title: Epithelial MAPK Signaling Directs Endothelial NRF2 Signaling and IL-8 Secretion in the Alveolar Capillary Region

city: College Station

first: Eva

last: Vitucci

address: 212 Adriance Lab Road

institute: Texas A&M University

summary: Particulate matter 2.5 (PM2.5) deposition in the lung’s alveolar capillary region (ACR) is significantly associated with respiratory disease development, yet the underlying molecular mechanisms are not completely understood. Adverse responses that promote respiratory disease development involve orchestrated, intercellular signaling between multiple cell types within the ACR.  Our goal was to use an organotypic, in vitro model of the ACR to investigate if alveolar epithelial PM2.5 exposure induces exposure responses in alveolar epithelial cells and in underlying microvascular endothelial cells in the ACR. Our findings demonstrate that alveolar epithelial PM2.5 exposure induces robust transcriptional responses in the microvascular endothelial cells within the ACR. We show that the underlying microvascular endothelial cells develop redox dysfunction and increase proinflammatory cytokine secretion, two exposure responses commonly associated with respiratory disease development. Moreover, we identified intercellular signaling mechanisms between the alveolar epithelium and microvascular endothelium that modulate these adverse endothelial exposure responses. Our findings illustrate a new mechanism of intercellular communication between cells of the ACR that significantly improves our understanding of respiratory disease development following pulmonary exposure to inhaled materials.

overall_design: Two different human cell lines are used within this study: 1) NCI-H441 cells, an alveolar-like epithelial cell line and 2) HULEC, human lung endothelial cells. These cells were incorporated into the organotypic ACRE model and RNA-seq data was collected for comparative gene expression profiling analysis following a 6 and 24 h VEH or ACRE-DEP exposure. 3 indpendent experiments were run, serving as 3 biological replicates for each cell type, time point, and treatment. Average log2FC values were obtained by averaging the differential gene expression changes of the 3 biological replicates per condition. The average log2FC values per condition are the reported / published data.

first: Shaun

last: McCullough

first: Elizabeth

last: Martin

first: Alysha

last: Simmons


title: Effect of SHP2 Inhibition on mRNA Expression Profiles of GIST Cells

status: Public on Nov 30 2024

city: Shenzhen

first: Chunxiao

last: He

address: No.628, Zhenyuan Rd, Guangming (New) Dist.

country: China

institute: The seventh affiliated hospital of Sun Yat-sen University

type: Expression profiling by high throughput sequencing

summary: Secondary mutation of KIT/PDGFRA is the main reason that contributes to the multi-drug resistance phenotype of advanced GIST in the clinical setting. SHP2 is a specific signal transducer of KIT. Therefore, the combination of approved KIT/PDGFRA kinase inhibitors and SHP2 inhibitors is a promising treatment strategy for advanced GIST patients. Here, we treated GIST cells with the SHP2 inhibitor SHP099 and sequenced the total mRNA to analyze the effect of SHP2 inhibition on GIST cells.

overall_design: GIST cells were cultured in IMDM supplemented with 20% FBS. In the control group, cells were cultured for 24 hours. In the treatment group, cells were treated with SHP099 (20 µM) for 24 hours. Total mRNA was extracted, processed, and analyzed.

first: Xi

last: Xiang

first: Xinhua

last: Zhang

first: Yulong


title: Wildtype and PALS1 knockout MDCKII cells grown under non-confluent and in 3D cyst cultures

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

country: Germany

institute: University Münster

summary: To investigate how gradual differences in the tight junction formation could be linked to an altered gene expression, wildtype and PALS1 knockout cell lines were grown under non-confluent and in 3D cyst cultures. After preparation of the mRNA samples, mRNASeq was performed. Normalized gene expression data was then was analyzed for differentially expressed genes, and GO-Term enrichment studies were used to elucidate involved pathways.

overall_design: Wild-type (WT) MDCK cells and MDCKII cells with a targeted knock-out in the PALS1 gene (PALS1 KO) were grown under different growth conditions (non-confluent and in 3D cysts).

first: Thomas

last: Weide

first: Hermann

last: Pavenstädt


title: RORc expressing immune cells negatively regulate tertiary lymphoid structure formation and support their pro-tumorigenic functions [scRNA]

status: Public on Dec 01 2024

city: Jerusalem

first: Oren

last: Parnas

address: Faculty of Medicine, Ein-Kerem medical center

department: Immunology

country: Israel

institute: The Hebrew University of Jerusalem

summary: Background and aims: Tertiary lymphoid structures (TLSs) are formed in many cancer types and have been correlated with better prognosis and response to immunotherapy. In liver cancer, TLSs have been reported to be pro-tumorigenic as they harbor tumor progenitor cells and nurture their growth. The processes involved in TLS development and the acquisition of a pro- or anti-tumorigenic phenotype in cancer are largely unknown. RORc expressing immune cells have been previously implicated in TLS formation, however, their role in TLS development in the context of inflammation-associated liver cancer remains unexplored. Methods: IKKβ(EE)Hep mice, exhibiting chronic liver inflammation and TLS formation followed by liver cancer, were crossed with RORc knockout mice to explore the effect of RORc on TLS and tumor formation. Transcriptional, proteomic and immunohistochemical techniques were used to analyze TLS phenotypes. CD4, CD8 and B cell depletions were used to analyze their contribution to liver TLS and tumor formation. Results: RORc expressing cells were detected within TLSs of both human patients and mice which develop intrahepatic cholangiocarcinoma. In mice, RORc expressing cells negatively regulate TLS formation, since in their absence TLSs form in excess. CD4 cells are essential for liver TLS formation whereas B cells are required for TLS formation specifically in the absence of RORc expressing cells. Importantly, in chronically inflamed livers lacking RORc expressing cells, TLSs become anti-tumorigenic, resulting in reduced tumor load. Comparing liver pro- and anti-tumorigenic TLSs, revealed enrichment of exhausted CD8 cells that retained effector functions, as well as germinal center B cells and plasma cells in anti-tumorigenic TLSs. Cell depletion experiments revealed a role mainly for B cells in limiting tumor development, possibly via tumor-directed antibodies. Conclusions: RORc expressing cells negatively regulate B cell responses, and facilitate the pro-tumorigenic functions of hepatic TLSs.

overall_design: The goal of this experiment was to analyze the composition and phenotype of RORc+ immune cells from hepatic tertiary lymphoid structures (TLSs). RORc+ immune cells were analyzed in 6 months old DEN-injected mice with chronicly inflammed livers (Alb-IKKβ(EE)Hep;RORctm2Litt +/-  (termed: IKK RORc Het or control), which harbor a GFP reporter cDNA knocked-in at the site of RORγt translation initiation site). GFP positive immune cells (expressing RORc) were isolated from 5 IKK RORc Het mice (cells were pooled after isolation).

first: Einat

last: Cinnamon

first: Ilan

last: Stein

first: Elvira

last: Zino

first: Eli

last: Pikarsky

first: Yehuda

last: Shovman


title: The Landscape of N6-Methyladenosine in Localized Primary Prostate Cancer

city: TORONTO

first: Xin

last: Xu

state: Ontario

address: 101 COLLEGE ST EAST TOWER 11-601D

country: Canada

institute: Princess Margaret Cancer Center

summary: To investigate the molecular role of VCAN in prostate cancer, we knockdown the VCAN gene by two different shRNAs in PC-3 xenografts.

overall_design: Differential gene expression analysis of RNA-seq data for KD control xenografts and KD VCAN xenografts.

first: Housheng

middle: H


title: QTL mapping reveals novel genes and mechanisms underlying variations in H2S production during alcoholic fermentation in Saccharomyces cerevisiae

city: Montpellier cedex1

first: Jean-Luc

last: Legras

address: 2, place Viala

department: UMR1083, Science pour l'Oenologie

country: France

institute: INRA

summary: Saccharomyces cerevisiae’s requirement of reduced sulfur to synthesise methionine and cysteine during alcoholic fermentation, is mainly fulfilled through the sulfur assimilation pathway. S. cerevisiae reduces sulfate into sulfur dioxide (SO2) and sulfide (H2S), whose overproduction is a major issue in winemaking, due to its negative impact on wine aroma. The amount of H2S produced is highly strain-specific and depends as well on the SO2 concentration, often added to the grape must. Applying a Bulk Segregant Analysis to a 96 strain-progeny derived from two strains with different ability to produce H2S, and comparing the allelic frequencies along the genome of pools of segregants producing opposite H2S quantities, we identified two causative regions involved in H2S production in the presence of SO2. A functional genetic analysis allowed the identification of variants in four genes: ZWF1, ZRT2, SNR2 and YLR125W, able to impact H2S formation, involved in functions and pathways until now not associated with sulfur metabolism. This data points that redox status and zinc homeostasis are linked to H2S formation in wine fermentation conditions and provides new insights into the regulation of H2S production during wine fermentation, giving a new vision of the interplay between the sulfur assimilation pathway and cell metabolism. This archive contains  the transcriptome data  of the result of allelic swp for  three   genes  : ZWF1, ZRT2, YLR125w under fermentation.

overall_design: For each gene , we analyzed  the transcriptome of the  two parental strain (WT)  , and the transcripttome of the  mutant strain obtained after the replacement by the allele of the other parent. Each modality has been analylazed in triplicated.

first: Irene

last: De Guidi

first: Céline

last: Serre

first: Jessica

last: Noble

first: Anne

last: Ortiz-Julien

first: Bruno

last: Blondin


title: Expression data from mouse proximal tubules of the kidneys of adult female control mice and proximal-tubule specific IGF-1R KO mice, that were ovariectomized at postnatal day 21

city: Kyoto

first: Yuichiro

last: Kitai

address: Yoshidakonoecho Sakyo-ku

country: Japan

institute: Kyoto University

summary: We used RNA-Seq analysis to detail the global programme of gene expression underlying IGF-1R knockout from proximal tubules.

overall_design: We compared gene expression in proximal tubules of uninjured control mice and proximal-tubule specific IGF-1R knockout mice, that were ovariectomized at postnatal day 21.

first: Naoya

last: Toriu

first: Shoko

last: Tarumoto

first: Taro

last: Tsujimura

first: Motoko

last: Yanagita


title: Expression data from mouse proximal tubules of the kidneys of sham-operated adult male mice, and female mice ovariectomized/sham-operated at postnatal day 21

summary: We used RNA-Seq analysis to detail the global programme of gene expression underlying pre-pubertal ovariectomy.

