title: Therapeutic targeting of BAP1/ASXL3 sub-complex in ASCL1-dependent small cell lung cancer

status: Public on Feb 23 2022

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) is an aggressive disease, with patients diagnosed with either early-stage, limited stage, or extensive stage of SCLC tumor progression. Discovering and targeting the functional biomarkers for SCLC will be crucial in understanding the molecular basis underlying SCLC tumorigenesis to better assist in improving clinical treatment. Emerging studies have demonstrated that dysregulations in BAP1 histone H2A deubiquitinase complex are collectively associated with pathogenesis in human SCLC. Here, we investigated the function of the oncogenic BAP1/ASXL3/BRD4 epigenetic axis in SCLC by developing a next-generation BAP1 inhibitor, iBAP-II, and focusing on the epigenetic balance established between BAP1 and non-canonical PRC1 complexes in regulating SCLC-specific transcriptional programming. We further demonstrated that pharmacologic inhibition of BAP1’s catalytic activity dramatically disrupted BAP1/ASXL3/BRD4 epigenetic axis by inducing protein degradation of the ASXL3 scaffold protein, which bridges BRD4 and BAP1 at active enhancers. Furthermore, treatment of iBAP-II dramatically inhibits SCLC cell viability and tumor growth in vivo via repression of neuroendocrine lineage-specific ASCL1/MYCL/E2F signaling in cells.

overall_design: This study aims to provide mechanistic insight into the oncogenic function of BAP1 in SCLC and highlighted the potential of targeting BAP1’s activity as a novel SCLC therapeutic.

first: Zibo

last: Zhao


title: Agelena koreana whole body and venom gland transcriptome

city: Goyang-si

first: Jungsuk

last: Sung

state: Gyeonggi-do

address: 32, Dongguk-ro, Ilsandong-gu

country: South Korea

institute: Life science

type: Expression profiling by high throughput sequencing

summary: Agelena koreana is indigenous spider in South Korea that lives on piles of trees building webs. RNA-sequencing was performed for venom gland tissue and whole body except venom gland.

overall_design: Agelena koreana mRNA profiles of venom gland and whole body without venom gland

first: Jung-Suk

first: Min-Kyoung

last: Shin

first: Byungjo

last: Lee

first: Seung-Tae

last: Kim

first: Jung-Sun

last: Yoo


title: Selection of RNA aptamers against human islets by SELEX and toggle SELEX

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

summary: Type 1 Diabetes is still an incurable disease characterized by autoimmune destruction of insulin-producing beta cells within the islet of Langerhans in the pancreas. Currently, there are no methods to monitor beta-cell mass in humans or deliver therapeutics specifically to beta cells. Here we performed Cluster Systematic Evolution of Ligands by Exponential Enrichment (SELEX) experiments and toggle SELEX experiments to identify RNA aptamers specific for human islets.  In the cluster SELEX, we started from a random library of RNA nucleotides composed of a 40 nucleotide long variable region flanked by two constant regions. We performed eight selection cycles using hand-picked islets and islet-depleted acinar tissue from 4 cadaveric human donors as positive and negative selectors. In the toggle SELEX, we conducted eight cycles of selection using islets and acinar tissue from mice, followed by two cycles of selection using human tissues. The polyclonal libraries from the two selection strategies showed a convergent evolution of ligands and increased specificity for human islets.

overall_design: 8 cycles of Cluster-SELEX were perfomed using human islets and acinar tissues as positive and negative selectors.  In the Toggle SELEX, we performed 8 cycles of selection using islets and acinar tissue from mice followed by two cycles of selection using islets and acinar tissue from human cadaveric donors.

first: Jimmy

last: Caroli

first: Paolo

last: Serafini


title: A customized synthetic gene circuit selectively engages an immune-related transcriptional program in p53-negative LLC cells

city: Nanjing

first: Wang

last: Yafeng

state: Jiangsu

address: 12 Xuefu-Road, Pukou District

country: China

institute: Nanjing University

summary: Purpose: Cancer immunotherapy has shown promising results in both mouse models and clinical trials. However, to specifically reprogram the immune microenvironment of advanced tumor lesions remains a huge challenge. Therefore, we assembled a synthetic gene circuit aimed at specifically targeting p53-negative LLC cells, but not their p53+ derivatives, for immune activation. Methods: Firstly, we established an LLC-derived knock-in line (p53+), where the WT p53 coding region was re-introduced into the endogenous locus to rescue the bi-allelic point mutations (a nonsense mutation at E32, and a R334P mutation) in the parental LLC cells. Next, both the parental LLC cells and p53+ LLC cells were introduced with the AND-NOT gene circuits which contains the tumor-specific survivin promoter-driven dCas9 (Psuv-dCas9), U6 promoter-driven Ifng-activating sgRNA (or control sgRNA), and p53-responsive promoter PM2-driven AcrIIA4max. 48 hours after transfection, the total RNA was isolated and subjected to RNAseq services. Results: The p53+ LLC cell showed differences of hundreds of genes compared with the parental LLC cells. This group of genes contain a number of classical p53 targets. Notably, the logic circuit drove selective induction of a different gene set in the parental, but not the p53+ cells. Importantly, the vast majority of the circuit-induced genes are known downstream targets of IFN, confirming the specificity of a CRISPRa-driven transcriptional rewiring. Conclusion: Overall, this dataset provides evidence that the AND-NOT gene circuit selectively targets p53-negative LLC cells, but not their p53+ derivatives, and subsequently programs a highly specific immune-rewiring output.

overall_design: mRNA profiles of p53-negative LLC cells and their p53+ derivatives which introduced with the customized synthetic gene circuit

first: Yafeng

last: Wang

first: Jianghuai

last: Liu


title: Transcriptomic Analysis of Liver Indicates Novel Vaccine to Porcine Reproductive and Respiratory Virus Promotes Homeostasis in T-Cell and Inflammatory Immune Responses Compared to Commercial Vaccine in Pigs

city: Beltsville

first: Damarius

middle: S

last: FLEMING

state: Maryland

address: 10300 Baltimore Ave Bldg 1040, Barc East

department: ARS

country: USA

institute: USDA

summary: One of the largest impediments for commercial swine production is the presence of Porcine Reproductive and Respiratory Syndrome virus (PRRSV), a devastating RNA viral infection that is responsible for over $1 billion in loss in the U.S. annually. The challenge with combating PRRSV is a combination of the effect of an extraordinary rate of mutation, the ability to infect macrophages, and subversion of host immune response through a series of actions leading to both immunomodulation and immune evasion. Currently there are a handful of commercial vaccines on the market that have been shown to be effective against homologous infections, but struggle against heterologous or mixed strain infections. However, vaccination is the current best strategy for combating PRRSV, making research into new vaccine technology key. To address these issues with PRRSV and host antiviral functions a novel modified-live vaccine (MLV) able to stimulate known anti-viral interferons was created and examined for its ability to potentiate effective immunity and better protection. Here, we examine gene expression in the liver of pigs vaccinated with our novel vaccine, given the liver’s large role in anti-viral responses and vaccine metabolism. Our study indicated that pigs administered the novel vaccine experience homeostatic gene expression consistent with less inflammation and T-cell depletion risk than pigs administered the commercial vaccine.

overall_design: Liver 3' mRNA single-end profiles of novel vaccine, commercial vaccine, and sham-vaccinated PRRSV challenged pigs at 14 days post infection

last: Fleming

first: Laura

middle: C

last: Miller

first: Jiuyi

last: Li

first: Albert

last: Van Geelen

first: Yongming

last: Sang


title: Targeted gene expression profiling of human myeloid cells from blood and lung compartments of patients with Tuberculosis and other lung diseases

status: Public on Feb 22 2022

city: Parow

first: Gian

last: van der Spuy

address: Francie van Zijl Dr

department: Biomedical Sciences

country: South Africa

institute: Stellenbosch University

summary:
This was a pilot study aimed at uncovering the role of myeloid-derived suppressor cells (myeloid-derived  suppressor cell) in patients with Tuberculosis and differences between cells found in peripheral blood and in the lung.
Fluidigm™ RT-PCR technology was used to quantify expression levels of 43 genes in monocytecytes and myeloid-derived  suppressor cell from peripheral blood and monocytecytes and alveolar macrophages from bronchoalveolar lavage fluid taken from patients with Tuberculosis or other lung diseases.

overall_design: Gene expressions levels were compared between lung and blood derived cells within and between TB patients and healthy controls

first: L

middle: A

last: Kotze

first: G

middle: D


title: Mild SARS-CoV-2 infection in rhesus macaques is associated with viral control prior to antigen-specific T cell responses in tissues

city: Bethesda

first: Sivaranjani

last: Namasivayam

address: 33 North Drive

department: NIAID

institute: NIH

summary: SARS-CoV-2 primarily replicates in mucosal sites, and more information is needed about immune responses in infected tissues. We used rhesus macaques to model protective primary immune responses in tissues during mild COVID-19. Viral RNA levels were highest on days 1-2 post-infection and fell precipitously thereafter. 18F-fluorodeoxyglucose (FDG)-avid lung abnormalities and interferon (IFN)-activated myeloid cells in the bronchoalveolar lavage (BAL) were found on days ∼3-4. Virus-specific effector CD8 and CD4 T cells were detectable in the BAL and lung tissue on days ∼7-10, after viral RNA, lung inflammation, and IFN-activated myeloid cells had declined. Notably, SARS-CoV-2-specific T cells were not detectable in the nasal turbinates, salivary glands, and tonsils on day 10 post-infection. Thus, SARS-CoV-2 replication wanes in the lungs prior to T cell responses, and in the nasal and oral mucosa despite the apparent lack of Ag-specific T cells, suggesting that innate immunity efficiently restricts viral replication during mild COVID-19.

overall_design: Profiling of bronchoalveolar lavage fluid and PBMCs from SARS-CoV-2 infected rhesus macaques via single-cell sequencing

first: Christine

middle: E

last: Nelson

first: Taylor

middle: W

last: Foreman

first: Keith

last: Kauffman

first: Shunsuke

last: Sakai

first: Danielle

last: Dorosky

first: Nickiana

last: Lora

first: Kelsie

last: Brooks

first: E

middle: L

last: Potter

first: Mario

last: Roederer

first: Alan

last: Sher

first: Daniela

last: Weiskopf

first: Alessandro

last: Sette

first: Emmie

last: de Wit

first: Heather

last: Hickman

first: Jason

middle: M

last: Brenchley

last: Via

first: Daniel

last: Barber


title: Genome-wide analysis of osteosarcoma for comparison to healthy bone tissue

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: Analysis of common pediatric osteosarcoma cell lines SaOS2, U2OS and 143B and two patient derived xenograft samples in comparison of osteoblast cell line hFOB1.19.

