title: Effects of fumarate on the metabolic reprogramming of aging T-cells associated with rescue of the T-cell anti-tumor functions

city: Charleston

first: Mohamed Faisal

last: Kassir

state: SC

address: 86 Jonathan Lucas St HO509

institute: Medical University of South Carolina

summary: Changes in mitochondrial bioenergetics in aging T-cells play a key role in the decrease in T-cell function and tumor resistance with aging. The bioactive sphingolipid ceramide, induced by aging stress, is a major player in these changes, as its accumulation at the mitochondrial membranes of both mouse and human aging T-cells induces ceramide-dependent mitophagy, which decreases T-cell viability, cytokine secretion, and anti-tumor activity. Besides lipid signaling, our findings show a general depletion of tricarboxylic acid cycle (TCA) metabolites in aging T-cells, with pools of fumarate, malate, and argininosuccinate significantly decreasing in both mouse and human aging T-cells. In vivo supplementation of fumarate to mouse T-cells seemed to correct some of the functional defects observed in aging, with a protection of T-cell viability, cytokine production, and tumor killing capacity in co-cultures with tumor cells. The fumarate supplementation also led to a decrease in ceramide-dependent mitophagy in the aging T-cells, indicating an interplay between ceramide-dependent mitophagy and fumarate metabolism. Here, the RNAseq data shows a reversal of the genetic signature of aging in T-cells upon supplying fumarate, associated with a significant increase in different metabolic enzymes.

overall_design: 24-month old C57BL/6 mice were treated with 10mg/kg fumarate for 2 months. After two months of treatment, T-cells were collected from mice treated with fumarate or vehicle, as well as young 2 month old mice. T-cells were then activated in vitro with plate-bound CD3 (2ug/ml) and CD28 (5ug/ml) in the presence of IL-2 (100IU/ml). T-cells were then collected and RNA was extracted for RNAseq.


title: Effects of fumarate and Alzheimer's disease on the metabolic reprogramming of aging T-cells associated with rescue of the T-cell anti-tumor functions

status: Public on Jun 09 2025

country: USA

summary: Changes in mitochondrial bioenergetics in aging T-cells play a key role in the decrease in T-cell function and tumor resistance with aging. The bioactive sphingolipid ceramide, induced by aging stress, is a major player in these changes, as its accumulation at the mitochondrial membranes of both mouse and human aging T-cells induces ceramide-dependent mitophagy, which decreases T-cell viability, cytokine secretion, and anti-tumor activity. Besides lipid signaling, our findings show a general depletion of tricarboxylic acid cycle (TCA) metabolites in aging T-cells, with pools of fumarate, malate, and argininosuccinate significantly decreasing in both mouse and human aging T-cells. In vivo supplementation of fumarate to mouse T-cells seemed to correct some of the functional defects observed in aging, with a protection of T-cell viability, cytokine production, and tumor killing capacity in co-cultures with tumor cells. The fumarate supplementation also led to a decrease in ceramide-dependent mitophagy in the aging T-cells, indicating an interplay between ceramide-dependent mitophagy and fumarate metabolism. Interestingly, T-cells from aging mice with Alzheimer's disease are protected against the aging-induce increase in mitophagy, and their fumarate pools are also protected. Here, the NanoString data shows the changes in metabolic and immune markers in aging T-cells with/out fumarate supplementation, as well as in T-cells from Alzheimer's mice, associated with a significant increase in different metabolic enzymes.

overall_design: 4 different condtions, 3 biological replicates for each.


title: Spatial transcriptomics analysis of a panel of PDX models of GBM

city: London

first: Simona

last: Parrinello

address: 72 Huntley Street

country: United Kingdom

institute: UCL Cancer Institute

summary: Visium spatial transcriptomics was carried out on ten glioblastoma PDX models and one tumour free age-matched control brain.

sample_organism:
Homo sapiens
Mus musculus
Homo sapiens/Mus musculus xenograft

overall_design: Patient derived cell lines transduced with luciferase-GFP were injected into the striatum of immunocompromised NSG mice. Tumours were allowed to develop and progression monitored by IVIS signalling. When mice began to demonstrate signs of disease (weight loss and behaviouraly indicators), brains were snap frozen in cold methylbutane prior to OCT embedding, cryostat sectioning  (10um) onto 10xGenomics Visium Spatial Gene Expression Slides.

first: Melanie

last: Clements

first: Wenhao

last: Tang

first: Samuel

last: Marguerat


title: Leveraging chorionic villus biopsies for the derivation of patient-specific trophoblast stem cells

status: Public on Jun 10 2025

city: Kansas City

first: Kaela

middle: Margaret

last: Varberg

state: MO

address: 2401 Gillham Road; CMRI 7902.19

department: Pediatrics

institute: Children's Mercy

type: Expression profiling by high throughput sequencing

summary: Human trophoblast stem (TS) cells are an informative in vitro model for the generation and testing of biologically meaningful hypotheses. The goal of this project was to derive patient-specific TS cell lines from clinically available chorionic villus sampling (CVS) biopsies. Cell outgrowths were captured from human CVS tissue specimens cultured in modified human TS cell medium. Cell colonies emerged early during the culture and cell lines were established and passaged for several generations. Karyotypes of the newly established CVS-derived trophoblast stem (TSCV) cell lines were determined and compared to initial genetic diagnoses from freshly isolated chorionic villi. Phenotypes of TSCV cells in the stem state and following differentiation were compared to cytotrophoblast-derived TS (TSCT) cells. TSCV and TSCT cells uniformly exhibited similarities in the stem state and following differentiation into syncytiotrophoblast. These shared features included morphology and gene expression. TSCV cell differentiation into extravillous trophoblast cells exhibited cell line dependent phenotypes. CVS tissue specimens provide a valuable source for TS cell derivation. They expand the genetic diversity of available TS cells and are associated with defined clinical outcomes. TSCV cell lines provide a new set of experimental tools for investigating trophoblast cell lineage development.

overall_design: Chorionic villus tissue specimens were cultured in Complete TS Cell Medium (Okae et al., 2018) on type IV collagen-coated dishes and cell outgrowths formed and expanded from attached tissue specimens. Human TS cell colonies emerged after first passage and lines were expanded with subsequent passaging. TS cells were propogated in tissue culture treated dishes pre-coated with type IV collagen in Complete TS Cell Medium.  EVT cell differentiation (2018 protocol) was induced by plating human TS cells onto 6-well plates pre-coated with 1 μg/mL collagen IV at a density of 80,000 cells per well. Cells were cultured in EVT Differentiation Medium and analyzed on day 8 of EVT cell differentiation (Okae et al., 2018). Alternatively, EVT cell differentiation (2022 protocol) was induced by plating human TS cells into 6 cm petri dishes at a density of 1x105 TS cells per dish and cultured for two days in Spheroid Medium. After two days spheroids collected and replated in EVT Differentiation Medium and Matrigel. Cells were analyzed on day 7 of EVT cell differentiation. Syncytiotrophoblast cell differentiation was induced by plating TS cells into 6 cm petri dishes at a density of 300,000 cells per dish in Three-dimensional (3D) Syncytiotrophoblast Differentiation Medium (Okae et al., 2018). Cells were analyzed on day 6 of syncytiotrophoblast cell differentiation.

middle: M

first: Ayelen

last: Moreno-Irusta

first: Allynson

last: Novoa

first: Boryana

last: Koseva

first: Brynne

last: Musser

first: Joseph

first: Jeremy

last: Goering

first: Irfan

last: Saadi

first: Khursheed

last: Iqbal

first: Hiroaki

last: Okae

first: Takahiro

last: Arima

first: John

last: Williams

first: Elin

last: Grundberg

first: Margareta

middle: D

last: Pisarska

first: Michael

middle: J

last: Soares


title: ChIP-Seq of H3K27me3 in MCF-7 cells overexpressing EPIC1

city: Pittsburgh

first: Min

last: Zhang

state: PA

address: Salk Hall, 3501 Terrace St

institute: University of Pittsburgh

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Chromatin immunoprecipitation assays followed by sequencing (ChIP-Seq) of H3K27me3 in MCF-7 cells overexpressing EPIC1.

overall_design: ChIP-seq of H3K27me3 in MCF-7 cells overexpressing EPIC1

first: Da

last: Yang

first: Zehua

last: Wang

first: Yifei

first: Sihan

last: Li


title: The response of human coronary artery endothelial cells to PPBP treatment

status: Public on Jun 07 2025

city: Nanjing

first: Dongqing

address: No.12, Jiangwangmiao Street, Xuanwu District, Nanjing, China

country: China

institute: Hospital for Skin Diseases, Institute of  Dermatology, Chinese Academy of Medical Sciences &  Peking Union Medical College

summary: Pro-platelet basic protein (PPBP), a platelet-derived member of the CXC chemokine family, activates neutrophils and other immune cells via CXCR1 and CXCR2 receptors. It is associated with various diseases, including chronic obstructive pulmonary disease, inflammatory bowel disease, and rheumatoid arthritis. In our study, PPBP was found to be significantly upregulated in both the dermal adipose tissue and plasma of patients with psoriasis. Administration of PPBP or imiquimod in Apoe-/- mice exacerbated atherosclerosis by inducing oxidative stress and mitochondrial dysfunction in coronary artery endothelial cells. Conversely, neutralizing PPBP or administering the mitochondria-targeted antioxidant Mito-TEMPO significantly reduced atherosclerotic plaque formation in these mice. To further explore the mechanisms by which PPBP contributes to atherosclerotic plaque development, we conducted transcriptomic analysis of human coronary artery endothelial cells (HCAEC) treated with PPBP

overall_design: HCAECs were treating with PPBP protein. The total RNA was isolated for subsequent RNA sequencing analysis.

first: Liping

last: Zhu


title: Bulk RNA-seq of CD11b+ cells from MC38 tumours in Kaede transgenic mice

city: Cambridge

first: Colin

middle: YC

last: Lee

address: Wellcome Genome Campus, Hinxton

institute: Molecular Immunity Unit

summary: Tumour-associated macrophages (TAMs) are a universal feature of cancers but variably influence outcome and treatment responses. Here, we used a photoconvertible mouse to distinguish newly entering, monocyte-derived (md)TAMs that were enriched at the tumour core, from resident-like (r)TAMs that localised with fibroblasts at the tumour–normal interface. The mdTAM pool was highly dynamic and continually replenished by circulating monocytes. Upon tumour entry, these monocytes differentiated down two divergent fate trajectories distinguished by the expression of MHC class II. MHC-II+ mdTAMs were functionally distinct from MHC-II– mdTAMs, demonstrating increased capacity for endocytosis and FcγR-mediated phagocytosis, as well as pro-inflammatory cytokine production. Both mdTAM subsets showed reduced expression of inflammatory transcripts and increased expression of PD-L1 with increasing tumour dwell-time. Treatment with anti-PD-L1 skewed mdTAM differentiation towards the MHC-II+ fate and attenuated the anti-inflammatory effects of the tumour environment. Anti-PD-L1 enhanced mdTAM–CD4+ T-cell interactions, establishing an IFNγ-CXCL9/10-dependent positive feedback loop. Altogether, these data resolve distinct temporal, spatial and functional properties of TAMs, and provide evidence of subset-specific effects of PD-L1 blockade.

overall_design: MC38-Ova tumours were collected 24h or 72h after photoconversion in Kaede transgenic mice. Live CD45+TER119–Kaede+CD11b+NK1.1– cells were isolated by FACS sorting for RNA-seq.