overall_design: We compared the global transcription profiles of mouse proximal tubules of  sham-operated adult male mice, and female mice ovariectomized/sham-operated at postnatal day 21


title: Functional screen for mediators of onco-mRNA translation specificity [II]

status: Public on Nov 29 2024

city: San Francisco

first: Joanna

last: Kovalski

state: CA

country: USA

institute: University of California San Francisco

summary: Oncogenic protein dosage is tightly regulated to enable cancer cells to adapt and survive. Whether this is regulated at the level of translational control and the key factors in cis and trans remain unknown. The Myc oncogene is a central paradigm of an exquisitely regulated oncogene and a major driver of pancreatic ductal adenocarcinoma (PDAC). Using a genome-wide 5’UTR CRISPRi screen in PDAC cells, we identified activators of selective MYC translation and validated four RNA binding proteins (RBPs), including epitranscriptome modifiers. Among these RBPs, RBM42 was our top hit, which is highly expressed in PDAC and predicts poor survival. Combining polysome sequencing and CLIP-seq analyses, we find that RBM42 binds and selectively regulates the translation of MYC and a precise, yet vital suite of pro-oncogenic transcripts, including JUN and EGFR. Mechanistically, employing IP-mass spectrometry analysis, we find that RMB42 is a novel ribosome-associated protein (RAP). Using DMS-Seq and mutagenesis analysis, we show that RBM42 directly binds and remodels the MYC 5’UTR RNA structure, facilitating the formation of the translation pre-initiation complex. Importantly, RBM42 is necessary for human PDAC cell growth and fitness and PDAC tumorigenesis in xenograft mouse models in a Myc-dependent manner in vivo. In PDAC patient samples, RBM42 expression is correlated with Myc protein levels and transcriptional activity. This work transforms our understanding of the translational code in cancer and offers a new therapeutic opening to target the expression of oncogenes.

overall_design: To investigate the EGFR and JUN 5'UTR RNA structure, we conducted Dimethyl sulfate (DMS) treatment followed by RNA-sequencing for the EGFR or JUN 5'UTR.

first: Davide

last: Ruggero


title: Functional screen for mediators of onco-mRNA translation specificity [DMS-seq]

overall_design: To investigate the role of RBM42 in PDAC cells in remodeling the MYC 5'UTR RNA structure, we conducted Dimethyl sulfate (DMS) treatment followed by RNA-sequencing for the MYC 5'UTR. We depleted RBM42 and compared the structures in the presence or absence of RBM42 in duplicate with 2 independent shRNAs.

first: Vishvak

last: Subramanyam


title: Single Cell Analysis Reveals The Essential Role of TGFbeta Pathway in Shaping Immune-suppressive Microenvironment and Promoting CRPC Development (bulk RNA-Seq)

city: Beijing

first: Zhenpeng

last: Wu

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

summary: To understand the dynamic changes of different cell populations within the Pten-null prostate cancer model in response to ADT, we carried out scRNA-seq transcriptome analysis on CD45- and CD45+ FACS-sorted cells from Pten-null intact (CP), early-(nmCRPC-4wks) and late-(nmCRPC-12wks) stage castrated prostates, respectively. To systematically investigate the effects of androgen deprivation therapy (ADT) on the cellular landscapes of primary and nmCRPC as well as intra- and extra-tumoral immune cells and their functional status at single cell level, we conducted scRNA-seq on CD45+ cells from bone marrow, blood, spleen and thymus of intact, early- and late-stage castrated Pten-null mice.

overall_design: Epithelial cells and fibroblasts of CP and CRPC prostates were FACS isolated for RNA-seq. CaP2/8 epithelial cell lines were treated with TGFβ1, FGF9, or SB431542 for indicated periods, then RNA was purified for RNA-seq.

first: Jinping

last: Li


title: Functional screen for mediators of onco-mRNA translation specificity [polysome-seq]

overall_design: To investigate the function of RBM42 on translation in PDAC cells, we knocked down RBM42 in Panc-1 cells with shRNA. We then performed total RNA-sequencing on pooled polysome fractions (poly-seq) in triplicate shSCR (control) and shRBM42-1.


title: Functional screen for mediators of onco-mRNA translation specificity

overall_design: To investigate the function of RBM42 in PDAC cells, we knocked down RBM42 in Panc-1 cells with shRNA. We then perfromed total RNA-sequencing in triplicate shSCR (control) and shRBM42-1.


title: A torpor-like state in mice slows blood epigenetic aging and prolongs healthspan [ET0301]

status: Public on Nov 28 2024

city: Cambridge

first: Sinisa

last: Hrvatin

state: MA

address: 455 Main Street

department: Whitehead Institute

institute: MIT

type: Methylation profiling by genome tiling array

summary: Torpor and hibernation are extreme physiological adaptations of homeotherms associated with pro-longevity effects. Yet the underlying mechanisms of how torpor affects aging, and whether hypothermic and hypometabolic states can be induced to slow aging and increase health span, remain unknown. We demonstrate that the activity of a spatially defined neuronal population in the avMLPA, which has previously been identified as a torpor-regulating brain region, is sufficient to induce a torpor like state (TLS) in mice. Prolonged induction of TLS slows epigenetic aging across multiple tissues and improves health span. We isolate the effects of decreased metabolic rate, long-term caloric restriction, and decreased core body temperature (Tb) on blood epigenetic aging and find that the decelerating effect of torpor-like states on aging is mediated by decreased Tb. Taken together, our findings provide novel mechanistic insight into the decelerating effects of torpor and hibernation on aging and support the growing body of evidence that Tb is an important mediator of aging processes.

platform_organism:
Macaca mulatta
Homo sapiens
Mus musculus
Rattus

overall_design: Samples beginning with CR are from the  caloric restriction experiment in figure 4 of the paper. Samples beginning with C (experimental) or F (control) (date added to the end) are from long-term experiments in figure 3 of the paper. The title of each sample explains what treatment group the sample is from.

first: Jayne

last: Lorna

first: Hrvatin

last: Sinisa


title: Gene expression profiles of sorted D1- and D2-expressing cells in mouse ventral hippocampus

city: New York

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

summary: The hippocampus, as well as dopamine circuits, coordinate decision-making in anxiety-eliciting situations. Yet, little is known about how dopamine modulates hippocampal representations of emotionally-salient stimuli to inform appropriate resolution of approach versus avoidance conflicts. We here study dopaminoceptive neurons in mouse ventral hippocampus (vHipp), molecularly distinguished by their expression of dopamine D1 or D2 receptors. We show that these neurons are transcriptionally distinct and topographically organized across vHipp subfields and cell types. While both D1 and D2 vHipp neurons are recruited during anxiogenic exploration, they mediate opposite approach/avoidance responses, and are differentially modulated by dopaminergic transmission. We propose that vHipp dopamine dynamics operate as a feedback loop to gate exploratory behaviors, implicating dopaminoception in the complex computation engaged in vHipp to govern emotional states.

overall_design: Single-nuclei RNA-sequencing of D1- and D2-expressing nuclei from mouse vHipp dissection isolated by Fluorescence-Activated Nuclei Sorting

first: Arthur

last: Godino

first: Marine

last: Salery

first: Angelica

middle: M

last: Minier-Toribio

first: Vishwendra

last: Patel

first: John

middle: F

last: Fullard

first: Eric

last: Parise

first: Freddyson

middle: J

last: Matrinez-Rivera

first: Carole

last: Morel

first: Panos

last: Roussos

first: Robert

middle: D

last: Blitzer

last: Nestler


title: A torpor-like state in mice slows blood epigenetic aging and prolongs healthspan [9155]

overall_design: Samples beginning with C (TLS) or F (control) are from long-term experiments (date added to the end) in figure 3 of the paper.


title: A torpor-like state in mice slows blood epigenetic aging and prolongs healthspan [ET0283]

overall_design: Samples beginning with C (TLS) or F (control) are from long-term experiments (date added to the end) in figure 3 of the paper. Samples beginning with TC are from temperature clamp experiments from figure 4 of paper. The title of each sample explains what treatment group the sample is from.


title: Epitranscriptomic rRNA fingerprinting reveals tissue-of-origin and tumor-specific signatures

city: Barcelona

first: Ivan

last: Milenkovic

state: Catalonia

address: Dr. Aiguader 88

country: Spain

institute: Centre for Genomic Regulation

summary: Mammalian ribosomal RNA (rRNA) molecules are highly abundant RNAs, decorated with over 220 different rRNA modifications, changing their chemical and biological properties. Previous works have shown that some types of rRNA modifications can be dynamically regulated; however, a comprehensive analysis of how the mammalian rRNA modification landscape is remodeled across time, cell types and upon disease conditions, remains largely unexplored. Here, we employ direct RNA nanopore sequencing to generate maps of human and mouse rRNA modifications across tissues, developmental stages, cell types and disease conditions. Our analyses reveal multiple rRNA sites that are differentially modified in a tissue- and/or developmental stage-specific manner. Notably, the adult brain exhibits the most distinct rRNA modification patterns, including previously unannotated rRNA modified sites. We then demonstrate that dynamic rRNA modification patterns can be used for tissue and cell type identification, which we hereby term ‘epitranscriptomic fingerprinting’. We then explored rRNA modification patterns in normal-tumor matched samples from lung cancer patients, finding that rRNA epitranscriptomic fingerprinting accurately classified clinical samples into normal and tumor groups from only 250 reads per sample, demonstrating the potential of rRNA modifications as diagnostic biomarkers, and revealing rRNA modifications as a rich source of information for tissue, cell type and disease identification.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Direct-RNA sequencing of rRNA from mouse tissues, cell lines and human matched normal-tumor lung samples.

first: Novoa

last: Eva Maria

first: Milenkovic

last: Ivan

first: Cruciani

last: Sonia

first: Llovera

last: Laia

first: Medina

last: Rebeca


title: scRNA sequencing of the small intestine lamina propria of laboratory and rewilded mice

city: Philadelphia

first: Ken

last: Cadwell

state: PA

address: 421 Curie Boulevard

institute: University of Pennsylvania Perelman School of Medicine

summary: In rewilded mice, we observed B cells in circulation with increased signs of maturation, alongside heightened germinal center responses within secondary lymphoid organs. Rewilding also expanded B cells in the gut, which was accompanied by elevated systemic levels of IgG and IgM antibodies reactive to the microbiota. Our findings indicate that exposing laboratory mice to a more natural environment enhances B cell development to better reflect the immune system of free-living mammals.

overall_design: Laboratory and rewilded mice (C57BL/6J) were compared after 6-7 weeks. Small intestine lamina propria cells were harvested and 4 mice per condition were pooled and then used on individual lanes for sequenceing.

first: Ying-Han

last: Chen

first: Kimberly

last: Zaldana


title: Unravelling AURKB as a potential therapeutic target in pulmonary arterial hypertension using integrated transcriptomic analysis and pre-clinical studies

city: Quebec city

first: Francois

last: Potus

address: 2725 Ch Ste-Foy

institute: IUCPQ-Laval university

summary: To illuminate new actionable targets involved in pulmonary vascular remodeling in pulmonary arterial hypertension (PAH), we performed RNA sequencing on pulmonary artery smooth muscle cells (PASMCs) isolated from PAH patients and control donors. We then enriched our own experiment with publicly available datasets. Aggregation of gene expression datasets followed by functional enrichment and connectivity map analyses on common upregulated genes in PAH-PASMCs revealed Aurora kinase B (AURKB), the enzymatic core of the chromosomal passenger complex with BIRC5, as a potential driver and therapeutic target in PAH. Using pharmacological and molecular tools, we demonstrated that inhibition of AURKB in PAH-PASMCs blocks cell cycle progression, induces cell death, and reverses the gene signature of PAH-PASMCs. In addition, we provided evidence that AURKBi-treated PAH-PASMCs that escape apoptosis, acquire a senescence-associated secretory phenotype. In vivo, AURKB inhibition using Barasertib significantly improved hemodynamics in two preclinical models of established PAH by attenuating pulmonary vascular remodeling. A therapeutic effect was also observed in precision-cut lung slices generated from human lungs, thus confirming the predictive value of AURKB interference as a potential therapeutic for PAH progression.Finally, we demonstrated that the combination of Barasertib with the anti-senescent agent UC2288 was more effective in reducing vascular remodeling than either drug alone.

