting LC neurons only followed by sequencing of the vHC 45min after stimulation. Three groups, homecage control without virus injection/stimulation, control virus and ChR2 virus.

first: Sian

last: Duss


title: Autophagy mediates p53 degradation and is essential for human myelopoiesis

status: Public on Jan 25 2023

city: Guangzhou

first: Jiaming

last: Gu

state: Guangdong

address: Kaiyuan Street

institute: Guangzhou Institutes of biomedicine and health, Chinese Academy of Sciences

summary: Emergency myelopoiesis (EM) is critical for immune defense against pathogens, which requires rapid replenishing of mature myeloid cells. The EM process involves a rapid cell cycle switch from the quiescent hematopoietic stem cells (HSCs) to highly proliferative myeloid progenitors (MPs). How this cell cycle switch is regulated remains poorly understood. Here, we reveal that ATG7, a critical autophagy factor is essential for the rapid proliferation of MPs during human myelopoiesis. Peripheral blood (PB) mobilized HSPCs with ATG7 knock-down or HSPCs derived from ATG7-/- human embryonic stem cells (hESCs) exhibit severe defect in proliferation at MP stage during myeloid/granulocytes differentiation. ATG7 deficient MPs show substantially elevated P53 protein and up-regulation of P53 signaling pathway genes. Mechanistically, ATG7 dependent autophagy mediates P53 degradation in lysosome that allows normal proliferation of MPs. Together, we reveal an essential role of autophagy for P53 degradation in cell cycle switch during human myelopoiesis

overall_design: We compared the transcriptome of  the  WT and  ATG7 knocked down peripheral blood derived myeloid progenitors by RNA-Seq

first: Yanling

last: Zhu

first: Huaisong

last: Lin

first: Guangjin

last: Pan


title: Transcriptome analysis of freshly isolated young and aged mouse natural regulatory T cells

status: Public on Jan 31 2023

city: Belfast

first: Denise

last: Fitzgerald

address: 97 Lisburn Rd

country: United Kingdom

institute: QUB

summary: Remyelination efficiency declines wiith aged leading to axonal loss and irreversible disability. Regulatory T cells have been previously shown

overall_design: Young and aged natural Tregs were isolated from spleen and lymphnodes of C57Bl6/J mice. In brief, spleen and lymph nodes were mashed through a 70µm strainer and red blood cells lysed. Natural Tregs were then magnetically isolated  using CD4 negative selection (Stemcell technologies) followed by CD25 positive selection (Stemcell technologies). CD25+ cells were then lysed with Trizol and frozen at -80C. young and aged natural Tregs were always isolated simultaneosly and once all samples were obtained, RNA was isolated.

first: Alerie

middle: G

last: de la Fuente

first: Vijay

middle: K

last: Tiwari

middle: C


title: Tregs constrain CD8+ T cell priming required for curative intratumorally anchored anti-4-1BB immunotherapy

status: Public on Jan 30 2023

city: Cambridge

first: Joseph

last: Palmeri

address: 500 Main St., Attn: 76-291: Joseph Palmeri

department: Chemical Engineering

institute: Massachusetts Institute of Technology

summary: Costimulation of T cells with agonist antibodies targeting 4-1BB (CD137) improves antitumor immune responses in preclinical studies, but clinical development has been hampered by on-target, off-tumor toxicity. Here, we report the development of a tumor-anchored ɑ4-1BB agonist, termed ɑ4-1BB-LAIR, which consists of an ɑ4-1BB antibody fused to the collagen binding protein mLAIR1. Combination treatment with an antitumor antibody (TA99) displayed only modest efficacy, but surprisingly cured >90% of mice upon depletion of CD4+ cells. We elucidated two mechanisms of action for this synergy: ɑCD4 increased priming and activation in the tumor draining lymph node , and TA99 + ɑ4-1BB-LAIR supported the cytotoxic program of these newly primed CD8+ T cells within the tumor microenvironment.  Replacement of ɑCD4 with ɑCTLA-4, a more clinically relevant agent to enhance T cell priming, produces equivalently high cure rates while generating significantly more robust immunological memory against secondary tumor rechallenge.

overall_design: RNA-sequencing was performed on CD45+ cells isolated from tumors (B16F10) and tumor draining lymph node samples from mice treated with various immmunotherapy combinations at two different time points

first: Brianna

last: Lax

first: Lauren

last: Duhamel

first: Jordan

last: Stinson

first: Luciano

last: Santollani

first: Joshua

last: Peters

first: Emi

last: Lutz

first: William

last: Pinney III

first: K

last: Wittrup

first: Bryan

last: Bryson


title: Single cell 5' RNA sequencing of 9 Korean ovarian cancer patients

status: Public on Jan 09 2023

city: Daejeon

first: Jung Kyoon

last: Choi

address: 291, Daehak-ro, Yuseong-gu

department: Department of Bio and Brain Engineering

institute: Korea Advanced Institute of Science and Technology

summary: To investigate the tumor-associated antigens and their functional relationships in ovarian cancer, we provide single-cell 5’ RNA sequencing data of 18,299 cells from 9 patients with ovarian high-grade serous ovarian carcinoma (HGSOC). In the heterogeneous complexity, we refined single-cell profiles by public methods for cell-type annotation and aneuploid prediction, resulting in the cellular composition of the epithelial tumor, tumor-infiltrating immune cells, and the other stromal cells. The extraction of the expressional pattern to discriminate tumor and the other normal cells was performed, which could provide the clue for the prioritization of antigens for ovarian cancer.

overall_design: Single-cell mRNA expression data were derived from nine patients (mean age, 56 years old) who were undertaken cytoreductive surgery with ovarian high-grade serous ovarian carcinoma (HGSOC). For quality control of the data, we carried out filtering the cells with low UMI and RNA features, and high mitochondrial percentages. To efficiently predict the amount of copy number variation, cells with sufficient expression values that could be compared within cells were selected for further analysis. 18,299 cells that passed the final criteria were used for initial clustering, dimensional reduction, and cell-type identification with the definition of tumor cells.

first: Hee

last: An


title: Analysis of human subcutaneous adipose tissue from an 8-week training-intervention

status: Public on Feb 01 2023

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary: The participants performed an 8-week supervised aerobic endurance exercise intervention program. Biopsies of both adipose tissue and skeletal muscle were collected at associated timepoints and a matched analysis was performed.

overall_design: We performed gene expression microarray analysis in human adipose tissue biopsies from subjects before and after acute exercise as well as before and after training interventions