overall_design:
Pediatric osteosarcomas (OS) exhibit extensive genomic instability that has complicated the identification of new targeted therapies. Here we report that the vast majority of 108 patient tumor samples and patient-derived xenografts (PDXs), which display an unusually dilated endoplasmic reticulum (ER) haver reduced expression of four COPII vesicle components that trigger aberrant accumulation of procollagen-I protein within the ER. OS cell lines were used as an experimentally tractable system.
Total RNA obtained from cells and tumor tissue of PDXs

first: Linda

last: Hendershot

first: Rachael

middle: K

last: Wood


title: Human Fibroblast-Like Synoviocytes Derived Extracellular Vesicles miRNA sequencing

status: Public on Feb 21 2022

city: Guangzhou

first: Yixiong

last: Chen

address: No. 600 Tianhe Road, Tianhe District

institute: The Third Affiliated Hospital of Sun Yat-sen University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose:The goal of this study is to compare the miRNA expressions in LPS stimulated RA FLSs derived EVs between trauma FLSs derived EVs.
Methods:Total RNA of EVs was extracted with trizol LS (Invitrogen, USA), and quantified with Nanodrop. Agarose electrophoresis was used for quality inspection, and library was constructed after passing the quality inspection. Then, Agilent 2100 Bioanalyzer was used to determine the quality of the library. RNA was denatured with 0.1 M NaOH and sequenced on Illumina NextSeq500.
Results:In total of 24 miRNAs were changed in the 650 scanned miRNAs in LPS stimulated RA FLSs derived EVs, compared to Trauma FLSs derived EVs, with 13 up-regulated miRNAs and 11 down-regulated miRNAs(P<0.05; Fold change>=1.5).Next, we analyzed the possible biological functions of the expression changed miRNAs using GO analysis. Of note, the results showed that expression altered miRNAs may principally correlate with blood vessel morphogenesis, cardiovascular system development, vasculature development and tube development.
Conclusions:RNA parts of LPS-RA FLSs derived EVs may play key role in stimulating angiogenesis of ECs.

overall_design: Examination of the different microRNA in 2 FLSs  derived extracellular vesicles.

first: Junlong

last: Dang

first: Manli

last: Wang


title: Effect of nitrate on the transcriptome of the primary root tip in Medicago truncatula

status: Public on Feb 20 2022

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

country: France

institute: INRA

summary: Comparison of R108, a wild and nitrate sensitive genotype, with npf6.8-3, a mutant and insensitive line, deficient in the nitrate transceptor MtNPF6.8 (Pellizzaro et al, 2014 Plant Physiol).

overall_design:
Comparison between treated and untreated plants for the mutant and the wild type
NOTE:
The full original/unedited raw data files from multi-chip blades (slides) which contain complete information for various hybridizations are included as Series supplementary files.
Experiments were technically as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but processed the results as though they are single channel (Cy3 and Cy5 signals are calculated, instead of Cy3/Cy5 ratios). Each raw data file generated from each Cy3 and Cy5-labeled pair is linked to the corresponding *_Cy5 sample records.

first: Lili

last: Zang

first: Marie

last: Morère-Le Paven

first: Thibault

last: Clochard

first: Françoise

last: Montrichard

first: Sandrine

last: Balzergue

first: Muriel

last: Bahut


title: Affymetrix SNP array data for analysis of peanut agronomic traits

city: Jinan

first: rz

last: Tian

state: Shandong

address: 202 North Industrial Road

institute: SAAS

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

summary:
Peanut is one of the most important cash crops with high quality oil, high protein content, and many other nutritional elements, and grown globally. Cultivated peanut (Arachis hypogaea L.) is allotetraploid with a narrow genetic base, and its genetics and molecular mechanisms controlling the agronomic traits are poorly understood.
The array SNP data was used for revaling of key candidate loci and genes associated with important agronomic traits in peanut

overall_design: Total of 333 samples

first: Ruizheng

first: Chuanzhi

last: Zhao


title: RNA aptamers specific for transmembrane p24 trafficking protein 6 and Clusterin for the targeted delivery of imaging reagents and RNA therapeutic to human β cells

first: Silvio

last: Bicciato

summary: The ability to detect and target β cells in vivo can drastically refine the way diabetes is studied and treated. By an unsupervised Systematic evolution of ligands by exponential enrichment (SELEX) we identified two RNA aptamers  that specifically recognize mouse and human β cells in vitro and in vivo.  Here we took advantage of commercially available high density protein arrays to identify putative target of the two islet specific aptamers. Briefly, 5' biotynilated RNA aptamer 1-717 and m12-3773 were chemically produced , complexed with Alexafluor 647-streptavidin and used as probe on the HuProt™ v2.0 19K protein array. Putative binders were further confirmed by cold target inhibition assays, silencing experiments, and surface plasmon resonance.

overall_design: Commercially available human protein arrays were blocked with yeast RNA-enriched blocking buffer and stained with astreptavidin Alexafluor 647 conjugated with 5' biotinylated aptamers. After several washes, images were acquired with a microarray scanner and the fluorescence signal was quantified. Data from 2 different replica (for a total of 4 independent spots per each protein) were background (average fluorescence around the protein spots) corrected, quantile normalized and the differential binding of the aptamer 1-717 and m12-3773 to the spotted protein evaluated.

first: Dimitri

last: Van Simaeys

first: Adriana

last: De la Fuente

first: Alessia

last: Zoso

first: Serena

last: Zilio

first: Andrea

last: Grilli

first: Jo'neil

last: Williams

first: Jimmy

last: Caroli

first: Paolo

last: Serafini


title: Cohesin protein STAG2 regulates expression of IRF9 and interferon signaling in melanoma via  enhancer loop reprogramming [HiChIP]

city: Bad Nauheim

first: Lei

last: Gu

state: MASSACHUSETTS

address: parkstreet 1

country: Germany

institute: Max Planck Institute for heart and lung research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The cohesin complex participates in the organization of 3D genome through generating and maintaining DNA loops. Stromal antigen 2 (STAG2), a core subunit of the cohesin complex, is frequently mutated in various cancers. However, the impact of STAG2 inactivation on 3D genome organization and subsequent gene expression in cancer remain poorly understood. Here we show that depletion of STAG2 in melanoma cells leads to expansion of topologically associating domains (TADs) and enhances the formation of H3K27Ac-associated DNA loops at sites where binding of STAG2 is switched to its paralog STAG1. We further identify Interferon Regulatory Factor 9 (IRF9) as a major direct target of STAG2 in melanoma cells via integrated RNA-Seq, STAG2 ChIP-Seq and H3K27Ac HiChIP analyses. We demonstrate that loss of STAG2 activates IRF9 through modulating the 3D genome organization, which in turn enhances type I interferon signaling and increases the expression of PD-L1. Our findings not only establish a previously unknown role of the STAG2 to STAG1 switch in 3D genome organization, but also reveal a functional link between STAG2 and interferon signaling in cancer cells, which may contribute to malignant phenotype in STAG2-mutant cancer.

overall_design: We investigated how STAG2 KD affact 3D genome structure and its related functional consequnece in malignant phenotype in STAG2-mutant melanomas.

first: Bin

last: Zheng

first: Zhaowei

last: Chu


title: Cohesin protein STAG2 regulates expression of IRF9 and interferon signaling in melanoma via enhancer loop reprogramming.

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

overall_design: Refer to individual Series


title: Cohesin protein STAG2 regulates expression of IRF9 and interferon signaling in melanoma via enhancer loop reprogramming [Hi-C]


title: Cohesin protein STAG2 regulates expression of IRF9 and interferon signaling in melanoma via  enhancer loop reprogramming [ChIP-seq]


title: Cohesin protein STAG2 regulates expression of IRF9 and interferon signaling in melanoma via  enhancer loop reprogramming [RNA-seq]


title: RNAseq analysis of genes differentially expressed in H1299 cells with anti-circadian rhythm dysfunctional treatment

status: Public on Feb 19 2022

city: Wuhan

first: Yixian

last: Fan

state: Hubei

address: Hangkong Road 13, Wuhan

institute: Huazhong University of Science and Technology

summary: We examined the biological difference between H1299 cells with the treatments targeting circadian rhythm  in order to better understand circadian rhythm disruption as a feature of cancer. To this end, we  knocked down CLOCK using siRNA (siCLOCK) or melatonin pre-treatment and  assessed the gene expression pattern by RNA-Seq.

overall_design: Nine samples obtained from H1299 cells including serum free medium (as control), siCLOCK and  0.1mM melatonin treatment group were analyzed. Three independent samples were analyzed for each group.

last: He

first: Fahu

last: Yuan


title: RNA-seq analysis of Wild Type and Mll5-/- Retinal Transcriptomes

city: Singapore

first: Xiaoming

last: Zhang

address: 10 Medical Drive

country: Singapore

institute: National University of Singapore

summary: Analysis of differential gene expression in wild type vs Mll5-/- Retinal Transcriptomes. The aim is to identify potential genes that are regulated by MLL5.

overall_design: Total RNA obtained from 18-day old wild type (WT) and Mll5-/- mice retinas are used for RNA-seq

first: Bo-Wen

first: Lue

last: Xiang

first: Hui

last: Wu

first: SUPIT

last: Alexander

first: Peipei

last: Zhou

first: Melvin

middle: Z

last: Dai

first: Xiaoyun

last: Wang

first: Wenjun

last: Xiong

first: Yan

first: Zi-Bing

last: Jin

first: Lih-Wen

last: Deng


title: single cell RNA sequencing of xenograft prostate cancer model under different treatment

status: Public on Feb 17 2022

city: Bellinzona

first: Andrea

last: Alimonti

address: Via vela 6

department: Molecular Oncology

country: Switzerland

institute: Institute of oncology research

summary: We performed single cell RNA sequencing of xenograft prostate cancer models to analyse effect of different drugs.

overall_design: Examination of epithelium and senescence of xenograft prostate cancer tumour to analyse senolytic therapy of different drugs.

first: Martina

last: Troiani


title: Transcription Factor Protein Interactomes Reveal Genetic Determinants in Heart Disease

status: Public on Feb 18 2022

city: San Francisco

first: Deepak

last: Srivastava

state: CA

address: 1650 Owens St

institute: J David Gladstone Institutes

summary: Congenital Heart Disease (CHD) is present in 1% of live births, and while large-scale genetic studies have uncovered genes associated with CHDs, identifying causal mutations remains a challenge. We hypothesized that genetic determinants for CHDs could be found in the protein interactomes of GATA4 and TBX5, two cardiac transcription factors (TFs) that cause CHDs. Defining their interactomes in human cardiac progenitors via affinity purification-mass spectrometry and integrating the results with genetic data from the Pediatric Cardiac Genomic Consortium (PCGC) revealed an enrichment of de novo variants among proteins that interact with GATA4 or TBX5. A consolidative score designed to prioritize TF interactome members based on distinctive variant, gene, and proband features identified numerous likely CHD-causing genes, including the epigenetic reader GLYR1. GLYR1 and GATA4 widely co-occupied cardiac developmental genes, resulting in co-activation, and the GLYR1 variant associated with CHD disrupted interaction with GATA4. This integrative proteomic and genetic approach provides a framework for prioritizing and interrogating the contribution of genetic variants in CHD and can be extended to other genetic diseases.