first: David

last: Withers

first: Menna

last: Clatworthy


title: Phagosome-mediated anti-bacterial immunity is governed by the proton-activated chloride channel in peritoneal macrophages

city: Baltimore

first: Henry Yi

last: Cheng

state: MD

address: 725 N Wolfe st, WBSB216

institute: Johns Hopkins University

summary: Phagosome-mediated degradation is a well-conserved and highly effective innate immune response against pathogen infections. However, its role in shaping immune responses remains underappreciated. The molecular mechanisms underlying how phagosomes mature are also poorly understood. Here, we identify proton-activated chloride (PAC) channel as a key negative regulator of phagosome maturation. PAC deletion facilitates phagosomal acidification and protease activation, leading to augmented bactericidal activity in peritoneal macrophages upon Escherichia coli infection. Moreover, enhanced phagosome bacterial degradation in PAC-deficient macrophages promotes downstream STING-IRF3 activation and type 1 interferon (IFN) responses through the release of bacterial ligands. Such ligand release also activates the inflammasome, leading to gasdermin D (GSDMD) cleavage and secretion. The secreted N-terminus GSDMD directly participates in bacterial killing by forming GSDMD pores on bacterial surfaces. Eventually, this macrophage hyperactivation is terminated by pyroptotic cell death. In mice, PAC deletion in macrophages reduced overall peritoneal inflammation and proinflammatory neutrophil and monocyte infiltrations, as well as improved survival after peritoneal infection. Our study thus provides new insights into mechanisms of phagosome maturation and the dynamics of host defense response following phagosome-mediated bacterial degradation.

overall_design: Mice were subjected to intraperitoneal E. coli infection for 30 minutes and underwent peritoneal lavage to acquire peritoneal cells. Cells were washed with ice-cold PBS and collected in FACS buffer. Cells further underwent surface staining for LPM gating. Subsequently, Sony MA900 Multi-Application Cell Sorter was used for isolating LPM cells. 3 samples from PBS- and infection-treated mice from control or Cx3cr1-PAC−/− mice were collected. Total RNA was extracted using the RNeasy Micro kit (Qiagen). In brief, libraries were constructed using the NEBNext Ultra II RNA library Prep Kit for Illumina (New England Biolabs) and sequenced on an illumina NovaSeq 6000 System. Reads were mapped to GRCm38/mm10 reference mouse genome with Hisat2 v2.0.5. FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Fragments per kilobase per million mapped reads (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene. Further differential expression analysis, Gene Set Enrichment analysis, Gene Ontology analysis, and KEGG pathway analysis were carried out by clusterProfiler R package.

first: Henry

middle: Y

first: Yingzhi

last: Ye

first: Shuying

last: Sun

first: Zhaozhu

last: Qiu


title: Spatial Transcriptomics of Developing Wheat Seed Reveals Concentric Gene Expression Zones and Subgenome Biased Expression of Key Genes

status: Public on Jun 08 2025

city: St Lucia

first: Tori

middle: Jewel

last: Millsteed

state: QLD

address: 306 Carmody rd

department: Queensland Alliance for Agriculture and Food Innovation

country: Australia

institute: The University of Queensland

summary: Gene expression of developing seeds drives essential processes such as nutrient storage, stress tolerance and germination. However, the spatial organisation of gene expression within the complex structure of the seed remains largely unexplored. Here we report the use of the STOmics spatial transcriptomics platform to visualise spatial expression patterns in the wheat (Triticum aestivum) seed at the critical period of grain filling in mid seed development. We analysed >4,000,000 spatially resolved transcripts, achieving subcellular resolution of transcript localization across multiple tissue domains, and identified gene expression clusters linked to eight functional cellular groups. Notably, our analysis characterised four distinct clusters within the endosperm, which exhibited radial expression patterns from the inner to outer regions of the grain, and identified novel marker gene candidates for the clusters found. We further investigated known tissue-specific genes and identified subgenome biased expression between paralogs of puroindoline-B, metallothionein protein, and α-amylase/subtilisin inhibitor. These findings provide new detail about gene expression across and within different functional cellular groups of the developing seed and demonstrate that spatial transcriptomics could further our understanding of subgenome differences in polyploid plants.

overall_design: The STOmics spatial transcriptomics platform was used to measure spatial gene expression in the developing wheat seed. Sections of 14 DPA seeds were cut in a cryostat to a thickness of 20 µm and mounted onto the STOmics transcriptomics assessment chips, covered in an array of spatially tagged DNA nanoballs (DNBs). The RNA content of the chips were sequenced and aligned to the reference genome to generate a gene expression matrix with spatial data.

last: Kainer

first: Robert

last: Sullivan

first: Xiaohuan

first: Ka-Leung

first: Likai

last: Mao

first: Arlie

last: Macdonald

last: Henry


title: Transcriptome analysis of subcutaneous adipose tissue from psoriatic lesion skin and peripheral non-lesional skin

summary: Psoriasis, a prevalent chronic inflammatory skin disease, affects over 100 million individuals globally and is increasingly acknowledged as a systemic condition impacting the heart, blood vessels, and joints. A substantial body of research highlights a strong correlation between the severity of psoriasis and an elevated risk of cardiovascular diseases. Notably, treatments that alleviate dermatological symptoms have also been shown to reduce the formation of coronary plaques. Adipose tissue, functioning as a significant endocrine organ, secretes pro-inflammatory mediators that perpetuate the chronic low-grade inflammation typical of obesity. To investigate the molecular changes in adipose tissue associated with psoriasis, we collected subcutaneous adipose tissue samples from both psoriatic lesion skin (LS, n=8) and peripheral non-lesional skin (NLS, n=8), and conducted comprehensive transcriptomic analyses.

overall_design: The total RNA was isolated from subcutaneous adipose tissue samples from 8 psoriatic lesion skin and 8 peripheral non-lesional skin.  The whole transcriptome analysis was perfrom by microarray

first: Mona

last: Ståhle

first: Ning

last: Xu Landén


title: RNA-seq revealed the protective effect of Huangqi Guizhi Wuwu Decoction against cisplatin induced PC12 cell injury

city: Baotou

first: Jie

address: Baotou Medical College

institute: Baotou Medical College

summary: Chemotherapy-induced peripheral neuropathy (CIPN) not only impacts chemotherapy regimens but also causes intolerable and long-lasting effects on cancer patients. Currently, duloxetine is the only drug used to treat CIPN. However, the clinical use of this drug still faces several challenges. Therefore, we focused on traditional Chinese medicine (TCM) to find an effective and safe alternative medicine. Huangqi Guizhi Wuwu Decoction (HGWD) is a traditional Chinese medicine that has been clinically used for treating nerve pain for thousands of years. This study aimed to investigate the neuroprotective effect of HGWD on cisplatin-induced injury in PC12 cells and to elucidate its potential mechanism of action.

overall_design: We investigated the effect of cisplatin and HGWD treatment on rat PC12 cell gene expression. For RNA-seq analysis, three groups were divided into a control group, a cisplatin group, and an HGWD+ cisplatin group. Each group had three biological replicates.

first: C

last: Jie

first: D

last: Yuan

first: T

last: YuChen

last: ZhiQiang


title: SOX2 regulates foregut squamous epithelial homeostasis and is lost during Barrett’s esophagus development [scRNA-seq]

status: Public on Jun 06 2025

city: St. Louis

first: Ramon

last: Jin

address: 600 S Euclid

institute: Washington University School of Medicine

summary: Esophageal adenocarcinoma (EA) is increasingly prevalent and is thought to arise from Barrett’s esophagus (BE), a metaplastic condition in which chronic acid and bile reflux transforms the esophageal squamous epithelium into a gastric-intestinal glandular mucosa. The molecular determinants driving this metaplasia are poorly understood. We developed a human BE organoid biobank that recapitulates BE’s molecular heterogeneity. Bulk and single-cell transcriptomics, supported by patient tissue analysis, revealed that BE differentiation reflects a balance between SOX2 (foregut/esophageal) and CDX2 (hindgut/intestinal) transcription factors. Using squamous-specific inducible Sox2 knockout (Krt5CreER/+; Sox2∆/∆; ROSA26tdTomato/+) mice, we observed increased basal proliferation, reduced squamous differentiation, and expanded metaplastic glands at the squamocolumnar junction, some tracing back to Krt5-expressing cells. CUT&RUN analysis showed SOX2 bound and promoted differentiation-associated (e.g., Krt13) and repressed proliferation-associated (e.g., Mki67) targets. Thus, SOX2 is critical for foregut squamous epithelial differentiation and its decreased expression is likely an initiating step in progression to BE and thence to EA.

overall_design: sc-RNA seq data for human BE organoids lines WU002, WU010, WU012, and WU014

middle: U

first: Jason

middle: C

last: Mills


title: SOX2 regulates foregut squamous epithelial homeostasis and is lost during Barrett’s esophagus development [CUT&Run]

overall_design: CUT&RUN for WT control forestomach organoids and SOX2 KO forestomach organoids using SOX2 antibody, H2K27Me3 positive control, and IgG negative control


title: Histone β-hydroxybutyrylation underlies the reno-protective effect of β-hydroxybutyrate in hypertensive Dahl Salt-Sensitive Rats [RNA-seq]

city: Toledo

first: Bina

last: Joe

state: OH

address: Block health Science building

institute: University of Toledo health science center

summary: Background: Previously, we demonstrated that the ketone body, β-hydroxybutyrate, is a potent antihypertensive and reno-protective metabolite in Dahl Salt-Sensitive rats.  However, the mechanism by which β-hydroxybutyrate confers these beneficial effects is understudied. Here we focused on determining whether the reno-protective effect of β-hydroxybutyrate is due to its known ability to epigenetically remodel chromatin via histone β-hydroxybutyrylation. Methods: We used the same animal protocol previously used for the discovery of the renoprotective effect of β-hydroxybutyrate. Briefly, post-weaning, male and female Dahl Salt-Sensitive rats were split into two groups and supplemented with or without 1,3-Butanediol for 6 weeks. At euthanasia, circulating β-hydroxybutyrate was quantitated. Renal homogenates were examined for histone 3 lysine 9 β-hydroxybutyrylation, chromatin occupancy, transcriptomic and proteomic profiles with validations.  Results: Rats supplemented with 1,3-butanediol had higher circulating β-hydroxybutyrate, renal histone β-hydroxybutyrylation and significant remodeling of chromatin.  Notably, regions of the genome associated with lipid catabolism were predominantly in an open chromatin configuration, leading to active transcription and translation. The most highly upregulated gene actively transcribed and translated was 3-hydroxy-3-methyglutaryl CoA Synthase 2 (Hmgcs2), a gene responsible for the biosynthesis of β-hydroxybutyrate in mitochondria. In contrast, regions with more compact chromatin structures contained immune function genes, protein tyrosine phosphatase receptor type C (Ptprc) and lymphocyte cytosolic protein 1 (Lcp1), which were suppressed. Conclusions: These results reveal that renal epigenetic histone β-hydroxybutyrylation is a novel mechanism by which transcriptional regulation of both energy metabolism and immune function occur concomitantly and contribute to renoprotection in the hypertensive Dahl rat.

overall_design: Male and female Dahl Salt-Sensitive rats were split into two groups and supplemented with or without 1,3-Butanediol for 6 weeks. At euthanasia, circulating β-hydroxybutyrate was quantitated. Renal homogenates were examined for histone 3 lysine 9 β-hydroxybutyrylation, chromatin occupancy, transcriptomic and proteomic profiles with validations.

first: Mandal

last: Juthika

first: Aryal

last: Sachin

first: Manandhar

last: Ishan

first: Chakraborty

last: Saroj

first: Mei

last: Xue

first: Yeoh

last: Beng

first: Mell

last: Blair

first: Kleinhenz

last: Andrew

first: Tummala

last: Ramakumar

first: Yang

last: Tao

first: Saha

last: Piu

first: Gunning

last: William

first: Vijay-Kumar

last: Matam

first: Basrur

last: Venkatesha

first: De la Serna

last: Ivana

first: Joe

last: Bina


title: Cohesin recruitment to promoters and enhancers by general transcription factors and chromatin regulators

city: Chapel Hill

first: Alexis

last: Stutzman

state: NC

address: 250 Bell Tower Drive

institute: University of North Carolina at Chapel Hill

summary:
Background
Cohesin is a major regulator of three-dimensional genome organization and gene expression. Cohesin binds to DNA and dynamically extrudes a DNA loop, often bringing two cis-regulatory elements physically close together. Extruding cohesin molecules can be stalled or stabilized when they encounter a CTCF insulator protein on DNA, thereby anchoring a DNA loop.  However, many enhancer-promoter loops that are bound by cohesin lack CTCF and it is not clear how cohesin is recruited to these sites in the genome.