first: Simon

middle: I

last: Dreher

first: Martin

last: Irmler

first: Olga

last: Pivovarova-Ramich

first: Katharina

last: Kessler

first: Karsten

last: Jürchott

first: Carsten

last: Sticht

first: Louise

last: Fritsche

first: Patrick

last: Schneeweiss

first: Jürgen

last: Machann

first: Andreas

middle: F

last: Pfeiffer

last: Hrabe de Angelis

middle: L

last: Birkenfeld

last: Peter

last: Niess

first: Cora

last: Weigert

first: Anja

last: Moller


title: Specificity, synergy, and mechanisms of splice-modifying drugs

city: Cold Spring Harbor

first: Carlos

last: Martí-Gómez

email: carlos199m1@gmail.com, martigo@cshl.edu

state: New York

address: 1 Bungtown Rd

department: Quantitative Biology

institute: Cold Spring Harbor Laboratory

summary: Drugs that target pre-mRNA splicing hold great therapeutic potential, but the mechanistic understanding of how these drugs function is limited. Here we introduce a biophysical modeling framework that can quantitatively describe the sequence-specific and concentration-dependent behavior of splice-modifying drugs. Using massively parallel splicing assays, RNA-seq experiments, and precision dose-response curves, we apply this framework to two drugs, risdiplam and branaplam, developed for treating spinal muscular atrophy. The results quantitatively define the specificities of risdiplam and branaplam for 5’ splice site sequences, suggest that branaplam recognizes 5’ splice sites via two distinct interaction modes, and disprove the prevailing two-site hypothesis for risdiplam activity at SMN2 exon 7. The results also show, more generally, that single-drug cooperativity and multi-drug synergy are widespread among splice-modifying drugs. Our biophysical modeling approach thus clarifies the mechanisms of existing splice-modifying treatments and provides a quantitative basis for the rational development of new therapies.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design:
Comparative alternative splicing profiling analysis of RNA-seq data for HeLa cells treated with splice modifying drugs risdiplam and branamplan, and DMSO as control
Massively parallel splicing assay of 5'splice site sequences in HeLa cells treated with splice modifying drugs risdiplam and branamplan, and DMSO as control in 3 different genetic contexts (MPSA samples)

first: Yuma

last: Ishigami

first: Mandy

last: Wong

first: Andalus

last: Ayaz

first: Mahdi

last: Kooshkbaghi

first: Sonya

last: Hanson

first: David

last: McCandlish

first: Adrian

last: Krainer

first: Justin

last: Kinney


title: Comparison of wild-type Synechocystis sp. PCC 6803 with strains overexpressing wild-type or 5’-sensing-deficient RNase E

status: Public on Jan 20 2023

city: Freiburg

first: Ute

middle: A.

last: Hoffmann

address: Schänzlestr. 1

department: Institute of Biology III

institute: University of Freiburg

summary: We compared transcriptomic changes, 5'-triphosphorylated (TSS) and 5'-monophosphorylated (PSS) RNA ends of different strains of the cyanobacterium Synechocystis sp. PCC6803. Comparison encompassed wild-type Synechocystis (WT), a strain overexpressing RNase E and RNase HII (rne(WT)) and a strain overexpressing 5’-sensing-deficient RNase E and RNase HII (rne(5p)). Analysis of changing 5'-monophosphorylated ends revealed 5’ sensing depedent processing sites on a transcriptome-wide level.

overall_design: Triplicates of RNA samples of WT and rne(WT) as well as duplicates of rne(5p) grown at 30°C were analysed

first: Said

last: Rogh

first: Florian

last: Heyl

first: Rolf

last: Backofen

first: Wolfgang

last: Hess

first: Claudia

last: Steglich

first: Annegret

last: Wilde


title: Kidney inner medulla from mice treated with or without cisplatin

status: Public on Jan 01 2023

city: Birmingham

first: Kelly

middle: Anne

last: Hyndman

state: Al

address: 1918 University BLVD

department: Medicine

institute: University of Alabama at Birmingham

summary: We are interested in the inner medulla of the kidney and how the nephrotoxic drug, cisplatin, may affect the transcriptome.  Furthermore, we are interested in male and female inner medullary transcriptomic differences.

overall_design: Kidney inner medulla RNA profiles from male and female mice treated with saline control or 72 h following cisplatin-induced acute kidney injury


title: Effect of TMEM43 overexpression on gene expression in adult zebrafish hearts

status: Public on Dec 31 2022

city: Wuerzburg

first: Miriam

last: Zink

address: Am Schwarzenberg

institute: University Hospital Wuerzburg

summary:
To determine transcriptional changes caused by the overexpression of wild-type and mutant TMEM43 and to gain insights into the mechanisms responsible for the phenotype of arrhythmogenic cardiomyopathy
We performed RNA-sequencing in adult zebrafish hearts

overall_design: Comparative gene expression profiling analysis of RNA-seq data for adult non-transgenic (NTG), wild-type TMEM43 (TMEM43-WT), p.P111L mutant TMEM43 (TMEM43-p.P111L) and p.S358L mutant TMEM43 zebrafish hearts

first: Brenda

last: Gerull


title: Analysis of transcriptomic transcriptomic consequences of Tyrobp deletion in a Huntington’s disease mouse model

city: New York

first: Jordi

last: Creus Muncunill

state: NY

address: 1391 Madison Ave, Apt. 3F

institute: Mount Sinai

summary: We report the gene expression alterations observed in the striatum 10-month-old Q175 mice with and without Tyrobp

overall_design: Examination of gene expression alterations in the striatum of Q175 with and without Tyrobp

last: Creus-Muncunill

first: Daniele

last: Mattei

first: Angie

last: Ramirez

first: Michelle

middle: E

last: Ehrlich


title: Advanced auxin-inducible degron system deciphers unique functions of CTCF in transcriptional regulation [ChIP-seq]

status: Public on Dec 28 2022

city: Doha

first: Mohamed Nadhir

last: Djekidel

state: Doha

address: Gharafa

department: Translational Medicine Department

country: Qatar

institute: Sidra Medicine

summary: ChIPseq was performed on cells depleted for CTCF by  AID2 auxin degradation to examine CTCF DNA binding affinity.  ChIP seq was also performed on cells depleted for endogenous CTCF and expressing HA tagged WT CTCF and CTCF mutants (deltaZF1, deltaZF10 and deltaRBR) to examine how functional deletions affect CTCF DNA binding affinity.

overall_design: AID2 auxin degradation was combined with endogenous AID tagged CTCF in the human B-ALL cell line SEM.  Cells were depleted for endogenous CTCF and induced to express HA tagged WT CTCF and CTCF mutants (deltaZF1, deltaZF10 and deltaRBR). ChIPseq was performed to examine CTCF DNA binding affinity.

first: Judith

last: Hyle

first: Mohamed

last: Williams

first: Shaela

last: Wright

first: Ying

last: Shao

first: Beisi

last: Xu

first: Chunliang

last: Li


title: Transcriptomic analyses of a Cyberlindnera jadinii strain (NBRC0988) grown in glucose and xylose

status: Public on Dec 11 2022

city: Tianjin

first: Feiyu

last: Fan

state: Tianjin

address: 32 West 7th Avenue, Tianjin Airport Economic Area

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

summary: Strand-specific RNA-seq libraries were constructed for two samples, including (I) wild-type strain NBRC0988 grown in YEP medium containing 2% w/v glucose;(II) wild-type strain NBRC0988 grown in YEP medium containing 2% w/v xylose. For preparation of RNA samples, NBRC0988 cells grown overnight were inoculated into 100 ml liquid Yeast Extract Peptone Dextrose (YEPD) medium with the initial inoculation amount of OD600= 0.1, and cultured for 15 hours at 30℃ and 250 rpm. The cells were collected by centrifugation at 6,000g for 5 minutes. After washing twice with phosphate buffer saline (PBS), they were inoculated into new 100 mL YEP medium containing 2% w/v glucose or xylose.After flask culturing at 30°C and 250 rpm for an additional 5 hours, the yeast cells were collected by centrifugation for total RNA isolation and Illumina RNA-seq library construction.  Total RNA for samples were isolated using TRIzol reagent (Invitrogen, Grand Island, USA), then used for high-throughput RNA sequencing. The 150-nt paired-end strand-specific RNA-seq libraries (SS_lib_type RF) were generated commercially at Novogene Biotechnology Co. Ltd (Tianjin, China) by using Illumina’s novaseq 6000 platform (Illumina, San Diego, USA).