overall_design:
3 replicates for each condition were ran for Bulk RNAseq after siRNA knockdown of GATA4 or siControl in hiPSC-derived cardiac progenitors (3x siRNA Control and 3 x siRNA GATA4).
2 replicates for each sample were ran for Bulk RNAseq after siRNA knockdown of GLYR1 or siControl in hiPSC-derived cardiac progenitors (2x siRNA Control and 2x siRNA GLYR1 ).
4-5 replicates for each sample were ran for Bulk RNAseq of day6 hiPSC derived cardiac progenitors (CPs) (5x WT CPs, 4x GATA4 knockout CPs and 5x TBX5 knockout CPs).
3-1 replicates for each sample were ran for ChIPseq on day6 WT hiPSC derived cardiac progenitors (CPs),  (3x GLYR1 WT CPs, 2x H3K36me3 WT CPs, 2x GATA4 WT CPs, 2x TBX5 WT CPs, 2x NKX2-5 WT CPs, 1x MEIS1 WT CPs, 1x ISL1 WT CPs).
2 replicates for each sample were ran for Bulk RNAseq of day0 WT hiPSC (2x GLYR1 WT hiPSC and 2x H3K36me3 WT hiPSCs, ).
1-3 replicate single-cell RNA-seq samples at 3 time-points (hiPSC, Day 6 and Day 18 into cardiac differentiation) under two genotypes (WT and P496L GLYR1 mutant) were processed across 3 batches (see column Y). For the analyses to infer differential binding between the two genotypes (WT and P496L GLYR1 mutant), 3 replicates for each genotype  were used for GLYR1 ChIPseq in hiPSC-derived cardiac progenitors processed in batch 2 (see column Y). 5 replicates under each of the hiPSC and cardiac progenitor stages of GLYR1 ChIPseq were used to infer differential GLYR1 binding between the two stages.

first: Barbara

last: Gonzalez-Teran


title: A transcriptomic study reveals that fish vibriosis due to the zoonotic pathogen Vibrio vulnificus is an acute inflammatory disease.

city: Burjassot

first: Carmen

last: Amaro

state: Valencia

address: Dr. Moliner, 50

department: Microbiology and Ecology

country: Spain

institute: University of Valencia

summary: Vibrio vulnificus is a marine zoonotic pathogen associated with fish farms that is considered a biomarker of climate change. Zoonotic strains trigger a rapid death of their susceptible hosts (fish or humans) by septicemia that has been linked to a cytokine storm in mice.  A toxin called RtxA1 produced by the bacteria might play an important role in bacterial invasion and subsequent death by septic shock since animals infected with a mutant deficient in rtxA1 suffer from septicemia but do not die. The aim of this study was to globally analyze the early eel immune response in blood against V. vulnificus, as well as the role of the RtxA1 toxin on this interaction.

overall_design: We used the eel immersion infection model and then analyzed the transcriptome in RBCs, white BCs, and whole blood using an eel-specific microarray platform.

first: Carla

last: Hernández-Cabanyero

first: Eva

last: Sanjuán

first: Felipe

last: Reyes-López

last: Vallejos-Vidal

first: Lluis

last: Tort


title: RNA-seq approaches to understand the biological effects of sialic acid on murine synovial fibroblasts

city: Glasgow

first: Miguel

last: Pineda

address: 120 university avenue

country: United Kingdom

institute: University of Glasgow

summary:
The aim of this study was to explore the role sialic acid in synovial fibroblasts using NGS-derived transcriptome analysis (RNA-seq).
Methods: Synovial fibroblasts were extracted from the synovium of healthy mice and expanded ex vivo. RNA was extracted from sialidase buffer (NT)  and Clostridium perfringens Neuraminidase (CP) treated synovial fibroblast.
Methods:  Whole Transcriptome Profiling  was generated by deep sequencing, in triplicate, using Illumina NextSeq™ 500 platform.  Libraries were prepared using polyA selection (TruSeq stranded mRNA kit).
Methods: The sequence reads that passed quality filters were  aligned to mouse reference genome (GRCM38) using Hisat2 version 2.1.0.  we mapped about 30 million sequence reads per sample (75 bp, paired-end)
Methods: Featurecounts version 1.4.6 was used to quantify reads counts. Data quality control, non-expressed gene filtering, median ratio normalization (MRN) implemented in DESeq2  package and identification of differentially expressed (DE) genes were done  using the R bioconductor project DEbrowser.
Results: we detected differentially expressed genes in CP treated synovial fibroblast compared to NT synovial fibroblast, which pass the threshold of >2 fold, adjp <0.01. DE genes reflect increased cellular inflammatory response after CP treatment
Conclusions: These findings underline the ability of sialic acid to modulate homeostatic and inflammatory responses in non-immune synovial fibroblasts, suggesting that sialylation plays a key role in perpetuating local inflammation in the arthritic joint.

overall_design: Our results show the transcriptome profile of NT and CP treated synovial fibroblast expanded ex vivo


title: Ion AmpliSeq mouse transcriptome profiles in non-involved mammary tissue from Brca1f/f Trp53+/- or HMMR Tg/Tg Brca1f/f Trp53+/- mice

city: Barcelona

first: Miguel Angel

last: Pujana

address: Gran Via 199

institute: Institut Catala d'Oncologia IDIBELL

summary: Comprehensive transcriptome profiling of mouse contralateral premalignant mammary glands to identify altered pathways to promote mammary tumors in the context of HMMR overexpression

overall_design: RNA sequencing of bulk mouse mammary tissues.

first: Zhengcheng

last: He

first: Chris

last: Maxwell


title: single cell RNA sequencing of murine prostate cancer models

summary: We performed single cell RNA sequencing of Epcam+ sorted cells from murine prostate cancer models to characterize the epithelial compartment of the tumors.

overall_design: Examination of epithelium from 2 different prostate cancer genetic enrineering mouse models


title: Transcriptome profiles of mammary tumors from Brca1f/f Trp53+/- or HMMR Tg/Tg Brca1f/f Trp53+/- mice

summary: Comprehensive transcriptome profiling of mouse mammary tumors to identify altered genes and pathways that promote Brca1-mutant carcinogenesis in the context of HMMR overexpression.

overall_design: RNA sequencing of bulk mouse mammary tumors.

first: Roderic

last: Espin

first: Miquel


title: Nuclear Lamina binds the EBV genome during latency and regulates viral gene expression [RNA-seq]

status: Public on Mar 11 2022

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Approximately 90% of the world population is infected with EBV and carries the virus in a silent, asymptomatic state for life. In immunocompromised individuals, EBV infection can cause B-cell transformation and malignancies.  One approach to control EBV infectivity is by changing the expression of viral genes.   We are interested in how epigenetics contributes to regulating the gene expression patterns adopted by EBV during latency.   The host’s hijacking is a well know strategy adopted by viruses to modify the epigenome, the trascriptome and the proteome of the host with the aim to survive and remain silent in the host.   We observed that in B cells, EBV infection mimics antigen-mediated activation, resulting in the induction of specific proteins named Lamin A/C.   Lamins have multiple and central roles they: provide nuclear physical support; anchor the heterochromatin to the nuclear periphery and seem to play a role in several nuclear functions requing the chromatin structure rearrangement.  The interaction with lamins has already been study in the context of EBV lytic reactivation, but their role in the control of the EBV latency states and as epigenetic regulators of different EBV genes expression profiles as not been investigated.  The binding of the Lamin AC to important regulatory regions of EBV genome was assessed through ChIP-Seq and, and gene expression (RNA-Seq) profiles, were evaluated in wild type and Lamin AC KO cell lines.   Differences in protein and RNA expressions in B cells activated by using both EBV and a simulation of the immune response were analyzed.  Our data suggest two main conclusion: lamins might contribute to the epigenetic control of EBV genes expression during latency changing the interaction of the host structural proteins with key regulatory regions in the viral genome and a possible mechanism with who EBV modifies the nucleus and hijacks cellular mechanisms.

sample_organism:
Homo sapiens
human gammaherpesvirus 4

platform_organism:
Homo sapiens
human gammaherpesvirus 4

overall_design: RNA-seq experiment in LAMIN A/C WT and KO cells under control and G9a inhibitor treatment

first: Lisa

last: Caruso

first: Italo

last: Tempera


title: Single-cell Multiomics Reveals Clonal T-cell Expansions and Exhaustion in Blastic Plasmacytoid Dendritic Cell Neoplasm

status: Public on Feb 16 2022

city: Cincinnati

first: Erica

last: DePasquale

state: OH

address: 3333 Burnet Ave.

department: Gastroenterology

institute: Cincinnati Children's Hospital

summary: The immune system represents a major barrier to cancer progression, driving the evolution of immunoregulatory interactions between malignant cells and T-cells in the tumor environment. Blastic plasmacytoid dendritic cell neoplasms (BPDCN), a rare acute leukemia with plasmacytoid dendritic cell (pDC) differentiation, provides a unique opportunity to study these interactions. pDCs are key producers of interferon alpha (IFNA) that play an important role in T-cell activation at the interface between the innate and adaptive immune system. To assess how uncontrolled proliferation of malignant BPDCN cells affects the tumor environment, we catalog immune cell heterogeneity in the bone marrow of five healthy controls and five BPDCN patients by analyzing 52,803 single-cell transcriptomes, including 18,779 T-cells. We test computational techniques for robust cell type classification and find that T-cells in BPDCN patients consistently upregulate interferon alpha (IFNA) response and downregulate tumor necrosis factor alpha (TNFA) pathways. Integrating transcriptional data with T-cell receptor sequencing via shared barcodes reveals significant T-cell exhaustion in BPDCN that is positively correlated with T-cell clonotype expansion. Our results highlight new mechanisms of T-cell exhaustion in BPDCN and demonstrate the value of single-cell multiomics to understand immune evasion in the tumor environment. These findings improve our understanding of the development and response to this disease and the mechanisms by which BPDCN cells evade immune destruction.

overall_design: Paired Single-cell RNA sequencing and T-cell receptor sequencing on 5 BPDCN bone marrow samples and 5 healthy controls

first: Daniel

last: Ssozi

first: Marina

last: Ainciburu

first: Jonathan

last: Good

first: Jenny

last: Noel

first: Martin

last: Villanueva

first: Charles

middle: P

last: Couturier

first: Alex

last: Shalek

first: Sary

middle: F

last: Aranki

first: Hari

middle: R

last: Mallidi

first: Gabriel

last: Griffin

first: Andrew

last: Lane

first: Peter

last: van Galen


title: Single-cell landscapes of primary glioblastomas and matched organoids and cell lines reveal variable retention of inter- and intra-tumor heterogeneity [scRNA-seq]

city: Vancouver

first: Marco

last: Marra

state: BC

address: 675 W 10th Ave, 7th Floor

country: Canada

institute: Canada's Michael Smith Genome Sciences Centre

summary: Glioblastomas (GBMs) are aggressive primary malignant brain tumors characterized by extensive levels of inter- and intra-tumor genetic and phenotypic heterogeneity. Patient-derived organoids (PDOs) have recently emerged as useful models to study such heterogeneity. Here, we present bulk exome as well as single-cell genome and transcriptome profiles of primary IDH wild type GBMs from ten patients, including two recurrent tumors, as well as PDOs and brain tumor-initiating cell (BTIC) lines derived from these patients. We find that PDOs are genetically similar to and variably retain gene expression characteristics of their parent tumors. At the phenotypic level, PDOs appear to exhibit similar levels of transcriptional heterogeneity as their parent tumors, whereas BTIC lines tend to be enriched for cells in a more uniform transcriptional state. The datasets introduced here will provide a valuable resource to help guide experiments using GBM-derived organoids, especially in the context of studying cellular heterogeneity.

