title: CUT&Tag of H3K4me1 and H3K27ac from Nutlin-3a-treated MCF-7 cells

first: Martin

last: Fischer

state: Thuringia

department: Computational Biology

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

summary: CUT&Tag of H3K4me1 and H3K27ac from MCF-7 cells treated with Nutlin-3a or DMSO control

overall_design: MCF-7 cells were treated with Nutlin-3a 10 µM or DMSO control for 24 h

first: Konstantin

last: Riege

first: Steve

last: Hoffmann


title: Unraveling the battle between a highly virulent PEDV strain and the host via single-cell transcriptomic analysis

status: Public on Apr 22 2025

city: Harbin

first: Yanan

last: Wang

address: 600 Changjiang Road, Xiangfang District, Harbin City

country: China

institute: Northeast Agricultural University

type: Expression profiling by high throughput sequencing

summary: Porcine epidemic diarrhea virus (PEDV) causes severe intestinal damage and high mortality in neonatal piglets. The continuous emergence of new strains has brought new challenges to prevention and control. In this study, we isolated and characterized a prevalent PEDV virulent strain, and analyzed 19,612 jejunal cells from PEDV-infected and control piglets using single-cell sequencing, revealing significant changes in cellular composition, gene expression, and intercellular communication. In response to PEDV infection, epithelial repair was enhanced through increased proliferation and differentiation of stem cells, transit-amplifying (TA) cells, and intestinal progenitor cells into enterocytes. Additionally, PEDV disrupted intercellular communication, compromising epithelial functionality while triggering immune responses, with IFN-II and IL-10 signaling activation acting as critical regulators of immune balance and tissue homeostasis. Beyond enterocytes, viral genes were detected in various other cell types. Further experiments confirmed that PEDV could initiate replication in B and T lymphocytes but was unable to produce infectious progeny, with T cells additionally undergoing virus-induced apoptosis. These findings provide new insights into PEDV tropism, immune evasion, and epithelial repair, revealing complex host-pathogen interactions that shape disease progression and tissue regeneration, thereby contributing to a better understanding of enteric coronavirus pathogenesis.

overall_design: One case jejunum sample from PEDV-infected piglets (pooled from three piglets' jejunum tissues); one control jejunum sample from non-infected piglets (pooled from three piglets' jejunum tissues).

first: Yijing

last: Li

first: Li


title: GFI1-driven transcriptional and epigenetic programs maintain memory CD8+ T cell persistence [scMultiome-seq].

status: Public on Apr 23 2025

city: Brisbane

first: M. Zeeshan

last: Chaudhry

state: Queensland

address: 37 Kent Street

country: Australia

institute: The University of Queensland

type: Genome binding/occupancy profiling by high throughput sequencing

summary: CD8+ T cells play a pivotal role in restricting chronic virus infection and provide long-term protective immunity. The molecular mechanisms that govern long-term persistence of antiviral memory CD8+ T cells are poorly understood. Growth factor independent-1 (GFI1), a transcriptional repressor, plays a crucial role in T cell development. We show that following T cell activation, GFI1 expression is selectively maintained in memory CD8+ T cells, and GFI1 marks transcriptionally distinct antiviral CD8+ T cells with superior recall and expansion capacity. Conditional deletion of GFI1 in CD8+ T cells revealed that plays a crucial role in long-term persistence of CD8+ T cells responses following chronic virus infection. Single-cell multiome sequencing demonstrated that GFI1 epigenetically controls the gene regulatory networks that promote memory CD8+ T cell proliferation. GFI1 mediated eomesodermin expression protects the CD8+ T cells from activation induced cell death. Moreover, temporal mapping revealed that continuous GFI1 expression is required to maintain long-term memory CD8+ T cells persistence. Thus, GFI1 is central regulator of the molecular programs that shape memory features and is pivotal in promoting CD8+ T cell self-renewal and long-term protective memory formation.

overall_design: WT and GFI1-KO P14 T cells were adoptively transferred into congenic recipients followed by chronic LCMV clone-13.  WT and GFI1-KO CD8+ T cell isolated at day 7 following LCMV infection were sequenced with 10x singel cell multiome ATAC +GEX kit.

first: M

middle: Z

first: Gabrielle

last: Belz


title: Effect of EZH2 Inhibition on peripheral Blood Circulating CART19 (day 20)

status: Public on Apr 24 2025

city: Philadelphia

first: Marco

last: Ruella

state: PA

address: 3400 Civic Center Blv

department: Center for Cellular Immunotherapies

country: USA

institute: University of Pennsylvania

summary: Molecular carachterization of CART19-vehicle vs CART19-tazemetostat circulating T cells

overall_design: OCI-Ly18 xenograft lymphoma model treated with vehicle or tazemetostat and infused with CART19. Cell sorting and SCRNA sequencing on 3 vs 3 animals infused with CART19 vs CART19-tazemetostat

first: Patrizia

last: Porazzi

first: Linhui

last: Chen

first: Ruchi

middle: P

last: Patel

first: Puneeth

last: Guruprasad

first: Siena

last: Nason


title: Antibody response against Influenza and SARS-CoV-2 antigens

city: Irvine

last: Liang

state: CA

address: MedSurge II

institute: University of California Irvine

summary: A protein microarray was used to measure antibody response in the plasma of mice immunized with mRNA vaccine formulations at d14 and d28 post prime immunizations (n = 53). The results demonstrate antigen- specific antibody response was elicited by a bivalent mRNA vaccine to combat Influenza and SARS-CoV-2 infections.

platform_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: Antibody profiling against 16 antigens in triplicates from Influenza and SARS-CoV-2 variants

first: Jiin

last: Felgner

first: Jenny

middle: E

last: Hernandez-Davies

first: Erwin

last: Strahsburger

first: Emily

last: Silzel

first: Rie

last: Nakajima

first: Aarti

last: Jain

first: Jacob

last: Laster

first: Jui-Lin

last: Chiang

first: Yali

last: Tsai

first: Philip

middle: L

first: D

last: Huw Davies


title: RNA-binding protein Ars2 mediates transcriptional silencing of telomeric repeats and transposable elements in the Drosophila germline [chromRNA-seq]

city: Moscow

first: Anastasiya

last: Kobelyatskaya

address: Vavilov str, 32

country: Russia

institute: Engelhardt Institute of Molecular Biology, RAS

summary: Telomeres ensure genome stability and the levels of telomeric RNA reflect the integrity of telomeric chromatin. The highly conserved RNA-binding protein Arsenite-resistance protein 2 (Ars2) plays an essential role in the nuclear metabolism of many types of RNAs and negatively regulates the expression of telomeric transcripts in human cells and in Drosophila. We found that germline knockdown of Drosophila Ars2 does not affect small RNA abundance but causes overexpression of telomeric repeats and transposable elements (TEs) which accompanies by their chromatin decompaction. The expression of transgene containing the HeT-A telomeric retrotransposon was also affected by Ars2 knockdown. The mutation of the G-rich region, which is prone to the formation of G-quadruplex structures, reduces the HeT-A transgene's sensitivity to Ars2 depletion. Intriguingly, Ars2-regulated TEs are also enriched by G-quadruplex structures, implying their role in the Ars2 target recognition. Ars2 also prevents the formation of R-loops at telomeres, which are most likely caused by the accumulation of unreleased transcripts. Surprisingly, Ars2 is required for the expression of R1 retrotransposons, which are integrated in rRNA genes and essential for their amplification.  Our findings point to a new mechanism of Ars2-mediated control of expression of telomeric repeats and TEs in the germline.

overall_design: Deep-sequencing of chromatin-associated RNAs, small RNAs (19-30 nt), and chromatin immunoprecipitated genomic DNA ofDrosophila melanogaster ovaries


title: GFI1-driven transcriptional and epigenetic programs maintain memory CD8+ T cell persistence [ATAC-seq].

first: M. Zeeshan

last: Chaudhry

overall_design: WT and GFI1-KO P14 T cells were adoptively transferred into congenic recipients followed by chronic LCMV clone-13 or MCMV-ie2-gp33 infection.  Three samples each of WT and GFI1-KO CD8+ T cell isolated at day 7 following LCMV infection, and day 7 after MCMV infection were sequenced. To test the chromatin accessibility of naive CD8 T cells, naive P14 T cells were isolated from age matched naive WT and Gfi1fl/fl.Cd8acre animals.

first: M Zeeshan

first: Gabrielle

last: Belz


title: GFI1-driven transcriptional and epigenetic programs maintain memory CD8+ T cell persistence

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

overall_design: Refer to individual Series


title: GFI1-driven transcriptional and epigenetic programs maintain memory CD8+ T cell persistence [RNA-seq]

overall_design:
For transcriptional analyses of GFI1dTomato reporter CD8+ T cells, activated (CD11a+CD44+) GFI1high and GFI1low CD8+ T cells were isolated from spleen of Gfi1dTomato mice infected with LCMV clone 13 or LCMV Armstrong strains. Three samples each of GFI1high and GFI1low CD8+ T cells from both LCMV clone-13 and LCMV Armstrong infections were sequenced.
To understand the transcriptional program regulated by GFI1, WT and GFI1-KO P14 T cells were adoptively transferred into congenic recipients followed by chronic LCMV clone-13 infection. Similarly, WT and GFI1-KO P14 T cells were isolated from MCMV-ie2-gp33 infected mice. Three samples each of WT and GFI1-KO CD8+ T cell isolated at day 7 following LCMV infeciton, and day 7 after MCMV infection were sequenced.


title: PSME3 Regulates Migration and Differentiation of Myoblasts [CUT&Run]

city: Klosterneuburg

first: Kenneth

middle: David

last: Kuhn

address: Am Campus

country: Austria

institute: Institute of Science and Technology Austria

summary: The acquisition of cellular identity requires large-scale alterations in cellular state. The non-canonical proteasome activator PSME3 is known to regulate diverse cellular processes, but its importance for differentiation remains unclear. Here, we demonstrate that PSME3 binds dynamically to highly active promoters over the course of differentiation. However, loss of PSME3 does not globally affect mRNA transcription. We find instead that PSME3 influences the levels of several adhesion-related proteins and acts upstream of the HSP90 co-chaperone NUDC to regulate cell motility and myoblast differentiation in a proteasome-independent manner. Our findings reveal several new facets of PSME3 functionality and highlight its particular importance for the differentiation of myogenic cells.