overall_design: RNA profiles of C. jadinii wild-type strain NBRC0988 grown in YEP medium containing 2% w/v glucose or xylose were generated by deep sequencing, using Illumina’s novaseq 6000 platform

first: Lishan

last: Gu

first: Rongxin

last: Zhang

first: Xuqian

first: Yu

last: Wang

first: Kaiyu

last: Ma

first: Jingjing

last: Jiang

first: Gen

first: Honglei

first: Xueli


title: Intracellular differential gene expression detected by transcriptome sequencing after lactate treatment of nucleus pulposus cells

status: Public on Dec 06 2022

city: Chongqing

first: Yuyao

address: No.83, Xinqiao Zhengjie, Shapingba District

institute: Xiqiao hospital

summary: The accumulation of metabolites in the intervertebral disc is regarded as an important inducement of intervertebral disc degeneration (IVDD). Lactate, a metabolite produced by the cellular anaerobic glycolysis process, has been proved to be closely associated with IVDD. However, little was known about the role of lactate in nucleus pulposus cells (NPCs) senescence. This study attempted to investigate the effect and molecular mechanism of lactate on NPCs senescence in vitro and in vivo. A puncture-induced disc degeneration model was established in rats. Metabolomics analysis proved that lactate was significantly increased in the rat degenerated intervertebral disc. Eliminating extra lactate using lactate oxidase (LOx)-overexpressing lentivirus alleviated the progression of IVDD. In vitro experiments showed that high concentration lactate could induce senescence and oxidative stress in NPCs. High-throughput RNA sequencing (RNA-seq) results and bioinformatic analysis exhibited that lactate-stimulated NPCs senescence may be related to the PI3K/Akt signaling pathway. Further study verified that high concentration lactate could induce NPCs senescence and oxidative stress via inhibiting PI3K/Akt signaling and downstream Akt/p21/p27/cyclinD1 and Akt/Nrf2/HO-1 pathway. Utilizing molecular docking, we found that lactate may suppress the Akt phosphoactivation via binding to Lys39 and Leu52 in the PH domain of Akt. In conclusion, this study illuminates that lactate could promote the senescence of NPCs to aggravate IVDD by suppressing the PI3K/Akt signaling pathway and the expression of its downstream genes. These results highlight the involvement of lactate NPCs senescence, which may become a novel potential therapeutic target for the treatment of IVDD.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NP cells and NP cells after treated with lactate.

first: Changqing

last: Zhai

first: Libangxi

last: Liu

first: Yuhan

last: Qi


title: Long-read transcriptome profiling of the rat hippocampal neurons in primary culture at different time points after activation using Nanopore sequencing

status: Public on Nov 25 2022

city: Moscow

first: Alexander

last: Beletsky

address: Butlerova street, building 5a

country: Russia

institute: IHNA

summary: Long-read transcriptome sequencing provides us with a convenient tool for thorough study of biological processes such as neuronal plasticity. In this study, we aimed to perform transcriptional profiling of rat hippocampal primary neuron cultures after stimulation with picrotoxin (PTX) to further understand molecular mechanisms of neuronal activation. To overcome limitations of short-read RNA-Seq approaches we performed a Oxford Nanopore Technologies (ONT)-based long-read sequencing and transcriptome assembly of rat primary hippocampal culture mRNA at three time points after the PTX activation (30 min; 1 h and 5 h). Overall, we found 23652 novel transcrits in comparison to reference annotations, out of which ~6k were entirely novel and mostly transposable element-derived loci. Analysis of differentially expressed genes (DEG) showed that a total of 3046 genes were differentially expressed, of which 2037 were upregulated and 1009 were downregulated at 30 min after the PTX application, with only 446 and 13 genes differentially expressed at 1 h and 5 h time points respectively. Most notably, multiple genes encoding ribosomal proteins, with high basal expression level, were downregulated after 30 min incubation with PTX; we suggest that this indicates redistribution of transcriptional resources towards activity-induced genes.  Novel loci and isoforms, observed in this study, could help us further understand the functional mRNA repertoire in neuronal plasticity processes. Together with other NGS techniques, the result of differential gene expression analysis of sequencing data obtained using MinION platform might provide a simple method to optimize further study of neuronal plasticity.

overall_design: 20 primary hippocampal neuronal cultures under control and PTX-treated conditions were subjected to long-read Oxford Nanopore RNA sequencing and transcriptome assembly. 12 cultures (with noticeable response to PTX) were subjected to differential expression analysis.

last: Beletskiy

first: Anastasia

last: Zolotar

first: Polina

last: Fortygina

first: Ekaterina

last: Chesnokova

first: Leonid

last: Uroshlev

first: Pavel

last: Balaban

first: Peter

last: Kolosov


title: Effect of ferroportin on placental gene expression

status: Public on Nov 18 2022

city: BOSTON

first: CHANG

last: CAO

address: 185 CAMBRIDGE ST.

department: CENTER FOR GENOMIC MEDICINE

institute: Mass General Brigham

summary:
To investigate the function of ferroportin, we deleted ferroportin gene in mouse placenta using cre.
We performed RNA-sequencing on six ferroportin knockout and four control placentas.

overall_design: Compare gene expression in ferroportin knockout (KO) and the control (C) placentas.

first: Chang

last: Cao

first: Mark

last: Fleming


title: Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation

status: Public on Dec 09 2022

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

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

overall_design: Refer to individual Series


title: Centromere evolution in Brachypodium genomes with different polyploid levels

status: Public on Dec 01 2022

city: Wuhan

first: Handong

last: Su

state: Hubei

address: No.1,Shizishan Street · Hongshan District

institute: Huazhong Agricultural University

summary: Centromeric repetitive DNA sequences are highly variable during evolution, which are the hub for genome stability in almost all the eukaryotic organisms. However, how centromeric repeat sequences diverge rapidly among closely related species and populations, and how polyploidy contributed to the diversity of centromere among co-evolved subgenomes are largely unknown. Here, we applied the Brachypodium system to investigate the track of centromere evolution within this taxa, and their adaptation to alloploidization process. Subgenome divergent centromeric satellite repeat were discovered in tetraploid B. hybridum, and this divergent was originated form their two diploid progenitors. Furthermore, differential sequences influence the association sites with CENH3 nucleosomes on the monomer satellite repeats, and positioning of CENH3 nucleosomes on the satellite DNA are stable in each subgenome after alloploidization. Only minor intrasubgenomic variations were observed on these satellite repeats from diploid to tetraploid in B. hybridum, and no evident intersubgenomic transfer of centromeric satellite repeats after alloploidization. Pan-genome analysis reveals that the general principle of centromere dynamic within the populations in Brachypodium genomes with different polyploidy level. Our results provide an unprecedented information regarding the genomic and functional diversity of centromeric repeat DNA during evolution.

sample_organism:
Brachypodium distachyon
Brachypodium hybridum
Brachypodium stacei

overall_design: ChIP-seq was carried out with anti-CENH3 antibodies using material from young leaves of different Brachypodium lines.