overall_design:
Single-cell RNA-seq profiles of primary glioblastoma samples and organoids and neurosphere cell lines derived from them
***Raw data files will be deposited to EGA, since they are derived from human samples and need controlled access***

first: Veronique

middle: G

last: LeBlanc

first: Diane

last: Trinh

first: Shaghayegh

last: Aslanpour

first: Martha

last: Hughes

first: Dorothea

last: Livingstone

first: Dan

last: Jin

first: Bo Young

last: Ahn

first: Michael

last: Blough

first: J

last: Cairncross

first: Jennifer

last: Chan

first: John

last: Kelly


title: CFIm-mediated alternative polyadenylation remodels cellular signaling and miRNA biogenesis

city: Basel

first: Mihaela

last: Zavolan

state: BS

address: Klingelbergstrasse 50-70

department: Biozentrum

institute: University of Basel

summary: The mammalian cleavage factor I (CFIm) has been implicated in alternative polyadenylation (APA) in a broad range of contexts, from cancers to learning deficits and parasite infections. To determine how the CFIm expression levels are translated into these diverse phenotypes, we carried out a multi-omics analysis of cell lines in which the CFIm25 (NUDT21) or CFIm68 (CPSF6) subunits were either repressed by siRNA-mediated knockdown or over-expressed from stably integrated constructs. We established that more than 800 genes undergo coherent APA in response to changes in CFIm levels, and they cluster in distinct functional classes related to protein metabolism. The activity of the ERK pathway traces the CFIm concentration, and explains some of the fluctuations in cell growth and metabolism that are observed upon CFIm perturbations. Furthermore, multiple transcripts encoding proteins from the miRNA pathway are targets of CFIm-dependent APA. This leads to an increased biogenesis and repressive activity of miRNAs at the same time as some 3’ UTRs become shorter and presumably less sensitive to miRNA-mediated repression. Our study provides a first systematic assessment of a reference set of core APA targets, that respond to changes in CFIm protein subunit levels (CFIm25/CFIm68), and the elicited signalling pathways downstream of CFIm, to improve our understanding of the key role of CFIm in integrating RNA processing with other cellular activities.

overall_design: mRNA profiles of control, CFIm25/68 over-expression and siRNA treated CFIm25/68 knock-down HEK 293 cell lines were generated by next-generation sequencing.

first: Souvik

last: Ghosh

first: Meric

last: Ataman

first: Maciej

last: Bak

first: Anastasiya

last: Börsch

first: Alexander

last: Schmidt

first: Katarzyna

last: Buczak

first: Beatrice

last: Dimitriades

first: Christina

last: Herrmann

last: Kanitz


title: Basal-like cell-conditioned medium exerts anti-fibrotic effects in vitro and in vivo

first: DBM Bioinformatics

last: Core Facility

address: Hebelstrasse 20

department: Departement of Biomedicine

summary: We performed a single-cell transcriptome analysis of basal-like cells cultured from peripheral lung tissue of patients with idiopathic pulmonary fibrosis (IPF).

overall_design:
Single-cell suspensions were generated from basal-like cells grown from cultured peripheral lung tissue biopsies from 3 IPF patients and were loaded on separate wells of a 10X Genomics Chromium Single Cell Controller.

***Please note that raw data are not available due to patient privacy concerns.

first: Petra

last: Khan

first: Katrin

last: Hostettler

first: Julien

last: Roux


title: A GRAS family transcription factor negatively regulates cell division and positively affects cell size through SIM/SMR transcription

status: Public on Feb 15 2022

city: Paris

first: Jing

last: An

address: 630 Rue Noetzlin

institute: Universite Paris Saclay

summary:
Purpose: To elucidate the role of E1M and SNOS1 (transcription factors) during the process of G2/M phases of cell cycle.
Methods: We integrated ChIP-seq, Mnase-seq and ATACseq
Results:   It showed that E1M associates with AP2-type transcription factor and E1M has an important role for determing final cell size and organ functions.

overall_design: Analysis  of E1M and  SNOS1 target genes

first: Ying

last: Huang

first: Masaki

last: Ito

first: Moussa

last: Benhamed


title: Single-cell landscapes of primary glioblastomas and matched organoids and cell lines reveal variable retention of inter- and intra-tumor heterogeneity [scWGS]

first: Marco

last: Marra

overall_design:
Single-cell whole-genome profiles of primary glioblastoma samples and organoids derived from them
***Raw data files will be deposited to EGA, since they are derived from human samples and need controlled access***

first: Veronique

last: LeBlanc

first: Diane

last: Trinh

first: Shaghayegh

last: Aslanpour

first: Martha

last: Hughes

first: Dorothea

last: Livingstone

first: Dan

last: Jin

first: Bo Young

last: Ahn

first: Michael

last: Blough

first: J

last: Cairncross

first: Jennifer

last: Chan

first: John

last: Kelly


title: Single-cell landscapes of primary glioblastomas and matched organoids and cell lines reveal variable retention of inter- and intra-tumor heterogeneity [multi-generation scRNA-seq]

overall_design:
Single-cell RNA-seq profiles of first-, second-, and third-generation patient-derived glioblastoma explants
Raw data files have been deposited to EGA (EGAD00001008431) since they contain patient data and require controlled access.


title: N7-methylguanosine tRNA modification promotes esophageal squamous cell carcinoma tumorigenesis via the RPTOR/ULK1/autophagy axis

first: Shuibin

last: Lin

state: China

address: Zhongshan 2nd road, Guangzhou

department: Clincial for Translational Medicine

institute: The First Affliliated Hospital, Sun Yat-sen University

summary: The cancer cells selectively promote the translation of oncogenic mRNAs to facilitate cancer progression, while the molecular mechanisms remain unclear. The tRNA N7-methylguanosine (m7G) modification is not essential for yeast growth, but in mammals mis-regulations of tRNA m7G modification cause stem cell defect and developmental disorders. Here we found that tRNA m7G methyltransferase complex components METTL1 and WDR4 are elevated in esophageal squamous cell carcinoma (ESCC) tissues and associated with poor ESCC prognosis. Functionally, depletion of METTL1 or WDR4 suppresses proliferation, migration, and invasion of ESCC cells. In addition, forced expression of METTL1 or WDR4 promotes ESCC progression depending on the tRNA m7G methyltransferase activity. Mechanistically, METTL1 knockdown leads to reduced tRNA m7G modification and decreased expression of m7G-modified tRNAs. Depletion of METTL1 selectively reduces the translation of a subset of oncogenic transcripts, including the genes related to mTOR signaling and autophagy in m7G related codon dependent manner. Rescue assays revealed the essential function of RPTOR/ULK1/autophagy axis in METTL1 driven ESCC progression. Furthermore, ESCC initiation and progression models using Mettl1 conditional knockout and knockin mice uncovered the strong physiological function of Mettl1 in promoting in vivo ESCC tumorigenesis. Our study uncovered a new layer of translation regulation mechanism mediated by tRNA m7G modification, provided strong evidence to support the important physiological function of mis-regulated tRNA modification in cancer, and suggested that targeting METTL1 and its downstream signaling axis could be a promising strategy for ESCC treatment.

overall_design: TRAC-Seq were developed to identify the tRNA m7G methylome in ESCC cell line. Polyribosome-bound-RNA-seq was used to study the differentially translated genes in the METTL1 knockdown and control cells. Ribo-seq was performed to study the differentially translated genes and ribosome processivity in the METTL1 knockdown and control cells. RPTOR-rescued polyribosome-bound-RNA-seq was used to distinguish the m7G-dependent and RPTOR-dependent mRNA translation in the K150 cells.

first: Hui

last: Han


title: RNA-seq raw data and analysis for APP, Shal495 and TrpA1 Drosophila melanogaster mutants

city: Shanghai

first: Yong

last: Ping

address: 800 Dongchuan Rd. Life Science Buildings #1,RM204

institute: Shanghai Jiao Tong University

summary: Evidence suggests that impaired synaptic and firing homeostasis represents a driving force of early Alzheimer’s disease (AD) progression. Here, we examine synaptic and sleep homeostasis in a Drosophila model by overexpressing human amyloid precursor protein (APP), whose duplication and mutations cause familial early-onset AD. We find that APP overexpression induces synaptic hyperexcitability. RNA-seq data indicate exaggerated expression of Ca2+ related signaling genes in APP mutants, including genes encoding Dmca1D, calcineurin (CaN) complex, and IP3R, but not in hyperexcitable mutants caused by TrpA1 or Shal/Kv4. We further demonstrate that increased CaN activity triggers transcriptional activation of Itpr (IP3R) through activating nuclear factor of activated T cells (NFAT). Strikingly, APP overexpression causes defects in both synaptic downscaling and sleep deprivation induced sleep rebound, and both defects could be restored by inhibiting IP3R. Our findings uncover IP3R as a shared signaling molecular in synaptic downscaling and sleep homeostasis, and its dysregulation may lead to synaptic hyperexcitability and AD progression at early stage.

overall_design:
We performed RNA sequencing (RNA-seq) on dissociated adult heads (5-7 days) to explore the possible downstream pathways that might be affected by APP, Shal495, TrpA1 and hyperexcitability induced in these mutants.
For each sample, total RNA was isolated from approximately 50 adult male heads.

first: Lingzhan

last: Shao

first: Yan

last: Zhang


title: Single cell RNA-seq developmental series in mouse hypothalamus in wild-type and Eed-cKO

status: Public on Feb 14 2022

city: Brisbane

first: Brad

last: Balderson

state: QLD

address: Chemistry Bld, 68 Cooper Rd

department: The School of Chemistry and Molecular Bioscience

country: Australia

institute: The University of Queensland

summary: Neuronal sub-type diversity in the hypothalamus is staggeringly immense. To investigate the role of epigenetic regulation in hypothalamic development in the generation of this cellular diversity; a floxed Eed allele was crossed to the early, pan-CNS Cre deleter Sox1-Cre, resulting in loss of H3K27me3 in the entire Mus musculus CNS by E11.5. E12.5, E13.5, E15.5, and E16.5 embryonic mouse hypothalamic cells were dissected and analysed by single cell RNA sequencing, on the Illimina/BioRad platform.

overall_design: Control and mutant Eed conditional knock-out at embryonic time points E12.5, E13.5, E15.5, and E16.5 were analysed by scRNA-seq in the mouse hypothalamus.

first: Behzad

middle: Y

last: Salmani

first: Susanne

last: Bauer

first: Helen

last: Ekman

first: Annika

last: Starkenberg

first: Thomas

last: Perlmann

last: Piper

first: Mikael

last: Boden

first: Stefan

last: Thor


title: MicroRNAs profile in Human Circulating CD4+ T Cells in Patients with Atherosclerosis Obliterans：Healthy persons vs. patients

city: Guangzhou

first: Siwen

last: Wang

address: 58# Zhongshan 2nd Rd

institute: The First Affiliated Hospital of Sun Yat-sen University

summary: MicroRNAs profile of circulating CD4+ T Cells in Aged Patients with Atherosclerosis Obliterans comparing healthy persons without symptoms or lesion associated with atherosclerosis.

platform_organism:
Homo sapiens
Human alphaherpesvirus 2
Lymphocryptovirus
Rhadinovirus
JC polyomavirus
Human immunodeficiency virus 1
Merkel cell polyomavirus

overall_design: Two-condition experiment, patients CD4+ T cells vs. healthy control CD4+ T cells. Biological replicates: 6 healthy control, 8 patients, independently harvested. One replicate per array.