overall_design: CUT&RUN was performed on C2C12 cells at two separate stages of serum deprivation-induced differentiation: prior to differentiation (cycling) and after 48 hours (day 2). CUT&RUN was performed using antibodies targeting the proteasome regulator PSME3, H3K4me3, or a control IgG

middle: D

first: Ukrae

middle: H

last: Cho

first: Martin

middle: W

last: Hetzer


title: RNA-binding protein Ars2 mediates transcriptional silencing of telomeric repeats and transposable elements in the Drosophila germline [ChIP-Seq]


title: TANGO2 binds crystallin alpha B and its loss causes desminopathy

status: Public on Apr 21 2025

city: Perth

first: Stefan

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

institute: The Kids Research Institute Australia

summary: Mutations in the TANGO2 gene cause an autosomal recessive disorder characterised by developmental delay, stress-induced episodic rhabdomyolysis, and cardiac arrhythmias along with severe metabolic crises. Although TANGO2 mutations result in a well characterised disease pathology, the function of TANGO2 is still unknown. To investigate the function of TANGO2, we knocked out the TANGO2 gene in human cells and mice. We identify that loss of TANGO2 impairs intermediate filament structure, resulting in fragmented mitochondrial networks and formation of cup-like mitochondria. In mice loss of TANGO2 caused heart defects, reduced muscle function and hypoglycemia that were caused by remodelling of intermediate filaments, resulting in changes in the mitochondrial and cytoplasmic proteomes and glycosylation. We identify that TANGO2 binds the small heat shock protein crystallin alpha B (CRYAB) to prevent the aggregation of the intermediate filament desmin and in the absence of TANGO2, mice develop desminopathy, which is consistent with features found in patients carrying mutations either in desmin or CRYAB.

overall_design: Total RNA differential gene expression changes between TANGO2 knockout and wild type CAL51 cells grown under glucose and galactose.

first: Maike

last: Stentenbach

first: Laetitia

middle: A

last: Hughes

first: Blake

last: Payne

first: Danielle

last: Rudler

first: Samuel

middle: V

last: Fagan

first: Tim

last: McCubbin

first: Kara

last: Perks

first: Judith

last: Ermer

first: James

last: Hendry

first: Henrietta

middle: C

last: Szappanos

first: Joel

last: Eliades

first: Livia

last: Hool

first: Nicolle

last: Packer

first: Edward

last: Moh

first: Benjamin

middle: S

last: Padman

first: Oliver

last: Rackham

first: Aleksandra

last: Filipovska


title: RNA-binding protein Ars2 mediates transcriptional silencing of telomeric repeats and transposable elements in the Drosophila germline [smallRNA-seq]

first: Anastasiya

last: Kobelyatskaya

type: Non-coding RNA profiling by high throughput sequencing


title: The effects of YTHDC1 on brown adipose tissue

status: Public on Apr 17 2025

first: Zheng

last: Chen

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

summary:
The goal of this study is to investigate how YTHDC1 regulates brown adipose tissue
Methods: Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from iBATs of Ythdc1flox/flox and Ythdc1-BKO mice at 8 weeks old. Three independent biological replicates for each group were used for RNA-seq. RNA-seq was performed by deep sequencing using an Illumina Novaseq 6000 platform. Paired-end clean reads were aligned to the mouse reference genome(GRCm38/mm10) with Hisat2 v2.0.5, and the aligned reads were used to quantify mRNA expression by using featureCounts v1.5.0-p3.
Our study represents the first detailed analysis of iBAT transcriptomes from Ythdc1flox/flox and Ythdc1-BKO mice, generated by RNA-seq technology.

overall_design: mRNA profiles in brown adipose tissues of Ythdc1flox/flox and Ythdc1-BKO mice were generated by deep sequencing using Illumina Novaseq 6000 platform (n=3 for each group).

first: Yuqin

last: Wang


title: Deep Spatial Sequencing Revealing Differential Immune Responses in Human Hepatocellular Carcinoma [AVITI]

status: Public on Apr 16 2025

city: Pittsburgh

first: Shuchang

last: Liu

address: 203 Lothrop Street

institute: University of Pittsburgh

summary: Hepatocellular carcinoma (HCC) is one of the most lethal cancers for humans. HCC is highly heterogeneous. In this study, we performed ultra-depth (~1 million reads per spot) spatial sequencing on a case of HCC. Sixteen distinct spatial expression clusters were identified. Each of these clusters was spatially contiguous and had distinct gene expression patterns. In contrast, benign liver tissues showed minimal heterogeneity in terms of gene expression. Numerous immune cell-enriched spots were identified in both HCC and benign liver regions. Cells adjacent to these immune cell-enriched spots showed significant alterations in their gene expression patterns. Interestingly, the responses of HCC cells to the nearby immune cells were significantly more intense and broader, while the responses of benign liver cells to immune cells were somewhat narrow and muted, suggesting an innate difference in immune cell activities towards HCC cells in comparison with benign liver cells. When standard-depth sequencing was performed, significant numbers of genes and pathways that were associated with these changes disappeared. Qualitative differences in some pathways were also found. These results suggest that deep spatial sequencing may help to uncover previously unidentified mechanisms of liver cancer development.

overall_design: A case of HCC sample with moderate differentiation was obtained from archived tissue slide storage. The case was fully anonymized. The cancer and benign liver regions were identified by a board-certified pathologist. Two spatial slides were measured: J259B (with HCC tumor and adjacent tissue) and J259X (HCC tumor). Samples were sequenced by AVITI platform.

first: Yan-ping

last: Yu

first: Silvia

first: Caroline

last: Obert

first: Bao-Guo

last: Ren

first: Kyle

last: Metcalfe

first: Jia-Jun

last: Krajacich

first: Jian-Hua

last: Luo


title: Single cell profiling to determine influence of wheeze and early-life viral infection on developmental programming of airway epithelium

city: chicago

first: Nana-Fatima

last: Haruna

state: Illinois

address: 200 E Chestnut St., Apt 705

department: Department of Medicine, Division of Allergy and Immunology

institute: Northwestern University

summary: Although childhood asthma is in part an airway epithelial disorder, the development of the airway epithelium in asthma is not understood. We sought to characterize airway epithelial developmental phenotypes in those with and without recurrent wheeze and the impact of infant infection with respiratory syncytial virus (RSV). Nasal airway epithelial cells (NAECs) were collected at age 2-3 years from an a priori designed nested birth cohort of children from four mutually exclusive groups of wheezers/non-wheezers and RSV-infected/uninfected in the first year of life. NAECs were cultured in air-liquid interface differentiation conditions followed by a combined analysis of single cell RNA sequencing (scRNA-seq) and in vitro infection with respiratory syncytial virus (RSV). NAECs from children with a wheeze phenotype were characterized by abnormal differentiation and basal cell activation of developmental pathways, plasticity in precursor differentiation and a delayed onset of maturation. NAECs from children with wheeze also had increased diversity of currently known RSV receptors and blunted anti-viral immune responses to in vitro infection. The most dramatic changes in differentiation of cultured epithelium were observed in NAECs derived from children that had both wheeze and RSV in the first year of life. Together this suggests that airway epithelium in children with wheeze is developmentally reprogrammed and characterized by increased barrier permeability, decreased antiviral response, and increased RSV receptors, which may predispose to and amplify the effects of RSV infection in infancy and susceptibility to other asthma risk factors that interact with the airway mucosa.

overall_design:
Nasal airway epithelial cells were collected from children at age 2-3 from different groups: wheezers/non-wheezers and RSV-infected/uninfected in their first year of life. The cells underwent scRNA-sequencing targetting 10,000 cells.

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human privacy issue
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first: Sergejs

last: Berdnikovs

first: Dawn

last: Newcomb

first: Kaitlin

last: McKernan

first: Shelby

middle: N

last: Kuehnle

first: Tebeb

last: Gebretsadik

first: Christopher

last: McKennan

first: Siyuan

last: Ma

first: Jacqueline-Yvonne

last: Cephus

first: Christian

last: Rosas-Salazar

first: Larry

last: Anderson

first: James

last: Gern

first: Tina

last: Hartert


title: Deep Spatial Sequencing Revealing Differential Immune Responses in Human Hepatocellular Carcinoma

first: Shuchang

last: Liu


title: Phosphatase-independent activity of smooth-muscle calcineurin orchestrates a gene expression program leading to arterial hypertension

city: Madrid

first: Paula

middle: Sofia

last: Yunes-Leites

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

summary: Objective: Angiotensin-II (Ang-II) drives pathological vascular wall remodeling in hypertension and abdominal aortic aneurysm (AAA). Previous studies showed that the phosphatase activity of calcineurin (Cn) mediates Ang-II-induced AAA, but the cell type involved in the action of Cn in AAA formation remained unknown.  Methods: Smooth muscle cell (SMC)-specific and endothelial cell (EC)-specific Cn-deficient mice (SM-Cn-/- and EC-Cn-/- mice, respectively) were created and assessed for Ang-II-induced AAA formation and hypertension vs controls. Osmotic minipumps were used to administer Ang-II and cyclosporine A (CsA), a pharmaceutical Cn inhibitor. AAA formation and hypertension were monitored by ultrasonography, arterial blood pressure monitoring, and histological analysis. Deep RNA sequencing was used to identify the Ang-II-regulated transcriptome sensitive to Cn deletion or pharmacological inhibition. Arterial and SMC contractility were also assessed.  Results: Cn expressed in SMCs, but not ECs, was required for Ang-II-induced AAA. SMC Cn also played an unexpected structural role in the early onset and maintenance of Ang-II-induced hypertension independently of Cn phosphatase activity. Nearly 90% of the genes regulated by Ang-II in the aorta required Cn expression in SMCs. Cn orchestrated, independently of its enzymatic activity, the induction by Ang-II of a gene expression program closely related to SMC contractility and hypertension. Cn deletion in SMCs, but not its pharmacological inhibition, impaired the regulation of arterial contractility. Among the genes whose regulation by Ang-II required Cn expression but not its phosphatase activity, Serpine1 was critical for Ang-II-induced hypertension. Indeed, pharmacological inhibition of PAI-1, the protein encoded by Serpine1, impaired SMCs contractility and regressed hypertension. Conclusions: Whereas the phosphatase activity of Cn mediates Ang-II-induced AAA, a phosphatase-independent action of SMC Cn underlies blood pressure regulation by orchestrating a gene expression program closely related to contractility regulation and hypertension.

overall_design: For RNAseq 1: Aortic samples from Cn-Ctl and SM-Cn-/- male mice treated or non-treated with Ang-II for 2h, 6h or 24h. For RNAseq 2: Aortic samples from WT and WT male mice treated with Cyclosporin A, both treated or non-treated with Ang-II for 2h or 24h.