title: Comparison of the effects of mutaions modelling early-onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae

status: Public on Nov 08 2022

city: Adelaide

first: Karissa

last: Barthelson

state: South Australia

address: North Terrace Campus

country: Australia

institute: The University of Adelaide

summary: Neural cells are under immense pressure to maintain proper degradation of molecules using their endo-lysosomal pathway (ELP). In Alzheimer’s disease (AD), the gradual cognitive worsening of this age-related disorder is partially due to dysfunction of the ELP. However, AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia (mucopolysaccharidosis type III, MPSIII) is an extreme consequence of ELP dysfunction, where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide, which ultimately accumulates and interferes with the function of the ELP. Unlike AD, Sanfilippo is genetically simple (all causative genes are identified). The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes, they likely share disease-associated mechanisms. Here, we dissect the similarity between AD and Sanfilippo using RNA-seq. We have generated zebrafish knock-in models of both diseases: the early-onset familial AD-like (EOfAD-like) mutation psen1 Q96_K97del  and the MPSIII-like mutation naglu A603fs. We generated a family of zebrafish containing wild type, heterozygous EOfAD-like and homozygous MPSIII-like genotypes. We raised the family until 7 days post fertilisation and performed mRNA-seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained ~50% power to detect differentially expressed genes. Nevertheless, changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS-III mutant larvae, suggesting a homeostatic response as the cells which make up the larval RNA-seq samples respond to dysfunctional lysosomes.

overall_design: We first paired fish a female zebrafish with genotype psen1 Q96_K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 days post fertilisation. The, the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then, the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations, a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae, n = 8 EOfAD-like/+ larvae and n = 8 MPS-IIIB homozygous larvae.

first: Michael

last: Lardelli


title: Assessment of Spatial Genomics for Oncology Discovery

status: Public on Nov 01 2022

first: Anna

last: Lyubetskaya

address: 100 Binney St

institute: Bristol-Myers Squibb

summary: Tumor heterogeneity is a major challenge for oncology drug discovery and development. Understanding of the spatial tumor landscape is key to identifying new targets and impactful model systems. Here, we test the utility of spatial transcriptomics (ST) for Oncology Discovery by profiling 40 tissue sections and 80,024 capture spots across a diverse set of tissue types, sample formats, and RNA capture chemistries. We verify the accuracy and fidelity of ST by leveraging matched pathology analysis that provide a ground truth for tissue section composition. We then use spatial data to demonstrate the capture of key tumor depth features, identifying hypoxia, necrosis, vasculature, and extracellular matrix variation. We also leverage spatial context to identify relative cell type locations showing the anti-correlation of tumor and immune cells in syngeneic cancer models. Lastly, we demonstrate target identification approaches in clinical pancreatic adenocarcinoma samples, highlighting tumor intrinsic biomarkers and paracrine signaling.

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Anna, Lyubetskaya

first: Brian

last: Rabe

first: Andrew

last: Fisher

first: Anne

last: Lewin

first: Isaac

last: Neuhaus

first: Connie

last: Brett

first: Todd

first: Ethel

last: Pereira

first: Ryan

last: Golhar

first: Sami

last: Kebede

first: Alba

last: Font-Tello

first: Kathy

last: Mosure

first: Nicholas

last: Van Wittenberghe

first: Konstantinos

last: Mavrakis

first: Kenzie

last: MacIsaac

first: Benjamin

last: Chen

first: Eugene

last: Drokhlyansky


title: A Transcription Factor Atlas of Directed Differentiation

status: Public on Jan 05 2023

first: Julia

last: Joung

address: 75 Ames St

institute: Broad Institute

sample_organism:
Escherichia coli
Homo sapiens
Lentivirus


title: Ustekinumab as Induction and Maintenance Therapy for Crohn's Disease

city: Spring House

first: Patrick

last: Branigan

address: 1400 McKean Road

institute: Johnson and Johnson

summary:
Whole blood samples were collected from patients at baseline, 6 weeks and 8 weeks after induction (Ustekinumab or placebo) therapies for RNA extraction and microarray analysis from patients with moderate-to-severe CD who participated in stelara CD phase 3 studies (UNITI-2). These patients failed conventional therapies previously and largely naive to anti-TNF therapy.
We used microarrays to detail the transcriptional programme underlying placebo and stelara treatment in the periphery at WK0, WK6, WK8.

overall_design: A gene expression profiling study was conducted in whole blood samples and samples were collected for RNA extraction and hybridization to microarrays from patients with moderate-to-severe Crohn's disease

first: Venkat

last: Swati

first: Branigan

last: Patrick


title: High-content CRISPR screens link coronary artery disease genes to endothelial cell programs [Pilot scRNA-seq]

city: Stanford

first: Jesse

last: Engreitz

state: CA

address: 240 Pasteur Drive

institute: Stanford University

summary: Genome-wide association studies (GWAS) have discovered thousands of risk loci for common, complex diseases, each of which could point to genes and gene programs that influence disease. For some diseases, it has been observed that GWAS signals converge on a smaller number of biological programs, and that this convergence can help to identify causal genes. However, identifying such convergence remains challenging: each GWAS locus can have 2-20 candidate genes, the cellular programs a gene participates in are difficult to define in an unbiased fashion, and it remains unclear which genes and programs would be likely to influence disease risk. Here, we explored a new approach to address this challenge, by creating an unbiased catalog of gene programs and their regulators in endothelial cells to link variants to functions for coronary artery disease (CAD). To do so, we applied CRISPRi-Perturb-seq to knock down all expressed genes within 500 Kb of all CAD GWAS loci (2,285 genes in total) and measure their effects on the transcriptome using single-cell RNA-seq. We used consensus non-negative matrix factorization to define 60 gene expression programs—including core cellular programs, such as ribosome biogenesis, and endothelial cell-specific programs, such as flow response and angiogenesis—and link these programs to upstream regulators including transcription factors, chromatin regulators, metabolic enzymes, and signaling cascades. By combining this gene-to-program catalog with variant-to-gene maps, we find that candidate CAD genes converge onto 6 interrelated gene programs, together involving known and novel genes in 39 of 229 CAD GWAS loci. Analysis of these programs revealed that the cerebral cavernous malformations (CCM) complex—whose potential connection to CAD has not been previously explored—acts upstream to regulate other CAD genes involved in cytoskeletal organization, extracellular matrix remodeling, and cell migration. The strongest regulator of these programs is TLNRD1, a highly conserved but poorly studied gene that we show acts in the CCM pathway and regulates actin organization and endothelial cell barrier function. Together, our study nominates new genes that likely influence risk for CAD, identifies convergence of CAD risk loci into certain gene programs in endothelial cells, and demonstrates a generalizable strategy to catalog gene programs to connect disease variants to functions.

overall_design: This series contains pilot Perturb-seq studies, which were used to optimize conditions for and cross validate the larger Perturb-seq study reported in GSE210681. Human immortalized endothelial cells engineered to contain doxycycline inducible CRISPR interference machinery (CRISPRi TeloHAEC or CRISPRi Eahy926), were transduced with one of two guide RNA libraries targeting gene promoters (referred to as the 50gene & 200gene libraries), in a CROP-seq vector. After 5 days of doxycycline treatment, cells were run on a single lane of a 10X Chromium Controller and scRNA-seq libraries generated. For Eahy926, the maximum number of cells recommended in the 10x protocol was used (16k), or the lane was "superloaded" with ~10x more cells (150k). For TeloHAEC, only the superloading condition was used. polyA+ cDNA surrounding the guide sequences was amplified to make "dialout" libraries, used to link guide RNA sequences to scRNAseq cell barcodes.