first: Shenming


title: Selective Involvement of PRC2 in Mouse Hypothalamus Cell Specification

summary: Neuronal sub-type diversity in the hypothalamus is staggeringly immense. To investigate the role of epigenetic regulation in hypothalamic development in the generation of this cellular diversity; a floxed Eed allele was crossed to the early, pan-CNS Cre deleter Sox1-Cre, resulting in loss of H3K27me3 in the entire Mus musculus CNS by E11.5. The E18.5 embryonic hypothalamus was dissected and analysed by single cell RNA sequencing, on the Illimina/BioRad platform. Cell specification was surprisingly unaffected, with the majority of cell types - except Hcrt and dopamine neurons - sucessfully generated. This indicates that the role of the PRC2 complex - past E11.5 - is surprisingly limited in Mus musculus hypothalamic development.

overall_design: Control and mutant Eed conditional knock-out E18.5 embryos were analyzed by scRNA-seq in the hypothalamus.

first: Michael


title: dCas9 Fusion to Computer Designed PRC2 Inhibitor Reveals Functional TATA Box in Distal Promoter Region [ChIP-seq]

status: Public on Feb 12 2022

city: Seattle

first: Hannele

last: Ruohola-Baker

state: WA

address: 850 Republican Street

institute: Institute for Stem Cell and Regenerative Medicine

summary: The critical process in development, bifurcation of cellular fates, requires epigenetic H3K27me3 marks propagated by PRC2 complex. However, the precise chromatin loci of functional H3K27me3 marks are not yet known. Here we identify critical PRC2 functional sites at high resolution. We fused a computationally designed protein, EED binder (EB) that competes with EZH2 and thereby disrupts PRC2 function, to dCas9 (EBdCas9) to direct PRC2 inhibition at a precise locus using gRNA. We targeted EBdCas9 to 4 different genes ( TBX18, p16, CDX2  and  GATA3 ) and observed epigenetic remodeling at a single nucleosome resulting in gene activation. Remarkably, while traditional TATA box is located 30bp upstream of TSS, we identified a functional TATA box, >500bp of TSS, normally repressed by PRC2 complex. Deletion of this TATA box eliminates EBdCas9 dependent TBP recruitment and transcriptional activation. Targeting EBdCas9 to  CDX2  and  GATA3  results in trophoblast trans-differentiation. EBdCas9 technology may provide a broadly applicable tool for epigenetic regulation at a single locus to control gene expression

overall_design: biological samples were isolated from iPSC WTC cell lines expressing either EB-Flag or EBdCas9 for 3 days, or no expressing cells. ChIP-seq H3K27me3 was preform for each sample.

first: Weng

middle: I

last: Ng


title: dCas9 Fusion to Computer Designed PRC2 Inhibitor Reveals Functional TATA Box in Distal Promoter Region [AutoCUT&RUN]

overall_design: Cleavage under targets and Release using nuclease (Cut-and-Run), a chromatin profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing, was used to profile protein-DNA interactions in ES cells genome-wide.


title: CD45RA+CD62L- ILCs represent a quiescent local reservoir for the generation of mature ILC in human tissues

city: Huddinge

first: Jenny

last: Mjösberg

state: Stockholm

address: Alfred Nobels allé 8

department: Department of Medicine

country: Sweden

institute: Karolinska Institutet

summary: Innate lymphoid cells (ILCs) are highly plastic and predominantly mucosal tissue-resident cells that contribute to both homeostasis and inflammation depending on the microenvironment. The recent discovery of naïve-like tissue-resident ILCs suggests an ILC differentiation process that is akin to naïve T cell differentiation. Delineating the naïve-like ILC heterogeneity and the transcriptional, epigenetic and functional mechanisms that underlie ILC differentiation in tissues is crucial for understanding ILC biology in health and disease. Here we show that CD62L distinguishes two subsets of naïve-like CD45RA+ ILCs in tonsil tissue. While both subsets contain uni- and multipotent precursors of ILC1/NK cells and ILC3, CD62L+ ILCs resemble bona fide naïve ILCs with metabolism reminiscent of naïve T cells, lacking transcriptional and epigenetic signatures of mature ILCs. CD62L- ILCs are epigenetically similar to, but transcriptionally distinct from CD62L+ naïve-like ILCs including transcripts of cytokine signaling and metabolic pathways related to mature ILCs. A similar population of CD62L- quiescent ILCs with preferential differentiation capacity towards IL-22-producing ILC3 accumulate in the inflamed mucosa of patients with inflammatory bowel disease (IBD). These data suggest that naïve-like and quiescent ILCs are imprinted by their tissue microenvironment that poises their differentiation potential. Our findings identify restoration of homeostatic IL-22-producing ILC3 from CD62L- quiescent ILCs as a potential approach to improve tissue healing in IBD.

overall_design:
Transcriptional, epigenetic and functional characterization of naive-like ILCs in human mucosal tissues
***Please note that, due to the privacy of patients,  the raw data is not provided***

first: Efthymia

last: Kokkinou

first: Ram

middle: V

last: Pandey

first: Irene

last: Guierrez-Perez

first: Whitney

last: Weigel

first: Tea

last: Soini

first: Anna

last: Carrasco

last: Rao

first: Christopher

last: Tibbitt

first: Luca

last: Mazzurana

first: Maho

last: Nagasawa

first: Suzanne

last: Bal

first: Mattias

last: Jangard

first: Danielle

last: Friberg

first: Ulrik

last: Lindforss

first: Caroline

last: Nordenvall

first: Malin

last: Ljunggren

first: Staffan

last: Haapaniemi

first: Åsa

last: Keita

first: Johan

last: Söderholm

first: Charlotte

last: Hedin

first: Hergen

last: Spits

first: Yenan

last: Bryceson


title: Single-cell landscapes of primary glioblastomas and matched organoids and cell lines reveal variable retention of inter- and intra-tumor heterogeneity.

first: Marco

last: Marra

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

overall_design: Refer to individual Series


title: Gene expression data from the hippocampus of rats with prenatal valproic acid exposure

city: Honjo, Chuo-ku, Kumamoto

first: Kazuya

last: Matsuo

department: IMEG

country: Japan

institute: Kumamoto University

summary:
In this study, we explored molecular alterations in the hippocampus of prenatal valproic acid (VPA)-exposed rats as a model of autism spectrum disorders (ASD). In addition, we assessed effects of chronic administration of intranasal oxytocin, a promising peptide for ASD treatment.
Comparative analyses revealed that prenatal VPA exposure altered gene expression, a part of which is involved in key features including memory, developmental process, and epilepsy. Oxytocin partly improved these gene expression, which were predicted to interact with those involved in social behaviors and hippocampal-dependent memory. The present study documented molecular profiling in the hippocampus related to ASD and improvement by chronic treatment of oxytocin.

overall_design: Pregnant rats were treated with valproic acid (VPA) and the male offspring were used as a model of autism spectrum disorders. VPA-treated rats were separated with or without postnatal treatment with oxytocin (OXT). Control, VPA, and VPA+OXT were used in this study (n=3 for each group). RNA samples prepared from hippocampi were subjected to microarray analysis using the Affymetrix Rat Gene 2.0 ST platform (GPL17117).

first: Kohji

last: Fukunaga


title: Chemical-induced chromatin remodeling reprograms mouse ESCs to totipotent-like stem cells [CUT&Tag 2]

status: Public on Feb 11 2022

city: GuangZhou

first: Hanwen

last: Yu

state: GuangDong

address: North Campus, Sun Yat-Sen University, No. 74, 2nd Yat-*Sen Road, Yuexiu District, Guangzhou City, Guangdong Province, 510080, PRC

institute: SUN YAT-SEN UNIVERSITY

summary: Totipotent cells have more robust developmental potency than any other cell types, giving rise to both embryonic and extraembryonic tissues. Stable totipotent cultures and deciphering the principles of totipotency regulation would be invaluable to understand cell plasticity and lineage segregation in early development. Our approach of remodeling the pericentromeric heterochromatin and re-establishing the totipotency-specific broad H3K4me3 domains promotes the pluri-to-totipotency transition. Our protocol establishes a closer match of mouse 2-cell (2C) embryos than any other 2C-like cells. These totipotent-like stem cells (TLSCs) are stable in culture and possess unique molecular features of the mouse 2C embryo. Functionally, TLSCs are competent for germline transmission and give rise to both embryonic and extraembryonic lineages at high frequency. Therefore, TLSCs represent a highly valuable cell type for studies of totipotency and embryology.

overall_design: We investigated H3K4me1, H3K4me3, H3K27me3, H3K27ac and H3K9me2 landscape on the genome of  mESC and TPSC cells using CUT&Tag. CUT&Tag was performed  with the indicated antibody and IgG as control.

first: Mingzhu

last: Yang

first: Xiu

first: Jichang

last: Wang


title: Single-cell dissection of the human brain vasculature

city: Cambridge

last: Sun

state: MA

address: 455 Main St

department: EECS

institute: Whitehead Institute

summary: Here, we perform the first single-cell characterization of the human cerebrovasculature using both ex vivo fresh tissue experimental enrichment and post mortem in silico sorting of human cortical tissue samples. We capture 16,681 cerebrovascular nuclei across 11 subtypes, including endothelial cells, mural cells, and three distinct subtypes of perivascular fibroblasts along the vasculature. We uncover human-specific expression patterns along the arteriovenous axis and determine previously uncharacterized cell type-specific markers. We use our newly discovered human-specific signatures to study changes in 3,945 cerebrovascular cells of Huntington’s disease patients, which reveal an activation of innate immune signaling in vascular and glial cell types and the concomitant reduction to proteins critical for maintenance of blood-brain barrier integrity. Finally, our study provides a comprehensive resource molecular atlas of the human cerebrovasculature to guide future biological and therapeutic studies.

overall_design: Dissect cerebrovascular cell types in health and Huntington's disease

first: Myriam

last: Heiman

first: Manolis

last: Kellis

first: Francisco

last: Garcia


title: Transcriptome profiling of wild-type (WT) and USP8 knockout (KO) CT26 cell lines

city: Wuhan

first: Wenjun

last: Xiong

address: Room 1106, Medical Research Institute, Wuhan University, Donghu Road, No. 115, Wuchang District, Wuhan, Hubei Province, P.R. China.

department: Medical Research Institute

institute: Wuhan University

summary: USP8 is one of DUBs and is frequently overexpressed or gain-of-function mutated in multiple types of human cancer. Importantly, USP8 has been identified as an immunomodulatory DUB as T cell-specific Usp8 deficiency disrupts regulatory T cell functions, leading to recruiting abundant CD8+ T cells in colons and resulting in the inflammatory bowel disease in mice. However, whether targeting USP8 can enhance anti-tumor immunity has not been reported. To further explore the physiological function of USP8, we performed the transcriptomic analysis to comprehensively understand which signaling pathways are mainly regulated by USP8 in cancer cells. Usp8 WT and KO CT26 cells were harvested for RNA-sequencing (RNA-seq).

overall_design: Usp8 was knock out via sgRNA. SgControl was used as a control(WT) and RNA-seq experiment was performed with biological replicates.