Results
Here, we investigate the localization patterns of cohesin, as well as general chromatin state and localization of transcription factors WDR5, SP1, and NFYA in mouse embryonic stem cells.  The SP1 and NFYA transcription factors are ubiquitously expressed proteins known to regulate expression of genes associated with a variety of cellular processes, while WDR5 is a core component of multiple complexes that regulate chromatin. Cohesin co-binds promoters and enhancers with WDR5, with SP1, or with NFYA in mESCs and other cell types. Cohesin co-immunoprecipitates with WDR5, SP1, and NFYA and cohesin simultaneously binds to the same chromatin molecules with these proteins.  At co-bound sites, depletion of cohesin does not alter binding of WDR5, SP1, or NFYA;, however depletion of WDR5, SP1, or NFYA decreases cohesin binding.

Conclusions
These results indicate that general transcription factors and chromatin regulators recruit cohesin to specific sites in chromatin and thereby serve as structural regulators of enhancer-promoter loops via the recruitment of cohesin.

overall_design: ChIP-seq of WDR5, NFYA, SP1, and SMC1 from mESCs that are either wildtype or depleted for WDR5, SP1, or NFYA using siRNA. ChIP of these proteins from siGlo controls are also included.

first: Audra

middle: F

last: Bryan

first: Megan

last: Justice

middle: V

first: Daniel

last: McKay

first: Jill

last: Dowen


title: SOX2 regulates foregut squamous epithelial homeostasis and is lost during Barrett’s esophagus development [SOX2mousetissue]

first: Ramon

last: Jin

summary:
Differentially expressed genes in SOX2 KO vs control forestomachs
In this dataset, we include expression data from 4 SOX2 KO forestomachs and 3 control forestomaches

overall_design: In this dataset, we include expression data from 4 SOX2 KO forestomachs and 3 control forestomachs. To induce gene deletion but not gastric injury, “low-dose” tamoxifen (1 mg/20 g body weight) was injected intraperitoneally for 7 consecutive days. Mouse forestomach tissues from four Krt5CreER/+; Sox2∆/∆; ROSA26tdTomato/+ mice and three wildtype control mice were harvested and flushed with PBS. Corpus and antrum were removed. The forestomach tissues were mechanically dissociated using a tissue Homogenizer 850. RNA was isolated using RNeasy Mini Kit, following the manufacturer’s protocol. For microarray, samples were processed and hybridized to Affymetrix Mouse Gene 2.0 ST by the Washington University Genome Technology Access Core (GTAC). Mouse forestomach tissue GeneChips were analyzed with Partek Flow Genomic Analysis Software using default settings for array QC, data normalization, and to generate differential expression analyses including hierarchical clustering and volcano plots.

first: Jason

last: Mills


title: SOX2 regulates foregut squamous epithelial homeostasis and is lost during Barrett’s esophagus development

summary:
Differentially expressed genes in SOX2 KO vs control forestomach organoids
In this dataset, we include expression data from SOX2 KO forestomach organoid and control forestomach organoid

overall_design: In this dataset, we include expression data from SOX2 KO and control forestomach organoids generated from mouse forestomach tissues from Krt5CreER/+; Sox2∆/∆; ROSA26tdTomato/+ mice and wildtype control mice. Organoids were expanded and mechanically dissociated from Matrigel, dispersed using 0.05% Trypsin-EDTA and manual pipetting. RNA was isolated using RNeasy Mini Kit, following the manufacturer’s protocol. For microarray, samples were processed and hybridized to Affymetrix Mouse Gene 2.0 ST by the Washington University Genome Technology Access Core (GTAC). Mouse forestomach organoid GeneChips were analyzed with Transcriptome Analysis Console (Applied Biosystems) analysis software to perform array QC, data normalization, and differential expression analyses.


title: Histone β-hydroxybutyrylation underlies the reno-protective effect of β-hydroxybutyrate in hypertensive Dahl Salt-Sensitive Rats [ATAC-seq]

first: Bina

last: Joe

first: Mandal

last: Juthika

first: Aryal

last: Sachin

first: Manandhar

last: Ishan

first: Chakraborty

last: Saroj

first: Mei

last: Xue

first: Yeoh

last: Beng

first: Mell

last: Blair


title: Allergens Abrogate the Anti-inflammatory Property of DNA and Unmasks Macrophage/ILC2-STING-TNFα-driven Neutrophilic Asthma

city: Denver

first: Rafeul

last: Alam

state: Colorado

address: 1400 Jackson Street

department: Medicine

institute: National Jewish Health

summary: The mechanism of neutrophilic and mixed neutrophilic-eosinophilic asthma is poorly understood. We found that extracellular DNA and nucleosomes (Nucs) were elevated in the airways from neutrophilic-eosinophilic asthma patients and correlated with bronchoalveolar lavage neutrophils. Bronchial tissue from neutrophilic-eosinophilic asthma expressed increased DNA sensor-positive cells. Intranasally administered DNA did not induce airway hyperreactivity (AHR) or any pathology but induced AHR and neutrophilic-eosinophilic inflammation when co- administered with the allergen Alternaria (Alt). Nucs alone induced anti-inflammatory/defensive genes whereas the Nuc-Alt combo increased TNFα and innate cytokines. The Alt-Nuc phenotype was abolished in cGas-/- , Alr-/- , Sting-/- , LysMcre:Stingf/f, Il7rcre:Roraf/f and Tnfrsf1b-/- mice. Alt, unexpectedly, played an essential role in the Nuc-induced phenotype. It abrogated Nuc-induction of anti_x0002_inflammatory genes, facilitated Nuc uptake, induced ILC2s, which, in presence of Nucs, produced high levels of TNFα and promoted neutrophilic infiltration. We established a paradigm where allergens inhibit the anti-inflammatory effects of DNA/Nucs and facilitate STING-TNFα-driven neutrophilic-eosinophilic inflammation in asthma.

overall_design: Total 12 samples from lung tissue of wild-type C57B/6 mice . Study groups: Saline, Nucleosome, Alternaria and Alternaria +Nucleosome. Each groups had three replicates.

first: Anand

last: Sripada


title: SOX2 regulates foregut squamous epithelial homeostasis and is lost during Barretts esophagus development [humanBEorganoids]

summary: Differentially expressed genes in human BE organoids compared to control esophageal squamous organoids.

overall_design: In this dataset, we include expression data from 12 BE organoids and 4 esophageal squamous organoids


title: The role of extracellular vesicle miRNA released in response to influenza A virus

city: Southampton

first: Karl

last: Staples

address: MP810 Southampton General Hospital, Tremona Road

institute: University of Southampton Faculty of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: Influenza is a major cause of human disease and mortality and a key cause of exacerbation in chronic disease like COPD. Recent studies have shown that airway epithelial cells, the primary target of influenza, release lipid bilayer particles known as Extracelluar vesicles (EVs) which contain biological molecules such as micro-RNA (miRNA). Emerging evidence suggests that these small non-coding RNA molecules are selectively packaged into EVs and can regulate recipient cell gene expression including major pathways involved in inflammation and fibrosis. Further understanding the role of EVs and their miRNA cargo in cellular communication in response to infection may identify biomarkers of disease or lead to novel theraputics.  This study utilised a 3D model of IAV infection to explore the impact of IAV on the miRNA profile of EVs released from bronchial epithelial cells in vitro. Infection with IAV at 3.6 x 106 IU/ml for 24 hours was determined to be a suitable condition for EV analyses due to the detection of significant upregulation of anti-viral genes without high levels of cell death or loss of barrier integrity.

overall_design: miRNA-seq profiling of EVs isolated from the apical wash of ALI differentiated BCi-NS1.1 cells. Samples were either uninfected (n=5) or IAV infected at 3,600,000 IU/ml for 24 hours (n=5).

first: Laura

last: Reid


title: Investigate FOXA2-driven lineage plasticity in prostate cancer cells by Single-cell nanopore RNA sequencing (scNanoRNA-seq)

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

summary: Emerging evidence suggests that the epigenetic state, including the DNA methylation, chromatin accessibility and histone modification, is substantially remodeled, leading to transcriptional reprogramming during the transformation of castration resistant adenocarcinoma (CRPC-Adeno) to neuroendocrine (CRPC-NE) lineage and LUAD to LUAD-SCLC lineage . However, the underlying mechanism is largely unknown. Here, we found FOXA2 transdifferentiates prostate adenocarcinoma away from an AR+/AR gene signature positive (AR+/ARS+) luminal cell lineage to an embryonic and neuroendocrine-lineage by inducing a population of AR+/ARS- transient cells through NKX2-1. Mechanistically, as a pioneer factor, FOXA2 primes NE lineage enhancers by inducing regional chromatin accessibility and DNA demethylation at early stage of transformation. Whereas, once the expression of NKX2-1 is induced by FOXA2, FOXA2 interacts with NKX2-1, mediates gene promoter and enhancer looping and cooperatively recruits P300/CBP complex to NE lineage enhancers, thereby activates NE lineage gene transcription. Interestingly, similar mechanism is also observed in SCLC cancer, suggesting FOXA2 and NKX2-1 are general regulators orchestrating the epigenetic landscape of NE lineage cancer. Finally, therapeutic targeting P300/CBP with CCS1477 which is in clinical trial for lethal PCa significantly impairs NEPC tumor growth.

overall_design: To identify cells at transitioning stage  and clonal evolution during FOXA2-induced NEPC transformation, we performed scNanoRNA-seq in LNCaP+FOXA2 D0 and D28 cells

first: Xiaodong

last: Lu

first: Viriya

last: Keo

first: Jonathan

last: Zhao


title: Transcriptomic analysis of first molars in a mouse model of Loeys-Dietz Syndrome Type II harboring a G357W mutation in the Tgfbr2 gene

city: Bethesda

first: Olivier

last: Duverger

address: 30 Convent Drive - Bldg 30 - Room 202

institute: National Institute of Dental and Craniofacial Research

summary: Loeys Dietz Syndrome (LDS) is a connective tissue disorder caused by mutations along the TGF-beta signaling pathway and characterized by severe aortic aneurysm and craniofacial anomalies. Patients with LDS Type II (LDS2), caused by mutations in the TGFBR2 gene also exhibit enamel defects. A mouse model for LDS2, harboring a G357W mutation in the Tgfbr2 gene, recapitulates the cardiovascular, craniofacial and dental phenotype of the disease. This transcriptomic analysis aimed at identifying genes that are differentially regulated in first molars of Tgfbr2-G357W/+ mice at postnatal day 5 and 11. Total RNA was extracted from enamel organs from Tgfbr2-G357W/+ mice (LDSR2, KI) and Tgfbr2-+/+ wild-type littermates (WT).

overall_design: Total RNA from first mandibular molars at P5 and P11 from five Tgfbr2-G357W/+ mice (LDSR2, Het) and eight Tgfbr2-+/+ wild-type littermates (WT)  was collected for bulk RNA-seq analysis.