first: Gavin

middle: R

last: Schnitzler

first: Helen

last: Kang

first: Vivian

last: Lee-Kim

first: X

last: Ma

first: Tony

last: Zeng

first: Shamsudheen

last: Vellarikkal

first: Ronghao

last: Zhou

first: Katherine

last: Guo

first: Oscar

last: Sias-Garcia

first: Alex

last: Bloemendal

first: Glen

last: Munson

first: Philine

last: Guckelberger

first: Tung

middle: H

last: Nguyen

first: Drew

middle: T

last: Bergman

first: Deepak

last: Atri

first: Nathan

last: Cheng

first: Brian

last: Cleary

first: Eric

middle: S

last: Lander

first: Hilary

last: Finucane

first: Rajat

last: Gupta


title: Modulation of type-I interferon responses in Rhesus Macaque whole blood

status: Public on Nov 16 2022

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

summary: RNA-sequencing used to investigate the transcriptome response to Sars-cov-2 in the presence of IFN treatment

overall_design: Rhesus macaques treated with an IFNα2 modulator to supress IFN response and infected with Sars-CoV-02.

first: Timothy

middle: N

last: Hoang

first: Leanne

last: Whitmore

first: Elise

last: Viox

first: Jennifer

last: Tisonick-Go

last: Smith

first: Jean

last: Chang

last: Gale Jr

first: Steven

last: Bosinger

first: Mirko

last: Paiardini


title: High-content CRISPR screens link coronary artery disease genes to endothelial cell programs

first: Jesse

last: Engreitz


title: Single-cell transcriptional profiling reveals anti-CTLA-4 therapy remodels the intestinal immune landscape in inflammation-prone conditions

city: Beijing

first: Yifan

last: Zhou

address: No. 30 Shuangqing Road

department: School of Medicine

institute: Tsinghua University

summary:
Aim: Understanding of irAE-driving mechanisms using an irAE animal model
Methods: Adult Stat3Δ/Δ (STAT3 is deleted from DCs via the Cre-recombinase system)  and Stat3+/+ mice were challenged with B16-OVA melanoma tumors, treated biweekly for 2 weeks with anti-CTLA-4 (clone 9H10) or control IgG. Colonic lamina propria (LP) immune cells were isolated and sorted for live CD45+ cells by fluorescence-activated cell sorting (FACS) 18-19 d after tumor establishment and following completion of therapy. Colonic LP immune cells were subjected to single-cell RNA sequencing (scRNAseq, 10x Genomics).
Results: The scRNAseq data, representing 14039 cells from our 4 experimental groups, were concatenated and graphed using unsupervised clustering to identify transcriptionally-related populations. This resulted in elaboration of 19 discrete clusters, including 16 immune and 3 non-immune clusters.
Conclusion:This work provides mechanistic insight into irAE development and models for pre-clinical investigation.

overall_design: scRNAseq of CD45+ colonic lamina propria  (LP) immune cells purified from melanoma-bearing Stat3+/+ and Stat3Δ/Δ mice (Stat3Δ/Δ mice = Stat3 deleted from CD11c+ cells by the Cre recombinase system) treated with anti-CTLA-4 or control IgG

first: Yusra

middle: B

last: Medik

first: Daniel

last: Zamler

first: Sijie

last: Chen

first: Stephanie

last: Watowich


title: A single-cell analysis reveals tumor heterogeneity and immune environment of acral melanoma [scRNA-Seq]

status: Public on Oct 30 2022

first: Chao

last: Zhang

address: 1 Huahuxi Road, Hexi

institute: Tianjin Medical University Cancer Hospital & Institute

summary: Acral melanoma is considered as a special subtype of melanoma. We performed 11 single cell RNA sequencing (scRNA seq), 57 Bulk RNA sequencing, 8 whole exon sequencing（WES seq）, and 6 TCR sequencing to analyze the tumor heterogeneity and immune environment characteristics of acral melanoma.

overall_design: We used the single cell data of 5 cases of acral melanoma and 3 cases of cutaneous melanoma as the discovery set for comparative analysis, and used 57 cases of Bulk-RNA data and 3 cases of single cell RNA data to verify the results. 8 WES data were used to analyze the mutation characteristics of the discovery set samples, and 6 TCR data were used to analyze the T cell clone diversity of the two subtype melanoma samples.

first: Hongru

last: Shen

first: Tielong

last: Yang

first: Ting

last: Li

first: Xinyue

last: Liu

first: Jin

last: Wang

first: Zhichao

last: Liao

first: Junqiang

last: Wei

first: Jia

last: Lu

first: Haotian

first: Lijie

last: Xiang

first: Yichen

first: Meng

first: Yang

first: Ruwei

last: Xing

first: Sheng

last: Teng

first: Jun

last: Zhao

first: Yun

first: Gang

first: Kexin

first: Xiangchun

first: Jilong


title: Generation and Maturation of Human iPSC-derived 3D Organotypic Cardiac Microtissues in Long-Term Culture

status: Public on Oct 18 2022

city: Brno

first: Ece

last: Ergir

address: Studentska 6

department: Center for Translational Medicine (CTM)

country: Czech Republic

institute: St. Anne´s University Hospital Brno - International Clinical Research Centre (FNUSA-ICRC)

summary: We have established a scaffold-free protocol to generate multicellular, beating and self-organized human organotypic cardiac microtissues (hOCMTs) in vitro from human induced pluripotent stem cells (hiPSCs) that can be cultured for long term. This is achieved by differentiation of hiPSC in 2D monolayer culture towards cardiovascular lineage, followed by further aggregation on low-attachment culture dishes in 3D. The generated hOCMTs containing multiple cell types that physiologically compose the heart, gradually self-organize and beat without external stimuli for more than 50 days. We have shown that 3D hOCMTs display improved cardiac specification, survival and maturation as compared to standard monolayer cardiac differentiation in 2D. We also confirmed the functionality of hOCMTs by metabolic flux analysis and their response to cardioactive and cardiotoxic drugs in long term culture. This study could help to develop more physiologically-relevant cardiac tissue models, and represent a powerful platform for future translational research in cardiovascular biology.

overall_design: Cross-comparison of bulk RNA-seq for hiPSC-derived 3D organotypic cardiac microtissues/organoids on Day 30 and Day 50 time points, vs 2D monolayer iPSC-derived cardiac differentiation on Day 30 and Day 50 timepoints

first: Jorge

last: Oliver-De La Cruz

first: Soraia

last: Fernandes

first: Marco

last: Cassani

first: Francesco

last: Niro

first: Daniel

last: Pereira-Sousa

first: Jan

last: Vrbský

first: Vladimír

last: Vinarský

first: Ana

last: Perestrelo

first: Doriana

last: Debellis

first: Natália

last: Vadovičová

first: Stjepan

last: Uldrijan

first: Francesca

last: Cavalieri

first: Stefania

last: Pagliari

first: Heinz

last: Redl

first: Peter

last: Ertl

first: Giancarlo

last: Forte


title: High-content CRISPR screens link coronary artery disease genes to endothelial cell programs [ATACseq]

first: Jesse

last: Engreitz

overall_design: Chromatin was collected from parental human endothelial cell lines (TeloHAEC and Eahy926) grown in normal growth media, or media supplemented with 10ng/ml interleukin 1 beta (IL1b) or tumor necrosis factor alpha (TNFa) for 24 hours. Briefly, one well of a 12-well plate (~200,000 cells) was directly lysed using a custom TN5 buffer (33mM Tris Acetate pH 7.8, 66mM Potassium Acetate, 10 mM Magnesium Acetate, 16% dimethylformamide & 0.1% NP40). 47.5 ul of lysed cells was added to 2.5 ul Tn5 tagmentation enzyme (Illumina) & incubated at 37C for 1hr, and the reaction stopped by addition of 20 ul buffer RLT (Qiagen). Products were purified by addition of 1.8 volumes Ampure XP beads (Beckman-Coulter) & magnetic separation of beads, followed by two 80% ethanol washes, brief drying of pellets & resuspension in 23 ul water. Barcoded ATAC-seq libraries were then generated as described in (Fulco, C. P., Nasser, J., Jones, T. R. & Munson, G. Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations. Nature (2019)), and sequenced to a depth of 10-20 million reads per library.