first: Paula-Sofía

first: Yilin

last: Sun

first: Sara

last: Martinez-Martinez

first: Álvaro

last: Alfayate

first: Jesús

last: Vázquez

first: Juan-Miguel

last: Redondo

first: Miguel

middle: R

last: Campanero


title: Therapeutic Potential of Regulatory T Cells for Stem Cell Regulation: Insights from Treg-Mediated Enhancement of Limbal Stem Cell Functions

city: Shanghai

first: Chunyi

last: Shao

state: Shanghai

address: Number 639, Zhizaoju Road

institute: Shanghai Jiao Tong University School of Medicine

summary: Regulatory T cells (Tregs) play a key role in immunomodulation and tissue regeneration. Limbal stem cells (LSCs) maintain corneal epithelial homeostasis, and limbal stem cell deficiency (LSCD) leads to visual impairment. Current LSCD treatments face donor shortages and graft rejection risks. The present study explored Tregs’ therapeutic potential for LSCD in a mouse model of graded LSCD, and further explore the direct effect of Tregs on LSCs function by in vitro coculturing human-derived cells. Subconjunctival Tregs injection effectively treated mild and moderate LSCD in mouse models. Coculturing human LSCs with human Tregs promotes LSCs migration, proliferation, and stemness maintenance. Furthermore, amphiregulin (AREG), secreted by Tregs, was crucial to their therapeutic effects, as AREG-/- Tregs resulted in diminished efficacy on LSCD mice compared to wild-type Tregs. These findings highlighted Tregs as a promising treatment for LSCD, enhancing LSC function partially via AREG production.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human limbal stem cells

first: Fei

last: Fang

first: Yao

last: Fu


title: Single-Cell Roadmap of generating human induced hepatocyte-like cells from fibroblasts using two-step lineage reprogramming strategy

city: luzhou

last: Jiang

state: sichuan

address: 1st xianglinlu

institute: southwest medical university

summary: Background: Hepatocytes are crucial for drug screening, disease modeling, and clinical transplantation, yet generating large numbers of hepatocytes in vitro faces challenges, particularly with traditional direct reprogramming methods. These methods often result in cells with limited functionality and residual memory of their original state. To address these issues, we have a novel two-step lineage reprogramming strategy, which converts fibroblasts into human induced hepatocytes (hiHeps) via an intermediate hepatic progenitor-like cell stage. hiHeps resembled closely with primary human hepatocytes in molecular and functional identity, showing great potential for hepatocyte-based application, however the mechanism underlying the two-step reprogramming is unclear. Methods: This study employs high-throughput single-cell RNA sequencing (scRNA-seq) to explore the molecular and cellular dynamics of this process. Besides, we applied fluorescence-activated cell sorting, RT-qPCR, and shRNA knockdown to validate the key findings of the scRNA-seq results. Results: The findings reveal that the two-step reprogramming mimics a trajectory of liver development, with similar transcriptional waves of developmental genes during reprogramming process. CD24 and DLK1 were identified as markers for two different hepatic progenitor populations, both contributing to hepatocyte maturation. Notably, Lipid metabolism was found to enhance the maturation of progenitors into functional hepatocytes. Additionally, HNF4A and HHEX play roles in determining cell fate between hepatocytes and intestinal cells in the late reprogramming stages. Conclusions: This research provides a comprehensive single-cell roadmap for generating hiHeps in vitro, enhancing our understanding and optimization of the two-step reprogramming protocol.

overall_design: 7 single-cell samples of hiHeps and hHPLCs were sequenced using 10x genomics to analyze the roadmap of hepatocyte reprogramming.

first: Bingqing

last: Xie

first: Sen

last: Luo


title: Image-based identification and isolation of micronucleated cells to dissect cellular consequences

status: Public on Apr 15 2025

city: Seattle

first: Emily

middle: M

last: Hatch

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

summary: Recent advances in isolating cells based on visual phenotypes have transformed our ability to identify the mechanisms and consequences of complex traits. Micronucleus (MN) formation is a frequent outcome of genome instability, triggers extensive disease-associated changes in genome structure and signaling coincident with MN rupture, and is almost exclusively defined by visual analysis. Automated MN detection in microscopy images has proved extremely challenging, limiting unbiased discovery of the mechanisms and consequences of MN formation and rupture. In this study we describe two new MN segmentation modules: a rapid model for classifying micronucleated cells and their rupture status (VCS MN), and a robust model for accurate MN segmentation (MNFinder) from a broad range of fluorescence microscopy images. As a proof-of- concept, we define the transcriptome of non-transformed human cells with intact or ruptured MN after inducing chromosome missegregation by combining VCS MN with photoactivation-based cell isolation and RNASeq. Surprisingly, we find that neither MN formation nor rupture triggers a strong unique transcriptional response. Instead, transcriptional changes appear correlated with small increases in aneuploidy in these cell classes. Our MN segmentation modules overcome a significant challenge with reproducible MN quantification, and, joined with visual cell sorting, enable the application of powerful functional genomics assays, including pooled CRISPR screens and time-resolved analyses of cellular and genetic consequences, to a wide-range of questions in MN biology.

overall_design: RNA-seq profiling of cells treated with BAY1217389 or DMSO. Cells further isolated and compared based on presence/absence of micronuclei and/or micronucleus rupture. Where noted, cells first synchronized with RO-3306 treatment.

first: Lucian

last: DiPeso

first: Sriram

last: Pendyala

first: Heather

last: Huang

first: Douglas

last: Fowler


title: Single-Cell Transcriptomic Analysis of Cellular Composition and Signaling Pathways in Cerebral Cavernous Malformation

city: Beijing

first: Yutong

last: Liu

address: Dongdan

institute: Peking Union Medical College

summary: Lesional brain vascular tissues from CCM patients and normal brain vascular tissues from healthy controls were collected. Multiplex fluorescent immunohistochemistry and single-cell RNA sequencing were performed on the lesional tissues. Differential gene expression, pathway enrichment analysis, and cell-cell communication analysis were conducted to investigate disease-related changes. We identified 8 major cell types in the lesion tissues of CCM patients. We observed an increased proportion of monocytes, neutrophils, and NK cells in the lesion tissues of CCM patients. Twenty-eight significantly differentially expressed genes were identified, and pathways such as Natural Killer cell-mediated cytotoxicity showed alterations. Cell-cell communication analysis revealed an increase in both the types and strength of communication between cells in the CCM lesion tissues.

overall_design: STA samples and  CCM sample were obtained from 3 epileptics (as healthy control in this research) and 1 CCM patient during surgery respectively. The samples were then isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNA sequencing.

first: Zhiguang

last: Han

first: Chengxu

last: Lei


title: Deep Spatial Sequencing Revealing Differential Immune Responses in Human Hepatocellular Carcinoma [NextSeq]

first: Shuchang

overall_design: A case of HCC sample with moderate differentiation was obtained from archived tissue slide storage. The case was fully anonymized. The cancer and benign liver regions were identified by a board-certified pathologist. Two spatial slides were measured: J259B (with HCC tumor and adjacent tissue) and J259X (HCC tumor). Samples were sequenced by Illumina NextSeq 550 platform.

first: Yan-ping

last: Yu

first: Silvia

first: Caroline

last: Obert

first: Bao-Guo

last: Ren

first: Kyle

last: Metcalfe

first: Jia-Jun

first: Benjamin

last: Krajacich

first: Jian-Hua


title: CXCL12-CXCR4 signaling mediates the formation of a macrophageal niche for mammary tumorigenesis [scRNA-seq]

city: Plainsboro

first: Yong

last: Wei

state: NJ

address: LTL227 Wathington Road

department: Molecular Biology

institute: Princeton University

summary: Niche-associated signals, essential for the maintenance of normal stem cells and tumor-initiating cells, are spatially confined and exert their influence locally among adjacent cells. Here, we demonstrate that CXCR4+ macrophages are enriched in the normal mammary ducts and enhance regenerative activity in basal cells in response to the CXCL12 secreted by luminal cells. Conditional knockout of CXCR4 in macrophages or CXCL12 in luminal cells results in similar phenotypes, including impaired branching morphogenesis, decreased regenerative functionality in basal cells, and diminished ductal association of macrophages. CXCL12 stimulation of macrophages triggers an AKT-mediated stabilization of β-catenin, increasing the expression of pro-migratory genes and multiple Wnt ligands, which enhances the infiltration of macrophages and their ability to support stem-like regenerative functions of basal cells. Importantly, the identical CXCR4+ niche macrophages also govern the tumor-initiating activity of breast tumors by promoting the survival and tumor-forming capacity of tumor-initiating cells and inducing early immune evasion through the accumulation of regulatory T cells. Our findings elucidate a crucial role of the CXCL12-CXCR4 axis in facilitating a complex interaction among niche macrophages, two mammary epithelial cell lineages, and other stromal components, thereby establishing a supportive environment for both normal tissue regeneration and mammary tumor initiation.

overall_design: Normal mammary gland from 8-weeks-old wild type C57BL/6 mice, spontaneous mouse mammary tumors developed in MMTV-PyMT mice carrying myeloid specific KO of Cxcr4, or littermatter control mouse with wild type Cxcr4 were used for single cell RNAseq. The normal mammary gland or tumor samples are dissociated and all live cell transcriptome profiles were determined using single cell RNAseq, and single cell composition from these samples are determined accordingly.

first: Eunmi

last: Lee

first: Yibin

last: Kang


title: Immune cell infiltration into brain tumor microenvironment is mediated by Rab27-regulated vascular wall integrity

city: Montreal

first: Janusz

last: Rak

state: Quebec

address: 1001 Decarie Blvd. Room E01.4366

department: Department of Pediatrics

country: Canada

institute: McGill University

summary: To investigate the functional role of Rab27a/b in glioblastoma. We established different roles of brain endothelial cells at physoilogical and in tumor states in the genetically mutated Rab27a/b double knock out murine tissues. We performed single cells gene expression profiling analysis using data obtained from RNA-seq from the brains of non-tumor and glioma tissues derived by injection of GL261 tumor cells in Rab27a/b dHET and Rab27a/b dKO mice.

overall_design: Comparative single cells gene expression profiling analysis of RNA-seq data for Rab27a/b dHET (non-tumor, BEC), Rab27a/b dKO (non-tumor, BEC), Rab27a/b dHET (GL261 glioma, TEC) and Rab27a/b dKO (GL271 glioma, TEC),

first: Lata

last: Adnani

first: Brian

last: Meehan

first: Minjun

last: Kim

first: Dongsic

last: Choi

first: Cristopher

last: Rudd

first: Yasser

last: Riazalhosseini


title: CXCL12-CXCR4 signaling mediates the formation of a macrophageal niche for mammary gland stem cells

summary: Niche-associated signals, essential for stem cell maintenance, are spatially confined and exert their influence locally among adjacent cells. Here, we demonstrate that CXCR4+ macrophages are enriched in the mammary ducts and enhance MaSC activity in basal cells in response to the CXCL12 secreted by luminal cells. Conditional knockout of CXCR4 in macrophages or CXCL12 in luminal cells results in similar phenotypes, including impaired branching morphogenesis, decreased stem cell functionality in basal cells, and diminished ductal association of macrophages. CXCL12 stimulation of macrophages triggers an AKT-mediated stabilization of β-catenin, increasing the expression of pro-migratory genes and multiple Wnt ligands. This process enhances the infiltration of macrophages into intraepithelial regions and their ability to support MaSC functions. Our findings elucidate a crucial role of the CXCL12-CXCR4 axis in facilitating a complex interaction among ductal macrophages and two mammary epithelial cell lineages in establishing a supportive environment for MaSCs during mammary gland development.

overall_design: Mammary gland macrophage and MaSC enriched basal cells were sorted using cell identity markers from mice with conditional knockout of Cxcl12 and Cxcr4 genes. Furthermore, mammary gland macrophages were cultured in vitro and treated with Cxcl12 and/or AKT inhibitors. Transcriptome profiles were determined in these cells to delinate the signaling transductions of CXCL12 and CXCR4 axis between MaSC/Luminal and macrophage populations.