overall_design: we performed a comparative transcriptomic analysis between control and PAH-PASMCs, and then aggregated our results with publicly available databases to establish a disease signature. Based on this signature, we next applied a computational drug repositioning pipeline that revealed an antimitotic agent (AURKB inhibitor), which has never been tested in PAH preclinical research, as the top reverser. We then investigated the role of AURKB in PAH progression.

first: Boucherat

last: Olivier


title: Distinct Gene Regulatory Dynamics Drive Skeletogenic Cell Fate Convergence During Vertebrate Embryogenesis [scRNA-Seq]

status: Public on Nov 27 2024

city: Basel

first: Patrick

last: Tschopp

address: Vesalgasse 1

department: Department of Environmental Sciences

country: Switzerland

institute: University of Basel

summary: Cell type repertoires have expanded extensively in metazoan animals, with some clade-specific cells being paramount to their evolutionary success. A prime example are the skeletogenic cells of vertebrates that form the basis of their developing endoskeletons. Depending on anatomical location, these cells originate from three different embryonic precursor lineages – the neural crest, the somites, and the lateral plate mesoderm – yet they converge developmentally towards similar cellular phenotypes. Furthermore, these lineages have gained ‘skeletogenic competency’ at distinct timepoints during vertebrate evolution, thus questioning to what extent different parts of the vertebrate skeleton rely on truly homologous cell types. Here, we investigate how lineage-specific molecular properties of the three precursor pools are integrated at the gene regulatory level, to allow for phenotypic convergence towards a skeletogenic cell fate. Using single-cell transcriptomics and chromatin accessibility profiling along the precursor-to-skeletogenic cell continuum, we examine the gene regulatory dynamics associated with this cell fate convergence. We find that distinct transcription factor profiles are inherited from the three precursor states, and that lineage-specific enhancer elements integrate these different inputs at the cis-regulatory level, to execute a core skeletogenic program. We propose a lineage-specific gene regulatory logic for skeletogenic convergence from three embryonic precursor pools. Early skeletal cells in different body parts thus share only a partial ‘deep homology’. This regulatory uncoupling may render them amenable to individualized selection, to help to define distinct morphologies and biomaterial properties in the different parts of the vertebrate skeleton.

overall_design: single-cell RNAseq data from chicken embryonic tissues

first: Tschopp

last: Patrick


title: Distinct Gene Regulatory Dynamics Drive Skeletogenic Cell Fate Convergence During Vertebrate Embryogenesis [scATAC]

type: Genome binding/occupancy profiling by high throughput sequencing


title: Exploring the mechanism of AGR2 regulating the progression of pancreatic ductal adenocarcinoma and remodeling of the tumor microenvironment

status: Public on Nov 26 2024

city: Nanjing

first: Hongzhen

last: Li

state: Jiangsu

address: No. 321 Zhongshan Road, Nanjing, Jiangsu, 210008, China

institute: The Affiliated Hospital of Nanjing University Medical School

summary: Pancreatic ductal adenocarcinoma (PDAC) is a highly invasive and lethal malignant tumor characterized by extensive desmoplasia. We found that AGR2 deletion reshapes the tumor microenvironment by affecting the activation of the IGF1 signaling pathway. On the one hand, AGR2, as an endoplasmic reticulum protein, promoted correct folding and cell surface distribution of IGF1R. On the other hand, AGR2 was secreted into the extracellular space, promoting IGF1 transcription by activating the WNT pathway in cancer-associated fibroblasts (CAFs). Through these mechanisms, AGR2 significantly enhanced the IGF1 signal in the PDAC tumor microenvironment, accelerating the formation of desmoplasia and an immunosuppressive microenvironment.

overall_design: In order to investigate the effect of AGR2 on pancreatic ductal adenocarcinoma (PDAC) tumor cells, we knocked out AGR2 in panc1 and capan2 cells using CRISPR/Cas9 technology and selected monoclonal cell lines. We performed RNA sequencing on the above-mentioned cell lines after AGR2 knockout. To investigate the effect of secreted AGR2 on cancer-associated fibroblasts (CAFs), we subjected CAFs derived from human PDAC to 12 hours of serum starvation followed by treatment with rAGR, TGFβ, and IL1α for 24 hours.

first: Shanshan

last: Shen

first: Bo

last: Kong


title: Exploring the mechanism of AGR2 regulating the progression of pancreatic ductal adenocarcinoma and remodeling of the tumor microenvironment [CUT&Tag]

overall_design: In order to investigate the transcriptional regulation of AGR2 by c-JUN, Panc1 cells were subjected to Cleavage Under Targets and Tagmentation (CUT&Tag) assays using c-JUN antibody after 12 hours of serum starvation with or without IGF1 treatment.


title: NK cell cytotoxicity shapes the clonal evolution of B cell leukemia [DNA barcoding]

city: Vienna

first: CCRI

last: BiCU

address: Zimmermannpl. 10

department: Bioinformatics Core Unit

country: Austria

institute: St. Anna Children's Cancer Research Institute

summary: The term cancer immunoediting describes the dual role by which the immune system can suppress and promote tumour growth and is divided into three phases: elimination, equilibrium and escape. The role of NK cells has mainly been attributed to the elimination phase. Here we show that NK cells play a role in all three phases of cancer immunoediting. Extended co-culturing of DNA barcoded mouse BCR/ABLp185+ B acute lymphoblastic leukaemia cells with NK cells allowed for a quantitative measure of NK cell-mediated immunoediting. Whereas most tumour cell clones were efficiently eliminated by NK cells, a certain fraction of tumour cells harboured an intrinsic primary resistance. Furthermore, DNA barcoding revealed tumour cell clones with secondary resistance, which stochastically acquired resistance to NK cells. NK cell cytotoxicity put a selective pressure on B-ALL cells inducing primary and secondary resistance, while resistant tumour cells were characterised by a full-blown IFN-g signature. Besides well-known regulators of immune evasion, our analysis of NK resistant tumour cells revealed the upregulation of novel genes, including Ly6a, which we found to drive NK cell resistance in leukaemic cells. We further translated our findings to the human system and showed that high LY6E expression on tumour cells impaired the physical interaction with NK cells and led to worse prognosis in leukaemia. Our results demonstrate that tumour cells are actively edited by NK cells during the equilibrium phase and use different avenues to escape NK cell-mediated eradication.

overall_design: Experiment includes B-ALL alone  and B-ALL cultured with WT, Ifng-/- and Prf-/- NK cells samples, which were anaylsed on different timepoints. Experiments was conducted in biological triplicates with 2 to 4 cell lines. DNA barcode amplicons are sequenced in technical duplicates.

first: Michelle

middle: C

last: Buri

first: Mohamed

middle: R

last: Shoeb

first: Aleksander

last: Bykov

first: Peter

last: Reiscak

first: Hayeon

last: Baik

first: Alma

last: Dupanovic

first: Faith

middle: O

last: David

first: Boris

last: Kovacic

last: Hall-Glenn

first: Sara

last: Dopa

first: Jos

last: Urbauns

first: Lisa

last: Sippl

first: Susanne

last: Stofner

first: Dominik

last: Emminger

first: Jason

last: Cosgrove

first: Dagmar

last: Schinnerl

first: Anna

last: Poetsch

first: Manfred

last: Lehner

first: Xaver

last: Koenig

first: Leïla

last: Perié

first: Ton

middle: N

last: Schumacher

last: Gotthardt

first: Florian

last: Halbritter

first: Eva

last: Putz


title: NK cell cytotoxicity shapes the clonal evolution of B cell leukemia [ATAC-seq]

first: CCRI

last: BiCU

first: Michelle

last: Buri

first: Mohamed

last: Shoeb

first: Aleksander

last: Bykov

first: Peter

last: Reiscak

first: Hayeon

last: Baik

first: Alma

last: Dupanovic

last: David

last: Kovacic


title: A decision point between transdifferentiation and programmed cell death priming controls

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

summary: The involvement of cell death pathways in the early stage of pancreatic ductal adenocarcinoma (PDAC) development, especially KRAS-dependent acinar-to-ductal metaplasia (ADM), remains to be investigated. Here, we show that TAK1 mediates cell survival during ADM transdifferentiation through suppression of Caspase-8/3-dependent apoptosis and RIPK3-MLKL-dependent necroptosis, which could be targeted for prevention and treatment of PDAC. Given that mutations are a driving force of PDAC development and TAK1 might modulate chromosomal stability and the mutational spectrum of PDAC via NF-κB, we performed an array comparative genomic hybridization (aCGH) analysis on pancreatic tissue of five KRASG12D TAK1/CASP8ΔAc RIPK3-/- mice and five KRASG12D mice. Interestingly, both genotypes showed distinct chromosomal abnormalities with gain or loss of genetic regions. Further analysis of these chromosomal regions showed they contained genes known to be involved in the pathogenesis of human PDAC, such as Trp53, Cdkn2a, Smad4, Rnf43 and Arid1a. However, we did not observe a consistent pattern of chromosomal/gene alterations in the majority of samples/tumors between KRASG12D single transgenic mice and KRASG12D TAK1/CASP8ΔAc RIPK3-/- mice, arguing against the hypothesis that TAK1 deficiency mediated late stages of tumor promotion through changes in chromosomal stability.

overall_design: the genomic DNA of pancreatic tissue from 5 KRAS mutant mice (KRASG12D) and 5 mice which were  KRAS mutant (KRASG12D), TAK1/CASP8 deficient and  RIPK3-/- knockout  was hybridized against the genomic DNA from a pooled normal DNA reference from the same mouse strain and the resulting copy number profiles compared to each other.

first: Mihael

last: Vucur


title: Spatially restricted immune and microbiota-driven adaptation of the gut [scRNA-seq]

first: Ramnik

last: Xavier

address: 415 Main Street

institute: Broad Institute of MIT and Harvard

summary: The intestine is characterized by an environment where host requirements for efficient nutrient and water absorption are consequently paired with the requirement to establish and maintain tolerance to the outside environment. The organ is anatomically organized into the small intestine (SI) which specializes in nutrient absorption and the colon which specializes in water resorption. The transcriptional and cellular circuits that define intestinal regionalization and their robustness, adaptability, and resilience to changes in the local environment are not well characterized. Here, we generated a comprehensive survey of the spatial and cellular landscape of the murine intestine to demonstrate the steady state transcriptional landscape of the murine intestine is robust, adaptable, and resilient to perturbation. We characterized the transcriptional landscape of the full length of the intestine and show it is established independently of the microbiota and is not under circadian regulation. In the colon, these regional circuits were characterized by unique subsets of structural cells. Moreover, we identified a spatial adaptation to the microbiota in the colon characterized by the emergence of unique structural cell subsets including an enterocyte, fibroblast, and goblet cell, with the later two co-occurring in space. Employing a model of acute spatiotemporal damage allowed us to show the spatial landscape and adaptations we identified are both resilient to inflammation. Our results demonstrate that intestinal circuits are under host control and spatial adaptations in the steady state as well as in the process of recovery from tissue damage in the inflamed state are primarily characterized by changes to structural cell types such as epithelial and stromal cells.