first: Gavin

last: Schnitzler

first: Helen

last: Kang

first: Vivian

last: Lee-Kim

first: X

last: Ma

first: Tony

last: Zeng

first: Shamsudheen

last: Vellarikkal

first: Ronghao

last: Zhou

first: Katherine

last: Guo

first: Oscar

last: Sias-Garcia

first: Alex

last: Bloemendal

first: Glen

last: Munson

first: Philine

last: Guckelberger

first: Tung

last: Nguyen

first: Drew

last: Bergman

first: Deepak

last: Atri

first: Nathan

last: Cheng

first: Brian

last: Cleary

first: Eric

last: Lander

first: Hilary

last: Finucane

first: Rajat

middle: M

last: Gupta


title: High-content CRISPR screens link coronary artery disease genes to endothelial cell programs [ChIPseq]

first: Jesse

last: Engreitz

overall_design: Chromatin was collected from parental human endothelial cell lines (TeloHAEC and Eahy926) grown in normal growth media, or media supplemented with 10ng/ml interleukin 1 beta (IL1b) or tumor necrosis factor alpha (TNFa) for 24 hours. Chromatin was immunoprecipitated using an anti-histone H3 lysine 27 acetyl (H3K27ac) antibody, and ChIP-seq libraries prepared using KAPA Hyper Prep Kits (KAPA Biosystems). For some samples, libraries were also prepared from INPUT chromatin (not immunoprecipitated).

first: Gavin

last: Schnitzler

first: Helen

last: Kang

first: Vivian

last: Lee-Kim

first: X

last: Ma


title: A single-cell analysis reveals tumor heterogeneity and immune environment of acral melanoma [RNA-Seq]

first: Chao

last: Zhang

first: Hongru

last: Shen

first: Tielong

last: Yang

first: Ting

last: Li

first: Xinyue

last: Liu

first: Jin

last: Wang

first: Zhichao

last: Liao

first: Junqiang

last: Wei

first: Jia

last: Lu

first: Haotian

first: Lijie

last: Xiang

first: Yichen

first: Meng

first: Yang

first: Ruwei

last: Xing

first: Sheng

last: Teng

first: Jun

last: Zhao

first: Yun

first: Gang

first: Kexin

last: Chen

first: Xiangchun

first: Jilong


title: POU2AF2/C11orf53 functions as a co-activator of POU2F3 by maintaining chromatin accessibility and enhancer activity

status: Public on Sep 28 2022

city: Chicago

first: Lu

state: Illinois

address: 303 E. Superior Street Simpson Querrey 7-414

department: Biochemistry and Molecular Genetics

institute: Northwestern University

summary: Small cell lung cancer (SCLC), accounting for around 15% of all lung cancers, often results in rapid tumor growth, early metastasis, and acquired therapeutic resistance. The POU class 2 homeobox 3 (POU2F3) is a master regulator of tuft cell identity and defines a subtype of SCLC tumors (SCLC-P subtype) that lack the expression of neuroendocrine markers. Here, we have identified a previously uncharacterized protein C11orf53, which is co-expressed with POU2F3 in both SCLC cell lines and patient samples, and defines the same SCLC subtype. C11orf53 is an essential gene for SCLC-P subtype cells’ survival based on genome wide CRISPR screen, and genetic depletion of C11orf53 or POU2F3 induces apoptosis in different SCLC-P subtype cell lines. Furthermore, our biochemical and genome-wide studies have demonstrated that C11orf53 is a novel chromatin-bound protein that occupies broad active enhancer domains and regulates gene expression at active enhancers. Mechanistically, C11orf53 directly interacts with POU2F3 at the POUs domain, and is recruited to chromatin by POU2F3. Depletion of C11orf53 dramatically reduced enhancer H3K27ac levels and chromatin accessibility, resulting a reduction of the expression of POU2F3-dependent tuft cell markers.  Based on the expression pattern and molecular function, we have renamed C11orf53 as "POU Class 2 Homeobox Associating Factor 2" (POU2AF2). In summary, our study has identified a new co-activator of POU2 family transcription factors, and sheds light on the therapeutic potential of targeting POU2AF2/POU2F3 heterodimer in human SCLC.

overall_design: This study aims to provide mechanistic insight into the function of a previously uncharacterized protein C11orf53 in SCLC

first: Zibo


title: A single-cell analysis reveals tumor heterogeneity and immune environment of acral melanoma

first: Chao


title: Expression data from actinic lentigines in Japanese volunteers

status: Public on Oct 14 2022

city: Aulnay sous Bois

first: Emilie

last: Warrick

address: 1 avenue Eugène Schueller

institute: L'Oreal R&I

summary: Actinic lentigines (AL) are very common hyperpigmented lesions that develop on chronically sun-exposed skin and represent a visible sign of skin ageing. In this study, a homogeneous group of advanced AL lesions was selected using epiluminescence imaging and pigmented pattern scoring. Gene expression profiling was performed  on AL compared with adjacent non lesional (NL) skin.

overall_design: Twelve Japanese women aged 54-71 years, phototype III-IV were included in the study. Pairs of 3-mm biopsies (AL lesion and adjacent NL skin) were obtained on the back of hands from each volunteer.

first: Christine

last: Duval

first: Françoise

last: Bernerd


title: Single Cell Multiomics of Healthy, COVID-19 positive and Recovered Individuals

status: Public on Nov 17 2022

city: Delhi

first: Rajesh

last: Pandey

address: Mall road

country: India

institute: CSIR-IGIB

summary: We performed scRNA sequencing to understand the cellular heterogeneity and immune response landscape behind COVID-19 pathophysiology. We combine this with Ab-Seq, oligo-attached antibody based quantification of cell surface proteins to better understand the cell type and state of the cells. Samples were multiplexed using BD single-cell multiplexing kit (Human) in order to measure these data simultaneously

overall_design: PBMCs were isolated from Healthy (n = 4), COVID-19 (n = 16) and recovered (n = 13) individuals, using BD vaccutainers cell prepataion tubes. PBMCs were isolated as per manufacturer's recommendation, and stored for future use. Samples were multiplexed using BD single cell multiplexing kit (Human), followed by tagging with a pool of 40 oligo-attached antibody for surface markers (Ab-Seq). Around 30000 cells were loaded per cartridge, followed by cell lysis, cDNA synthesis and final library preparation using BD WTA amplification kit as per manufacturer's recommendation. A poly-A transcripts library (WTA), Ab-Seq library and library from oligos of Sampe multiplexing kit (SMK) were constructed from each batch, and were sequenced on NovaSeq 6000 platform.

first: Chattopadhyay

last: Partha

first: Davas

last: Manish

first: Wadhwa

last: Saruchi

first: Sahni

last: Shweta

first: Maurya

last: Ranjeet

first: Mishra

last: Pallavi

first: Pandey

last: Rajesh

first: Kumar

last: Anil

first: Rawat

last: Nisha


title: Effect of inhibiting Glucose transporters by Glutor or Glupin on gene expression in primary human NK cells

status: Public on Oct 23 2022

city: Essen

first: Bettina

last: Budeus

address: Virchowstrasse 173

department: Institute for Cell Biology

institute: University Hospital Essen

summary: To study the effect of Glucose transporter inhibition we isolated human NK cells from PBMCs of six healthy donors and expanded them with feeder cells and cytokines in the presence of 100nM Glutor, 100nM Glupin or 0.1% DMSO for 21 days. We then performed gene expression analysis using RNAseq.