title: A lineage-specific super-enhancer for MYB controls the development of gastrointestinal adenocarcinomas

first: Fuyuan

last: Li

address: No. 2005, Songhu Road, Xinjiangwancheng Street, Yangpu District

department: School of life science

institute: Fudan University


title: CXCL12-CXCR4 signaling mediates the formation of a macrophageal niche for mammary tumorigenesis [tumor]

overall_design: Spontaneous mouse mammary tumors are developed in MMTV-PyMT mice carrying myeloid specific KO of Cxcr4 or littermatter control mice with wild type Cxcr4. 3 pairs of intratumoral macrophage samples and 2 pairs full primary tumor samples are harvested to determine full trascriptome profiles and compared to determine the molecular consequences of of Cxcr4 in macrophage and tumor progression.


title: A lineage-specific super-enhancer for MYB controls the development of gastrointestinal adenocarcinomas (ChIP-seq)

summary: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for MYB in HT55 cells.

overall_design: MYB ChIP-seq were performed using antibodies recognizing endogenous protein.

first: Jin


title: A lineage-specific super-enhancer for MYB controls the development of gastrointestinal adenocarcinomas (RNA-Seq)

summary: To investigate the downstream target genes regulated by MYB, we performed  gene expression profiling analysis  in HT55 cells in which  target gene has been knocked down by shRNA.

overall_design: Comparative GSEA analysis of RNA-seq data for HT55 cells and its KD derivative (shMYB).


title: MeRIP-seq to identify putative Mettl3 targets in the nephron progenitor cells

status: Public on Apr 14 2025

city: Dallas

first: Vishal

last: Patel

state: Texas

address: 5323 Harry Hines Blvd, RM F5.206, MC8856

department: Internal Medicine Nephrology

institute: UTSW

summary: Mettl3 is an mRNA methyl transferase enzyme. It catalzyes the methylation of the most common mRNA biochemical modification N6-methyl adenosine (m6A). The role of Mettl3/m6A pathway is unknown in the developing kidney. Through genetic and pharmaceutical approaches we found that Mettl3 is required for the differentiation of nephron progenitor cells.  nephron progenitors.  Genetic deletion of Mettl3 in the nephron progenitor cells blocks their differentiation. We sought to identify the mechanism of Mettl3 activity. We performed RNA-sequencing and RNA-m6A pull down assay followed by next-generation sequencing (MeRIP-seq) on wild type and Mettl3 deleted kidneys to determine the mRNA targets of Mettl3.

overall_design: m6A RNA immunoprecipitation was performed using the m6A antibody precipitation approach. RNA isolated from kidneys of Six2Cre or Six2Cre-Mettl3-KO E16.5 pups was subjected to fragmentation to obtain fragments of 100 nucleotides or smaller in length. Magnetic immunoprecipitation was performed. Two biological replicate samples per group were analyzed, each sample containing pooled fragmented RNA from 4-6 pairs of kidneys. The samples were subjected to Illumina Illumina's next-generation sequencing.

first: Harini

last: Ramalingam


title: Seasonal tissue-specific transcriptomic responses of the Andean Killifish Orestias ascotanensis

city: Santiago

first: Rodrigo

last: Maldonado

address: Avenida Pedro de Valdivia 1509

country: Chile

institute: Universidad Finis Terrae

summary: The Andean killifish Orestias ascotanensis inhabits the high-altitude Ascotán Salt Pan, an environment with variable salinity, high UV exposure, low oxygen, and extreme daily temperature fluctuations. These conditions make it an excellent model for studying high-altitude fish biology. However, the transcriptomic responses of O. ascotanensis to seasonal acclimation remain unexplored. To investigate seasonal and tissue-specific transcriptomic profiles, RNA-seq was performed on 42 libraries from gills, skin, and muscle tissues of 14 individuals collected in summer (n=7) and winter (n=7). Each library had a median of 105 million reads. Principal component analysis revealed strong tissue-specific expression, and seasonal differential expression analyses identified significant transcriptomic changes within each tissue. Additionally, a bioinformatics pipeline identified 10,365 high-confidence long non-coding RNAs (lncRNAs), predicted by at least three computational tools. Compared to protein-coding genes, lncRNAs exhibited higher tissue specificity, with a predominance of monoexonic structures and shorter exon lengths. This dataset provides the first comprehensive view of seasonal mRNA and lncRNA expression in O. ascotanensis tissues.

overall_design: Total RNA was extracted from three different tissues (gills, skin, and muscle) samples obtained from each of the 14 individuals captured during either summer (n=7) or winter (n=7), using TRIzol (Invitrogen) following the manufacturer's protocol. The concentration and quality of the extracted RNA were assessed using a Qubit fluorometer (Invitrogen) and a Bioanalyzer 2100 (Agilent), determining the integrity and purity of each sample. Unstranded poly-A libraries were prepared from each tissue sample using the Illumina TruSeq RNA sample preparation kit (Illumina) according to the manufacturer’s instructions. The prepared RNA samples were sent to Quick Biology (Pasadena, CA, USA) for sequencing, where they were processed on the Illumina HiSeq 4000 platform to generate 150 bp paired-end reads.

first: Martin

last: Montecino

last: Maldonado-Agurto


title: PSME3 Regulates Migration and Differentiation of Myoblasts

first: Kenneth

last: Kuhn

summary: The acquisition of cellular identity requires large-scale alterations in cellular state. The non-canonical proteasome activator PSME3 is known to regulate diverse cellular processes, but its importance for differentiation remains unclear. Here, we demonstrate that PSME3 binds dynamically to highly active promoters over the course of differentiation. However, loss of PSME3 does not globally affect mRNA transcription. We find instead that PSME3 influences the levels of several adhesion-related proteins and acts upstream of the HSP90 co-chaperone NUDC to regulate cell motility and myoblast differentiation in a proteasome-independent manner. Our findings reveal several new facets of PSME3 functionality and highlight its particular importance for the differentiation of myogenic cells.

overall_design: RNA-seq profiling of C2C12 cells at their cycling stage, or at either day 0 or day 2 of serum starvation-induced differentiation, treated with either control siRNA or that targeting proteasomal subunit PSME3. Included additionally at day 0 are cells not treated by siRNA.

first: Ukrae

last: Cho

last: Hetzer


title: Constitutive differences in immune gene expression and energy storage phenotypes co-vary with winter environment in wood frogs

city: STORRS MANSFIELD

first: Grace

last: Vaziri

state: CT

address: 77 Forest Rd., Apt A

institute: University of Connecticut

summary: Many terrestrial ectotherms have gone to great evolutionary lengths to adapt to long cold winters; some have even evolved the ability to tolerate the freezing of most of the water in the body. Now, however, high-elevation, and high-latitude winters are experiencing an accelerated period of warming. Specialized winter adaptations that promoted fitness in a seasonally frozen environment may soon be superfluous or even maladaptive. We ask whether winter adaptations include changes in immune functions, and whether changing winter conditions could exert disparate effects on populations of a wide-ranging terrestrial ectotherm, the wood frog (Lithobates sylvaticus). By rearing wood frogs from ancestral winter environments that vary in length and temperature in a common garden, and reciprocally crossing post-metamorphic frogs into unfrozen and frozen artificial winter conditions in the lab, we were able to decompose transcriptomic differences in ventral skin gene expression into those that were environmentally induced (responsive to temperature), genetically determined, and those that varied as an interaction between genotype and environment. We found that frogs from harsh ancestral winter environments upregulated immune processes, including cellular immunity, inflammatory processes, and adaptive immune processes, as compared to frogs from mild ancestral winter environments. Further, we saw that expression of several genes varied in an interaction between genotype and artificial winter environment, a pattern that was recapitulated at the level of hepatosomatic index (the proportion of body mass comprising liver). We suggest that just as winter climates likely served as the selective force resulting in remarkable winter adaptations such as freeze tolerance, they also induced constitutive changes in immune gene expression.

overall_design: We tested the hypothesis that immune gene expression would vary differentially based on whether expression is promoted by glycolysis or lipid metabolism, and with respect to an interaction between artificial winter treatment temperature and origin winter environments (‘harsh’ or ‘mild’). We performed a common garden and reciprocal exposure experiment by rearing wood frogs from egg masses in a laboratory. The egg masses were sourced from across the eastern US. Seventeen weeks post-metamorphosis, we sampled frogs for a "pre winter" timepoint, or exposed them to -2° or +2° C. Then we allowed them to overwinter for 9 days, euthanized them, and collected a ventral skin sample for tag-seq analysis of gene expression.

middle: I

first: Noah

last: Reid

first: Tracy

last: Rittenhouse

first: Daniel

last: Bolnick


title: A macrophage-predominant, immunosuppressive immune microenvironment and subtype-specific therapeutic vulnerabilities in advanced salivary gland cancer [bulk RNA-seq]

city: Berlin

first: Damian

middle: Tobias

last: Rieke

address: Charitéplatz 1

department: Comprehensive Cancer Center

country: Germany

institute: Charité – Universitätsmedizin Berlin

summary: Salivary gland cancers are rare, diverse malignancies characterized by poor response to immunotherapy. The tumor immune environment in these cancers remains poorly understood. To address this, we perform an integrative analysis of the tumor immune microenvironment in a large cohort of advanced salivary gland cancer samples. Most tumors exhibit low immune activity with limited immune cell infiltration. Inflammation is linked to higher tumor mutational burden in non-adenoid cystic carcinoma histologies. Subtype specific expression of immune checkpoints is identified with prominent expression of VTCN1 in luminal-like cells within adenoid cystic carcinoma. Macrophages with immunosuppressive properties dominate the immune microenvironment across subtypes. Responses to immunotherapy are limited and associated with a higher ratio of T-cells relative to macrophages in individual cases, warranting further investigation. Here, we show an immunosuppressive environment in salivary gland cancers and identify subtype-specific immune vulnerabilities that could inform tailored therapeutic strategies.

overall_design:
Tumor biopsies from 93 advanced SGC were sequenced for bulk mRNA. Samples were derived from different tumor entities and from different sites (primary/metastatic). A total of 95 samples for 93 patients are included.