overall_design: Single cell suspensions were generated for single cell RNA sequencing from 4 different segments (A-D) of mouse colon from WT SPF and GF mice and 2 segments (B-C) from WT FMT mice. 3 biological replicates were generated for each segment for both SPF and GF mice. 2 biological replicates were generated for each segment for FMT mice. Samples were compared within SPF mice to establish the cellular complexity of different regions in the steady state and subsequently compared to GF mice and FMT mice to establish those that are dependent on the microbiota.

first: Toufic

last: Mayassi

first: Chenhao

last: Li


title: Spatially restricted immune and microbiota-driven adaptation of the gut [Spatial Transcriptomics]

overall_design: Intestinal tissue was collected from WT SPF, GF, or FMT treated mice as well as DSS treated mice. Tissue was partitioned into segments covering the duodenum, jejunum, ileum, and colon and then swiss rolled and embedded in OCT for freshly frozen sample generation used for spatial transcriptomics data generation using 10x Visium technology. Samples were compared to establish the steady state spatial transcriptome of the intestine, the spatial transcriptome regulated by microbiota, and finally the impact of inflammation and recovery from inflammation on the spatial transcriptome of the intestine. 3 biological replicates were included for each tissue segment for SPF and GF mice and 2 biological replicates were included for each tissue segment for FMT treated mice. 1 biological replicate was generated for DSS treated tissue.


title: Spatially restricted immune and microbiota-driven adaptation of the gut

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

overall_design: Refer to individual Series


title: A targetable PREX2/RAC1/PI3Kb signalling axis confers resistance to clinically relevant therapeutic approaches in melanoma

status: Public on Nov 22 2024

city: Glasgow

first: Kathryn

last: Gilroy

address: Switchback Road

country: United Kingdom

institute: Cancer Research UK Scotland Institute

summary: Metastatic melanoma remains a major clinical challenge. Large-scale genomic sequencing of melanoma has identified bona fide activating mutations in RAC1, with mutations of its upstream regulator, the RAC-GEF PREX2, also commonly detected. Crucially, RAC1 mutations are associated with resistance to BRAF-targeting therapies. Despite the role of its homologue PREX1 in melanomagenesis, and evidence that some truncating PREX2 mutations drive increased RAC1 activity, no hotspot mutations have been identified, and the impact of PREX2 mutation remains contentious. Here, we use genetically engineered mouse models and patient-derived BRAFV600E-driven melanoma cell lines to dissect the role of PREX2 in melanomagenesis and response to therapy. We show that while PREX2 is dispensable for the initiation and progression of melanoma, its loss confers sensitivity to clinically relevant therapeutics. Importantly, genetic and pharmacological targeting of the RAC1 effector kinase PI3Kβ phenocopies PREX2 loss, sensitizing our model systems to therapy. Our data reveal a druggable PREX2/RAC1/PI3Kβ signalling axis in BRAF-mutant melanoma that could be exploited clinically.

overall_design: Gene expression data of Braf Pten melanoma in mice treated with combinations of AZD6244 (MEK1/2 inhibitor), AZD8835 (p110a inhibitor) and AZD8186 (p110b/d inhibitor).

first: Catriona

last: Ford

first: Andrew

last: Campbell

first: Owen

last: Sansom


title: A Ralstonia solanacearum effector targets splicing factor SR34a to reprograms alternative splicing and regulates host immunity

city: Shanghai

first: Yingji

last: Chen

address: 2005 Songhu Road, Yangpu District

department: School of Life Sciences

institute: Fudan University

summary: Alternative splicing (AS) is a critical post-transcriptional regulatory mechanism in eukaryotes. While infection with Ralstonia solanacearum GMI1000 significantly alters plant AS patterns, the underlying molecular mechanisms remain unclear. Herein, we investigate the effects of GMI1000 Type III secretion system (T3SS) effector proteins on AS in the tomato cultivar Heinz 1706. RNA sequencing (RNA-seq) confirmed genome-wide AS changes induced by the T3SS in tomato, in-cluding 1386 differential alternative splicing events in 1023 differentially alternatively spliced genes, many of which are associated with plant defense. Seven nucleus-localized Type III effec-tors(T3Es) were transiently expressed in an RLPK splicing reporter system transgenic tobacco, identifying RipP2 as an effector that modulates AS levels. Sequence analysis, protein-protein in-teraction assays, and AlphaFold2 structural predictions revealed that RipP2 interacts with the tomato splicing factor SR34a.Furthermore, RipP2 acetylates a conserved lysine at position 132 within the SWQDLKD motif of SR34a, regulating its splicing pattern in defense-related genes and modulating plant immunity. This study elucidates how the "Rip-SR34a module" influences plant immune responses by regulating the alternative splicing of immune-related genes, providing new insights into the molecular mechanisms of pathogen-plant interactions, particularly in splicing regulation.

overall_design: The study includes RNA samples extracted from Solanum lycopersicum (tomato plants) to investigate the regulatory effects of Type III secretion system effectors from Ralstonia solanacearum strain GMI1000 on alternative splicing (AS). The experimental design comprises two main groups: a control group and an experimental group. Each group includes three biological replicates to ensure reproducibility and accuracy. Tomato plants treated with a non-virulent strain (hrcV mutant) of Ralstonia solanacearum (Samples: hrcV-1, hrcV-2, hrcV-3). Tomato plants treated with the wild-type strain GMI1000 of Ralstonia solanacearum (Samples: GMI1000-1, GMI1000-2, GMI1000-3). The variables under investigation include the presence or absence of the effector proteins from R. solanacearum and their impact on alternative splicing patterns in the host plant. Control samples help to establish a baseline for comparison with the experimental samples, which are expected to exhibit changes in splicing patterns due to the presence of the effectors.


title: SPARROW reveals microenvironment zone-specific cell states in healthy and diseased tissues.

status: Public on Nov 24 2024

city: Seattle

first: Peiyao

middle: A

last: Zhao

state: WA

address: 615 Westlake Ave N

institute: Allen Institute

summary: Spatially resolved transcriptomics technologies have significantly enhanced our ability to understand cellular characteristics within tissue contexts. However, current analytical tools often treat cell type inference and cellular neighbourhood identification as separate and hard clustering processes, resulting in models that are not comparable across tissue feature scales and samples, thus hindering a unified understanding of tissue features. Our computational framework, SPARROW, addresses these challenges by representing cell types and cellular organization patterns as latent embeddings learned through an interconnected neural network architecture. SPARROW integrates clustering directly into the learning of these latent embeddings, enabling feature extraction specific to clustering while ensuring comparability across samples through shared latent spaces. When applied to diverse datasets, SPARROW outperformed state-of-the-art methods in cell type inference and microenvironment zone delineation and uncovered microenvironment zone-specific fine cell states that reveal underlying biology. Furthermore, SPARROW algorithmically achieves single cell spatial resolution and whole transcriptome coverage---an experimental challenge---by integrating spatially resolved transcriptomics and scRNA-seq data in a shared latent space. This formulation enabled SPARROW to uncover both established and novel microenvironment zone-specific ligand-receptor interactions in human tonsils---discoveries not possible with either data modality alone. Overall, SPARROW provides a comprehensive characterization of tissue features across scales, samples and conditions.

overall_design: Spatially resolved transcriptomics merFISH (Vizgen MERSCOPE) of human tonsil and lymph nodes


title: A CXCL8 Signaling Axis Enables Susceptibility to Infection by Human Respiratory Viruses

city: Changchun, Jilin

first: qingran

last: yang

address: 1 Xinmin Street, Chaoyang District

institute: First hospital of Jilin university

summary: Respiratory viruses pose an ongoing threat to human health, with excessive cytokine secretion playing a critical role in severe illness and mortality. However, the complex relationship between cytokine secretion and viral infection remains poorly understood. Here, we have unraveled the role of cxcl8 as an early response gene to respiratory EV-D68 infection. The upregulation of CXCL8 by viral infection is found to be crucial for EV-D68 replication. Importantly, silencing CXCL8 or its receptors, CXCR1/2, significantly impedes EV-D68 replication. Upon recognition of CXCL8 by CXCR1/2, the MAPK pathway is activated, facilitating the translocation of the essential host cofactor hnRNP K from the nucleus to the cytoplasm. This translocation enhances the recognition of viral RNA by hnRNP K in the cytoplasm, promoting the functionality of the 5’UTR region in the viral genome. Interestingly, the VP4 structural protein of EV-D68 contains a mimic motif of human immunoreceptor tyrosine-based activation motif (ITAM) that interacts with syk and triggers the PI3K/AKT signaling pathway, resulting in elevated CXCL8 gene expression for viral replication. Moreover, our investigations reveal the conservation and significance of the CXCL8 signaling pathway across various prominent human respiratory viruses, including SARS-CoV-2, influenza, and rhinovirus. In summary, our findings unveil a paradigmatic mechanism through which respiratory viruses exploit cytokine-mediated intercellular communication to transmit signals that optimize viral replication. This deepens our understanding of the shared evolutionary strategies employed by respiratory viruses and opens up new avenues for the development of broad-spectrum antiviral drugs targeting respiratory pathogens.

overall_design: To identify early host responses that modulate viral infection, we analyzed the effects of low-does viral infection (EV-D68, MOI=0.1)) on the entire transcriptome within respiratory A549 cells. The samples were collected for RNA-Seq assay at an early stage of infection (4 hpi.)


title: Gene expression analysis of macrophages exposed to LPS and LPS-coated beads

status: Public on Nov 25 2024

city: Amherst

first: Alissa

last: Rothchild

address: 661 N Pleasant Street

department: Veterinary and Animal Sciences Department

institute: University of Massachusetts Amherst

summary: The aim of this study was to measure the response of alveolar macrophages (AM) and bone marrow-derived macrophages (BMDM) to LPS, LPS-coated beads, and PBS-coated beads

overall_design: Mice were exposed to LPS-coated beads or PBS-coated beads using a nebulizer. Alveolar macrophages were isolated 4 hours after exposure by broncholaveolar lavage and by fluorescence activated cell sorting using the following surface markers (CD45+, Zombie Violet-, CD3-/CD19-, Siglec F+, CD64+, FITC-bead+ or FITC-bead-). Bone marrow-derived macrophages were collected 4 hours after exposure to LPS-coated beads, PBS-coated beads, or soluble LPS by fluorescence activated cell sorting using the following surface markers (CD45+, Zombie Violet-, CD3-/CD19-, F4/80+, FITC-bead+ or FITC-bead-). Samples were analyzed by RNA-sequencing.