first: Sean

middle: K

last: Wang

first: Quynh

last: Nguyen

first: Priyam

middle: H

last: Jani

first: Fabian

last: Mandoza

first: Yan

first: Daniel

last: Martin

first: Pamela

middle: A

last: Frishmeyer-Guerrerio

first: Janice

middle: S

last: Lee


title: Single-cell transcriptomics reveal diverging pathobiology and opportunities for precision targeting in scleroderma -associated versus idiopathic PAH

first: Catherine

last: Simpson

state: Maryland

address: 1830 E. Monument St. 5th Fl

summary: Pulmonary arterial hypertension (PAH) is characterized by progressive cellular and molecular changes within the pulmonary vasculature that lead to structural remodeling, rising pulmonary vascular resistance and, if untreated, right ventricular failure. In clinical practice, PAH treatments have evolved little over the last two decades, and until recently, all approved therapies have targeted one of three molecular pathways: the nitric oxide (NO) signaling pathway, the endothelin pathway, or the prostacyclin pathway. With these therapies, treatment responses have been modest and variable, with patients experiencing a heterogeneity of treatment effects. In particular, patients with PAH related to systemic sclerosis (SSc-PAH) have derived less benefit from PAH-specific therapies and have experienced worse clinical outcomes compared to other PAH subgroups. We and others have shown that in SSc-PAH, pathophysiologic differences at the molecular, cellular, and tissue levels underlie observed differences in clinical outcomes. A detailed understanding of the molecular aberration present in SSc-PAH versus idiopathic PAH (IPAH) might allow for exploitation of aberrant signaling pathways that are unique to SSc-PAH (and/or present in both of these two common PAH subtypes) for drug targeting. Recently, the approval of sotatercept, a novel ligand-trap molecule that targets TGF-beta signaling in PAH, was based on randomized controlled trial data demonstrating clinical improvement in patients already treated with drugs targeting NO, endothelin, and/or prostacyclin signaling. The success of sotatercept therefore lends credence to the notion that targeting as-yet unaddressed molecular aberrancies can bring about additional clinical benefit. Most previous omics investigations in PAH have examined circulating plasma or serum. With this study, we sought to identify distinct and overlapping gene expression patterns in SSc-PAH versus IPAH human lung tissue as a means of implicating abnormal biological processes, including inferred gene regulation and cell signaling, unique to the organ manifesting disease. To maximize biologic insight, we took a single-cell approach to RNA sequencing, in contrast to the bulk sequencing performed in most previous PAH studies. Finally, we leveraged cell-specific gene expression patterns and established computational methods to identify small molecule compounds with high potential to reverse disease-specific expression signatures, as a means of prioritizing candidates for drug repositioning. We posit that generation of phenotype-specific high-dimensional omics datasets, such as this one, will enable a precision-targeted approach to molecular aberration that might improve therapeutic responses and resolve heterogeneous treatment effects, thereby improving clinical outcomes across PAH subtypes.

overall_design:
There are four SSc-PAH lung specimens, four IPAH lung specimens, and four failed donor specimens judged suitable to serve as healthy controls.The PAH samples were compared to the failed donor using differential expression and gene set enrichment analysis. In order to infer gene regulatory differences between the two PAH subgroups, we performed differential transcription factor (TF) activity analysis for each cell cluster using UCell.

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

first: Tijana

last: Tuhy

first: Julie

last: Coursen

first: Tammy

last: Graves

first: Michael

last: Patatanian

first: Christopher

last: Cherry

first: Shannon

middle: E

last: Niedermeyer

first: Sarah

middle: L

last: Khan

first: Darin

last: Rosen

middle: P

last: Croglio

first: Mohab

last: Elnashar

first: Todd

last: Kolb

first: Stephen

last: Mathai

first: Rachel

last: Damico

first: Paul

last: Hassoun

first: Karthik

last: Suresh

first: Larissa

last: Shimoda

first: Micheala

last: Aldred


title: G-quadruplex structures regulate long-range transcriptional reprogramming to promote drug resistance in ovarian cancer [CUT&Tag]

first: Marco

last: Di Antonio

address: Molecular Sciences Research Hub, 82 Wood Lane

institute: Imperial College London

summary: Enhancers are regulatory elements of the genome involved in transcriptional regulation and reprogramming. Similarly, we propose that secondary DNA structures termed G-quadruplexes could also be impacting transcription in an enhancer based way via long-range interactions to bring together regulatory elements of the genome. In this study, we map G-quadruplex structures and h3k27ac enhancer marks in a paired ovarian cancer cell line; PEO1 and PEO4. We endeavour to use these findings to help link the transcriptional function of G-quadruplexes with enchancer in chemotherapy sensitive (PEO1) and chemotherapy resistant (PEO4) ovarian cancer cells.

overall_design: We performed CUT&Tag using either an anti- h3k27ac antibody, or the G-quadruplex targting BG4 antibody to map enhancer marks or G-quadruplex structures. For each mark, we did 2x technical of 3x biological repeats in each of the cell lines. Technical repeats have been merged.

first: Jenna

last: Robinson

first: Gem

last: Flint

first: Ian

last: Garner

first: Silvia

last: Galli

first: Thomas

last: Maher

first: Marina

last: Kuimova

first: Ramon

last: Vilar

first: Iain

last: McNeish

first: Robert

last: Brown

first: Hector

last: Keun


title: G-quadruplex structures regulate long-range transcriptional reprogramming to promote drug resistance in ovarian cancer [RNA-seq]

summary: G-quadruplexes are secondary DNA structures which have been shown to have an impact on gene transcription via a variety of mechanisms, In this study we generate RNA-seq data of wildtype chemotherpay sensitive (PEO1 A) and chemostherapy resistant (PEO4 A) ovarian cancer cells to intersect with G-quadruplex mapping data to assess how transcription is impacted by G-quadruplex formation. In another variation of the PEO1/4 cell line, in which the PEO1 B cell line has a reversion mutation to reinstate BRCA2, we used the G-quadruplex stabilising molecule pyridostatin (PDS) to treat PEO1 B and its counterpart PEO4 B for either 0, 2 or 6 hours to see how stabilising G-quadruplexes effects gene expression in a temporal manner.

overall_design: We performed RNA-seq on wildtype PEO1 (BRCA2-) and PEO4 (BRCA2+) cells (which we term PEO1 A and PEO4 A) to assess differential expression between the two. We then performed RNA-seq on another variation of the PEO pair in which BRAC2 has been reinstated in PEO1, before and after treatment with PDS for 2 and 6 hours. We term this pair with the altered BRCA2 status PEO1 B and PEO4 B. 3x biological replicates were performed for each sample type.


title: Neutrophils recruited by NKX2-1 suppression via activation of CXCLs/CXCR2 axis promote lung adenocarcinoma progression

city: Taipei

first: Pinghsing

last: Tsai

state: Taiwan

address: Rm. 825, 7F., No.322, Sec. 2, Shipai Rd., Beitou D

country: Taiwan

institute: Taipei Veterans General Hospital

summary: Background: Lung adenocarcinoma (LUAD) progression is dependent on the immune tumor microenvironment through paracrine signaling. Lineage-specific transcription NKX2-1 is a well-developed pathology marker to define LUAD with progressive impact in patients. However, the involvement of NKX2-1 in modeling the tumor immune microenvironment is still unclear. Here, we demonstrated that NKX2-1-low tumors expedite tumor progression in LUAD through increased tumor-promoting neutrophils. Method: Single-cell RNA sequencing and Visium in situ capturing profiling were used to characterize the infiltration of neutrophils in NKX2-1-low LUAD tumors at high resolution. Clinical relevance of NKX2-1 expression and disease status were evaluated by immunohistochemical analysis of LUAD tissue arrays and the overall survival analysis was performed by TCGA databases. qRT-PCR validated the level of CXC chemokines, and proinflammatory genes in LUAD cells, meanwhile chemokine array confirmed the secretion of chemokines. Mechanistically, ATAC-seq was used to confirm the modulatory role of NKX2-1 on the chromatin accessibility of CXC chemokine genes.  Results: NKX2-1 downregulation was observed in high-grade LUAD with increased neutrophil recruitment and infiltration. NKX2-1 knockdown promoted the expression and secretion of CXCL1, CXCL2, CXCL3, and CXCL5 in LUAD cells. Mechanistically, ATAC-seq revealed the restrictive regulation of NKX2-1 on the promoters of CXCL1, CXCL2 and CXCL5. Single-cell RNA sequencing and Visium in situ capturing revealed the infiltrated neutrophil had strong cell-cell communication through the activation of CXCLs/CXCR2 signaling with increased tumor growth and vice versa when inhibited with CXCR2 antagonist SB225002. Conclusion: This study revealed that NKX2-1 negatively regulates the infiltration of tumor-promoting neutrophils by suppressing CXCLs/CXCR2-dependent mechanisms. Hence, targeting CXCR2 in NKX2-1-low tumors is a potential antitumor therapy that improves LUAD patient outcomes.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
In order to examine the suppressive function of NKX2-1 in the advancement of lung adenocarcinoma, we generated H1975 and HCC827 cell lines with depleted NKX2-1 expression using shRNA technology. We then performed gene expression profiling analysis including bulk, single cell, and spatial RNA sequencing.
In order to identify the specific DNA region affected by the presence of NKX2-1, ATAC-seq analysis was performed on H1975 cells under conditions of NKX2-1 knockdown and control.
To examine the impact of cytokines on neutrophils, we conducted a co-culture experiment involving HL60 neutrophil cells with either control or NKX2-1 knockdown H1975 cells, followed by bulk RNA sequencing analysis.

first: Anita

last: La’ah

first: Lo-Jei

last: Ching

first: Ping-Hsing

first: Mong-Lien

last: Wang


title: G-quadruplex structures regulate long-range transcriptional reprogramming to promote drug resistance in ovarian cancer [ATAC-seq]

summary: Chromatin accessibilty is a key regulator of gene expression. In this study we aim to map accessible chromatin regions in both chemotherapy sensitive (PEO1) and chemotherapy resistant (PEO4) ovarian cancer cell lines, to intersect with RNA-seq data to see how chromatin architecture changes and impacts gene expression between the two cell lines.

overall_design: Chromatin accessibilty was assessed using ATAC-seq on both PEO1 and PEO4 cells, with 4x biological repeats per cell line.


title: Gene context drift identifies drug targets to mitigate cancer treatment resistance

first: Amir

last: Jassim

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

summary: Cancer treatment often fails because combinations of different therapies evoke complex resistance mechanisms that are hard to predict. We introduce REsistance through COntext DRift (RECODR): a computational pipeline that combines co-expression graph networks of single-cell RNA sequencing profiles with a graph-embedding approach to measure changes in gene co-expression context during cancer treatment. RECODR is based on the idea that gene co-expression context, rather than expression level alone, reveals important information about treatment resistance. Analysis of tumours treated in preclinical and clinical trials using RECODR unmasked resistance mechanisms–invisible to existing computational approaches–enabling the design of highly effective combination treatments for mice with choroid plexus carcinoma, and the prediction of potential new treatments for patients with medulloblastoma and triple negative breast cancer. Thus, RECODR may unravel the complexity of cancer treatment resistance by detecting context-specific changes in gene interactions that determine the resistant phenotype.

overall_design: CPC cells (mc300) tagged with luciferase were grown in tissue culture in complete neurobasal media (with 20ng FGF, 20ng EGF and 0.1% BSA ). When neurospheres formed, 5000 cells were implanted in to CD1 nude mice. After 3 days, Bioluminescence (BLI) signals were taken using the IVIS to look for tumor growth. Mice were then randomised in to non-treatment and treatment arms to an average BLI signal of 1-5*10^5 p/s/cm2/sr. Tumour growth was monitored by IVIS imaging. When mice reached an endpoint (either through clinical signs or a BLI of 1-9*10^8 p/s/cm2/sr) mice were killed by exposure to carbon dioxide. Brains were harvested and tumors removed before undergoing enzymatic dissociation with 100µg/ml of DNAseI and 20U/ml Papain for one hour at 37°C. After an hour, samples were triturated 5-6 times before being passed through a 40μm filter. The original tube was washed with 5ml HBSS which was then passed through the same filter. Samples were centrifuged for 5 mins at 4°C and 300g. The supernatant was discarded and cells re-suspended in 10ml HBSS before being passed through a second 40μm filter. The cell suspension was then centrifuged for 5 mins at 4°C and 300g. Finally, the supernatant was discarded and cells were re-suspended and transferred to FACS tubes before being being sorted using a BD Aria II (BD Biosciences) with the following gating strategy, forward and side scatter, singlets and dual RFP (561nm-585/29) and YFP(488nm-530/40) positive cells. Dead cells were excluded with DAPI, UV (355nm-450/50).