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

first: Erika

last: Zuljan


title: FFPE-ATAC and PDX-ATAC sequence data of small cell lung cancer

status: Public on Apr 13 2025

city: NEW YORK

first: Kenta

last: Kawasaki

state: NEW YORK

address: 417 East 68th Street

institute: Memorial Sloan Kettering Cancer Center

summary: Small cell lung cancer (SCLC) is known for its high metastatic potential, with most patients demonstrating clinically evident metastases in multiple organs at diagnosis. The factors contributing to this exceptional metastatic capacity have not been defined. To bridge this gap, we compared gene expression in SCLC patient samples who never experienced metastasis or relapse throughout their clinical course, versus primary SCLC patient samples from more typical patients who had metastatic disease at diagnosis. This analysis identified FOXA2 as a transcription factor strongly associated with SCLC metastasis. To clarify the contribution of ASCL1 with the interaction with FOXA2, we performed ATAC-seq on clinical FFPE samples, and PDX samples to analyze the chromatin accessibility in FOXA2+ and FOXA2- state. Furthermore, we confirmed the binding of ASCL1 by ChiP-sequence.

overall_design: ATAC-sequence on FFPE samples in comparison of their metastatic potential,  and ATAC-sequence on FOXA2+ and FOXA2- PDX samples

first: Eralda

last: Salataj

first: Pierre-Jacques

last: Hamard

first: Richard

middle: P

last: Koche

first: Joan

last: Massagué

first: Charles

last: Rudin


title: RNA-sequence data of clinically never-metastatic primary small cell lung cancer cases and small cell lung cancer metastasis cases, FOXA2 knock-down and overexpression in cell lines

summary: Small cell lung cancer (SCLC) is known for its high metastatic potential, with most patients demonstrating clinically evident metastases in multiple organs at diagnosis. The factors contributing to this exceptional metastatic capacity have not been defined. To bridge this gap, we compared gene expression in SCLC patient samples who never experienced metastasis or relapse throughout their clinical course, versus primary SCLC patient samples from more typical patients who had metastatic disease at diagnosis. This analysis identified FOXA2 as a transcription factor strongly associated with SCLC metastasis.

overall_design: We collected pathological slides from clinically never-metastatic primary small cell lung cancer cases and small cell lung cancer metastasis cases and extracted, processed for RNA-sequence

first: Yingqian

last: Zhan

first: Fanli

last: Meng

first: Brian

last: Loomis


title: Nerve-to-cancer transfers of mitochondria during cancer metastasis

city: Mobile, AL

first: Simon

last: Grelet

state: Alabama

address: 1660 Spring Hill Ave - USA Drive North,

institute: University of South Alabama - Mitchell Cancer Institute

summary: The nervous system plays a pivotal role in cancer biology, and pathological investigations have linked intratumoural nerve density to metastasis. However, the precise impact of cancer-associated neurons and the communication channels at the nerve–cancer interface remain poorly understood. Previous cancer denervation models in rodents and humans have highlighted robust cancer dependency on nerves, but the underlying mechanisms driving nerve-mediated cancer aggressivity remain unknown. Here we show that cancer-associated neurons enhance cancer metabolic plasticity by transferring mitochondria to cancer cells. Breast cancer denervation and nerve–cancer coculture models confirmed that neurons significantly improve tumour energetics. Neurons cocultured with cancer cells undergo metabolic reprogramming, resulting in increased mitochondrial mass and subsequent transfer of mitochondria to adjacent cancer cells. To precisely track the fate of recipient cells, we developed MitoTRACER, a reporter of cell-to-cell mitochondrial transfer that permanently labels recipient cancer cells and their progeny. Lineage tracing and fate mapping of cancer cells acquiring neuronal mitochondria in primary tumours revealed their selective enrichment at metastatic sites following dissemination. Collectively, our data highlight the enhanced metastatic capabilities of cancer cells that receive mitochondria from neurons in primary tumours, shedding new light on how the nervous system supports cancer metabolism and metastatic dissemination.

overall_design: RNA-seq of 4T1 cancer cells extracted from xenografts in the mammary fat pad of mice, comparing control (PBS-treated) versus Botox-predenerverated (Botox-treated) conditions at the injection site

first: Gregory

last: Hoover

first: Shila

last: Gilbert

first: Olivia

last: Curley

first: Clemence

last: Obellianne

first: Mike

middle: T

last: Lin

first: William

last: Hixson

first: Terry

last: Pierce

first: Joel

middle: F

last: Andrews

first: Mikhail

last: Alexeyev

first: Fariba

last: Behbod

last: Medina

first: Yi

last: Ding

first: Ping

last: Bu

first: Jeffrey

last: Chang

first: Gustavo

last: Ayala


title: Sensitive monitoring of xenograft cancer models using cell-free DNA

city: Shenzhen

first: Kun

last: Sun

state: Guangdong

address: Rm A1921, Guangming International Innovation Center,

institute: Shenzhen Bay Laboratory

summary: Tumor-derived xenograft mouse models are widely used tools in cancer studies. We reported that in xenograft models without recognizable tumors, however, circulating tumor-derived cell-free DNA (cfDNA) was persistently detectable in peripheral blood long after engraftment, suggesting that measurement of tumor-derived cfDNA could be more sensitive for tumor assessment in xenograft models as well as serve as valuable supplementary parameters in outcome interpretations, especially for those without visible tumors.

overall_design: We inoculated immunodeficiency mice with luciferase-eGFP expressing human HCC1937, A427, or A2058 cells, and performed whole genome sequencing of the cfDNA from mice plasma to detect the human original DNA in xenograft mice, with cfDNA from wild-type mice without engraftment as control.

first: Yunyun

last: An

first: Huizhen

first: Bianbian

last: Tang

first: Fanglei

last: Gong


title: A macrophage-predominant, immunosuppressive immune microenvironment and subtype-specific therapeutic vulnerabilities in advanced salivary gland cancer [Single nuclei RNAseq]

first: Damian

last: Rieke

overall_design:
Tumor biopsies from 13 advanced SGC were sequenced for single nuclei mRNA. Samples were derived from different tumor entities and from different sites (primary/metastatic). A total of 16 samples for 13 patients are included (3 technical replicates)

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

first: Erika

last: Zuljan


title: Osteocyte-derived extracellular vesicles mediate the bone-to-cartilage crosstalk and promote osteoarthritis progression [EVs  from plasma]

status: Public on Apr 12 2025

city: Nanjing

last: Liu

address: 321 Zhongshan Road

institute: Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University

summary: Osteoarthritis (OA) is the most common degenerative joint disease. During its initiation and early progression a disruption in subchondral bone (SCB) remodeling, induced by excessive and cumulative mechanical loading, occurs before cartilage degeneration. While it is known that osteocytes in the SCB are mainly responsible for mechanosensing, their role in the early phases of OA are still unclear. Here, we found that mechanical stress induces SCB osteocytes to secrete extracellular vesicles (EVs) that accelerate cartilage metabolic dysregulation. By gain- and loss-of function experiments we show that such EVs via miR-23b-3p promote cartilage catabolism while inhibiting their anabolism. Mechanistically, miR-23b-3p inhibits mitophagy by targeting OTUD4 to promote this metabolic skewing. Further, by inhibiting miR-23b-3p in either osteocytes or chondrocytes we could alleviate cartilage degeneration and OA progression in a mouse model. Together, our findings show that SCB osteocytes communicate with chondrocytes via EVs and that targeting a key EV-derived miRNA can ameliorate OA progression.

overall_design: To gain further insights into the underlying mechanisms by which miR-23b-3p regulates chondrocyte function during OA progression, we conducted RNA-sequencing analysis on human primary osteoarthritic chondrocytes infected with negative control (nc) or a miR-23b-3p mimic (mimic).

first: Yuze

last: Ma

first: Tianshu

last: Shi


title: Osteocyte-derived extracellular vesicles mediate the bone-to-cartilage crosstalk and promote osteoarthritis progression [primary chondrocytes]

first: Pu

last: Wang

first: Wentian

last: Gao


title: ASCL1-ChiP sequence data of small cell lung cancer cell lines

first: Kenta

last: Kawasaki

overall_design: ASCL1- ChiP-sequence on H1836 and SHP77 small cell lung cancer cell lines to identify the binding of ASCL1 to FOXA2 locus

first: Yingqian

last: Zhan

first: Jun Ho

last: Lee

first: Joan

last: Massagué

first: Charles

last: Rudin


title: Osteocyte-derived extracellular vesicles mediate the bone-to-cartilage crosstalk and promote osteoarthritis progression [only osteocyte-enriched subchondral bone]


title: Mitochondrial Calcium Signaling Regulates Branched-Chain Amino Acid Catabolism in Fibrolamellar Carcinoma

status: Public on Apr 11 2025

first: Yasemin

last: Sancak

address: 1959 NE Pacific Street K526

department: Pharmacology

institute: University of Washington

summary: Metabolic adaptations are essential for survival. The mitochondrial calcium uniporter plays a key role in coordinating metabolic homeostasis by regulating mitochondrial metabolic pathways, and calcium signaling. However, a comprehensive analysis of uniporter-regulated mitochondrial pathways has remained unexplored. Here, we investigate consequences of uniporter loss- and gain-of-function using uniporter knockout cells and fibrolamellar carcinoma (FLC), which we demonstrate to have elevated mitochondrial calcium levels. We find that branched-chain amino acid (BCAA) catabolism, and the urea cycle are uniporter-regulated pathways. Reduced uniporter function boosts expression of BCAA catabolism genes, and the urea cycle enzyme ornithine transcarbamylase. In contrast, high uniporter activity in FLC suppresses their expression. This suppression is mediated by the transcription factor KLF15, a master regulator of liver metabolism. Thus, uniporter plays a central role in FLC-associated metabolic changes, including hyperammonemia. Our study identifies an important role for the uniporter in metabolic adaptation through transcriptional regulation of metabolism and elucidates its importance for BCAA and ammonia metabolism in FLC.

overall_design: RNAseq profiling of WT and MCU KO HeLa cells. 500,000 HeLa cells were plated in 6-well plates. After two days, total RNA was isolated and sequenced.


title: A boundary-defining protein facilitates megabase-scale regulatory chromosomal loops in Drosophila neurons [ChIP-seq]

city: Lausanne

first: Maria Cristina

last: Gambetta

address: Genopode Building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

summary: Regulatory elements, such as enhancers and silencers, control transcription by establishing physical proximity to target gene promoters. Neurons in flies and mammals exhibit long-range three-dimensional genome contacts, proposed to connect genes with distal regulatory elements. However, the relevance of these contacts for neuronal gene transcription and the mechanisms underlying their specificity necessitate further investigation. Here, we precisely disrupt several long-range contacts in fly neurons, demonstrating their importance for megabase-range gene regulation and uncovering a hierarchical process in their formation. We further reveal an essential role for the chromosomal boundary-forming protein Cp190 in anchoring many long-range contacts, highlighting a mechanistic interplay between boundary and loop formation. Finally, we develop an unbiased proteomics-based method to systematically identify factors required for specific long-range contacts. Our findings underscore the essential role of architectural proteins such as Cp190 in cell-type-specific genome organization enabling specialized neuronal transcriptional programs.

overall_design: Anti-hemmaglutinin (HA) ChIP-seq was performed on dissected larval central nervous systems of lola-I[KO] mutants rescued by an HA-tagged lola-I cDNA expressed under lola-I regulatory sequences, or on wildtype animals lacking HA-tagged lola-I transgene as negative control.

first: Marion

last: Mouginot

first: Sahar

last: Hani

first: Pascal

last: Cousin

first: Julien

last: Dorier

first: Arianna

last: Ravera


title: A boundary-defining protein facilitates megabase-scale regulatory chromosomal loops in Drosophila neurons [Hi-C]

overall_design: Neurons purified by fluorescence-activated cell sorting (FACS) from old (16-24-hour old) embryos were isolated from mutants or their matched wildtype (WT) controls, and subjected to Hi-C in biological duplicates. More specifically, neurons were immunostained and FACS-purified from CTCF0 or Cp1900 mutants and their matched WT (called WT0) controls. Neurons endogenously expressing mCherry under elav regulatory sequences were FACS-purified from two independent lola-IKO mutants (considered as biological duplicates) and their matched WT controls.