first: Xueliang

last: Gao

first: Tiantian

last: Zhang

first: Jinfang


title: dCas9 Fusion to Computer Designed PRC2 Inhibitor Reveals Functional TATA Box in Distal Promoter Region [ATAC-seq]

first: Hannele

last: Ruohola-Baker

overall_design:
WTC EBdCas9 induced cells and WTC NCdCas9 induced cells were transfected with TBX18 g6 RNA for 2 days and were harvested on day 3 for ATACseq analysis.
hESC Elf 1 cells were either induced with EB using Dox for 3 days or not induced and harvest for ATAC seq analysis.

first: Weng

last: Ng


title: Chemical-induced chromatin remodeling reprograms mouse ESCs to totipotent-like stem cells


title: dCas9 Fusion to Computer Designed PRC2 Inhibitor Reveals Functional TATA Box in Distal Promoter Region [bulk RNA-seq]

overall_design: We performed bulk RNA-seq of the EEDBinder-dCas9 cell lines reprogrammed to EPS and trophoblast stem cells

first: Yuliang

first: WengI


title: single-cell RNA-seq of embryonic Drosophila somatic muscle cells

city: Heidelberg

first: Jessica

last: Velten

address: Im Neuenheimer Feld 230

department: Centre for Organismal Studies

institute: University of Heidelberg

summary: This data set contains single-cell RNA-seq data from stage 16-17 embryonic somatic muscle cells that express GFP from a Mhc-TAU-GFP marker construct.

overall_design: Cells were sorted for GFP fluorescence into individual wells and processed using the smart-seq2 protocol.

first: Lars

first: Ingrid

last: Lohmann


title: dCas9 Fusion to Computer Designed PRC2 Inhibitor Reveals Functional TATA Box in Distal Promoter Region


title: Structural basis for PoxtA-mediated resistance to Phenicol and Oxazolidinone antibiotics

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

institute: ScilifeLab - Karolinska Institutet

summary: PoxtA and OptrA are ATP binding cassette (ABC) proteins of the F subtype (ABCF) that confer resistance to oxazolidinone, such as linezolid, and phenicol antibiotics, such as chloramphenicol. PoxtA/OptrA are often encoded on mobile genetic elements, facilitating their rapid spread amongst Gram-positive bacteria. These target protection proteins are thought to confer resistance by binding to the ribosome and dislodging the antibiotics from their binding sites. However, a structural basis for their mechanism of action has been lacking. Here by investigating 5'P mRNA decay intermediates, that provide ribosome protection data, we show that PoxtA protects against Linezolid specific stalls. Furthermore, we present cryo-electron microscopy structures of PoxtA in complex with the Enterococcus faecalis 70S ribosome at 2.9–3.1 Å, as well as the complete E. faecalis 70S ribosome at 2.2–2.5 Å. The structures reveal that PoxtA binds within the ribosomal E-site with its antibiotic resistance domain (ARD) extending towards the peptidyltransferase center (PTC) on the large ribosomal subunit. At its closest point, the ARD of PoxtA is still located >15 Å from the linezolid and chloramphenicol binding sites, suggesting that drug release is elicited indirectly. Instead, we observe that the ARD of PoxtA perturbs the CCA-end of the P-site tRNA causing it to shift by ~4 Å out of the PTC, which correlates with a register shift of one amino acid for the attached nascent polypeptide chain. Given that linezolid and chloramphenicol are context-specific translation elongation inhibitors, we postulate that PoxtA/OptrA confer resistance to oxazolidinones and phenicols indirectly by perturbing the P-site tRNA and thereby altering the conformation of the attached nascent chain to disrupt the drug binding site.

overall_design: Here we investigate 5'P mRNA decay intermediates in Enterococcus faecalis to investigate context-specific ribosome stalls in response to Linezolid in presence or absence of PoxtA. We analyzed 12 samples using HT-5PSeq (Zhang and Pelechano,  https://doi.org/10.1016/j.crmeth.2021.100001) optimized for bacteria (Huch, Nersisyan et al, https://doi.org/10.1101/2021.04.08.439066). We performed three biological replicates for two strains (with and without PoxtA expression) in the presence and absence of Linezolid treatment at sub-MIC concentrations.

first: Caillan

last: Crowe-McAuliffe

first: Victoriia

last: Murina

first: Marje

last: Kasari

first: Kathryn

last: Turnbull

first: Hiraku

last: Takada

first: Yury

middle: S

last: Polikanov

first: Arnfinn

last: Sunsfjord

first: Kristin

last: Hegstad

first: Gemma

middle: C

last: Atkinson

first: Vasili

last: Hauryliuk

first: Daniel

middle: N

last: Wilson

first: Susanne

last: Huch

first: Lilit

last: Nersisyan


title: Transcriptome of Lactobacillus plantarum NMM.1 isolated from  Inner Mongolia raw milk

status: Public on Feb 10 2022

first: Kailin

last: Li

address: Tian Ping

department: Shanghai Institute of Nutrtion and Health

institute: Chinese Academy of Sciences

summary: We report the transcriptome profile of the  Lactobacillus plantarum NMM.1  treated by 5 μg/mL deoxynivalenol-3-glucoside (D3G),aiming to search for some different expression genes and pathways to reveal the change caused by D3G.

overall_design: Lactobacillus plantarum NMM.1 mRNA profiles of 1-hour non-treated(control) cells and 5 μg/mL D3G-treated cells.

first: Li

last: Kailin

first: Wu

last: Aibo


title: Regulation of stem cell identity by miR-200a during spinal cord regeneration

city: Woods hole

first: Karen

last: Echeverri

address: 7 MBL ST

department: Eugene Bell Center for Regeneration Biology and Tissue Engineering

institute: MARINE BIOLOGICAL LAB

summary: Salamanders have the remarkable ability to functionally regenerate after spinal cord transection. In response to injury, GFAP+ glial cells in the axolotl spinal cord proliferate and migrate to replace the missing neural tube and create a permissive environment for axon regeneration. In this paper we show that miR-200a acts to repress expression of Brachyury in sox2 positive progenitor cells in the axoltol spinal cord after spinal cord injury but after tail amputation when multiple tissue types must be regenerated then mir-200a is downregualted allowing progenitor cells in the spinal cord to naturally become bipotent progenitors which can give rise to muscle and neural cell types. When  miR-200a is inhibited after spinal cord injury then these cells also express BRachyury cna can form muscle.

overall_design: All axolotls used in these experiments were bred in the axolotl facility at the University of Minnesota or at the MBL under the IACUC protocols #1710-35242A, #18-49. Axolotls of 2–3 cm were used for all in vivo experiments, and animals were kept in separate containers and fed daily with artemia; water was changed daily. Animals were anesthetized in 0.01% p-amino benzocaine (Sigma) before microinjection was performed.

first: Sarah

last: Walker

first: Keith

last: Sabin

first: Micah

last: Gearhart

first: Kenta

last: Yamamoto


title: Death Associated Protein 3 (DAP3) Coordinates Splicing Regulatory Networks to Modulate Global Alternative Splicing in Cancer

city: Singapore

first: Polly Leilei

last: Chen

address: #12-01, MD6, 14 Medical Drive

department: Department of Anatomy

institute: Cancer Science Institute of Singapore NUS

summary: The dynamic regulation of transcriptome requires coordinated participation of multiple RNA binding proteins (RBPs) in RNA processing. Dysregulated RNA processing, such as aberrant alternative splicing, is implicated in many cancers. Therefore, it is critical to explore the cancer-related RNA processing regulation and the underlying mechanisms. Many RBPs lack classical RNA-binding domains and their functions in RNA processing regulation remain unclear. Through an unbiased transcriptome-wide analysis, we report DAP3 binds ubiquitously to endogenous RNAs in vivo and its depletion reshapes the alternative splicing landscape in cancer cells. Mechanistically, we show DAP3 coordinates splicing regulatory networks, not only via mediating the formation of ribonucleoprotein (RNP) complexes, but also via modulating splicing of numerous splicing factors. Specific DAP3-regulated splicing changes such as non-productive splicing of WSB1 and RBM6, play important roles in tumorigenesis. Together, these findings provide critical mechanistic insights into the molecular functions of DAP3 in cancer development as a master regulator of RNA processing.

overall_design: We constructed strand-specific cDNA libraries of 3 total RNA samples and sequenced the libraries using Illumina NovaSeq 6000 PE150 platform achieving 100 millions of mappable reads per sample. Then we examined alternative splicing in EC109 cells after RBM6 depletion.

first: Leilei

first: Jian

last: Han

first: Omer

last: An


title: Sequencing of HepaRG cells with functional knockout of PXR

city: Memphis

first: William

middle: C.

last: Wright

state: Tennessee

address: 262 Danny Thomas Pl

department: Computational Biology

institute: St. Jude Children's Research Hospital

summary: Purpose: To assess effect of PXR functional knockout

overall_design:
Methods: We obtained expression profiles of cancer cell line HepaRG by RNA-sequencing in various conditions.
mRNA profiles of each cell line were obtaiend in triplicate using Illumina-based RNA-Sequencing. Sequencing was conducted as paired-end 100bp reads. The HepaRG WT group is considered as the control.

first: Monicah

last: Bwayi

first: Taosheng


title: Transcriptome analysis of mouse WT and CD22 KO GC B cells

status: Public on Feb 09 2022

city: Edmonton

first: Jhon

last: Enterina

state: AB

address: 6-020 KATZ Group Centre

department: Medical Microbiology and Immunology

institute: University of Alberta

summary: Germinal centres (GC) are specialized sites where B cells expand and diversify their antibody genes through somatic hypermutation. GC B-cells are routinely identified through distinct changes on their surface carbohydrates, known as glycans. One striking modification relates to the monosaccharide sialic acid. In mice, this change is mediated through downregulation of an enzyme called CMAH, which results in a GC-specific loss of preferred ligand for CD22, a member of the sialic acid-binding immunoglobulin-type lectins (Siglecs) and an inhibitory co-receptor of the B-cell antigen receptor (BCR). Here, we identified that glycan remodeling, mediated by downregulation of CMAH, is crucial for the GC B-cell response, and production of memory B-cells, plasma cells, and high affinity antibodies. We also demonstrated that the function of these altered glycans is dependent on CD22, highlighting that coordinated loss of preferred ligands acts to modulates the CD22 activity in the GC B-cells. Overall, our study reveals that intrinsic glycan remodeling functions to optimize the B-cell responses in the GC by controlling CD22.

overall_design: WT and CD22 KO mice were immunized with chicken ovalbumin-displaying liposomes. Dark zone (B220+CD19+IgD-GL7+CXCR4highCD86low) and light zone (B220+CD19+IgD-GL7+CXCR4lowCD86high) sorted from splenocytes of mice, at day 14 post-immunization. RNA was isolated and processed for next-generation RNA sequencing.