title: G-quadruplex structures regulate long-range transcriptional reprogramming to promote drug resistance in ovarian cancer [ChIP-seq]

first: Marco

summary: G-quadruplex ChIP-seq has been performed to establish genomic maps of G-quadruplex structures in chemotherapy sensitive (PEO1) and chemotherapy resistant (PEO4) ovarian cancer cell lines to uncover how the changes in G-quadruplex landscape may contribute to the development of chemotherapy resistance for the first time.

overall_design: Endogenous maps of G-quadruplexes were established through ChIP-seq using the BG4 antibody in PEO1 and PEO4 cells. 2 x technical of 3x biological replicates were performed.


title: Investigate FOXA2 driven lineage plasticity in prostate cancer cells by single-cell Multiome ATAC + Gene Expression assay.

first: Jindan

last: Yu

overall_design: To identify cells at transitioning stage during FOXA2 induced NEPC transformation, we performed single cell Multiome (gene expression + ATAC) in D0, D14 and D21 LNCaP+FOXA2 cells.

first: Xiaodong

last: Lu

first: Viriya

last: Keo

first: Jonathan

last: Zhao


title: High-throughput differentiation of human blood vessel organoids reveals overlapping and distinct functions of the cerebral cavernous malformation proteins

city: Greifswald

first: Dariush

last: Skowronek

address: Fleischmannstraße 43

country: Germany

institute: Institut für Humangenetik

summary: We used single cell RNA sequencing to compare gene expression between WT, CCM1 knockout, CCM2 knockout and CCM3 knockout blood vessel organoids.

overall_design: Comparative gene expression profiling and cell cluster analysis of single cell RNA-seq data for wild-type and CCM1, CCM2 and CCM3 knockout blood vessel organoids differentiated from hiPSCs after gene inactivation with CRISPR/Cas9

first: Skowronek

last: Dariush

first: Pilz

last: Robin A.

first: Felbor

last: Ute

first: Rath

last: Matthias


title: Inhibition of inflammation in adipose tissue accelerates mammary tumor development in mice

city: Dallas

first: Philipp

last: Scherer

state: Texas

address: 5323 Harry Hines Blv

department: Touchstone Diabetes Center

institute: UT Southwestern Medical Center

summary: Proinflammatory signaling in adipocytes is essential for healthy adipose expansion, remodeling, and tissue integrity. We investigated the effects of targeting adipocyte inflammation, specifically in the context of mammary tumor development, through local adipocyte-specific expression of the anti-inflammatory adenoviral RIDα/β protein complex. Suppression of adipose tissue inflammation (“RIDad mice”) in a mammary tumor model driven by MMTV-PyMT (“PyMT-RIDad mice”) led to an elevated number of tumor-associated macrophages (TAMs) in the mammary fat pad (MFP). This was accompanied by metabolic dysfunction and abnormal mammary gland development. Importantly, this phenotype correlated with accelerated mammary tumor onset, enhanced growth, and lung metastasis. Tumors in PyMT-RIDad mice exhibited upregulated CD36 expression, suggesting enhanced fatty acid uptake. Conversely, inhibition of tumor cell inflammation by RIDα/β in ductal epithelial cells delayed mammary tumor growth but had no effect on tumor onset or macrophage accumulation. These findings highlight the differential impact on tumor development exerted through the suppression of inflammatory signals in different cell types in the microenvironment. Our results underscore the role of the suppression of adipocyte inflammation leading to a tumor-friendly microenvironment, promoting mammary cancer progression. This study sheds light on the complex interplay between inflammation specifically driven by the adipocyte in breast cancer pathogenesis.

overall_design: To investigate the in vivo impact of inhibiting inflammation in adipocytes on mammary tumor development, we performed RNA-seq on both tumor tissue and mammary fat (adipocytes) to evaluate changes in mRNA expression following inflammation suppression in adipocytes using PyMT and PyMT-RIDad mice

first: Daeseok

last: Kim

first: Toshiharu

last: Onodera


title: Investigate FOXA2 mediated chromatin 3D confirmation reorganization during NEPC transformation by Hi-C.

overall_design: To examine whether the chromatin 3D structure was regulated by FOXA2 during NEPC transformation.  We performed Hi-C experiment in D14, D21 and D28 LNCa+FOXA2 cells, as well as LuCaP/CRPC PDX: LuCaP35CR and LuCaP147, NEPC PDX: LuCaP93 and LuCaP145.2, NEPC cell line NCI-H660.


title: Investigate FOXA2 mediated DNA demethylation during NEPC transformation by Nanopore Long Read sequencing.

type: Methylation profiling by high throughput sequencing

overall_design: To examine whether FOXA2 overexpression mediated regional DNA demethylation during NEPC transformation, we performed directed methylation with long-read sequencing (DiMeLo-seq) which enables us to analyze DNA CpG methylation and FOXA2 binding simultaneously on the same single DNA molecule in D2, D14 and D28 LNCaP+FOXA2 cells. In addition, to validate the findings in LNCaP+FOXA2 model, we performed Reduced representation methylation sequencing (RRMS) in LuCaP CRPC PDX (LuCaP35CR, LuCaP77CR and LuCaP147) and LuCaP NEPC PDX (LuCaP93, LuCaP145.2 and LuCaP173.1).


title: Investigate FOXA2 regulated chromatin state program  during NEPC transformation by ATAC-seq.

overall_design: To examine  whether the chromatin state was regulated by FOXA2 during NEPC transformation.  We performed the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) in LNCaP FOXA2 time course cells (FOXA2-D0, D2, D7, D14, D21 and D28).


title: Investigate FOXA2, NKX2-1 and P300 regulated transcription program by RNA-seq in prostate cancer cells.

overall_design: 1. To delineate the transcription program regulated by FOXA2 during NEPC transformation, we performed bulk RNA-seq in LNCaP FOXA2 time course cells (FOXA2-D0, D2, D7, D14, D21 and D28) and 22Rv1 cells with FOXA2 overexpression for 4 weeks.  2. To examine whether FOXA2 driven embryonic and neuron lineage transcription program was mediated by NKX2-1, we performed RNA-seq in FOXA2 stable transformed LNCaP cells (LuNE) with FOXA2 or NKX2-1 KO alone, or both KO using gRNAs. 3.To determine NKX2-1 and FOXA2 driven embryonic and NEPC like transcription program whether also regulated by P300/CBP in LuNE cells,  we performed RNA-seq in LuNE cells with control,  P300, CBP alone or P300 and CBP double KD or LuNE cells treated with P300/CBP inhibitor CCS1477.


title: Investigate FOXA2, NKX2-1, CTCF and P300 cistrome and enhancer (H3K27ac and H3k4me1) reprogramming during NEPC transformation by ChIP-seq.

overall_design: 1. To investigate FOXA2, NKX2-1, CTCF and P300 cistrome and enhancer (H3K27ac and H3k4me1) reprogramming during NEPC transformation, we performed FOXA2, NKX2-1, CTCF, H3K27ac and H3K4me1 ChIP-seq  in LNCaP FOXA2 time course cells (FOXA2-D7, D14, D21 and D28) with sgNC or sgNKX2-1 knockdown  2. To examine whether FOXA2 driven enhancer reprogram was mediated by NKX2-1, P300 and CBP,  we performed H3K27ac ChIP-seq  in FOXA2 stable transformed LNCaP cells (LuNE) with FOXA2, NKX2-1 KD alone or P300, CBP KD alone or treated with P300/CBP inhibitor CCS1477.  3. To  explore FOXA2, NKX2-1  cistrome in NEPC patient, we performed FOXA2 and NKX2-1 ChIP-seq in NEPC PDX LuCaP145.2 and NEPC cell line NCI-H660.


title: Transcriptomic analysis of young aortic tissue in a mouse model of Loeys-Dietz Syndrome Type II harboring a G357W mutation in the Tgfbr2 gene

first: Olivier

last: Duverger

summary: Loeys Dietz Syndrome (LDS) is a connective tissue disorder caused by mutations along the TGF-beta signaling pathway and characterized by severe aortic aneurysm and craniofacial anomalies. Patients with LDS Type II (LDS2), caused by mutations in the TGFBR2 gene also exhibit enamel defects. A mouse model for LDS2, harboring a G357W mutation in the Tgfbr2 gene, recapitulates the cardiovascular, craniofacial and dental phenotype of the disease. As part of our transcriptomic analysis aimed at identifying genes that are differentially regulated in the enamel organ of Tgfbr2-G357W/+ mice at postnatal day 11, we peformed a similar analysis on the aorta transcriptome at the same age. Total RNA was extracted from aortic arches from six Tgfbr2-G357W/+ mice (LDS2, Het) and five Tgfbr2-+/+ wild-type littermates (WT). This dataset provides a comprehensive list of genes affected in the aorta of an LDS2 mouse model at a young age.

overall_design: Total RNA from aortic arches dissected from six Tgfbr2-G357W/+ mice (LDSR2, Het) and five Tgfbr2-+/+ wild-type littermates (WT), at postnatal day 11, was collected for bulk RNA-seq analysis.

first: Sean

first: Quynh

last: Nguyen

first: Priyam

last: Jani

first: Fabian

last: Mandoza

first: Yan

first: Daniel

last: Martin

first: Pamela

last: Frishmeyer-Guerrerio

first: Janice

last: Lee


title: Rewiring of cortical glucose metabolism fuels human brain cancer growth

status: Public on Jun 05 2025

city: Ann Arbor

first: Wajd

middle: N.

last: Al-Holou

state: MI

address: 1500 E Medical Center Dr

department: Neurosurgery

institute: University of Michigan

summary: The brain avidly consumes glucose to fuel neurophysiology. Cancers of the brain, such as glioblastoma (GBM), relinquish physiological integrity and gain the ability to proliferate and invade healthy tissue. How brain cancers rewire glucose utilization to drive aggressive growth remains elusive. Here, we infused 13C-labeled glucose into patients and mice with brain cancer, coupled with quantitative metabolic flux analysis, to map the fates of glucose-derived carbon in tumor vs. cortex. Through the first direct and comprehensive measurements of carbon and nitrogen labeling in both cortex and glioma tissues, we uncover profound metabolic transformations. In human cortex, glucose carbons fuel essential physiologic processes including TCA cycle oxidation and neurotransmitter synthesis. Conversely, gliomas downregulate these processes and scavenge alternative carbon sources such as amino acids from the environment, repurposing glucose-derived carbons to generate molecules needed for proliferation and invasion. Targeting this metabolic rewiring in mice through dietary amino acid modulation selectively alters GBM metabolism, slows tumor growth, and augments the efficacy of standard-of-care treatments. These findings illuminate how aggressive brain tumors exploit glucose to suppress normal physiological activity in favor of malignant expansion and offer potential therapeutic strategies to enhance treatment outcomes.

overall_design: RNA-seq profiling of tumor tissues of three GBM patients.