title: Osteocyte-derived extracellular vesicles mediate the bone-to-cartilage crosstalk and promote osteoarthritis progression [EVs from osteocyte-enriched subchondral bone]

last: Liu


title: Atlas of pathogen-sensitive myeloid lncRNA networks in humans (SMyLR catalog) [ChIRP-seq]

city: Marburg

first: Leon

middle: Nicolas

last: Schulte

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

institute: Philipps-Universität Marburg

summary: Long noncoding RNAs (lncRNAs) play crucial roles in eukaryotic biology, yet their functions in the immune system are not fully understood. This study presents a comprehensive resource on the regulation, pathway dependencies, subcellular localizations, and protein interactomes of lncRNAs in immune cells exposed to pathogens. We developed GRADR, a methodology combining gradient profiling and RNA-bound proteome analysis, to map interactomes for all expressed RNAs in a single experiment. Using GRADR and targeted CRISPR multiomics, we identified a network of lncRNAs, including LINC01215, AC022816, and LINC01268 (ROCKI), that influence immunity, mainly through interactions with splicing factors. Our data are compiled into SMyLR, a web interface providing access to our lncRNA regulation and interactome atlas. This resource is expected to significantly advance research into RNA regulation in immunity.

overall_design: The LINC01268 (ROCKI) genome-occupancy profile was determined by ChIRP-seq, to test a potential chromatin-regulatory mode of action.


title: Catalytically distinct metabolic enzyme isocitrate dehydrogenase 1 mutants tune phenotype severity in tumor models [BiSulfite-seq]

city: San Diego

first: Christal

last: Sohl

address: 5500 Campanile Rd.

department: Chemistry and Biochemistry

institute: San Diego State University

type: Methylation profiling by high throughput sequencing

summary: Mutations in isocitrate dehydrogenase 1 (IDH1) impart a neomorphic reaction that produces D-2-hydroxyglutarate (D2HG), which can inhibit DNA demethylases to drive tumorigenesis. Mutations affect residue R132 and display distinct catalytic profiles for D2HG production. We show that catalytic efficiency of D2HG production is greater in IDH1 R132Q than R132H mutants, and expression of IDH1 R132Q in cellular and xenograft models leads to higher D2HG concentrations in cells, tumors, and sera compared to R132H. Though expression of IDH1 R132Q leads to hypermethylation in DNA damage pathways, DNA hypomethylation is more notable when compared to IDH1 R132H expression. Transcriptome analysis shows increased expression of many pro-tumor pathways upon expression of IDH1 R132Q versus R132H, including transcripts of EGFR and PI3K signaling pathways. Thus, IDH1 mutants appear to modulate D2HG levels via altered catalysis and are associated with distinct epigenetic and transcriptomic consequences, with higher D2HG levels appearing to be associated with more aggressive tumors.

overall_design:
To investigate the consequences of genome methylation as measured by reduced representation bisulfite (RRBS) analysis in mouse xenograft tumors generated from human cells stably overexpressing IDH! Wild type (WT), R132H, or R132Q in U87MG cells or in HT1080 cells modified to have the IDH1 R132C allele removed (WT/null alleles, or +/- here). Comparative gene expression profiling analysis of RRBS data for the resulting tumors are provided.
WT, R132H, and R132Q forms of IDH1 contained a C-terminal HA tag and were stably introduced into cells using an LEIH vector that contains an EF1a promoter for high expression in lentiviral based transfection.
Female athymic nude mice 6-8 weeks old were purchased from Jackson Labs were used. 27 mince per cell line (U87MG or HT1080) were used, with 9 mice per IDH type (WT, R132H, R132Q). The tumor from individual mice, if formed, were harvested if formed and a randomized subset were processed for RRBS analysis.

middle: D

first: Ashley

last: Schwartz


title: Atlas of pathogen-sensitive myeloid lncRNA networks in humans (SMyLR catalog) [RNA-seq]

overall_design:
To determine lncRNAs involved in anti-pathogen immunity and their pathway dependencies, human type II pneumocytes, alveolar macrophages and blood-derived macrophages were treated with microbial Toll-like-receptor (TLR)-ligands or Interferon-alpha (IFNa), as well as with TLR- and IFNa-signaling inhibitors. RNA was isolated and subjected to RNA-seq analysis.
The transcripts LINC01268 (ROCKI), AC010980.1, LINC00158, LINC01215 and AC022816.1, identified as immune-inducible lncRNAs, depending on the TLR-NFkB pathway, were silenced in THP1 cells by CRISPR interference, followed by RNA-seq analysis to determine their roles in macrophage immunity.
To narrow the subcellular sites of action of lncRNAs, RNA was isolated from cytplasmic and nulcear fractions of LPS-stimulated macrophages and subjected to RNA-seq analysis.


title: Catalytically distinct metabolic enzyme isocitrate dehydrogenase 1 mutants tune phenotype severity in tumor models

overall_design:
To investigate the consequences of gene expression as measured by RNAseq analysis in mouse xenograft tumors generated from human cells stably overexpressing IDH! Wild type (WT), R132H, or R132Q in U87MG cells or in HT1080 cells modified to have the IDH1 R132C allele removed (WT/null alleles, or +/- here). Comparative gene expression profiling analysis of RNAseq data for the resulting tumors are provided.
WT, R132H, and R132Q forms of IDH1 contained a C-terminal HA tag and were stably introduced into cells using an LEIH vector that contains an EF1a promoter for high expression in lentiviral based transfection.
Female athymic nude mice 6-8 weeks old were purchased from Jackson Labs were used. 27 mince per cell line (U87MG or HT1080) were used, with 9 mice per IDH type (WT, R132H, R132Q). The tumor from individual mice, if formed, were harvested if formed and a randomized subset were processed for RNAseq analysis.


title: Somatic muscle engineering faithfully recapitulates a molecular spectrum of high-risk sarcomas [RNA-Seq]

city: Heidelberg

first: Ana

last: Banito

address: Im Neuenheimer Feld 581

institute: KiTZ, DKFZ

summary: A particular challenge hampering therapeutic advancements for high-risk sarcoma patients is the broad spectrum of molecularly distinct sarcoma entities and the corresponding lack of suitable model systems to recapitulate and study these diseases. To overcome this predicament, we developed a novel genetically-controlled, yet versatile mouse modeling platform allowing delivery of different genetic lesions by electroporation (EPO) of the thigh muscle in wildtype mice. This sarcoma EPO-GEMM (EPO-based genetically engineered mouse model) platform allowed the generation of ten biologically distinct sarcoma entities and subtypes on an isogenic background, including the first model of ETV6::NTRK3-driven infantile fibrosarcoma and of BCOR-inactivated rhabdomyosarcoma. Comprehensive histological and molecular profiling revealed that this mouse sarcoma cohort recapitulates the molecular diversity observed across the human disease with gene fusion and Trp53 status acting as major determinants of sarcoma biology. Integrative cross-species analyses confirmed faithful recapitulation of the human disease, including the expression of relevant immunotherapy targets.

overall_design: Expression analysis (RNAseq) for characterization of murine sarcomas generated by muscle electroporation (EPO-GEMMs)

first: Roland

last: Imle


title: Somatic muscle engineering faithfully recapitulates a molecular spectrum of high-risk sarcomas [Illumina Array]

overall_design: DNA methylation analysis by Illumina BeadChip array of sarcoma EPO-GEMMs and conventional GEMMs.

first: Kevin

middle: B

last: Jones


title: Characterisation of a pathogenic non-migratory fibroblast population in systemic sclerosis skin [scRNA-Seq]

status: Public on Apr 10 2025

city: London

first: Kristina

middle: Elizabeth Neergaard

last: Clark

state: England

address: Royal Free Hospital, Pond Street

country: United Kingdom

institute: UCL

summary: Fibroblasts are central to pathogenesis of systemic sclerosis (SSc). However, studies of conventional explant fibroblast cultures incompletely reflect disease biology and treatment response. We isolated a second non-migratory “resident” population of fibroblasts from skin biopsies after outgrowth of explant “migratory” cells.  These non-motile resident fibroblasts were compared with migratory cells from the same biopsy, using functional studies, bulk and scRNAseq, and localised in situ by multichannel immunofluorescence.   Migratory and resident fibroblast populations in SSc showed distinct pro-fibrotic characteristics and gene expression for pathogenic pathways differing by stage and autoantibody subgroup.  TGFβ signalling was highly active in migratory fibroblasts in early stage dcSSc.  Conversely, resident fibroblasts had less upregulated TGFβ signalling, especially in late dcSSc.  Increased chemokine expression was a hallmark of resident fibroblasts at all stages.  In vitro studies confirmed differential response to TGF1 and CCL2 between migratory and resident cells. We suggest that migratory fibroblasts are especially important in early skin disease whereas non-migratory fibroblasts may have a regulatory role and contribute more to fibrosis in later stage disease. Thus, we have identified a pathogenic fibroblast population in SSc, not isolated by conventional explant culture, that could play an important role in fibrosis and be targeted therapeutically.

overall_design: Observational study comparing SSc whole skin forearm punch biopsies to HC whole skin forearm punch biopsies using scRNAsequencing

first: Shiwen

last: Xu

first: Moustafa

last: Attah

first: Voon

last: Ong

first: Christopher

last: Buckley

last: Denton


title: Characterisation of a pathogenic non-migratory fibroblast population in systemic sclerosis skin

summary: Fibroblasts are central to pathogenesis of systemic sclerosis (SSc). However, studies of conventional explant fibroblast cultures incompletely reflect disease biology and treatment response. We isolated a second non-migratory “resident” population of fibroblasts from skin biopsies after outgrowth of explant “migratory” cells.  These non-motile resident fibroblasts were compared with migratory cells from the same biopsy, using functional studies, bulk and scRNAseq, and localised in situ by multichannel immunofluorescence.   Migratory and resident fibroblast populations in SSc showed distinct pro-fibrotic characteristics and gene expression for pathogenic pathways differing by stage and autoantibody subgroup.  TGFβ signalling was highly active in migratory fibroblasts in early stage dcSSc.  Conversely, resident fibroblasts had less upregulated TGFβ signalling, especially in late dcSSc.  Increased chemokine expression was a hallmark of resident fibroblasts at all stages.  In vitro studies confirmed differential response to TGFb1 and CCL2 between migratory and resident cells. We suggest that migratory fibroblasts are especially important in early skin disease whereas non-migratory fibroblasts may have a regulatory role and contribute more to fibrosis in later stage disease. Thus, we have identified a pathogenic fibroblast population in SSc, not isolated by conventional explant culture, that could play an important role in fibrosis and be targeted therapeutically.