first: Matthew

last: Macauley


title: single-cell RNA-seq of embryonic Drosophila

first: Jessica

last: Velten


title: Gene expression between  normal and cancer tissue  for pancreatic cancer in Japan

city: Chiba city Chuo-ku

first: Yosuke

last: Iwatate

state: Chiba

address: Nitona-cho 666-2

department: Division of Hepato-Biliary-Pancreatic Surgery

institute: Chiba Cancer Center

summary: Transcriptomic analysis of cancer samples helps to identify the mechanism and molecular markers of cancer. However, transcriptomic analyses of pancreatic ductal adenocarcinoma from the Japanese population are lacking.  We performed RNA sequencing of flesh or frozen pancreatic ductal adenocarcinoma tissues and adjacent normal pancreatic tissue from 12 Japanese patients to identify genes critical for the clinical pathology of pancreatic cancer among the Japanese population.

overall_design: Examination of difference between normal and cancer in pancreatic dustal adenocarcinoma tissue.

first: Isamu

last: Hoshino

first: Yasutoshi

last: Tatsumi

first: Yuki

last: Nakamura


title: single-cell RNA-seq of embryonic Drosophila motoneurons

summary: This data set contains single-cell RNA-seq data from stage 16-17 embryonic motoneurons labeled by RFP expression driven by Ok371-GAL4

overall_design: Cells were sorted for RFP fluorescence into individual wells and processed using the smart-seq2 protocol.

first: Lars

first: Ingrid

last: Lohmann


title: RNAseq analysis of anti-BTLA vs control treated anti-CD3 stimulated mouse T cells or IgM stimulated mouse B cells

city: San Diego

first: John

last: Sedy

address: 10770 Wateridge Cir

institute: AnaptysBio

summary: This dataset comprises an analysis of BTLA signaling in wild-type mouse T cells or B cells. These purified CD4+ T cells or purified B cells were stimulataed through their antigen receptors and/or Interferon receptor and costimulated with anti-BTLA mAb that activates BTLA signaling. High throughput sequencing was performed on the RNA purified from stimulated populations to characterize how BTLA signaling regulates antigen receptor and type I interferon receptor signaling in T cells and B cells.

overall_design: One set of animals was not immunized and a second group was immunized with MOG peptide. B cells and CD4+ T cells were isolated from each of these groups. CD4+ T cells were either not stimulated or were stimulated with anti-CD3. B cells were either not stimulated or were stimulated with anti-TgM/G. Anti-CD3 stimulated CD4+ T cells or anti-IgM/G stimulated B cells were further treated with nothing, IFNb, anti-Btla, or both IFNb and anti-Btla. RNA was harvested from each of these groups for RNAseq analysis.


title: Transcriptome profiles of colonic stem cells of WT and AHR deficient mice treated with either DMSO or high affinity AHR ligand, FICZ for 4 hours

city: London

first: Brigitta

last: Stockinger

address: 1 Midland Road

institute: Francis Crick Insititue

summary: To identify aryl hydrocarbon receptor (AHR) dependent transcriptional changes in mouse colon stem cells, we performed RNA sequencing of colon organoids from wildtype and AhR deficient mice stimulated with an high affinity AHR ligand, 5nM FICZ for 4 hours.

overall_design: Organoids were prepared from colonic crypts of WT and AHR deficient mice and maintained in stem cell condition with WENR medium. Fully grown organoids were treated with either DMSO or 5nM FICZ for 4 hours in vitro and RNAseq was performed on total RNA.

first: Amina

last: Metidji


title: Genome-wide maps of chromatin state in WT and AHRKO colon organoids

summary: Identification of changes in chromatin accessibility between WT and AHR KO organoids under regenerative (WENR) and differentiating (d4 ENR) conditions

overall_design: Whole-genome ATAC-seq of WT or AHR KO colon organoids grown in either WENR or d4 ENR conditions

first: Kathleen

last: Shah

first: Muralidhara

last: Muradhana

first: Miriam

last: Sopena


title: Chromatin immunoprecipitation (ChIP) of aryl hydrocarbon receptor (AHR) in mouse colon stem cells

summary: To identify direct targets of the environmental sensor AHR, a nuclear transcription factor, in the colonic stem cells, we have performed ChIP sequencing of AHR bound DNA in wildtype colon organoids. ChIP sequencing of AHR knockout organoids was used as a control to filter out non-specific antibody targets.

overall_design: Colon organoids from wild type and AHR knockout mice were cultured in stem cell  condition with WENR medium and treated with high affinity AHR ligand, 5nM FICZ for 1 hour and immunoprecipitation was performed with anti-AHR antibody (Enzo, BML-SA210).

last: Maradana


title: Microarray analysis of E2a-/- and E2a/-Lef1F/F leukemia lines after retroviral Cre expression

city: Chicago

first: Barbara

last: Kee

state: Illinois

address: 924 E57th st

department: Pathology

institute: The University of Chicago

summary: We compared the transcriptome of E47-/- and E2a/-Lef1F/F leukemia lines 72 hours after transduction with MigR1 or MigR1-Cre. The GFP+ populations were isolated by flow cytometric sorting

overall_design: E2a-/- and E2a/-Lef1F/F leukemia lines were infected with retrovirus producing GFP (MigR1) or Cre (Migr2-Cre) and GFP+ cells were sorted 72 hours after infection. RNA was isolated from sorted cells using Trizol and subject to microarray analysis of 430.a arrays

first: Tiffany

last: Carr

first: Elizabeth

last: Bartom

first: Mikael

last: Sigvardsson


title: Multiple RSV strains infecting HEp-2 and A549 cells reveal cell line-dependent differences in resistance to RSV infection

city: Houston

first: Pedro

last: Piedra

state: TX

address: One Baylor Plaza

department: Virol & Micro

institute: Baylor College of Medicine

summary: A few transformed cell lines and two historic strains have been extensively used to study respiratory syncytial virus (RSV). We report a thorough molecular and cell biological characterization of HEp-2 and A549 cells infected with four strains of RSV representing both major subgroups as well as historic and more contemporary genotypes -- [RSV/A/Tracy (GA1), RSV/A/Ontario (ON), RSV/B/18537 (GB1), RSV/B/Buenos Aires (BA)] -- via measurements of viral replication kinetics and viral gene expression, immunofluorescence-based imaging of gross cellular morphology and cell-associated RSV, and measurements of host response including transcriptional changes and levels of secreted cytokines and growth factors. Our findings strongly suggest 1) the existence of a conserved difference in gene expression between RSV subgroups A and B; 2) the A549 cell line is a more stringent and natural host of replicating RSV than the HEp-2 cell line; and 3) consistent with previous studies, determining the full effects of viral genetic variation in RSV pathogenesis requires model systems as tractable as transformed cell lines but better representative of the human host.

sample_organism:
Homo sapiens
Respiratory syncytial virus type A
Respiratory syncytial virus type B

overall_design: Sequencing of viral genomes and transcriptomes and host transcriptomes in infections of two different cell lines, HEp-2 and A549, by four different RSV strains.

first: Anubama

last: Rajan

first: Felipe-Andrés

first: Letisha

last: Aideyan

first: Trevor

last: McBride

first: Matthew

last: Robertson

first: Hannah

last: Johnson

first: Gina

last: Aloisio

first: David

last: Henke

first: Cristian

last: Coarfa

first: Fabio

last: Stossi

first: Vipin

last: Kumar Menon

first: Harshavardhan

last: Doddapaneni

first: Donna

last: Muzny

first: Sara

last: Javornik Cregeen

first: Kristi

last: Hoffman

first: Joseph

last: Petrosino

first: Richard

middle: A

last: Gibbs

first: Vasanthi

last: Avadhanula


title: Regulation of Intestinal microbiome diversity by BTLA and HVEM

status: Public on Feb 08 2022

first: John

last: Sedy

state: CA

summary: The intestinal microbiome was examined from fecal pellets of animals with genetic targeting of the BTLA inhibitory receptor and the TNFR superfamily member HVEM, or in animals treated with agonist antibodies specific for BTLA.

overall_design: Fecal pellets were collected from cohorts, DNA collected, and submitted  for 16S sequencing and microbiome analysis. Groups consist of BTLA flox and cre expressing derivatives, HVEM flox and cre expressing derivatives, or C57BL/6 animals treated with anti-BTLA or control Ig. Each strain comparison contains replicate samples from different animals. Microbiome content was analyzed for relative differences in bacteria abundance.


title: ALPN-202 induces a more potent anti-tumor T cell response in MC38/hPD-L1 tumors than PD-L1 blockade alone

city: Seattle

first: Mark

last: Maurer

address: 188 E Blaine St. Suite 200

department: Translation Science

institute: Alpine Immune Sciences

summary:
Purpose: Use RNA-seq to characterize the anti-tumor immune response induced by ALPN-202 and compare to that of anti-PD-L1 treatment alone.
Methods: mRNA was isolated from MC38/hPD-L1 tumors 72 hours after a single dose of ALPN-202 (n=4), anti-PD-L1 mAb (durvalumab) (n=4), or Fc control (n=4).
Results: ALPN-202 treatment resulted in elevated expression of multiple T cell, NK cell, myeloid cell genes. Additionally, there was a strong increase in genes commonly associated with a proinflammatory response including cytokines, chemokines and surface markers.
Conclusions: ALPN-202 treatment resulted in a strong anti-tumor immune response that was more potent than that generated by blockade of PD-L1 alone.

overall_design: mRNA was isolated from MC38/hPD-L1 tumors 72 hours after a single dose of ALPN-202 (n=4), anti-PD-L1 mAb (durvalumab) (n=4), or Fc control (n=4). Gene expression was measured by RNA-seq using dual-index, single-read sequencing of pooled libraries was carried out on a HiSeq2500 sequencer (Illumina) with 58-base reads, using HiSeq v4 Cluster and SBS kits (Illumina) with a target depth of 5 million reads per sample.

first: Steve

last: Levin


title: The VarA-CsrA regulatory pathway influences cell shape in Vibrio cholerae

city: Lausanne

first: Melanie

last: Blokesch

address: Station 19 / EPFL-SV-UPBLO

department: School of Life Sciences

institute: Swiss Federal Institute of Technology Lausanne (EPFL)

summary: In this study, we determined the expression profile of V. cholerae strain A1552 and its varA-deficient mutant at two different growth stages (OD600 of 0.2 or 2.5)

overall_design: mRNA profiles of the indicated V. cholerae strains, which were grown in vitro in LB medium until they reached an optical density at 600 nm (OD600) of 0.2 or 2.5

first: Leonardo

last: Lemos Rocha


title: Determination of sRNAs interacting with vfr mRNA across three Pseudomonas aeruginosa strains

status: Public on Feb 07 2022

city: Zurich

first: Julian

last: Trouillon

address: Otto-Stern-Weg 3

department: Institute of Molecular Systems Biology

institute: ETH Zurich

summary: Determination of the RNA interacting with vfr mRNA  at two different time-points during growth on the three strains PAO1, PA14 and IHMA87, representing the three major P. aeruginosa phylogenetic lineages, using rGRIL-seq.

overall_design: rGRIL-seq. Interacting RNAs were ligated in live cell by overexpression of a T4 RNA ligase. After cell lysis, total RNA was isolated and enriched for vfr-containing chimeric transcripts using sDNA probes specific to vfr mRNA.

first: Kook

last: Han

first: Ina

last: Attrée

first: Stephen

last: Lory


title: Determination of the RNA interactome of the RNA-binding protein Hfq across three Pseudomonas aeruginosa strains

summary: Determination of the RNA interactome of the RNA-binding protein Hfq at three different time-point during growth on the three strains PAO1, PA14 and IHMA87, representing the three major P. aeruginosa phylogenetic lineages, using RIP-seq.