first: Andrew

last: Scott

first: Anjali

last: Mittal

first: Baharan

last: Meghdadi

first: Alexandra

last: O'Brien

first: Justine

last: Bailleul

first: Sravya

last: Palavalasa

first: Abhinav

last: Achreja

first: Weihua

last: Zhou

first: Jie

last: Xu

first: Angelica

last: Lin

first: Kari

last: Wilder-Romans

first: Ningning

last: Liang

first: Ayesha

last: Kothari

first: Navyateja

last: Korimerla

first: Donna

middle: M

last: Edwards

first: Zhe

last: Wu

first: Jiane

last: Feng

first: Sophia

last: Su

first: Li

last: Zhang

first: Peter

last: Sajjakulnukit

first: Anthony

last: Andren

first: Junyoung

middle: O

last: Park

first: Johanna ten

last: Hoeve

first: Vijay

last: Tarnal

first: Kimberly

last: Redic

first: Nathan

middle: R

last: Qi

first: Joshua

last: Fischer

first: Ethan

last: Yang

first: Michael

last: Regan

first: Sylwia

last: Stopka

first: Gerard

last: Baquer

first: Krithika

last: Suresh

first: Jann

middle: N

last: Sarkaria

first: Theodore

last: Lawrence

first: Sriram

last: Venneti

first: Nathalie Y

last: Agar

first: Erina

last: Vlashi

first: Costas

last: Lyssiotis


title: Transcriptomic analysis of enamel organ in a mouse model of Loeys-Dietz Syndrome Type II harboring a G357W mutation in the Tgfbr2 gene

first: Olivier

last: Duverger

summary: Loeys Dietz Syndrome (LDS) is a connective tissue disorder caused by mutations along the TGF-beta signaling pathway and characterized by severe aortic aneurysm and craniofacial anomalies. Patients with LDS Type II (LDS2), caused by mutations in the TGFBR2 gene also exhibit enamel defects. A mouse model for LDS2, harboring a G357W mutation in the Tgfbr2 gene, recapitulates the cardiovascular, craniofacial and dental phenotype of the disease. This transcriptomic analysis aimed at identifying genes that are differentially regulated in the enamel organ of Tgfbr2-G357W/+ mice at postnatal day 11. Total RNA was extracted from enamel organs from five Tgfbr2-G357W/+ mice (LDSR2, KI) and eight Tgfbr2-+/+ wild-type littermates (WT). This dataset indicates that the mutation in Tgfbr2 in the enamel organ minimally affects gene expression and suggests that the enamel phenotype in LDS2 is not dependent on canonical TGF-beta signaling.

overall_design: Total RNA from enamel organs (from mandibular incisors) micro-dissected from five Tgfbr2-G357W/+ mice (LDSR2, Het) and eight Tgfbr2-+/+ wild-type littermates (WT), at postnatal day 11, was collected for bulk RNA-seq analysis.

first: Sean

last: Wang

first: Quynh

last: Nguyen

first: Priyam

last: Jani

first: Fabian

last: Mandoza

first: Yan

first: Daniel

last: Martin

first: Pamela

last: Frishmeyer-Guerrerio

first: Janice

last: Lee


title: Multiplexed DNA Affinity purification sequencing (multiDAP-seq) of flowering plants [Solanum tuberosum]

city: Berkeley

first: Sharon

last: Greenblum

state: CA

address: 1 Cyclotron Road

institute: DOE Joint Genome Institute

summary: We applied multiplexed DNA affinity purification sequencing (multiDAP-seq) to profile the binding landscapes of 360 transcription factors (TFs) across ten flowering-plant genomes. Genomic DNA fragment libraries were assayed in 96-well plates against in vitro expressed HaloTag-fused TFs, generating nearly 3,000 genome-wide binding maps. These data provide a resource for identification of TF binding sites and comparative regulatory analyses, revealing deeply conserved TF-DNA interactions alongside lineage-specific rewiring events that underpin plant diversification. We also integreated these TF binding datasets with singe nuclei RNA-seq datasets produced from multiple tissues of five plant species to investigate the roles of TFs in driving cell type-specific gene expression patterns. The associated single nuclei RNA-seq datasets were submitted under BioProject ID PRJNA1262374.

overall_design: Transcription factors (TFs) were synthesized and cloned into an E. coli plasmid vector to generate Halo-tagged TFs driven by a T7 polymerase promoter. PCR primers were used to produce linear expression templates for in vitro protein production. Genomic DNA from each species was sheared to ~150 bp, uniquely barcoded by ligation of a single-indexed (i5 index only) Illumina adapter, PCR-amplified to erase native modifications, and pooled. Each pool was split into 96 wells, with each well containg a unique in vitro expressed transcription factor bound to magnetic Halo beads. Captured TF-bound DNA fragments were subsequently PCR amplified to add well-specific i7 Illumina adapters. Negative control wells were included on each plate using mock in vitro protein expression product, produced by using buffer in place of the linear TF protein expression templates. After sequencing, libraries were demultiplexed by the combined i5 and i7 indexed resulting in a unique fastq file per species species per TF. These were aligned to reference genomes and peaks were called against merged negative control backgrounds from the corresponding plate to identify TF binding sites in each genome.

first: Leo

last: Baumgart

first: Abraham

last: Morales-Cruz

first: Peng

first: Yu

last: Zhang

first: Ronan

last: O'Malley


title: Multiplexed DNA Affinity purification sequencing (multiDAP-seq) of flowering plants [Solanum lycopersicum]


title: Multiplexed DNA Affinity purification sequencing (multiDAP-seq) of flowering plants [Oryza sativa]


title: Multiplexed DNA Affinity purification sequencing (multiDAP-seq) of flowering plants [Sorghum bicolor]


title: LubriShieldTM - a permanent urinary catheter coating that prevents uropathogen biofilm formation in vitro independent of host protein conditioning

city: Solna

first: Ana

middle: I

last: Romero

address: Maria Aspmans Gata 44A

country: Sweden

institute: CytaCoat AB

summary: LubriShieldTM - a novel permanent coating was invented, and evenly applied to both the internal and external surfaces of indwelling urinary Foley catheters. Without releasing active substances, it effectively prevented pathogens from producing biofilm. The coating was superhydrophilic and incorporated a proprietary anti-fouling ligand, which created a surface that significantly inhibited up to 99% of colonizing uropathogens from forming biofilm for the duration of use without any microbial killing (p< 0.001).RNA-seq analysis revealed that gene expression associated with microbial extracellular polymeric substances formation was significantly downregulated on the coated surfaces. Additionally, microorganisms adhering to LubriShieldTM coated catheters were 78% more susceptible to antibiotics compared to those on uncoated silicone catheters (p=0.004).

overall_design: RNA-seq profiling of Pseudomonas aeruginos PA01 strain growing on Lubrishield-coated silicon catheters vs. uncoated one after 7 days growth under biofilm-promoting conditions in the artificial urine medium.

first: Serhiy

last: Surkov

first: Per

last: Wirsén

first: Graeme

last: Brookes

first: Linda

last: Bergström

first: Jan

last: Tejbrant

first: Elena

last: Dhamo


title: Epigenetic remodeling and 3D chromatin reorganization governed by NKX2-1 drive neuroendocrine prostate cancer

first: Jindan

last: Yu

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

overall_design: Refer to individual Series


title: Multiplexed DNA Affinity purification sequencing (multiDAP-seq) of flowering plants [Populus trichocarpa]

last: Wang


title: Multiplexed DNA Affinity purification sequencing (multiDAP-seq) of flowering plants [Fragaria vesca]


title: Joint representation and visualization of derailed cell states with Decipher [scATAC-seq]

city: New York

first: Joy

last: Fan

address: 520 West 120th Street

institute: Columbia University

summary: Biological insights often depend on comparing conditions such as disease and health. Yet, we lack effective computational tools for integrating single-cell genomics data across conditions or characterizing transitions from normal to deviant cell states. Here, we present Decipher, a deep generative model that characterizes derailed cell-state trajectories. Decipher jointly models and visualizes gene expression and cell state from normal and perturbed single-cell RNA-seq data, revealing shared and disrupted dynamics. We demonstrate its superior performance across diverse contexts, including in pancreatitis with oncogene mutation, acute myeloid leukemia, and gastric cancer.

overall_design: scATAC-seq on three patients from the TET2 cohort and a healthy bone marrow reference.

first: Achille

last: Nazaret

first: Joy Linyue

first: Vincent-Philippe

last: Lavallée

first: Cassandra

last: Burdziak

first: Andrew

last: Cornish

first: Vaidotas

last: Kiseliovas

first: Robert

last: Bowman

first: Ignas

last: Masilionis

first: Jaeyoung

last: Chun

first: Shira

last: Eisman

first: James

first: Justin

last: Hong

first: Lingting

last: Shi

first: Ross

last: Levine

first: Linas

last: Mazutis

first: David

last: Blei

first: Dana

last: Pe'er

first: Elham

last: Azizi


title: Multiplexed DNA Affinity purification sequencing (multiDAP-seq) of flowering plants [Brassica oleracea]

first: Sharon

last: Greenblum

first: Leo

last: Baumgart

first: Abraham

last: Morales-Cruz

first: Peng

last: Wang

first: Yu

last: Zhang

first: Ronan

last: O'Malley


title: Multiplexed DNA Affinity purification sequencing (multiDAP-seq) of flowering plants [Arabidopsis lyrata]


title: Multiplexed DNA Affinity purification sequencing (multiDAP-seq) of flowering plants [Capsella rubella]


title: Inactivation of the SRF cofactors Mrtfa and Mrtfb in MEFs results in proliferation defects and reduced expression of cytoskeletal and cell cycle progression genes

city: London

first: Richard

last: Treisman

address: 1 Midland Road

institute: The Francis Crick Institute

summary: The MRTFs (Myocardin-related transcription factors) are cofactors of the SRF transcription factor, and together they control dozens of growth factor-responsive, cytoskeletal and muscle specific genes. We used a conditional knockout strategy to demonstrate that in fibroblasts, inactivation of both Mrtfa and Mrtfb, or Srf, induces a severe defect in proliferation. This state exhibits features of both quiescence and senescence, with MRTF-null cells upregulating similar cell cycle regulators to serum-deprived wildtype cells, but is fully reversible by MRTF re-expression. We analysed gene expression in three MEF pools derived from Wildtype (Rosa26Tam-Cre) animals, and three MEF pools derived from Mrtfa-/-;Mrtfbfl/fl;Rosa26Tam-Cre mice. RNA was collected 0, 2, 4 or 12 days after 4-hydroxytamoxifen treatment, which inactivate Mrtfb in Mrtfa-/-;Mrtfbfl/fl;Rosa26Tam-Cre and generate MRTF-null cells. The data indicate that substantial numbers of genes exhibit altered expression in Mrtfa-/-;Mrtfb-/- cells, the difference being most pronouced 12 days following 4-OHT treatment. Genes downregulated at this point include many genes identified as serum-inducible MRTF-SRF target cells in NIH3T3 cells (Esnault et al, 2014, DOI: 10.1101/gad.239327.114) or as derepressed in MEFs following inactivation of all members of the TCF family of SRF cofactors (Gualdrini et al, 2016, DOI: 10.1016/j.molcel.2016.10.016). They are most enriched in GO categories related to actin cytoskeletal dynamics and cell signalling, and GSEA hallmarks connected with cell growth, division, and cell cycle.

overall_design: mRNA library was prepared using polyA_KAPA_mRNA_Hyper_Prep of 24 samples consisting of three biological replicates of WT MEFs (Rosa26Tam-Cre) and three biological replicates of MRTF-floxed MEFs (Mrtfa-/-;Mrtfbfl/fl;Rosa26Tam-Cre) each treated with 1µM 4-hydroxytamoxifen for 2 days before switching back to regular medium. RNA was collected 0, 2, 4, and 12 days after tamoxifen treatment.