overall_design: Gene expression profiling analysis of RNA-seq data for primary human NK cells isolated from six healthy donors treated for 21 days  with 100 nM Glutor, 100nM Glupin or 0.1% DMSO as a control.

first: Lea

last: Picard

first: Carsten

last: Watzl


title: Global transcriptional regulation of Sphingomonas melonis TY in response to hyperosmotic stress

status: Public on Sep 06 2022

city: Hangzhou

first: Xiaoyu

last: Wang

address: Yuhangtang Road

department: College of Life Sciences

institute: Zhejiang University

summary: To further elucidate the responsive patterns of S. melonis TY to hyperosmotic stress at transcriptional level, transcriptome sequencings were carried out on S. melonis TY cultured under three levels of salt stress (0%, 1%, 2%) for 10 or 30 minutes.

overall_design: RNA-seq

first: Lvjing

first: Haixia

first: Zhenmei

last: Lu


title: Identification and validation of key genes related to preferred flavour profiles in Australian commercial papaya (Carica papaya L.)

status: Public on Sep 19 2022

city: Brisbane

first: ziwei

last: zhou

state: QUEENSLAND

address: 170 Kessels Rd, Nathan

institute: Griffith University

summary:
To uncover a suit of genes related to the consumer preferred flavours, whole RNA sequencing followed by de novo genome assembly was performed on extreme flavoured papaya varieties RB1 (preferred with sweet flavour and floral aroma) and 1B (non-preferred with bitter flavour and musty aroma) fruits at ripe and unripe stages.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different papaya varieties at ripe and unripe stages.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for RB1 and 1B at ripe and unripe stages, three biological replicates were included for each variety at each maturity stage. While RB1 at ripe stage was set as control group.

first: Ziwei

last: Zhou

first: Ido

last: Bar


title: CircRNAs Are Here to Stay: A Perspective on the MLL Recombinome

status: Public on Sep 07 2022

city: Padova

first: Stefania

last: Bortoluzzi

address: via G. Colombo 3

department: Department of Molecular Medicine

country: Italy

institute: University of Padova

type: Non-coding RNA profiling by high throughput sequencing

summary: Chromosomal translocations harbored by cancer genomes are important oncogenic drivers. In MLL rearranged acute leukemia (MLLre) MLL/KMT2A fuses with over 90 partner genes. Mechanistic studies provided clues of MLL fusion protein leukemogenic potential, but models failed to fully recapitulate the disease. Recently, expression of oncogenic fusion circular RNAs (f-circ) by MLL-AF9 fusion was proven. This discovery, together with emerging data on the importance and diversity of circRNAs formed the incentive to study the circRNAs of the MLL recombinome. Through interactions with other RNAs, such as microRNAs, and with proteins, circRNAs regulate cellular processes also related to cancer development. CircRNAs can translate into functional peptides too. MLL and most of the 90 MLL translocation partners do express circRNAs and exploration of our RNA-seq dataset of sorted blood cell populations provided new data on alternative circular isoform generation and expression variability of circRNAs of the MLL recombinome. Further, we provided evidence that rearrangements of MLL and three of the main translocation partner genes can impact circRNA expression, supported also by preliminary observations in leukemic cells. The emerging picture underpins the view that circRNAs are worthwhile to be considered when studying MLLre leukemias and provides a new perspective on the impact of chromosomal translocations in cancer cells at large.

overall_design: CircRNA expression profiling analysis of RNA-seq data for patient-derived xenografts (PDX) with MLL::ENL (KMT2A::MLLT1) rearrangements.

first: Anna

last: Dal Molin

first: Silvia

last: Bresolin

first: Enrico

last: Gaffo

first: Caterina

last: Tretti Parenzan

first: Elena

last: Boldrin

first: Lueder

last: Meyer

first: Paola

last: Guglielmelli

first: Alessandro

last: Vannucchi

first: Geertruij

last: te Kronnie


title: Proteostasis governs differential temperature sensitivity across embryonic cell types

status: Public on Aug 08 2022

city: Seattle

first: Michael

last: Dorrity

state: Washington

address: 3720 15th Ave NE, Foege Building, Room S313

institute: University of Washington

summary: The genetic program of embryonic development is remarkably robust, but temperature stress can degrade its ability to generate animals with invariant anatomy. While the stereotyped, consistent phenotypes associated with environmental stress during vertebrate development suggest that some cell types are more sensitive to stress than others, the basis of this sensitivity is unknown. Here, we characterize hundreds of individual zebrafish embryos under temperature stress using whole-animal single cell RNA-seq to identify cell types and molecular programs within them that drive phenotypic variability. We find that temperature perturbs the normal proportions and gene expression programs of numerous cell types and also introduces asynchrony in their development. The notochord is particularly sensitive to temperature stress, which we show is due to a specialized cell type, sheath cells. Further analyses show that sheath cells accumulate misfolded protein at elevated temperature, leading to a cascading structural failure of the notochord and irreversible anatomic defects in the embryo. Our study demonstrates that whole-animal single cell RNA-seq can characterize mechanisms important for developmental robustness and pinpoint molecular programs within specific cell types that constitute key failure points.

overall_design: Whole zebrafish embryos were collected across multiple timepoints or in response to temperature perturbations (28C, 32C, 34C) with sci-RNA-seq3.

first: Cole

last: Trapnell


title: Efficacy and safety of ustekinumab treatment in patients with ulcerative colitis

city: London

first: Nick

last: Powell

address: Du Cane Road

department: Department of Metabolism, Digestion and Reproduction

institute: Imperial College London

summary: UNIFI was a randomized placebo-controlled phase 3 clinical trial evaluating the efficacy and safety of ustekinumab (ClinicalTrials.gov Identifier: NCT02407236). Gene expression profiling by microarrays was carried out at baseline on biopsies from the sigmoid colon (15-20cm from anal verge) of patients (n=550) with moderate-to-severe ulcerative colitis and of healthy subjects (n=18). Ulcerative colitis patients received placebo (n=186) or ustekinumab (n=364). The effects of two different dosages were investigated: 130mg (n=180) and 6mg/kg (n=184).

overall_design: Patients with moderate-to-severe ulcerative colitis were treated with ustekinumab (n=364) or placebo (n=186) at week 0. Biopsy samples were collected from 550 patients and 18 healthy subjects at baseline for RNA extraction and microarray profiling.