first: Alan

last: Diercks

first: Pamelia

last: Lim


title: Aberrant homeodomain-DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models [Coop-seq]

city: Saint Louis

first: Shiming

state: Missouri

address: 517 South Euclid Avenue

department: Department of Ophthalmology & Visual Sciences

institute: Washington University in St Louis

summary: Paired-class homeodomain transcription factors (HD TFs) play essential roles in vertebrate development, and their mutations are linked to human diseases. One unique feature of paired-class HD is cooperative dimerization on specific palindrome DNA sequences. Yet, the functional significance of HD cooperative dimerization in animal development and its dysregulation in diseases remain elusive. Using the retinal TF Cone-rod Homeobox (CRX) as a model, we have studied how blindness-causing mutations in the paired HD, p.E80A and p.K88N, alter CRX’s cooperative dimerization, lead to gene misexpression and photoreceptor developmental deficits in dominant manners. CRXE80A maintains binding at monomeric WT CRX motifs but is deficient in cooperative binding at dimeric motifs. CRXE80A’s dimerization defect impacts the exponential increase of photoreceptor gene expression in terminal differentiation and produces immature, non-functional photoreceptors in the CrxE80A retinas. CRXK88N is highly cooperative and localizes to ectopic genomic sites with strong enrichment of dimeric HD motifs. CRXK88N’s altered biochemical properties disrupt CRX’s ability to direct dynamic chromatin remodeling during development to activate photoreceptor differentiation programs and silence progenitor programs. Our study here provides in vitro and in vivo molecular evidence that paired-class HD cooperative dimerization regulates neuronal development and dysregulation of cooperative binding contributes to severe dominant blinding retinopathies.

overall_design: Two Coop-seq libararies containing dimeric HD motif variants on the sense or antisense strand were designed to profile the binding specificity of WT and mutant CRX HDs. The two libraries were mixed in equal molar ratio in the Coop-seq experiments.

first: Yiqiao

last: Zheng


title: Aberrant homeodomain-DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models [MPRA]

overall_design: A specific set of CRX bound genomic sequences were selected and tested for their regulatory activities in episomal plasmids in ex plant WT and CRX HD mutant mouse retinas.


title: H3K27me3 ChIP-seq in Burkitt lymphoma cells (Ramos cell line), wild type and SP140 knockout

status: Public on Nov 21 2024

city: Milano

first: Ettore

last: Zapparoli

address: via Olgettina 60

country: Italy

institute: Ospedale San Raffaele

summary: Sp140 is a lymphocytic-restricted protein, an epigenetic reader working as a corepressor of genes implicated in inflammation and orchestrating macrophage transcriptional programs to maintain cellular identity. Reduced Sp140 expression is associated both to autoimmune diseases and blood cancer. However, the molecular mechanisms that link Sp140 altered protein levels to detrimental effects on the immune response and cellular growth, as well as the interactors through which Sp140 promotes gene silencing, remain elusive. In this work, we have applied a multi-omics approach (i.e. interactomics, ChIP-seq and proteomics) in two Burkitt lymphoma cell lines to identify both interactors and target genes of endogenous Sp140. We found that Sp140 interacts with the PRC2 and NuRD complexes and we demonstrated that Sp140 interaction with PRC2 is functional and directs H3K27me3 deposition on a set of target genes related to cellular growth and leukaemia progression.

first: Simone

last: Tamburri

first: Zucchelli

last: Chiara

first: Angela

last: Bachi

first: Giovanna

last: Musco


title: ChIP-seq analysis done for MBD3 before and after SP140 knockout in Ramos cells

overall_design: We used ChIP-grade antibody for MBD3 and immunoprecipitated chromatin from wild type and SP140 KO Ramos cells

first: Zivojin

last: Jevtic

first: Fabio

last: Iannelli


title: Burkitt lymphoma cells (Ramos cell line), wild type and SP140 knockout


title: Aberrant homeodomain-DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct


title: Phenotypic plasticity and increased tissue infiltration of TREM1+ mono-macrophages following radiotherapy in rectal cancer. [scRNA-Seq]

status: Public on Nov 20 2024

city: wuhan

first: Mingjie

last: Li

address: union hospital

institute: Huazhong University of Science and Technology

summary: Our previously reported phase II and phase III trials have demonstrated that short-course radiotherapy (SCRT) combined with neoadjuvant immunochemotherapy (SIC) has led to clinical benefits in locally advanced rectal cancer (LARC). Characterization of the molecular mechanisms underlying responses to SIC may lead to improved treatment strategies. Here, we prospectively collected and applied multi-omic analyses to paired pre- and post-treatment LARC specimens undergoing SIC. The TREM1+ mono-macrophages subsets that display a pro-inflammatory phenotype are identified and correlate with complete response to SIC. Mechanically, ionizing radiation (IR) induces peripheral TREM1+ mono-macrophages expansion in tumors. Following IR, loss of TREM1 in mono-macrophages undermines antitumor immunity by altering mono-macrophages differentiation and inhibiting CD8+ T cell infiltration and activation. The TREM1+ mono-macrophages response may rely on activation of key inflammatory pathways, including NF-κB signaling and Toll-like receptor pathway. Pharmacological inhibition of TREM1 abolishes IR-induced immunoactivation and reduces combined IR and/or anti-PD-1 treatment. Thus, we establish a crucial role of a mono-macrophages state in mediating effective cancer therapy.

overall_design:
To investigate changes in peripheral blood mononuclear/macrophage system in LARC after neoadjuvant therapy with LC or SIC, we employed a large-scale transcriptomic analysis of peripheral blood mononuclear cells (PBMCs). Specimens were collected from 16 consecutive patients. To investigate the cellular and molecular contexture of the tumor immune microenvironment (TIME) following SIC treatment, we characterized CD45+ immune cells isolated from tumor tissue specimens before and after SIC by high-throughput single-cell RNA sequencing (scRNA-seq).

***************************************************************
no raw data due to patient privacy
***************************************************************


title: Phenotypic plasticity and increased tissue infiltration of TREM1+ mono-macrophages following radiotherapy in rectal cancer. [RNA-Seq]

overall_design:
To investigate changes in peripheral blood mononuclear/macrophage system in LARC after neoadjuvant therapy with LC or SIC, we employed a large-scale transcriptomic analysis of peripheral blood mononuclear cells (PBMCs). Specimens were collected from 16 consecutive patients. To investigate the cellular and molecular contexture of the tumor immune microenvironment (TIME) following SIC treatment, we characterized CD45+ immune cells isolated from tumor tissue specimens before and after SIC by high-throughput single-cell RNA sequencing (scRNA-seq). "HX-1A" represents the patient's RNA-seq data before treatment and "HX-4A" represents data after treatment.

***************************************************************
no raw data due to patient privacy
***************************************************************


title: Aberrant homeodomain-DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models [ATAC-seq]

overall_design: Whole retina bulk ATAC-seq experiments were performed on post-natal day 14 (P14) mouse retinas to understand how homeodomain missense mutations, p.E80A, p.K88N, p.R90W, affect chromatin remodeling in the developing mouse retinas.


title: NK cell cytotoxicity shapes the clonal evolution of B cell leukemia [RNA-seq]

first: CCRI

last: BiCU

overall_design: Experiment includes B-ALL alone  and B-ALL cultured with WT, Ifng-/- and Prf-/- NK cells samples, which were anaylsed on different timepoints. Experiments was conducted in biological triplicates with 2 to 4 cell lines. Cell lines A: DNA barcoded tumour cell line 1. Originating from BCR/ABLp185+ cell line #13. B: DNA barcoded tumour cell line 2. Originating from BCR/ABLp185+ cell line #13. C: DNA barcoded tumour cell line 1. Originating from BCR/ABLp185+ cell line #15. D: DNA barcoded tumour cell line 2. Originating from BCR/ABLp185+ cell line #15. DNA barcode amplicons are sequenced in technical duplicates.

first: Michelle

last: Buri

first: Mohamed

last: Shoeb

first: Aleksander

last: Bykov

first: Peter

last: Reiscak

first: Hayeon

last: Baik

first: Alma

last: Dupanovic

first: Faith

last: David

first: Boris

last: Kovacic

last: Hall-Glenn

first: Sara

last: Dopa

first: Jos

last: Urbauns

first: Lisa

last: Sippl

first: Susanne

last: Stofner

first: Dominik

last: Emminger

first: Jason

last: Cosgrove

first: Dagmar

last: Schinnerl

first: Anna

last: Poetsch

first: Manfred

last: Lehner

first: Xaver

last: Koenig

first: Leïla

last: Perié

first: Ton

last: Schumacher

last: Gotthardt

first: Florian

last: Halbritter

first: Eva

last: Putz


title: SP140 ChIP-seq for Daudi and Ramos cell lines

first: Ettore

last: Zapparoli

summary: Study of the effect of SP140 deletion on the distribution of H3K27me3 in two independent Burkitt''s Lymphoma cell lines (DAUDI and Ramos).

overall_design: Genetic deletion of human SP140 through CRISPR/Cas9. Chromatin has been extracted and then H3K27me3 has been performed.

first: Tamburri

last: Simone

first: Zucchelli

last: Chiara

first: Zapparoli

last: Ettore

first: Bachi

last: Angela

first: Musco

last: Giovanna


title: Spatial Analysis of a Complete DIPG-Infiltrated Brainstem Reveals Novel Ligand-Receptor Mediators of Tumor-to-TME Crosstalk

status: Public on Nov 18 2024

first: Anja

last: Kordowski

state: Washington

address: 1920 Terry Ave

institute: Seattle Children's Hospital

summary: Previous studies have highlighted the capacity of brain cancer cells to functionally interact with the tumor microenvironment (TME). This TME-cancer crosstalk crucially contributes to tumor cell invasion and disease progression. In this study, we performed spatial transcriptomic sequencing analysis of a complete annotated DIPG tumor-infiltrated patient brainstem. We identified four distinct tumor subpopulations and assessed respective ligand-receptor pairs that actively promote DIPG tumor progression via crosstalk with endothelial, neuronal and immune cell communities. These interactions might promote DIPG tumor progression and represent novel therapeutic targets.

overall_design:
In this study, we performed 10x Visium spatial transcriptomic sequencing of a complete annotated tumor-infiltrated brainstem from a single DIPG patient. Gene signatures from ten sequential tumor regions were analysed to assess mechanisms of disease progression, invasion and oncogenic interactions with the TME.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

first: Onkar

last: Mulay

first: Xiao

last: Tan

first: Tuan

last: Vo

first: Ulrich

last: Baumgartner

first: Mellissa

middle: K

last: Maybury

first: Timothy

middle: E

last: Hassall

first: Lachlan

last: Harris

first: Quan

last: Nguyen

first: Bryan

middle: W

last: Day


title: The matricellular protein Fibulin-5 regulates β-cell proliferation in an autocrine/paracrine manner

status: Public on Nov 19 2024

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

institute: Kanazawa University

summary: The matricellular protein Fibulin-5 (Fbln5) is a secreted protein that is essential for elastic fiber formation, and pancreatic islets are usually surrounded by the extracellular matrix (ECM), which includes elastic fibers. However, much uncertainty remains regarding the function of the ECM and its components in β-cells. Here, we describe the role of Fbln5 in β-cell replication. Fbln5 expression was increased upon glucose stimulation in β-cells of mouse and human islets. β-Cell-specific Fbln5-knockout (βFbln5KO) mice exhibit significantly reduced β-cell proliferation in vivo but not in vitro.  Secreted extracellular Fbln5 enhances β-cell replication. Fbln5-deficient β-cells exhibit downregulated expression of the gene encoding polo-like kinase 1 (PLK1), which is accompanied by ERK-mediated FoxM1 nuclear export. These data suggest that Fbln5 is secreted from β-cells in response to glucose and plays important roles in the appropriate maintenance of β-cell functions in an autocrine or paracrine manner.

overall_design: Comparison between the islets isolated from the βFbln5KO mice and those isolated from the floxed mice. There are four biological replicates for each condition.