overall_design: Observational study comparing SSc and HC explant and resident fibroblasts in skin 4mm biopsies

last: Clark'

last: Xu'

last: Attah'

last: Ong'

last: Buckley'

last: Denton'


title: single-cell RNA-sequence data of clinical small cell lung cancer samples

first: Kenta

last: Kawasaki

summary: Small cell lung cancer (SCLC) is known for its high metastatic potential, with most patients demonstrating clinically evident metastases in multiple organs at diagnosis. The factors contributing to this exceptional metastatic capacity have not been defined. To bridge this gap, we compared gene expression in SCLC patient samples who never experienced metastasis or relapse throughout their clinical course, versus primary SCLC patient samples from more typical patients who had metastatic disease at diagnosis. This analysis identified FOXA2 as a transcription factor strongly associated with SCLC metastasis. Subsequent analyses in experimental models demonstrated that FOXA2 induces a fetal neuroendocrine gene expression program and promotes multi-site metastasis. Moreover, we identified ASCL1, a transcription factor known for its initiating role in SCLC tumorigenesis, as a direct binder of the FOXA2 promoter and regulator of FOXA2 expression. Taken together, these data define the ASCL1-FOXA2 axis as a critical driver of multiorgan SCLC metastasis.

overall_design: We collected 19 small cell lung cancer patient samples and processsed for single-cell RNA-sequence

first: Sohrab

last: Salehi

first: Nicholas

last: Ceglia

first: Matthew

last: Zatzman

first: Eliyahu

last: Havasov

last: Shah

first: Joan

last: Massagué

first: Charles

last: Rudin


title: Somatic muscle engineering faithfully recapitulates a molecular spectrum of high-risk sarcomas

last: Banito

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

overall_design: Refer to individual Series


title: Spatial organization, chromatin accessibility and gene-regulatory programs defining sensory neurons

city: Solna

first: Patrik

last: Ernfors

address: Biomedicum, Solnavägen 9

department: MBB/Molneuro

country: Sweden

institute: Karolinska Institutet

summary: Heterogeneity among somatosensory neurons is necessary for internal and external sensation. Precise patterns of gene transcription orchestrated through enhancer activation maintain heterogeneity. Thus, high-resolution cell type classification, chromatin accessibility and its relation to enhancer activation can explain the governing principles for sensory neuron heterogeneity. Here, we generated an integrated atlas from high-quality scRNA-seq datasets of the dorsal root ganglion, including over 44,000 neurons. MERSCOPE spatial transcriptomics confirmed cell types in situ, including previously unrecognized neuronal types, and a spatial zonation of both neurons and non-neuronal cells. We generated a cell type specific open chromatin atlas that revealed enhancer driven regulons and gene-regulatory networks. These were organized into co-regulated gene-programs that together defined sensory neuron diversity. Cell type complexity was found to be generated by layered co-regulated transcriptional modules representing shared functions across different scales of the neuronal type hierarchy with cell type specific contribution as the exception.

overall_design: Multiome seq: Single nuclei were extracted from wild-type male and female mice aged 8-10 weeks. Joint snRNA- and snATAC libraries were prepared using the 10X Genomics platform.

first: Doris

last: Krauter

first: Jussi

last: Kupari

first: Dmitry

last: Usoskin

first: Jie

last: Su

first: Yizhou

last: Hu

first: Ming-Dong

last: Zhang


title: BAF60/SWP73 Subunits Define Subclasses of SWI/SNF Chromatin Remodelling Complexes in Arabidopsis

city: Warszawa

first: Sebastian

middle: Przemyslaw

last: Sacharowski

state: mazowieckie

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics PAS

summary: Evolutionary conserved SWI-SNF ATP-dependent chromatin remodeling complex changes nucleosome positioning and chromatin states, affecting gene expression to regulate developmental and hormonal pathways.  We showed the SWP73A and SWP73B - subunits of the SWI/SNF complex - differentially regulate gene expression related to metabolism and hormone biosynthesis, with opposite chromatin occupancy profiles.  The swp73b mutant exhibits hypersensitivity to auxin and salicylic acid (SA). SWP73B inactivation results in SA accumulation, but decreased gibberellin (GA) content and long-term GA treatment partially restored its phenotype.  Both SWP73 subunits are required for maintaining proper diurnal metabolite profiles, with SWP73A regulating essential genes of raffinose and glucosinolate metabolism.  Our study reveals that the duplication of the SWP73 subunit contributes to novel functions of the Arabidopsis SWI/SNF complex in gene transcription.

overall_design: 1. signle-end RNA-seq for 10 libraries, 2 replicas for each genotype. The aim was comparison of transcriptomes of Col-0, swp73a/+, swp73a, swp73b and swp73a/+swp73b

first: Bruno

last: Huettel

first: Tomasz

middle: J

last: Sarnowski


title: Shared roles of immune and stromal cells in the pathogenesis of human bronchiolitis obliterans syndrome

city: Philadelphia

first: Patrick

middle: Watson

last: Mellors

state: Pennsylvania

address: 3400 Civic Center Drive SCTR 8th Floor

institute: University of Pennsylvania

summary: We performed single cell RNA sequencing using the 10X genomics platform on explanted human lungs from 4 CLAD-BOS patients, 3 cGVHD-BOS patients, and 3 deceased controls to identify cell types, genes, and pathways enriched in BOS to better understand disease mechanisms

overall_design:
We analyzed distal lung specimens from patients undergoing first lung transplant for cGVHD-BOS, second lung transplant for CLAD-BOS, and healthy controls (NC) using the 10X Genomics Chromium Controller platform with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1. Sequencing was performed on an Illumina Novaseq 6000 instrument. We compared T-cell, macrophage, epithelial, and stromal transcriptomes between 1) CLAD-BOS and NC 2) cGVHD-BOS and NC 3) CLAD-BOS and cGVHD-BOS

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

first: Mellors

last: Patrick

first: Nottingham

last: Ana

first: Casino Remondo

last: Bruno

first: Shestov

last: Maxim

first: Planer

last: Joseph

first: Peterson

last: Andrew

first: Ying

last: Yun

first: Zhou

first: Christie

last: Jason

first: Diamond

last: Joshua

first: Cantu

last: Edward

first: Basil

last: Maria

first: Gill

last: Saar


title: Scalable ultra-high-throughput single-cell chromatin and RNA sequencing reveals gene regulatory dynamics linking macrophage polarization to autoimmune disease [NIH-3T3_K562_ATAC_with_blocking]

first: Mikael

last: Marttinen

address: Meyerhofstraße 1

institute: EMBL

summary: Enhancers and transcription factors (TFs) are crucial in regulating cellular processes, including disease-associated cell states. Current technologies to study these elements in gene regulatory mechanisms lack multiplexing capability and scalability. Here, we present SUM-seq, a cost-effective, scalable Single-cell Ultra-high-throughput Multiomic sequencing method for co-assaying chromatin accessibility and gene expression in single nuclei - enabling experiments at the million cell and hundreds of samples scale. SUM-seq outperforms current high-throughput single cell methods in sensitivity. We applied SUM-seq to dissect the gene regulatory mechanisms governing macrophage polarization, and explored their link to traits from genome-wide association studies (GWAS). Our analyses confirmed known TFs orchestrating M1 and M2 macrophage programs, unveiled new regulators, and suggested extensive enhancer rewiring. Integration with GWAS data further pinpointed the impact of specific TFs on a set of immune traits. Notably, enhancers regulated by the STAT1/STAT2/IRF9 (ISGF3) complex were enriched for rheumatoid arthritis (RA)-associated genetic variants, with the strongest link pointing to the CD40 gene, an emerging drug target for RA. This highlights the potential of SUM-seq for dissecting molecular disease mechanisms. In summary, SUM-seq provides a simple workflow for cost-effective, scalable single-cell ultra-high-throughput multiomic sequencing. It is particularly adept at elucidating complex gene regulatory networks in cell differentiation, response to perturbations, and disease contexts.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: To optimise and evaluate performance and quality, we performed SUM-seq on an equal mixture of human leukemia (K562) and mouse fibroblast (NIH-3T3) cell lines

first: Sara

last: Lobato-Moreno

first: Umut

last: Yildiz

first: Annique

last: Claringbould

first: Nila

middle: H

last: Servas

first: Evi

last: Vlachou

first: Christian

last: Arnold

first: Hanke

middle: G

last: Bauersachs

first: Victor

last: Campos-Fornés

first: Karin

last: Prummel

first: Kyung

last: Noh

first: Judith

last: Zaugg


title: Scalable ultra-high-throughput single-cell chromatin and RNA sequencing reveals gene regulatory dynamics linking macrophage polarization to autoimmune disease [NIH-3T3_K562_RNA_with_blocking]


title: Three-dimensional cell-cell interactions promote direct reprogramming of patient fibroblasts into functional and transplantable neurons

city: Lund

first: Petter

last: Storm

state: Select...

address: Sölvegatan 19, BMC A11

institute: Lund University

summary: Direct reprogramming of somatic cells into induced neurons (iNs) has become an attractive strategy for the generation of patient-specific neurons for disease modeling and regenerative neuroscience. To this end, adult human dermal fibroblasts (hDFs) present one of the most relevant cell sources. However, iNs generated from adult hDFs using traditional two-dimensional (2D) cultures are difficult to maintain long-term in vitro and face challenges in survival upon transplantation into the adult brain. These limitations impose considerable constraints on the biomedical applications and translational potential of iN technology. Here, we present a platform for direct in vitro reprogramming of adult hDFs inside three-dimensional suspension microcultures (3D-iNs) that eliminates some of the major bottlenecks in the direct neuronal reprogramming field. We show that the 3D environment favors neuronal over fibroblast cellular identity to yield more robust conversion into functional neurons with extended culturing span. The 3D reprogramming approach also provides a platform for fusion of different neuronal populations into induced assembloids. Importantly, unlike conventional iNs, 3D-iNs can be gently harvested and transplanted into the adult rodent brain to reproducibly generate functionally integrated neuron-rich grafts. Due to its simplicity, versatility, and robustness, our approach could readily be adapted as a culturing platform used for a broad range of in vitro and in vivo studies to improve disease modeling, drug screening, and other biomedical applications.

first: Mette

last: Habekost

first: Janko

last: Kajtex


title: Scalable ultra-high-throughput single-cell chromatin and RNA sequencing reveals gene regulatory dynamics linking macrophage polarization to autoimmune disease.


title: Cell Cycle by Light Intensity in Chlamydomonas reinhardtii

city: Berkeley

first: Sean

middle: D.

last: Gallaher

state: California

address: 176 Stanley Hall, room 408

department: California Institute for Quantitative Biosciences

institute: UC Berkeley

summary: Photosynthetic organisms coordinate their metabolism and growth with diurnal light, which can range in intensity from limiting to inhibitory. To gain a comprehensive understanding of how diurnal regulatory circuits interface with sensing and response to various light intensities, we performed a systems analysis of synchronized Chlamydomonas reinhardtii populations acclimated to low, moderate, and high diurnal light. Transcriptomic and proteomic data revealed that Chlamydomonas’ rhythmic gene expression program is resilient to limiting and excess light. Although gene expression is dynamic over the diurnal cycle, Chlamydomonas populations acclimated to low and high diurnal light exhibit constitutive phenotypes with respect to photosystem abundance, thylakoid architecture, and non-photochemical quenching that persist through the night. This suggests that cells harbor a “memory” or anticipation of the daylight environment. The integrated data constitute an excellent resource for understanding gene regulatory mechanisms and photoprotection in eukaryotes under environmentally relevant conditions.