first: Julie

last: Nielsen


title: Pooled scanning of protein variants identifies novel RNA-binding mutants

city: Philadelphia

first: Emily

last: Shields

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Binding to RNA has been observed for an ever-increasing number of proteins, which often have other functions. The contributions of RNA binding to protein function are best discerned by studying “separation-of-function” mutants that hamper interaction with RNA without affecting other aspects of protein function. To design these mutants, we need precise knowledge of the residues that contribute to the affinity of the protein to its RNA ligands. Here, we present RBR-scan: a technology to simultaneously measure RNA-binding affinity of a large number of protein variants. We fused individual variants with unique peptide barcodes optimized for detection by mass spectrometry (MS), purified protein pools from single bacterial culture, and assayed proteins in parallel for RNA binding. Mutations in the MS2 coat protein known to impair RNA-binding were correctly identified, as well as a previously unreported mutant, which we validated with orthogonal biochemical methods. We used RBR-scan to discover novel RNA-binding mutants in the cancer-associated splicing regulator SRSF2. Together, our results demonstrate that RBR-scan is a powerful and scalable platform for linking RNA-binding affinity to protein sequence, offering a novel strategy to decode the functional consequences of protein–RNA interactions.

overall_design: Nanopore sequencing of RBR-SCAN pools for two configurations for both MS2CP and SRSF2

first: Julia

last: Tasca

first: John

last: Doherty

middle: J

first: Shachinthaka

last: Dissanayaka Mudiyanselage

first: Lauren

last: Reich

first: Kavitha

last: Sarma

first: Benjamin

last: Garcia

first: Roberto

last: Bonasio


title: Regulation of epigenetics and chromosome structure by human ORC2 [RNAseq_2018]

city: Birmingham

first: Zhangli

last: Su

state: Alabama

address: 720 20th Street South

department: Department of Genetics

institute: University of Alabama

summary: The six subunit Origin Recognition Complex (ORC) is a DNA replication initiator that also promotes heterochromatinization in some species. A multi-omics study in a human cell line with mutations in three subunits of ORC, reveals that the subunits bind to DNA independent of each other rather than as part of a common six-subunit ORC. While DNA-bound ORC2 was seen to compact chromatin and attract repressive histone marks, the activation of chromatin and protection from repressive marks was seen at a large number of sites. The epigenetic changes regulate hundreds of genes, including some epigenetic regulators, adding an indirect mechanism by which ORC2 regulates epigenetics without local binding.  DNA-bound ORC2 also prevents the acquisition of CTCF at focal sites in the genome to regulate chromatin loops. Thus, individual ORC subunits are major regulators, in both directions, of epigenetics, gene expression and chromosome structure, independent of the role of ORC in replication.

overall_design: To understand epigenetic and chromosome structure changes that are dependent on ORC2, we performed RNA-seq, ATAC-seq, ChIP-seq, HiC in wild-type, ORC2 deletion and rescue HCT116 cells. To map ORC binding sites, we performed ChEC-seq.

first: Mengxue

last: Tian

first: Etsuko

last: Shibata

first: Yoshiyuki

first: Tianyi

last: Yang

first: Zhenjia

first: Fulai

last: Jin

first: Chongzhi

last: Zang

first: Anindya

last: Dutta


title: Regulation of epigenetics and chromosome structure by human ORC2 [RNAseq_2020]

last: Wang


title: Regulation of epigenetics and chromosome structure by human ORC2 [ATACseq 2]


title: Regulation of epigenetics and chromosome structure by human ORC2 [ATACseq 1]


title: Cagrilintide lowers bodyweight through brain amylin receptors 1 and 3

city: Zurich

first: Christelle

last: Le Foll

address: Winterthurerstrasse 260

department: Vetsuisse faculty

country: Switzerland

institute: Univeristy Of Zurich

summary: Amylin (AmyR) and calcitonin (CTR) receptor co-agonists are currently in Phase II/III clinical trials for obesity treatment. Amylin binds to a heterodimeric receptor composed of CTR and the receptor activity modifying proteins 1, 2 or 3 (RAMP1-3). We investigated the role of amylin 1 and 3 (AMY1R, AMY3R) receptors in modulating the pharmacological effects of the dual amylin–calcitonin receptor agonists, cagrilintide and salmon calcitonin (sCT), in RAMP1/3 knockout (KO) mice. Male wild-type (WT) and KO littermate mice were fed high-fat diet for 23 weeks prior to the 3-week treatment period with vehicle, 150 nmol/kg sCT or 3 nmol/kg cagrilintide (SC, SID). Body weight loss was observed in WT cagrilintide-treated mice (-3.4  +/-  0.51 g, P<0.005; n=8/group), whereas sCT rather increased it (0.60 +/- 0.38 g, P<0.01; n=8/group). The absence of RAMP1 and RAMP3 impeded cagrilintide’s potency but improved sCT’s efficacy on weight loss. Cagrilintide and sCT both decreased food intake during the first few days of treatment in WT mice only (Day 1: veh 2.7  +/-  0.2 g; cagri 1.2  +/-  0.1 g, P<0.0001; sCT 1.5 +/-  0.2 g, P<0.0021; n=7-8/group). Both peptides activated cFos signal in neurons of the dorsal vagal complex (DVC) and lateral parabrachial nucleus (LPBN) of WT mice while AP cFos signal was decreased in cagrilintide-treated RAMP1/3 KO mice by 57% compared to WT cagrilintide-injected mice (P<0.001, n=5-6/group). Differential gene expression was analyzed in the DVC, LPBN and mediobasal hypothalamic area (MBH) of WT and RAMP1/3 KO mice. After 3 weeks of treatment, neither sCT nor cagrilintide significantly altered gene expression in the DVC or LPBN in WT mice. However, mRNA bulk sequencing points to a role of RAMP1/3 in synaptic function and receptor trafficking. Altogether, these results demonstrate the dependency of cagrilintide on AMY1R and AMY3R to lower body weight.

overall_design: Wt and RAMP 1/3 male mice treated with vehicle, sct or cagrilintide for 21 days

first: Alexandra

last: Carvas

first: Andrea

last: Leuthardt

first: Patricia

last: Kulka

first: Greta

last: Lommi

first: Shad

last: Hassan

first: Bernd

last: Coester

first: Sofia

last: Lundh

first: Tune

last: Pers

first: Anna

last: Secher

first: Kirsten

last: Raun

first: Thomas

last: Lutz


title: Regulation of epigenetics and chromosome structure by human ORC2 [ChIPseq]

first: Zhangli

last: Su

first: Mengxue

last: Tian

first: Etsuko

last: Shibata

first: Yoshiyuki

first: Tianyi

last: Yang


title: Regulation of epigenetics and chromosome structure by human ORC2 [ORC1 ChECseq]

first: Zhenjia

last: Wang

first: Fulai

last: Jin

first: Chongzhi

last: Zang

first: Anindya

last: Dutta


title: Regulation of epigenetics and chromosome structure by human ORC2 [HiC]


title: Recruitment, rewiring, and deep conservation in flowering plant gene regulation

first: Sharon

last: Greenblum

summary: We conducted single-nuclei transcriptome profiling of multiple tissues from a range of flowering plant species. Individual samples from the same species and tissue were integrated to construct celltype-labeled snRNA atlases for four brassica species and one grass species (available as supplementary files). These atlases were used to track the activity of hundreds of transcription factors (TFs) across species and celltypes, by leveraging genome-wide TF binding site data from accompanying multi-species DAP-seq experiments (DAP-seq data available as SRA BioProject PRJNA1177505). The final integrated dataset revealed clear patterns of regulatory conservation across the plant phylogeny, as well as key examples of regulatory re-wiring to enable new cell types and lineage-specific adaptations.

sample_organism:
Arabidopsis thaliana
Brassica oleracea
Sorghum bicolor
Thlaspi arvense
Brachypodium distachyon
Arabidopsis lyrata
Capsella rubella
Camelina sativa
Panicum hallii

overall_design: Nuclei were extracted from fresh or flash-frozen tissue sampled from seedling roots, seedling shoots, whole seedlings, mature leaves, or flower buds of various flowering plant species grown in control conditions. Single-nuclei transcriptomes were then profiled using either the 10X Chromium droplet-based platform or the BD Rhapsody microwell-based platform. Note that in many cases, nuclei from the same tissue of different species were extracted simultaneously and profiled together in a single combined-species run. Sequences from these samples were then aligned to a combined-species reference and nuclei from each species were separated bioinformatically before downstream analysis.

first: Leo

last: Baumgart

first: Abraham

last: Morales-Cruz

first: Peng

first: Yu

last: Zhang

first: Ronan

last: O'Malley


title: Regulation of epigenetics and chromosome structure by human ORC2 [CUT&RUN]


title: Creb5 controls its own expression and directly induces the joint-interzone regulatory program [RNAseq_Prx1]

city: Boston

first: Andrew

middle: Bruce

last: Lassar

state: MA

address: 240 Longwood Ave.

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

summary: Our prior work indicated that the transcription factor Creb5 plays a crucial role in the genesis of synovial joints.  Here, we perform an integrative analysis of the transcriptome, chromatin accessibility, and Creb5-chromatin occupancy in Creb5-expressing synovial joint progenitor cells. This analysis revealed that Creb5 directly binds to both its own two promoters and to the regulatory regions of the early joint markers, Gdf5 and Sfrp2; each of whose expression in the joint-interzone is Creb5-dependent.  Functional enhancer analysis indicated that Creb5 binding sites in its own two promoters are necessary for these sequences to drive transgene expression in a pattern that mimics endogenous Creb5 expression.  While Creb5 directly regulates both Gdf5 and Sfrp2 expression in the inner joint-interzone by binding to either CREs or TREs in their regulatory elements,  Creb5 activates Barx1 expression specifically in the outer joint-interzone; and thus initiates both the formation of the joint-interzone and regionalization of cell fates within this tissue.

overall_design: Prrx1-Cre male mice were mated to Rosa26LSL-bovine-Creb5-ires-GFP/LSL-tdTomato female mice; yielding E14.5 embryos which express either bovine iCreb5HA-GFP(Prrx1-Cre) or itdTomato(Prrx1-Cre) in their limb bud mesenchyme.  Bulk RNA-Seq was performed on the isolated bovine iCreb5HA-EGFP(Prrx1-Cre) -expressing or itdTomato(Prrx1-Cre)-expressing  limb bud mesenchymal cells that had been isolated from 6 independent litters.

first: Cheng-Hai

first: Aref

last: Shahini

first: Laura

last: Cook

first: Meeta

last: Mistry

first: Jongkil

last: Kim

first: Heather

last: Wick

first: Len

last: Pennacchio

middle: B


title: Creb5 controls its own expression and directly induces the joint-interzone regulatory program [CutandRun_Sox9_GFP]

overall_design: To specifically identify Creb5 binding sites in the articular perichondrium of the zeugopods, we crossed Creb53XHA-P2A-tdTomato/+ mice with Hoxa11EGFP/+ mice to obtain E14.5 Creb53XHA-P2A-tdTomato/+; Hoxa11EGFP/+ embryos; employed FAC sorting to isolate cells that expressed both Creb5HA-tdTomato & Hoxa11EGFP  from either forelimbs or hindlimbs; and performed either Creb5- or HA- or IgG-(control) Cut&Run-Seq.    Creb5-Cut&Run-Seq was also performed with either Creb5+Sox9- cells or Creb5+Sox9+ cells (isolated from E14.5 Creb53XHA-P2A-tdTomato/+; Sox9iresEGFP/+ embryos).