first: Tomoko

last: Okuyama

first: Takahiro

last: Tsuno

first: Ryota

last: Inoue

first: Setsuko

last: Fukushima

first: Mayu

last: Kyohara

first: Anzu

last: Matsumura

first: Daisuke

last: Miyashita

first: Kuniyuki

last: Nishiyama

first: Yusuke

last: Takano

first: Yu

last: Togashi

first: Makiko

last: Meguro-Horike

first: Tatsuya

last: Kin

first: A.M. James

last: Shapiro

first: Hiromi

last: Yanagisawa

first: Yasuo

last: Terauchi

first: Jun

last: Shirakawa


title: Infection-induced vascular inflammation in COVID-19 links focal microglial dysfunction with neuropathologies through IL-1/IL-6-related systemic inflammatory states

first: Arthur

last: Liesz

address: Feodor-Lynen-Straße 17

department: Institute for Stroke and Dementia (ISD)

institute: LMU Hospital

summary: COVID-19 is associated with diverse neurological- and inflammatory states that predict poor acute- and long-term outcomes in patients. However, the mechanisms whereby infection-induced inflammation could affect complex neuropathologies through microglia, the main immune cells of the brain, is unclear. We developed a unique autopsy platform allowing the integration of molecular anatomy-, protein- and mRNA data sets in post-mortem mirror blocks of brain and peripheral organ samples from COVID-19 cases. Nanoscale microscopy, single-cell RNAseq and analysis of inflammatory and metabolic signatures revealed that focal loss of microglial P2Y12R occurs at sites of virus-associated vascular inflammation together with dysregulated microglia-vascular-astrocyte interactions, Cx3Cr1-fractalkine axis deficits and mitochondrial failure in severely affected medullary autonomic nuclei, and other brain areas. Microglial dysfunction occurs at sites of excessive synapse- and myelin phagocytosis and loss of glutamatergic terminals. These changes strongly correlate with the development of a generalized, but regionally heterogenous proinflammatory response across the brain related to interleukin-1 (IL-1), IL-6, and multiorgan virus load-related systemic inflammation via virus-sensing pattern recognition receptors (PRRs) and inflammasomes. Thus, SARS-CoV-2-induced central and systemic inflammation might lead to a primarily glio-vascular failure in the brain, promoting diverse neuropathologies through different, parallel mechanisms.

overall_design: To investigate how microglial dysfunction may contribute to inflammatory changes in COVID-19 brains, we performed single-nuclei mRNA sequencing from medulla samples of COVID-19 and control patients (n=2/group) by means of 10x Genomics.

first: Rebeka

last: Fekete

first: Alba

last: Simats

first: Eduárd

last: Bíró

first: Balázs

last: Pósfai

first: Csaba

last: Cserép

first: Anett

last: Schwarcz

first: Eszter

last: Szabadits

first: Zsuzsanna

last: Környei

first: Krisztina

last: Tóth

first: Erzsébet

last: Fichó

first: János

last: Szalma

first: Sára

last: Vida

first: Anna

last: Kellermayer

last: Dávid

first: Lászlo

last: Acsády

first: Levente

last: Kontra

first: Carlos

last: Silvestre-Roig

first: Judit

last: Moldvay

last: Fillinger

first: Attila

last: Csikász-Nagy

first: Tibor

last: Hortobágyi

first: Szilvia

last: Benko

first: Ádám

last: Dénes


title: Systems-level computational translation of mouse and human transcriptomics reveals a role for the unfolded protein response in Mycobacterium tuberculosis infection

city: Worcester

first: Christopher

last: Sassetti

state: Massachusetts

address: 55 Lake Avenue North

department: Microbiology

institute: University of Massachusetts Chan Medical School

summary: Numerous studies have identified similarities in blood transcriptomic signatures of tuberculosis (TB) disease phenotypes between mouse and human systems, such as type 1 interferon (IFN) production and innate immune cell activation, yet the pathophysiology observed in murine infection does not recapitulate some of the hallmarks of human TB disease. We hypothesized that some of these differences relate to quantitative differences in the importance of different biological pathways in the two systems, rather that completely distinct responses to infection. To test this hypothesis and address the critical animal-to-human gap, we applied a systems biology machine learning framework, Translatable Components Regression, which identifies axes of variation in the preclinical study that correspond with numerous biological pathways and processes and estimates their relative contributions to TB disease state in humans. Our modeling confirmed the presence of biological axes of variation that differed in their relative importance between species. Prominent among the pathways most predictive of human TB phenotype, beyond the previously established common signatures, is the infection-induced Unfolded Protein Response (UPR). To validate that this mechanism can be uncovered even in the murine context, wherein it has not previously been a major avenue of investigation, we show experimentally that this cellular stress pathway controls a variety of immune-related functions in Mycobacterium tuberculosis-infected mouse macrophages. Thus, our work here demonstrates how systems-level computational models enhance the value of animal studies for purpose of elucidating complex human pathophysiology.

overall_design: To determine the contribution of the three branches of the UPR, IRE1, ATF6 and PERK to infection outcomes, we infected bone marrow derived macrophages with Mycobacterium tuberculosis H37Rv in the presence and absense of UPR pathway inhibitors. Cells were pretreated with 4µ8c, Ceapin-A7 or GSK2606414 (targeting IRE1, ATF6, and PERK respectively) for 2 hours, and then were infected with H37Rv at an MOI of 9 for 24 h before cells were lysed and RNA extracted. Experiment was performed simultaneously for 4 biological replicates.

first: Krista

last: Pullen

first: Ryan

last: Finethy

first: Seung-Hyun

middle: B

last: Ko

first: Charlotte

last: Reames

first: Douglas

last: Lauffenburger


title: Effect of the FGFR kinase inhibitors AZD4547 and BGJ398 on gene expression in HaCaT cells

status: Public on Nov 17 2024

city: Zürich

first: Debora

last: Stefanova

address: Otto-Stern Weg 7

department: DBIOL

institute: ETH Zürich

summary: Fibroblast growth factors (FGF) play important roles during embryonic development as well as in the adult organism in tissue homeostasis, regeneration, repair and metabolism. We recently showed that inhibition of FGF receptor (FGFR) signaling in keratinocytes either pharmacologically or in a mouse FGFR1/2 knockout model, promoted expression of interferon-stimulated genes (ISGs) (Maddaluno et al, 2020). Here we analyzed the transcriptome of human HaCaT keratinocytes in response to treatment with the FGFR kinase inhibitors AZD4547 and BGJ398.

overall_design:
HaCaT cells were cultured to confluency in DMEM (10% FBS), then treated for 5 h in DMEM (5% FBS) with either vehicle (DMSO), 10 µM AZD4547 or 3.6 µM BGJ398.
contributor: Functional Genomics Center Zürich

first: Stefanova

last: Debora


title: A nucleoside signal generated by a fungal endophyte regulates host cell death and promotes root colonization

city: Cologne

first: Gregor

last: Langen

address: Zuelpicher Str. 47b

department: Institute for Plant Sciences

institute: University of Cologne

summary: Regulated host cell death is part of a plant defense strategy against pathogens but it is also involved in accommodating certain beneficial root microbes. We have identified extracellular metabolites and intracellular metabolic signals that contribute to beneficial root fungal endophyte colonization, and uncovered a conserved cell death mechanism likely co-opted for establishing plant-endophyte symbiosis.

overall_design: The response of 12-day-old  Arabidopsis thaliana Col-0 seedlings was analysed 3 and 12 hours after treatment with 500 µM dAdo in 2.5 mM MES buffer pH 5.6 or MES buffer alone. Gene expression was analysed using RNAseq, pseudoaligned to the TAIR10 transcriptome.

first: Nick

last: Dunken

first: Heidi

last: Widmer

first: Gerd

middle: U

last: Balcke

first: Henryk

last: Straube

first: Nyasha

last: Charura

first: Pia

last: Saake

first: Concetta

last: De Quattro

first: Hanna

last: Rövenich

first: Stephan

last: Wawra

first: Mamoona

last: Khan

first: Claus-Peter

last: Witte

first: Armin

last: Djamei

first: Matias

last: Zurbriggen

first: Jonas

last: Schön

first: Alain

last: Tissier

first: Alga

last: Zuccaro


title: Optimized CUT&RUN protocol for a non-histone protein in activated primary mouse B cells

status: Public on Nov 12 2024

city: Baltimore

first: Patricia

last: Gearhart

state: Maryland

address: 251 Bayview Blvd, Rm 06009C

department: Laboratory of Molecular Biology and Immunology

institute: NIH/NIA

summary: ChIP-seq has long been the standard for study of chromatin-protein interactions. However, development of a new technique, CUT&RUN, shows substantial advantages compared to ChIP-seq including higher quality signal while using substantially less sample. While a powerful technique, the original protocol was unsuitable for obtaining high-quality data for non-histone proteins from activated primary B lymphocytes. To adapt this protocol for B cells, cells were fixed prior to nuclear isolation, and several adjustments were introduced to the procedure and reagents. We measured binding of RNA polymerase II to five genes and used binding of H3K4me3 histone as a positive control. Robust peaks in transcribed genes were detected with as little as 100k nuclei.  Additionally, freeze-thaw of B cells prior to processing did not influence results, emphasizing the flexibility of this modified technique. Using the protocol described here will allow one to quantify low abundance proteins bound to DNA from limited numbers of B cells with more efficiency than can be achieved from the current standard, ChIP-seq.

overall_design: Naïve splenic follicular B cells were isolated from mice and stimulated in culture for 48 hours with 2 µg/mL anti-CD40 and 10 ng/mL IL-4. Cells were collected and processed for CUT&RUN at varying amounts of nuclei and on freshly isolated culture cells or cultured cells that were frozen and thawed. Target antibodies used were H3K4me3, IgG, RNA Pol II

first: Stormy

last: Ruiz

first: Robert

last: Maul


title: Investigating the effects of estrogen in the transcriptional regulation of SOX2 in breast cancer cells.

city: Toronto

first: Jennifer

last: Mitchell

address: 25 Harbord Street

department: Cell and Systems Biology

institute: University of Toronto

summary: We have evaluated the effects of estrogen over SOX2 expression by maintaining MCF-7 under three distinct conditions: estrogen deprivation for a year (LT -E2 MCF-7), treating MCF-7 cells with estrogen for 48 hours (48hr +E2 MCF-7), and maintaining cells under estrogenic conditions for a year (LT +E2 MCF-7).

overall_design: LT -E2 MCF-7 cells were maintained in estrogen-deprived conditions for a year; 48hr +E2 MCF-7 cells were treated with 10nM b-estradiol for 48 hours; LT -E2 MCF-7 cells were grown under 10nM b-estradiol for a year. Cells were submitted for ATAC-seq and ribo-depleted total RNA-seq in three replicates each.