overall_design: Cells were grown photoautotrophically in turbidostat mode in photobioreactors under diel cycles of 12 h light (LL 50 PFD, ML 200 PFD, or HL 1000 PFD) at 28°C and 12 h dark at 18°C for a minimum of two weeks in order to establish population synchrony and acclimate the population to the respective diurnal light intensity. Samples were collected for RNA-seq at five timepoints over the diel cycle (-2, +2, +6, +10, -10). These data are accompanied by proteomics, lipidomics, and physiological measurements. The moderate light (ML) condition served as the control, as it exhibited the highest degree of synchrony and has been reported on previously (Strenkert et al. 2019, PNAS).

first: Sunnyjoy

last: Dupuis

first: Valle

last: Ojeda

first: Anne

last: Glaesener

first: Sabeeha

middle: S

last: Merchant


title: Scalable ultra-high-throughput single-cell chromatin and RNA sequencing reveals gene regulatory dynamics linking macrophage polarization to autoimmune disease [NIH-3T3_K562_ATAC_without_blocking]

first: Mikael

last: Marttinen

first: Sara

last: Lobato-Moreno

first: Umut

last: Yildiz

first: Annique

last: Claringbould

middle: M


title: RNA-seq analysis of HeLa cells infected with YK410, a recombinant strain of HSV-1

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: To analyze the relationship between the expression of viral late protein and mRNA in cells infected with HSV-1, HeLa cells were infected with YK410, a recombinant strain of HSV-1, and fractionated based on the fluorescence intensity of Venus-Us11. The expression of viral mRNA in each subpopulation was analyzed by RNA sequencing (RNA-seq).

overall_design: HeLa cells infected with YK410 were analyzed by flow cytometry and sorted into six subpopulations based on the fluorescence intensity of Venus-Us11. The total RNA prepared from each subpopulation was subjected to RNA-seq analysis.

first: Moeka

last: Nobe

first: Yuhei

last: Maruzuru

first: Yasushi

last: Kawaguchi


title: To evaluate the transcriptome of ES cells upon CRE expression.

status: Public on Apr 08 2025

first: Yuzhuo

last: Xu

address: 12 Xue-fu Road, Pukou District

institute: Nanjing University

summary: RNA-seq was conducted to examine the effects of CRE recombinase on mouse embryonic stem cells.

overall_design: mRNA profiles of WT and WT-CRE embryonic stem cells were generated by deep sequencing, in triplicate, using Illumina Novaseq6000.

first: Jinzhong

last: Qin


title: Antigen-specific B cells from inflamed lung and lung-draining lymph node

first: Frederik

middle: Richard

last: Heinrich

state: Berlin

address: Chariteplatz 1

department: Bioinformatics

summary: Germinal center (GC) like B cells can be generated in unstructured non-ectopic T and B cell infiltrates in the in inflamed lung. We used single cell RNA sequencing (scRNA-seq) for gene expression and B cell receptor (BCR) to compare antigen-specific B cells from lung to those from the lung-draining lymph node.

overall_design: Antigen-specific B cells from B1-8i and T cells from Smarta mice were adoptively transferred into C57BL/6 recipients, which were repeatedly challenged intranasally with cognate antigen and LPS. On day 17, cells from lung (enzymatically digested) and the tracheal lymph node (Ln) were isolated and further purified for antigen-specific total B cells or germinal center (like) B cells.

first: Andreas

last: Hutloff

first: Laura

last: Bauer

first: Sarah-Sophie

last: Schacht

first: Pawel

last: Durek

first: Mir-Farzin

last: Mashreghi


title: Intestinal secretory differentiation reflects niche-driven phenotypic and epigenetic plasticity of a common signal-responsive terminal cell [scRNA-Seq]

city: Boston

first: Ramesh

middle: A

last: Shivdasani

state: MA

address: 450Brookline Ave.

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary:
Enterocytes and four classic secretory cell types derive from intestinal epithelial stem cells. Based on morphology, location, and canonical markers, goblet and Paneth cells are considered distinct secretory types. Here, we report high overlap in their transcripts and sites of accessible chromatin, in marked contrast to those of their enteroendocrine or tuft cell siblings. Mouse and human goblet and Paneth cells express extraordinary fractions of few antimicrobial genes, which reflect specific responses to local niches. Wnt signaling retains some ATOH1+ secretory cells in crypt bottoms, where absence of BMP signaling potently induces Paneth features. Cells that migrate away from crypt bottoms encounter BMPs and thereby acquire goblet properties. These phenotypes and underlying accessible cis-elements interconvert in post-mitotic cells. Thus, goblet and Paneth properties represent alternative phenotypic manifestations of a common signal-responsive terminal cell type. These findings reveal exquisite niche-dependent cell plasticity and
cis-regulatory dynamics in likely response to antimicrobial needs.

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

first: Swarnabh

last: Bhattacharya


title: Intestinal secretory differentiation reflects niche-driven phenotypic and epigenetic plasticity of a common signal-responsive terminal cell [scATAC-Seq]

summary:
Enterocytes and four classic secretory cell types derive from intestinal epithelial stem cells. Based on morphology, location, and canonical markers, goblet and Paneth cells are considered distinct secretory types. Here, we report high overlap in their transcripts and sites of accessible chromatin, in marked contrast to those of their enteroendocrine or tuft cell siblings. Mouse and human goblet and Paneth cells express extraordinary fractions of few antimicrobial genes, which reflect specific responses to local niches. Wnt signaling retains some ATOH1+ secretory cells in crypt bottoms, where absence of BMP signaling potently induces Paneth features. Cells that migrate away from crypt bottoms encounter BMPs and thereby acquire goblet properties. These phenotypes and underlying accessible cis-elements interconvert in post-mitotic cells. Thus, goblet and Paneth properties represent alternative phenotypic manifestations of a common signal-responsive terminal cell type. These findings reveal exquisite niche-dependent cell plasticity and
cis-regulatory dynamics in likely response to antimicrobial needs

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


title: Intestinal secretory differentiation reflects niche-driven phenotypic and epigenetic plasticity of a common signal-responsive terminal cell [ATAC-Seq]

overall_design:
Mouse duodenal organoids were treated with DAPT for 3 days, then continued for additional 4 days with DAPT and with WnthiBMPlo or Wntlo BMPhi conditions  along with DAPT, and cells were collected for bulk ATAC-seq.
Lgr5 GFP+ ISC or villi enterocytes from VilCreER-T2;Apcfl/fl mice 3 weeks after tamoxifen induction IP (1mg/ml) were harvested for bulkATAC-seq.


title: Intestinal secretory differentiation reflects niche-driven phenotypic and epigenetic plasticity of a common signal-responsive terminal cell [RNA-Seq]

overall_design:
Duodenal villi TOM+ cells from Atoh1CreERT2/+; R26Tom mice were isolated by flow cytometry 36 h after tamoxifen injection IP to specifically enrich for goblet cells.
Duodenal crypt TOM+ cells from Atoh1CreERT2/+; R26Tom mice were isolated by flow cytometry 12 days after tamoxifen injection IP to specifically enrich for Paneth cells.
To investigate the regulation of secretory differentiation, we established Dox inducible ATOH1 primary human cell lines, and EPCAM+ cells were taken without Dox treatment or with Dox treatment for 48 h and with Dox + WnthiBMPlo treatment or with Dox +WntloBMPhi treatment for 48 h.


title: VAL1/HSI2 promotes Arabidopsis flowering by repressing the organ boundary genes BLADE ON PETIOLE 1 (BOP1) and BOP2

status: Public on Apr 09 2025

city: Cerdanyola del Vallès

first: Julia

middle: I.

last: Qüesta

state: Barcelona

address: Carrer de la Vall Moronta

institute: Centre for Research in Agricultural Genomics

summary: The transition to reproductive development is a critical step in the plant lifecycle that relies on the integration of intrinsic and environmental signals. Several different pathways have been described for the control of flowering time that function downstream of the perception of environmental cues such as day length (photoperiodic pathway) and seasonal temperature (vernalization and ambient temperature pathways). In addition, the phytohormone gibberellin (GA) induces the floral transition under non-inductive photoperiod. In the model plant Arabidopsis thaliana, the transcriptional repressor VAL1/HSI2 triggers the stable repression of the floral repressor FLOWERING LOCUS C (FLC) during vernalization. However, the involvement of VAL1 in other flowering pathways has remained unclear. In this work, we combined a genetic and transcriptomic approach to investigate the requirement of VAL1 for the activation of flowering at different day length conditions. We found that VAL1, and not its sister protein VAL2, is required to induce the floral transition both under long and short days. Specifically in short days, the delayed flowering time of val1 mutant plants can be fully bypassed by the exogenous application of GA. We have been able to demonstrate that VAL1 induction of flowering occurs via the direct epigenetic repression of the organ boundary genes BLADE ON PETIOLE 1 (BOP1) and BOP2. Our work thus expands the repertoire of VAL target genes and further demonstrates the pleiotropic role of VAL factors in the regulation of Arabidopsis development.

overall_design: RNA-seq from 6 weeks old shoot apic meristem in Arabidopsis thaliana plants growth at short day.

first: Yajiao

last: Cheng

first: Benjamin

last: Tremblay

first: Vicente

last: Balanzá

first: Alvaro

last: Larran

middle: I


title: Protein phosphatase PfPPM2 signaling and dephosphorylation of  Heterochromatin HP1 is critical for  asexual division and sexual differentiation of malaria parasite.

city: New delhi

first: Pushkar

last: Sharma

address: Aruna Asaf Ali marg

country: India

institute: National Institute of Immunology

summary: We demonstrate that Protein Phosphatase PfPPM2 regulates both asexual and sexual development of human malaria parasite P. falciparum.  It is involved in  the division of the parasite during asexual development and promotes its sexual differentiation. Phosphoproteomics studies revealed that PfPPM2 targets in the parasite include key regulators of protein translation and chromatin remodelling. We demonstrate that it regulates dephosphorylation of S33 of Heterochromatin Protein 1 (HP1), a regulator of heritable gene silencing and contributes to both mitotic proliferation as well as sexual differentiation of the parasite into sexual forms. Detailed investigations revealed that PfPPM2 mediated dephosphorylation of HP1 at S33 is a signal for parasite sexual conversion. HP1- S33 dephosphorylation impairs its interaction with trimethylated form of histone 3 (H3) at lysine 9 (H3K9me3), which is known to stabilize the heterochromatin. As a result, the expression of transcription of ap2g-which is repressed by HP1-H3K9me3-was stimulated resulting in sexual conversion of the parasite. Interestingly, the state of HP1-S33 phosphorylation seems to largely reflect the fate of the parasite-its optimal phosphorylation is important for asexual division whereas it is dephosphorylated form favours sexual differentiation. PfPPM2 also regulates protein synthesis in the parasite by repressing a signaling pathway involved in the phosphorylation of initiation factor eIF2α, which are likely to contribute to parasite division and possibly differentiation.

overall_design: PfPPM2-HA-glmS:Nf54 parasites were either left untreated or treated with GlcN (cycle 0, rings)  and parasite pellets were prepared (schizonts, cycle 1) and  RNAseq analysis was perform  to compare global changes in transcriptome of these parasites upon PfPPM2 depletion.