first: Polychronis

last: Pavlidis

first: Anastasia

last: Tsakmaki

first: Eirini

last: Pantazi

first: Katherine

last: Li

first: Domenico

last: Cozzetto

first: Jonathan

last: Digby-Bell

first: Feifei

last: Yang

last: Lo

last: Alberts

first: Ana

last: Costa Sa

first: Umar

last: Niazi

first: Joshua

last: Friedman

last: Long

first: Yuchun

last: Ding

first: Christopher

last: Carey

last: Lamb

first: Mansoor

last: Saqi

first: Matthew

last: Madgwick

first: Leila

last: Gul

first: Agatha

last: Treveil

first: Tamas

last: Korcsmaros

first: Thomas

last: MacDonald

first: Graham

last: Lord

first: Gavin

last: Bewick


title: Dissecting the dynamic Q2 Q1 transcriptional landscape of early T helper cell differentiation into Th1, Th2, and Th1/2 hybrid cells

status: Public on Aug 05 2022

city: Bonn

first: Kevin

last: Thurley

address: Venusberg 1

department: Institute of Experimental Oncology

institute: University Hospital Bonn

summary: CD4+ T cell differentiation is a key element of the adaptive immune system driving appropriate immune responses by selective differentiation into specialized subsets such as Th1 and Th2 cells. Besides those canonical Th cell lineages, hybrid phenotypes such as Th1/2 cells have been identified in vivo, and their generation could be reproduced in vitro. While master transcription factors like T-bet and GATA-3 regulate and maintain differentiation into the canonical lineages, the transcriptional architecture of hybrid phenotypes is less well understood. In particular, it remains unclear whether a hybrid phenotype implies a mixture of the effects of several canonical lineages for each gene, or rather a bimodal behavior across genes. Th cell differentiation is a dynamic process in which the regulatory factors are modulated over time, but longitudinal studies of Th cell differentiation are sparse. Here, we present a dynamic transcriptome analysis following Th cell differentiation into Th1, Th2 and Th1/2 hybrid cells. We found that only a minority of ~20% of Th cell specific genes clearly shows mixed effects from both Th1 and Th2 cells on Th1/2 hybrid cells. While most genes follow either Th1 or Th2 cell gene expression, another fraction of ~20% of genes follows a Th1 and Th2 cell independent transcriptional program under control of the transcription factors STAT1 and STAT4. Overall, our results emphasize the key role of high-resolution longitudinal data for the characterization of cellular phenotypes.

overall_design: Time course microarray data for Th1, Th2 and hybrid Th12 differentiation, including Th0 control


title: Effect of Foxo1 deficiency in naive CD4 T cell activation in vitro

status: Public on Aug 02 2022

city: BAGNEUX

first: Bruno

last: Lucas

address: 5 rue Léon BERNARD

department: Immunology

institute: Institut Cochin, CNRS UMR8104, INSERM U1016

summary: Foxo1 deficiency promotes T-cell exhaustion.

overall_design: Naive CD4 T cells from peripheral lymph-nodes of mice deficient (C57BL/6 Foxo1TKO) or proficient (C57BL/6 Foxo1Ctrl) for Foxo1 expression in T cells were purified and 50 000 cells were cultured 4 days in the presence of an anti-CD3 antibody (145-2C11, 0.1 µg per ml) and 250 000 antigen presenting cells (splenocytes from C57BL/6 CD3eKO mice).

first: Aurélie

last: Durand


title: A tissue dissociation method optimized for ATAC-seq and CUT&RUN in Drosophila pupal tissues

status: Public on Aug 15 2022

city: Ann Arbor

first: Elizabeth

last: Fogarty

state: MI

address: 1105 N. University Ave

institute: University of Michigan

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

overall_design: Refer to individual Series


title: Gene expression dynamics of branching morphogenesis in pancreatic cancer organoids

city: Munich

first: Hans

middle: Carlo

last: Maurer

state: Bavaria

address: Ismaninger Str. 22

department: II. Medizinische Klinik

institute: Klinikum rechts der Isar

summary: The transcriptional dynamics occurring at the self-organizing glandular epithelial during branching morphogenesis are pivotal for deciphering various processes ranging from normal tissue growth to cancer formation.   For the past decade matrigel© has been widely used as extracellular matrix for the propagation of organoids, here we report that only in the presence of a higher than 70% collagen matrix symmetry breaking can be observed. Comparing the transcriptomic profile of collagen and matrigel grown-organoids we identified that matrigel organoids are more basal-like, have a higher EMT signature (GSEA) compared to the more classical collagen grown organoids.  In this study we used single primary murine pancreatic ductal adenocarcinoma cells (PDAC) cells embedded in floating collagen gels and adapted the media supplementation, thus allowing organoids to self-organize into highly complex branched structures, replicating the in vivo tumour architecture. During organoid development we identified four distinct morphogenetic phases, each characterized by a unique pattern of cell proliferation, invasion, matrix deformation and protein expression. In our search for novel molecular drivers of branching morphogenesis we compared the transcriptome of two distinct phases, an early development (day 7) vs a late mature time point (day 13). We compared these two distinct developmental time points in using PCA, GSEA and respective heat maps of major processes illustrating the overexpression of genes associated with: proliferation, ECM interaction, signalling by Rho GTPases and EMT in day-7 organoids and genes associated with ion channel transport at day-13 organoids.   An important aspect raised during our investigation was the effect of different genotypes (Ptf1aCre/+; KrasG12D/+, Pdx1Cre/+; KrasG12D/+; TP53fl/fl) on the branch formation of organoids. To this end we generated organoids derived from KC and KPC tumours, which interestingly gave rise to strikingly similar branching organoids. Although the morphology was not significantly altered the transcriptional profiling showed higher proliferation (Myc targets, E2F targets), EMT score for the KPC organoids.   We propose that the spatiotemporal synchronized processes of cell proliferation, matrix remodeling, contraction and ion channel flux are key-events of the different morphogenic phases and lead to the formation of these complex structures. Importantly, these dynamic processes are accompanied by strong transcriptional profile changes, with the organoids undergoing de-differentiation during branch elongation and later on activating an epithelial gene expression program upon maturation. Taken together, these results illustrate the ability of tumour cells to self-organize in multicellular complex structures and provide with a novel system to study branching morphogenesis and tumour biology in vitro.

overall_design: Bulk gene expression data from collagen and matrigel grown KC PDAC organoids. Early time points (day 7)  vs late time points (day 13) mature organoids & KC vs KCP branching PDAC organoids.

first: Aristeidis

last: Papargyriou

first: Carlo

first: Rupert

last: Öllinger

first: Roland

last: Rad

first: Maximilian

last: Reichert


title: Modeling human extraembryonic mesoderm cells using naive pluripotent stem cells [scRNA_seq_RACL_NACL]

status: Public on Aug 01 2022

city: Leuven

first: Vincent

last: Pasque

address: Herestraat 49 bus 804

department: Development and Regeneration

country: Belgium

institute: KU Leuven

summary: scRNAseq of day 6 RACL conversion and day 24 NACL conversion.

first: Thi

middle: X

last: Pham

first: Amitesh

last: Panda

first: Harunobu

last: Kagawa

first: Cankat

last: Ertekin

first: SanKit

last: To

first: Grigorios

last: Georgolopoulos

first: Sam

last: van Knippenberg

first: Ryan

last: Allsop

first: Alexandre

last: Bruneau

first: Jonathan

last: Chui

first: Lotte

last: Vanheer

first: Adrian

last: Janiszewski

first: Joel

last: Chappell

first: Michael

last: Oberhuemer

first: Raissa

last: Tchinda

first: Irene

last: Talon

first: Janet

last: Rossant

first: Frederic

last: Lluis

first: Laurent

last: David

first: Nicolas

last: Rivron

first: Bradley

middle: P

last: Balaton


title: Modeling human extraembryonic mesoderm cells using naive pluripotent stem cells [scRNA-seq]

first: Vincent

last: Pasque

summary: scRNAseq of day 30 of trophoblast conversion together with naïve and primed hPSCs. Cells were mixed using the following ratio (H9 primed: Sigma primed: H9 naive: Sigma naive: day 30 ASECRiAV conversion  = 1:1:1:1:2)

first: Thi

last: Pham

first: Amitesh

last: Panda

first: Harunobu

last: Kagawa

first: SanKit

last: To