first: Luis

last: Abatti


title: Cis-regulatory elements driving motor neuron-selective viral payload expression within the mammalian spinal cord

status: Public on Nov 16 2024

city: Boston

first: Mark

middle: Aurel

last: Nagy

address: 220 Longwood Ave

department: Department of Neurobiology

institute: Harvard Medical School

summary: Bulk RNA-seq and ATAC-seq of immunopurified CHAT+ and immunodepleted CHAT- nuclei of murine spinal cord

overall_design: Homozygous Chat-IRES-Cre (The Jackson Laboratory Stock # 006410) mice were crossed with homozygous SUN1-2xsfGFP-6xMYC (The Jackson Laboratory Stock # 021039) mice and GFP-positive nuclei were immunopurified from adult (6-12-week-old) heterozygous male and female F1 progeny via the INTACT approach for ATAC-seq and RNA-seq as previously described

first: Michael

last: Greenberg

first: Sinisa

last: Hrvatin


title: Transcriptome sequencing of SLC2A10 knock-down VSMCs

city: Wuhan

first: Zhipeng

last: Hu

address: 238 Jiefang Road

department: cardiovascular surgery

institute: Renmin hospital of Wuhan University

summary: shRNA was used to knock down SLC2A10 VSMCs. The effectiveness of gene interference was tested by qPCR. Transcriptome sequencing was performed and FASTQ files from RNA- seq experiments were clipped and trimmed. KEGG enrichment analysis on differently expressed genes was performed.

overall_design: VSMCs mRNA profiles of wild type (WT) and SLC2A10-/- mice

first: Qi

last: Wu

first: Lijuan

last: Jian


title: Effects of knockdown or overexpression of PNPLA6 in human retinal pigment epithelial cell line ARPE-19

city: Tokyo

first: Yoshitaka

last: Taketomi

address: 7-3-1 Hongo, Bunkyo-ku,

department: CDBIM, Graduate School of Medicine,

institute: The University of Tokyo

summary: Although mutations in human patatin-like phospholipase PNPLA6 are associated with hereditary retinal degenerative diseases, its mechanistic action in the retina is poorly understood. Here, we uncover the molecular mechanism by which PNPLA6 dysfunction disturbs retinal homeostasis and visual function. PNPLA6, by acting as a phospholipase B, regulates choline mobilization from phosphatidylcholine and subsequent choline turnover for phosphatidylcholine regeneration in retinal pigment epithelial (RPE) cells. PNPLA6-driven choline is supplied from RPE cells to adjacent photoreceptor cells to support their survival. Inhibition of this pathway results in abnormal morphology, proliferation, metabolism, and functions of RPE and photoreceptor cells, and mice with retina-specific PNPLA6 deletion exhibit retinitis pigmentosa-like retinal degeneration. Notably, these abnormalities are entirely rescued by choline supplementation. Thus, PNPLA6 plays an essential role in retinal homeostasis by controlling choline availability for phospholipid recycling and provide a framework for the development of a novel ophthalmic drug target for retinal degeneration.

overall_design: Cells, ARPE-19 retinal pigment epithelial cell line; Condition, Human PNPLA6 knockdown (siRNA) and control, PNPLA6 overexpression and mock; RNA, total RNA samples pooled from individual cells for 4 wells

first: Takashi

last: Ono

first: Yasumasa

last: Nishito

first: Makoto

last: Murakami


title: Effects of choline deficiency in mouse photoreceptor cell line 661W

overall_design: Cells, 661W mouse photoreceptor cells, Condition, cultured in choline-deficiency and sufficient medium (DMEM/f12); RNA, total RNA samples pooled from individual cells for 4 dishes


title: Crypt density and recruited enhancers underlie intestinal tumour initiation

status: Public on Nov 10 2024

first: Ramesh

last: Shivdasani

address: 450Brookline Ave.

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Oncogenic mutations that drive colorectal cancer can be present in healthy intestines for long periods without overt consequence. Mutation of Adenomatous polyposis coli (Apc), the most common initiating event in conventional adenomas, activates Wnt signaling, hence conferring fitness on mutant intestinal stem cells (ISCs). Apc mutations may occur in ISCs that arose by routine self-renewal or by dedifferentiation of their progeny. Although ISCs of these different origins are fundamentally similar, it is unclear if both generate tumours equally well in uninjured intestines. Also unknown is whether cis-regulatory elements are substantively modulated upon Wnt hyperactivation or as a feature of subsequent tumours. Here, we show in two mouse models that adenomas are not an obligatory outcome of Apc deletion in either ISC source but require proximity of mutant intestinal crypts. Reduced crypt density abrogates, and aggregation of mutant colonic crypts augments, adenoma formation. Moreover, adenoma-resident ISCs open chromatin at thousands of enhancers that are inaccessible in Apc-null ISCs not associated with adenomas. These cis-elements explain adenoma-selective gene activity and persist, with little further expansion of the repertoire, as other oncogenic mutations accumulate. Thus, cooperativity between neighbouring mutant crypts and new accessibility at specific enhancers are key steps early in intestinal tumourigenesis.

overall_design: To activate CreER-T2 in Atoh1CreER-T2;R26RTom, we administered 2 doses of 1 mg/mL tamoxifen (Sigma-Aldrich, T5648; stocks prepared in cornflower oil) by intraperitoneal (IP) injection 24 h apart; and 12 h later we harvested intestinal TOM+  crypt cells for scRNA-seq.

first: Swarnabh

last: Bhattacharya


title: miRNA analyses of genetic factors and the role of carotenoid accumulation in adductor muscles of QN Orange scallops

city: Qingdao

first: JunLin

last: Song

address: Changcheng Road

institute: JunLin Song

type: Non-coding RNA profiling by high throughput sequencing

summary: QN Orange scallop was interspecific hybrids with orange adductor muscles. Previous studies shown the accumulation of carotenoids was present in QN Orange scallops. In this study, analysis of miRNA expression profiles was performed to explore possibly regulatory patterns in carotenoid accumulation in adductor muscles of QN Orange scallops. Based on small RNA sequencing, a total of 3289 miRNAs and 91 differential expression miRNAs were identified between white and orange adductor muscles, respectively. GO and KEGG enrichment analysis of target genes of DE miRNA enriched in the transmembrane transporter activity-related pathways, kinase activity-related pathways, signal transduction-related pathways, ABC transporters, Retinol metabolism, lipid related metabolism and calcium signaling pathway.

overall_design: A total of nine adductor muscles from each strain were preserved for miRNA sequencing analysis. Samples were consolidated every three units to form a single sample for sequencing.


title: Gene expression of Tamoxifen induced control (TC), dormancy-like (TD) or relapse (TR) cell samples

status: Public on Nov 08 2024

city: Shen Zhen

first: Shu

last: Chen

address: Nanshan

institute: Tsinghua University

summary: To generate a dormancy state in vivo, female BALB/c athymic mice with ER+MC cell (MCF7) derived xenografts were treated with Tamoxifen (TAM). Throughout the treatment period, no significant differences in the body weight of the TAM-treated groups (TD and TR) compared to the vehicle-treated groups (TC) were observed. Whereas xenografts in the vehicle-treated group (as control group: TC) continued to increase in volume, the xenograft volumes of the TAM-treated group regressed 20%-30% in the first week and then remained stable during the four-week administration of TAM. Thereafter, half of the xenografts in TAM-treated mice were resected at random and designated as a dormancy-like group (TD). For the remaining TAM treated xenografts, treatment was discontinued and xenograft volume was observed to gradually increase. This group was defined as the relapse group (TR) and would mimic relapses observed after discontinuation of anti-estrogen therapy in patients.

overall_design: The TC, TD or TR cell lines were established in vitro from their corresponding xenografts for RNA-sequencing.

first: Xi

last: Zhang

first: Vijay

last: Pandey

first: Peter

last: Lobie


title: Gene expression of Fulvestrant induced control (FC), dormancy-like (FD) or relapse (FR) cell samples

summary: To generate a dormancy state in vivo, ovariectomized female BALB/c athymic mice (simulating the post-menopausal state) with ER+MC cell (MCF7) derived xenografts were treated with Fulvestrant (FUL). Throughout the treatment period, no significant differences in the body weight of the FUL-treated groups (FD and FR) compared to the vehicle-treated groups (FC) were observed. Whereas xenografts in the vehicle-treated group (as control group: FC) continued to increase in volume, the xenograft volumes of the FUL-treated group regressed 20%-30% in the first week and then remained stable during the four-week administration of FUL. Thereafter, half of the xenografts in FUL-treated mice were resected at random and designated as a dormancy-like group (FD). For the remaining FUL treated xenografts, treatment was discontinued and xenograft volume was observed to gradually increase. This group was defined as the relapse group (FR) and would mimic relapses observed after discontinuation of anti-estrogen therapy in patients.

overall_design: The FC, FD or FR cell lines were established in vitro from their corresponding xenografts for RNA-sequencing.


title: Comparative characterization of human accelerated regions in neurons

city: SAN FRANCISCO

first: Yin

last: Shen

state: CALIFORNIA

address: 513 Parnassus Ave

department: Department of Neurology

institute: UCSF

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

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design: Refer to individual Series


title: Effects of loss and gain of KAT6B on gene expression in neural stem and progenitor cells [NSC_Kat6b_RNAseq]

status: Public on Nov 06 2024

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: High histone acetylation is associated with high transcriptional activity. The lysine acetyltransferase KAT6B is known to be required for histone acetylation and KAT6B is essential for normal brain development. In this study we examined the effects of loss and gain of KAT6B on gene expression in forebrain neural stem and progenitor cells (NSPCs). We isolated NSPCs from the dorsal telencephalon of embryonic day 12.5 embryos, which is the primordium of the cerebral cortex, from mouse embryos that lacked KAT6B or overexpressed KAT6B. We cultured the cells in vitro for 3 to 5 passages before isolating RNA for library production and RNA-sequencing. We found that genes required for neuronal differentiation and brain development were downregulated in Kat6b null cells and upregulated in Kat6b transgenic overexpressing cells.

overall_design: RNA levels in E12.5 dorsal telencephalon neural stem and progenitor cells were compared between (a) Kat6b–/– and wild-type cells and (b) Tg(Kat6b) cells, which overexpressed Kat6b mRNA approximately 4.5-fold, and wild-type cells. Kat6b–/– and wild-type cells were derived from mouse embryos on a C57BL/6 genetic background. Tg(Kat6b) and their and wild-type control cells were derived from mouse embryos on a mixed FVBxBALB/c background, because the Tg(Kat6b) mice were not viable on an inbred background.

first: Maria

last: Bergamasco

first: Anne

last: Voss

first: Tim

last: Thomas

middle: L

first: Gordon

last: Smyth


title: Effects of loss and gain of KAT6B on gene expression in the developing cerebral cortex [Myst4_RNAseq]

summary: High histone acetylation is associated with high transcriptional activity. The lysine acetyltransferase KAT6B is known to be required for histone acetylation and KAT6B is essential for normal brain development. In this study we examined the effects of loss and gain of KAT6B on gene expression in the developing cerebral cortex. We isolated RNA from the dorsal telencephalon of embryonic day 12.5 embryos, which is the primordium of the cerebral cortex, and from the E15.5 foetal cortex of mouse embryos and foetuses that lacked KAT6B or overexpressed KAT6B. Genes required for brain development and neuronal differentiation were downregulated in Kat6b null tissues and upregulated in Kat6b transgenic overexpressing tissue.

overall_design: RNA levels in E12.5 dorsal telencephalon and E15.5 cortex were compared between (a) Kat6b–/– and wild-type tissue and (b) Tg(Kat6b) tissue, which overexpressed Kat6b mRNA approximately 4.5-fold, and wild-type tissue. Kat6b–/– and wild-type mice were on a C57BL/6 genetic background. Tg(Kat6b) and their and wild-type control mice were on a mixed FVBxBALB/c background, because the Tg(Kat6b) mice were not viable on an inbred background.