overall_design: RNA co-immunoprecipitation with 3xFLAG-tagged Hfq (RIP-seq) after 200, 400 and 600 minutes of growth in LB medium.


title: RNA-sequecing of disctinct cell states along the E-M phenotypic specturm

first: Yun

last: Zhang

email: zhangyunbio@gmail.com, barc@wi.mit.edu

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

summary: Analysis of HMLER-C1 cells,C2 cells and C1 cells with EED-KO or KMT2D-KO in order to understand the gene expression profiles associated with distinct EMT intermediate states.

overall_design: Examine the transcriptomes of cells in stable epitheli state (C1), plastic epithelial states (C2, C1-EED-KO-Epi, C1-KMT2D-KO-Epi), and distinct meenchymal states (C2-Mes, C1-EED-KO-Mes, C1-KMT2D-KO-Mes).

first: Robert

last: Weinberg


title: Gene-silencing activity of small RNAs controlled by TRMT6/61A-dependent base methylation

city: Birmingham

first: Zhangli

last: Su

state: Alabama

address: 720 20th Street South

department: Department of Genetics

institute: University of Alabama

summary: We identified human small RNAs containing m1A (N1-methyladenosine) by m1A RIP and TGIRT-seq. Small RNA-seq and long RNA-seq was performed after TRMT6/61A knock-down.

overall_design: 46 samples

first: Anindya

last: Dutta


title: CUT&RUN analysis of PRC2 and KMT2D-COMPASS direct targets in non-convertible HMLER cells

city: Cambridge

summary: Analysis of PRC2 and KMT2D-COMPASS binding sequences using CUT&RUN technique in non-convertible HMLER-C1 cells, convertible C2 epithelial cells, as well as C1 EED-KO epithelial and C1-KMT2D-KO epithelial cells.

overall_design: Cultured cells were processed using CUT&RUN with antibodies against EZH2 or ASH2L.


title: A leukemia-protective germline variant mediates chromatin module formation via transcription factor nucleation

first: Bart

last: Deplancke

address: EPFL SV IBI-SV UPDEPLA

institute: ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE

summary: Non-coding variants coordinate transcription factor (TF) binding and chromatin mark enrichment changes over regions spanning >100 kb. We named these molecularly coordinated regions “variable chromatin modules” (VCMs), providing a conceptual framework of how regulatory variation might shape complex traits. To better understand the molecular mechanisms underlying VCM formation, here, we mechanistically dissect an uncharacterized VCM-modulating non-coding variant that is associated with reduced chronic lymphocytic leukemia (CLL) predisposition and disease progression. This common, germline variant constitutes a 5-bp indel that controls the activity of an AXIN2 gene-linked VCM by creating a MEF2 binding site, which, upon binding, activates a super-enhancer-like regulatory element. This triggers a change in TF binding activity and chromatin state at an enhancer cluster spanning >150 kb, coinciding with subtle, long-range chromatin compaction and robust AXIN2 up-regulation. Our results support a model in which the indel acts as an AXIN2 VCM-activating TF nucleation event, which modulates CLL pathology.

overall_design: RNA-seq for the MEC1 CLL cell line with overexpression of AXIN2 or control using a lentiviral infection with the pLV-EF1a-IRES-Puro (#85132, Addgene) vector. ATAC-seq for crispred MEC1 cells to have both rs143348853 genotypes (homozygous ALT and REF). NGS Capture-C for the LCLs GM11931 and GM12282 using the rs143348853 locus as viewpoint.

first: Gerard

last: Llimos


title: RNA-Seq of inflammatory stimulated HUVECs transfected with microRNA-125a-5p or negative control.

city: Munich

first: Martin

middle: Bernhard

last: Mueller

address: Marchioninistrasse 15

department: Department of Anaesthesiology

institute: University Hospital, Ludwig-Maximilians-University Munich (LMU)

summary: Purpose: In recent years, research has revealed the role of microRNAs (miRs) as important regulators of endothelial function. Notably, miR-125a is upregulated in the blood of patients with acute vascular diseases. Since miRNAs act out their function in networks, we aimed at investigating the presence of a miR-125a-related network regulating the endothelial barrier. Method: We investigated transcriptional changes of human umbilical cord endothelial cells (HUVEC) after miR-125a overexpression in an acute inflammatory in-vitro setting using Next Generation Sequencing. Briefly, primary HUVECs from five different donors were transfected either with hsa-miR-125a-5p or negative control (NC). After transfection HUVECs were cultivated for 18 hours and stimulated with TNF (25 ng/ml) for additional 6 hours. We compared the following groups: NC (18047-0001, 18047-0002, 18047-0003, 18047-0004, 18047-0005) versus miR125a: (18047-0006, 18047-0007, 18047-0008, 18047-0009, 18047-0010) Results: MiR-125a overexpression in inflammatory activated HUVECs significantly altered gene expression of 468 genes (FC: +1.25 to -1.25 p<0.01). We found eight potential miR-125a direct target genes involved in endothelial barrier function.

overall_design: Transcriptome anlysis via Next Generation Sequencing of HUVECs overexpressing miR-125a-5p (n=5) versus control miRNA (n=5).

middle: B

first: Valena

last: Liesske

first: Lei

last: Li

first: Kreth

last: Simone


title: cDNA sequencing of Plasmodium falciparum field parasites 2015-2018

first: Zbynek

last: Bozdech

address: 60 Nanyang Drive

department: School of Biological Sciences

institute: Nanyang Technological University

summary: The objective of this study is to characterize gene expression signatures associated with in vivo artemisinin resistance phenotype and its transcriptional response to Artemisinin Combination Therapy (ACT) treatment . RNA-seq was applied to establish the global gene expression profiles for 196 and 180 isolates sampled from patients prior to and post to ACT treatment.

overall_design: P. falciparum isolates were sampled from the whole blood of patients from 6 countries and 13 sites across Southeast Asia (Ramu in Bangladesh; Thabeikkyin, Pyay, Pyin Oo Lwin and Ann in Myanmar; Phusing and Khun Han in Thailand; Pailin, Pursat, Ratanakiri and Preah Vihear in Cambodia; Sekong in Laos; Bin Phuoc in Vietnam) from 2015 to 2018.

last: Zhu

first: Sourav

last: Nayak

first: Michal

last: Kucharski


title: Fusobacterium nucleatum Reducing METTL3-mediated m6A Modification Contributes to Colorectal Cancer Aggressiveness

city: Hangzhou

first: Wei

last: Zhuo

state: Zhejiang

address: 866 Yuhangtang Road

department: School of Medicine

institute: Zhejiang University

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Fusobacterium nucleatum Reducing METTL3-mediated m6A Modification Contributes to Colorectal Cancer Aggressiveness [RNA-Seq]

summary: Transcriptome profiling revealed that KIF26B was associated with cell-cell junction and response to growth factor stimulation, which are important for CRC cell aggressiveness. And gene set enrichment analysis suggested that Hippo signaling pathway was significantly enriched in KIF26B-regulated gene signatures

overall_design: KIF26B induced gene expression in HCT116 colorectal cancer cells were measured at 48 h after transfection with siRNA control or siRNAs targeting KIF26B.

first: Lu


title: Fusobacterium nucleatum Reducing METTL3-mediated m6A Modification Contributes to Colorectal Cancer Aggressiveness [RIP-Seq]

summary: To investigate the role of Fusobacterium nucleatum-mediated m6A modification, we performed m6A-sequencing to map the m6A modification in control or Fusobacterium nucleatum-treated HCT116 cells.

overall_design: Examination of m6A modification variation in HCT116 cells treated with or without Fusobacterium nucleatum


title: The role of insulators and transcription in 3D chromatin organisation of flies

first: Nicolae Radu

last: Zabet

address: 4 Newark Street

department: Blizard Institute, Barts and The London School of Medicine and Dentistry

institute: Queen Mary University of London

summary: The DNA in humans and many animals is compartmentalised in topologically associating domains (TADs). In Drosophila, several architectural proteins are enriched at TAD borders, but we are still missing evidence that these proteins have a functional role in TAD maintenance. Here, we show that depletion of BEAF-32, Cp190 and Chro leads to changes in TAD organisation and chromatin loops. Their depletion affects mainly TAD borders in heterochromatin, while euchromatin TAD borders are resilient to these mutants. Furthermore, transcriptomic data identified thousands of genes displaying differential expression in these mutants and that majority of differentially expressed genes are in TADs that are reorganised. In contrast, we observed a lower effect on gene expression by the loss of chromatin loops. Our work identified for the first time a functional role for architectural proteins at TAD borders in Drosophila and a strong link between TAD reorganisation and changes in gene expression.

overall_design: Comparison of Hi-C and RNA-seq data in WT and mutant (BEAF-32; Cp190 and Chro; BEAF-32 and Dref) Drosophila melanogaster cell lines BG3 (derived from larval central nervous system)

first: Nicolae

first: Keerthi

middle: T

last: Chathoth

first: Liudmila

last: Mikheeva


title: Elevated ATGL in colon cancer cells and cancer stem cells promotes metabolic and tumorigenic reprogramming reinforced by obesity

status: Public on Feb 05 2022

city: New Orleans

first: Suzana

last: Savkovic

state: LA

address: 1324 Tulane Ave

institute: Tulane Univeristy

summary: Obesity is a worldwide epidemic associated with increased risk and progression of colon cancer. Here, we aimed to determine the role of adipose triglyceride lipase (ATGL), responsible for intracellular lipid droplet (LDs) utilization, in obesity driven colonic tumorigenesis. In local colon cancer patients, significantly increased ATGL levels in tumor tissue, compared to controls, were augmented in obese individuals. Elevated ATGL levels in human colon cancer cells (CCC) relative to non-transformed were augmented by an obesity mediator, oleic acid (OA). In CCC and colonospheres, enriched in colon cancer stem cells (CCSC), inhibition of ATGL prevented LDs utilization and inhibited OA-stimulated growth through retinoblastoma-mediated cell-cycle arrest. Further, transcriptomic analysis of CCC, with inhibited ATGL, revealed targeted pathways driving tumorigenesis and high-fat-diet obesity facilitated tumorigenic pathways. Inhibition of ATGL in colonospheres revealed targeted pathways in human colonic tumor crypt base cells (enriched in CCSC) derived from colon cancer patients. In CCC and colonospheres, we validated selected transcripts targeted by ATGL inhibition, some with emerging roles in colonic tumorigeneses (ATG2B, PCK2, PGAM1, SPTLC2, IGFBP1, ABCC3) and others with established roles (MYC, MUC2). These findings demonstrate obesity-promoted, ATGL-mediated colonic tumorigenesis and establishes therapeutic significance of ATGL in obesity reinforced colon cancer progression.

overall_design: Examination of ATGL dependent transcription in colon cancer HT29 and HCT116 cells and their  colonospheres

first: Rida

last: Iftikhar

first: Harrison

middle: M

last: Penrose

first: Angelle

last: King

first: Joshua

last: Samudre

first: Morgan

middle: E

last: Collins

first: Alifiani

last: Hartono

first: Sean

last: Lee

first: Frank

last: Lau

first: Melody

last: Baddoo

first: Erik

last: Flemington

first: Susan

last: Crawford

middle: D