title: Regulation of epigenetics and chromosome structure by human ORC2 [ORC2 ChECseq]

first: Zhangli

last: Su

first: Mengxue

last: Tian

first: Etsuko

last: Shibata

first: Yoshiyuki

first: Tianyi

last: Yang

first: Zhenjia

first: Fulai


title: Regulation of epigenetics and chromosome structure by human ORC2 [ORC5 ChECseq]

last: Wang

last: Jin

first: Chongzhi

last: Zang

first: Anindya

last: Dutta


title: Creb5 controls its own expression and directly induces the joint-interzone regulatory program

first: Andrew


title: Creb5 controls its own expression and directly induces the joint-interzone regulatory program [ATACseq_Prx1]

overall_design: Prrx1-Cre male mice were mated to Rosa26LSL-bovine-Creb5-ires-GFP/LSL-tdTomato female mice; yielding E14.5 embryos which express either bovine iCreb5HA-GFP(Prrx1-Cre) or itdTomato(Prrx1-Cre) in their limb bud mesenchyme.  ATAC-Seq was performed on the isolated bovine iCreb5HA-EGFP(Prrx1-Cre) -expressing or itdTomato(Prrx1-Cre)-expressing  limb bud mesenchymal cells that had been isolated from 3 independent litters.

first: Cheng-Hai

last: Zhang


title: Multiplexed DNA Affinity purification sequencing (multiDAP-seq) of flowering plants [Arabidopsis thaliana]

first: Sharon

last: Greenblum

first: Leo

last: Baumgart

first: Abraham

last: Morales-Cruz

first: Peng

first: Yu

first: Ronan

last: O'Malley


title: APOE Protects Against Severe Infection with Mycobacterium tuberculosis by Restraining Production of Neutrophil Extracellular Traps

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

summary: Mice lacking apolipoprotein E (APOE, Apoe-/- mice) are highly susceptible to infection with Mycobacterium tuberculosis (Mtb) but the underlying immune dysregulation has been unclear. We found that Mtb infected Apoe-/- mice have significantly elevated levels of neutrophils in their lungs compared to controls and demonstrated that depleting neutrophils, depleting pDCs, blocking type1 interferon signaling, and blocking LTB4 receptor signaling all improved the outcome of Mtb-infected Apoe-/- mice. Neutrophils can undergo a specialized form of cell death termed NETosis in which activation of the enzyme PAD4 leads to extrusion of neutrophil extracellular traps (NETs). NETs have been associated with severe tuberculosis in other mouse models and in humans but a role of NETs in the pathology has not been directly established. We demonstrate that blocking PAD4 activation leads to a decrease in NETs in the lungs and, strikingly, completely reverses the hypersusceptiblity of Apoe-/- mice.

overall_design:
To examine the role of Apoe in the resonses of pulmonary macrophages and neutrophils to infection with Mtb invivo, we generated 50:50 B6:Apoe-/- bone marrow chimeric mice on a B6 background and infected them with either~50 or ~4000 CFU of Mtb H37Rv expressing mCherry.
Alveolar macrophages, monocyte-derived macrophages, and neutrophils of each genotype were isolated by flow sorting at either 10 days following infection (for ~4000 CFU infections) or 28 days following infection (for ~50 CFU infections). Expression profiling of each group was performed by RNA-seq.

first: Alan

last: Diercks

first: Elizabeth

last: Gold

first: Dong

last: Liu

first: Dat

last: Mai


title: High-coverage allele-resolved single-cell DNA methylation profiling by scDEEP-mC reveals cell lineage, X-inactivation state, and replication dynamics

city: Grand Rapids

first: Peter

middle: W

last: Laird

address: 333 Bostwick Ave NE

department: Epigenetics

institute: Van Andel Institute

summary: DNA methylation is a relatively stable epigenetic mark with important roles in development and disease.1 Since cell-to-cell variation in epigenetic programming can reflect essential differences in cell state and fate, it is clear that single-cell methods are necessary to strengthen our understanding of DNA methylation’s biological roles. Existing single-cell whole-genome bisulfite sequencing (scWGBS) methods2 have substantial shortcomings, including very low CpG coverage3–7 or inefficient library generation requiring extremely deep sequencing.8 We report an improved method, single-cell Deep and Efficient Epigenomic Profiling of methyl-C (scDEEP-mC). High-coverage DNA methylation profiling by scDEEP-mC allows cell type identification, genome-wide profiling of hemi-methylation, and allele-resolved analysis of X-inactivation epigenetics in single cells. We further demonstrate how scDEEP-mC can profile single-cell copy number alterations, identify replicating cells, and track DNA methylation dynamics during and after DNA replication. The high coverage of scDEEP-mC creates an exceptional opportunity to explore DNA methylation biology in individual cells.

overall_design: Single-cell Deep and Efficient Epigenomic Profiling of methyl-C (scDEEP-mC) was conducted on 175 single cells isolated from mouse intestinal epithelium, as well as 199 cultured human fibroblasts at different passage levels and 93 TERT-immortalized human fibroblasts.

first: Nathan

last: Spix

first: Walid

last: Abi Habib

first: Zhouwei

first: Emily

last: Eugster

first: Hsiao-yun

last: Milliron

first: David

last: Sokol

first: KwangHo

last: Lee

first: Paula

last: Nolte

first: Jamie

last: Endicott

first: Kelly

middle: F

last: Krzyzanowski

first: Toshinori

last: Hinoue

first: Jacob

last: Morrison

first: Benjamin

last: Johnson

first: Wanding

last: Zhou

first: Hui

last: Shen


title: Multimodal profiling reveals tissue-directed signatures of human immune cells altered with age

city: Palo Alto

first: Lattice

last: Data Coordination

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

summary: The immune system comprises multiple cell lineages and heterogeneous subsets found in blood and tissues throughout the body. While human immune responses differ between sites and over age, the underlying sources of variation remain unclear as most studies are limited to peripheral blood. Here, we took a systems approach to comprehensively profile RNA and surface protein expression of over 1.25 million immune cells isolated from blood, lymphoid organs, and mucosal tissues of 24 organ donors aged 20-75 years. We applied a multimodal classifier to annotate the major immune cell lineages (T cells, B cells, innate lymphoid cells, and myeloid cells) and their corresponding subsets across the body, leveraging probabilistic modeling to define bases for immune variations across donors, tissue, and age. We identified dominant tissue-specific effects on immune cell composition and function across lineages for lymphoid sites, intestines, and blood-rich tissues. Age-associated effects were intrinsic to both lineage and site as manifested by macrophages in mucosal sites, B cells in lymphoid organs, and T and NK cells in blood-rich sites. Our results reveal tissue-specific signatures of immune homeostasis throughout the body and across different ages. This information provides a basis for defining the transcriptional underpinnings of immune variation and potential associations with disease-associated immune pathologies across the human lifespan.

overall_design: scRNA-seq and CITE-seq of immune cells from blood, lymphoid, and mucosal tissues from 24 donors aged 20-75 years

first: Nir

last: Yosef

last: Sims

first: Sarah

last: Teichmann

first: Joanne

last: Jones

first: Donna

last: Farber

first: Steven

last: Wells

first: Daniel

last: Rainbow

first: Michal

last: Mark

last: Szabo

first: Can

last: Ergen

first: Ana

last: Maceiras

last: Caron

first: Elior

last: Rahmani

first: Eli

last: Benuck

first: Valeh

middle: V

last: Pour Amiri

last: Chen

first: Allon

last: Wagner

middle: K

last: Howlett

first: Lorna

last: Jarvis

first: Karen. L

last: Ellis

first: Masaru

last: Kubota

first: Rei

last: Matsumoto

first: Krishnaa

last: Mahbubani

first: Kouresh

last: Saeb-Parsy

first: Cecilia

last: Dominguez-Conde

first: Laura

last: Richardson

first: Chuan

last: Xu

first: Shuang

last: Li

first: Lira

last: Mamanova

first: Liam

last: Bolt

first: Alicja

last: Wilk


title: Histone H3.14 variant is an early player in the abiotic stress response of Arabidopsis

city: Madrid

first: Crisanto

last: Gutierrez

address: Nicolas Cabrera 1

department: Genome Dynamics and Function

country: Spain

institute: Centro de Biologia Molecular Severo Ochoa

summary: Here we have focused on H3.14, a H3 variant which is expressed at very low levels under normal growth conditions. We found that it is expressed rapidly and transiently after abiotic stress in cells of the transition zone of the root, a subset of cells that seem to be responsive to the stress stimuli. To define its functional relevance we analyzed the phenotype of htr14 mutants and found that, contrary to the growth arrest phenotype of wild type plants, they show sustained growth in the presence of stress. The euchromatic localization of H3.14 suggested that it might be involved in transcriptional control. ChIP-seq identification of H3.14 genome-wide location after salt stress and RNA-seq of the htr14 mutant led us to identify three major H3.14 binding patterns that are associated with distinct clusters of genes involved in the early activation response to abiotic stress, in arresting cell growth and in maintenance of cellular homeostasis during abiotic stress. We conclude that the histone variant H3.14 is part of the early response required for the fast rewiring of transcriptional regulation after abiotic stress.

overall_design: Chromatin immunoprecipitation DNA sequencing (ChIP-seq) for histone variant H3.14

first: Rocio

last: Nunez-Vazquez

first: Sofía

last: Madeira

last: Rodriguez-Casillas

first: Diego

last: Gomez-Martinez

first: Bénédicte

last: Desvoyes


title: Histone H3.14 variant is an early player in the abiotic stress response of Arabidopsis [RNA-seq]

overall_design: To study the impact of H3.14 impairment in gene expression, we worked with both WT and htr14-1mutant plants during control (MSS) and stress (4h 140 mM NaCl) conditions. Seedlings were gown under long days (16h light - 8h dark) conditions and harvested 5 days after sowing. Only root tips (0.5 mm) were processed and studied. Three biological replicates were performed.


title: The m6A-mediated TGF-β-SMAD signaling axis regulates ccRCC progression [RIP-seq]

city: Nanjing

first: Shan

last: Gao

address: No. 2 Sipailou, Xuanwu District

institute: Southeast University

summary: TGF-β-SMAD signaling pathway plays an important role in progression of various tumors. However, posttranscriptional regulation such as N6-methyladenosine (m6A) of TGF-β-SMAD signaling axis remains incompletely understood. Here, we reveal that Insulin like growth factor 2 mRNA binding protein 2 (IGF2BP2) is low expression as well as associated with poor prognosis in clear cell renal cell carcinoma (ccRCC) patients and inhibits proliferation as well as promotes metastasis of ccRCC cells. To explore the underlying mechanism of IGF2BP2 in ccRCC, RNA-seq, RIP-seq and LACE-seq were performed to investigate the downstream targets of IGF2BP2.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for sh-IGF2BP2 and Anti-IGF2BP2 for RIP-seq and LACE-seq in 786-O cells.

first: Bo

last: Peng

first: Shuwen

last: Cheng

first: Liqiang

last: Duan


title: The m6A-mediated TGF-β-SMAD signaling axis regulates ccRCC progression [LACE-seq]


title: The m6A-mediated TGF-β-SMAD signaling axis regulates ccRCC progression [RNA-seq]


title: Creb5 controls its own expression and directly induces the joint-interzone regulatory program [RNAseq_Sox9_GFP]

first: Andrew

last: Lassar

overall_design: Guided by fluorescence of both tdTomato and EGFP, we dissected the developing knee joints of E14.5 Creb53XHA-P2A-tdTomato/+; Sox9iresEGFP/+ embryos.  Following collagenase treatment and filtration to isolate single cells, we sorted the cells from the developing knees into three populations: those that express either Creb5HA-tdTomato, Sox9-ires-EGFP, or both Creb5HA-tdTomato and Sox9-ires-EGFP.  Bulk RNA sequencing (RNA-Seq) was performed with mRNA isolated from the three cell populations that had been isolated from three independent litters.

first: Cheng-Hai

last: Zhang

first: Aref

last: Shahini

last: Cook

first: Meeta

last: Mistry

first: Jongkil

last: Kim

first: Heather

last: Wick

first: Len

last: Pennacchio