title: Uncovering the rewired IAP-JAK regulatory axis as an immune-dependent vulnerability of LKB1-mutant lung cancer

city: Atlanta

first: Changfa

last: Shu

state: GA

address: 1510 Clifton Rd

department: Pharmacology and Chemical Biology

institute: Emory University

summary: Harnessing the power of immune system to treat cancer has become a core clinical approach. However, rewiring of intrinsic circuitry by genomic alterations enables tumor cells to escape immune surveillance, leading to therapeutic failure. Uncovering the molecular basis of how tumor mutations induce therapeutic resistance may guide the development of intervention approaches to advance precision immunotherapy. Here we report the identification of the LKB1-IAP-JAK dynamic complex as a molecular determinant for immune response of LKB1-mut lung cancer cells. LKB1 alteration exposes a critical dependency of lung cancer cells on IAP for their immune resistance. Indeed, pharmacological inhibition of IAP re-established JAK-regulated STING expression and DNA sensing signaling, enhanced cytotoxic immune cell infiltration, and augmented immune-dependent anti-tumor activity in an LKB1-mutant immune-competent mouse model. Thus, IAP-JAK-targeted strategies, like IAP inhibitors, may offer a promising therapeutic approach to restore the responsiveness of “immunologically-cold” LKB1-mutant tumors to immune checkpoint inhibitors or STING-directed therapies.

overall_design: To probe the potential immune co-factors, we performed transcriptomic profiling to compare the differential expression genes (DEG) from LKB1-mut tumor cells in the absence or presence of immune cells upon birinapant treatment.

first: Xiulei

last: Mo

first: Haian

last: Fu


title: Comprehensive mapping of epigenetic events during the T-follicular helper-to-T-regulatory type-1 transdifferentiation pathway reveal a global poised state

status: Public on Nov 07 2024

city: Barcelona

first: Josep

last: Garnica

address: Rosselló, 149

institute: IDIBAPS

type: Methylation profiling by high throughput sequencing

summary: Chronic antigenic stimulation can trigger the formation of IL-10-producing T-regulatory type 1 (TR1) cells in vivo. We have recently shown that T follicular helper cells are precursors of TR1 cells and that the TFH-to-TR1 cell transdifferentiation process is underpinned by the progressive loss and acquision of opposing transcription factor gene expression programs that evolve through at least one transitional cell stage. Through a combination of wide-ranging bulk and single-cell transcriptional and epigenetic studies, here we demonstrate that TFH cells are epigenetically poised to differentiate into TR1 cells. Specifically, we find that the TFH-to-TR1 cell transition is accompanied by a significant reduction of the open chromatin regions (OCRs) found in TFH cells. However, the OCRs shared by TR1-like and TFH cells have a remarkably similar distribution of H3K27ac-marked active enhancers. Whereas the DNA regions that overlap these active enhancers are closed and hyper-methylated in conventional T cells, they are hypo-methylated in both TFH and TR1-like cells, even in genes silent in TFH cells, such as Il10. Furthermore, these enhancers are enriched for binding sites for the TFH and TR1-associated transcription factors (TFs) TOX-2, IRF4 and c-Maf. These data suggest that TFH cells are epigenetically poised to become TR1 cells, and that sustained TCR ligation-induced chromatin remodeling coupled to the acquisition of an alternative transcription factor expression profile are sufficient to drive their transdifferentiation into TR1 cells.

overall_design: pMHCII-NP-induced Tet+, vaccination-induced TFH, and Th0 (T conventional) cells were processed for bulk ATAC-seq, ChIP-seq for H3K27Ac, H3K4me3, and H327me3, whole genome methylome, as well as single-cell scRNA-seq + scATAC-seq multiome, in order to underpin the epigenetic changes during the transdifferenation of TFH into TR1 cells induced by pMHCII-NP.

first: Joel

last: Moro

first: Pere

last: Santamaria


title: Gastric Hypoplasia in mice lacking Fibroblast Growth Factor 9

status: Public on Nov 15 2024

city: St. Louis

first: Spencer

middle: G.

last: Willet

state: MO

address: 660 S. Euclid Avenue, Campus Box 8103

department: Department of Developmental Biology

institute: Washington University in St. Louis

summary: To determine the role of Fgf9 in gastric development, we collected E15.5 Fgf9 KO (Fgf9LacZ/LacZ) and Het (Fgf9LacZ/+) stomachs for RNA-seq analysis. 3 stomachs were pooled for each RNA-seq sample.

overall_design: E15.5 embryonic stomachs: FGF9KO versus FGF9HET

middle: G

first: Jason

last: Mills


title: Intrinsic electrical activity drives small-cell lung cancer progression

city: London

first: Leanne

last: Li

address: 1 Midland Road

institute: The Francis Crick Institute

summary: Elevated or ectopic expression of neuronal receptors and ion channels promotes tumor progression in many cancer types; neuroendocrine (NE) transformation of various adenocarcinomas has also been associated with increased aggressiveness. Whether the defining neuronal feature, namely electrical excitability, exists in cancer cells and whether this impacts cancer progression remains mostly unexplored. Small cell lung cancer (SCLC) is an archetypical example of highly aggressive NE cancers and is comprised of two major distinct subtypes of cancer cells: NE cells and non-NE cells. Here, we show that the NE cells are excitable, like neurons, while non-NE cells cannot fire action potentials, like astrocytes and other non-excitable cells. Action potential firing in NE cells directly promotes SCLC malignancy; however, the high ATP demand of electrical activity also leads to an unusual dependency on oxidative phosphorylation (OXPHOS) in NE cells. This finding contrasts with most cancer cells reported in the literature, which are non-excitable and heavily rely on aerobic glycolysis. Additionally, we find that non-NE cells metabolically support NE cells to supply their high ATP demand, promoting their excitability and malignancy, a process akin to the astrocyte-neuron metabolite shuttle. Lastly, we observe drastic changes in the innervation landscape during SCLC progression, which coincide with increased intratumoral heterogeneity (ITH) and elevated neuronal protein expression in SCLC cells, suggesting an induction of a tumor autonomous vicious cycle driven by cancer cell-intrinsic electrical activity, which confers long-term tumorigenic capability and metastatic potential.

overall_design: Eight mouse SCLC cell lines from both neuroendocrine and non-neuroendocrine subtypes were transcriptionally profiled for this study to identify differential gene expression signatures between the neuroendocrine and non-neuroendocrine subtypes.

first: Arjun

last: Bhutkar

first: Paola

last: Peinado


title: A CHD8-TRRAP axis facilitates MYC and E2F target gene regulation in human neural stem cells. [ChIP-seq]

city: Rotterdam

first: Raymond

last: Poot

address: Wytemaweg 80

department: Cell Biology

country: Netherlands

institute: Erasmus MC

summary: Mutations in ATP-dependent chromatin remodeler CHD8 cause one of the most frequent monogenetic forms of autism and is associated with brain overgrowth. Nevertheless, the activities of CHD8 in autism-relevant cell types are still poorly understood. Here, we purify the CHD8 protein from human neural stem cells and determine its interaction partners using mass spectrometry. We identify the TRRAP complex, a coactivator of MYC and E2F transcription factors, as a prominent CHD8 interaction partner. CHD8 colocalizes genome-wide with TRRAP and bind together at MYC and E2F target gene promoters in human neural stem cells. Depletion of CHD8 or TRRAP in human neural stem cells shows downregulation of MYC and E2F target genes as the most prominent gene-regulatory events. MYC and E2F transcription factors are established oncogenes known to regulate cell growth. Our results link CHD8 to TRRAP and suggest they act together in facilitating the regulation of MYC and E2F target genes in neural stem cells.

overall_design: Genome binding/occupancy profiling of CHD8 and TRRAP in human neural stem cells by high throughput sequencing.

first: Lize

last: Meert

first: Maarten

last: Fornerod

first: Mariana

last: Pelicano de Almeida

first: Zeliha

last: Ozgür

first: Mirjam

last: van den Hout

first: Wilfred

middle: F

last: van Ijcken


title: A CHD8-TRRAP axis facilitates MYC and E2F target gene regulation in human neural stem cells. [RNA-Seq]

overall_design: To investigate the function of CHD8, TRRAP and MYC in human neural stem cells, we performed shRNA-mediated knockdown experiments for each target band collected total RNA 72h after transfection. Gene expression profiling analysis was performed using data obtained from RNA-seq.


title: Aging activates, represses, and remodels the silent X chromosome and its escape across cell types of the female mouse hippocampus

status: Public on Nov 05 2024

first: Margaret

last: Gadek

address: 675 Nelson Rising Lane

department: Neurology

summary: Females show an advantage in lifespan and cognition in aging human populations.  The X chromosome is a major source of sex difference, as female mammals harbor an inactive (Xi) and active (Xa) following X chromosome inactivation (XCI).  Whether Xi – or the silent X – can activate in the aging brain and thus increase X dose is unknown. Here, we performed single nuclei RNA-sequencing in the young and aging hippocampus of female mice and applied allele-specific computational analysis. We show that aging remodels transcription of Xi and Xa across hippocampal cell types. Aging preferentially induced gene expression changes on the X chromosomes compared to the autosomes. Xi underwent activation and repression of select genes, particularly in dentate gyrus neurons, critical to learning and memory.

overall_design: Female M. musculus XistloxP +/-,Zp3-cre mice with a congenic C57BL/6J background, were crossed with male M. castaneous mice. XX progeny carrying the XistloxP +/-, Zp3-cre allele were used for single nuclei RNA sequencing. The fresh hippocampi of four young (3-4 month) and four old (23-24 month) mice were dissected and frozen for downstream snRNAseq studies.

first: Cayce

last: Shaw

first: Dena

last: Dubal


title: Effects of loss and gain of the histone acetyltransferase KAT6B on DNA accessibility (ATAC-seq)

first: Waruni

last: Abeysekera

department: Bioinformatics

summary: Heterozygous mutations in the histone acetyltransferase gene KAT6B (MYST4/MORF/QKF) cause cognitive disorders. Congruently, KAT6B is required for brain development, neural stem cell self-renewal and neuronal differentiation in mice. Despite the clear requirement for KAT6B in brain development, its molecular roles remain unexplored. Here we use ATAC sequencing to determine the effects of loss or gain of KAT6B on DNA accessiblity.

overall_design:
Kat6b knock-out mice were constructed on the C57BL/6 background. Transgenic Tg(Kat6b) mice that overexpress Kat6b were also constructed and maintained on a FVBxBALB/c hybrid genetic background. The mixed genetic background was chosen because Tg(Kat6b) mice are not viable on the C57BL/6 background.
Neural stem and progenitor cells were isolated from the dorsal telencephalon of E12.5 mouse embryos and ATAC-seq profiles were constructed. Samples were taken from four Kat6b–/– knockout embryos and four Kat6b+/+ wild-type embryos on the C57BL/6 background, as well as from four Tg(Kat6b) transgenic embryos and four Kat6b wild-type embryos on the FVBxBALB/c genetic background. All samples were also spiked with a fixed amount of DNA from Drosophila S2 cells to aid with normalization.

first: Gordon

last: Smyth

first: Anne

last: Voss

first: Tim

last: Thomas

first: Maria

middle: I

last: Bergamasc