title: Mutual Antagonism Between PRC1 Condensates and SWI/SNF in Chromatin Regulation

city: Boston

first: Philipp

last: Schneider

state: Massachusetts

address: 185 Cambridge Street

institute: Massachusetts General Hospital

summary: Opposing activities of conserved chromatin regulatory complexes, such as the Polycomb Repressive Complex 1 (PRC1) and the activating chromatin remodeler SWI/SNF play critical roles in regulating gene expression. However, the mechanisms by which these complexes compete to regulate chromatin states remain poorly understood. Here, we demonstrate that the condensate-forming properties of PRC1 play an important role in excluding SWI/SNF from chromatin. Consistently, PRC1 compositions with a higher propensity for condensate formation are more effective in preventing SWI/SNF binding. Conversely, SWI/SNF-bound chromatin significantly reduces PRC1 binding and subsequent condensate formation. Notably, SWI/SNF can suppress PRC1 condensate formation in an ATP-hydrolysis independent manner, suggesting a mechanism driven by competitive binding and steric hindrance rather than active remodeling. Our findings reveal a mutual antagonism between PRC1 condensates and SWI/SNF chromatin remodeling, highlighting the importance of PRC1 composition and condensate formation in regulating gene repression.

overall_design: RNA-Seq and CUT&RUN experiments using antibodies: BAF155, EZH2, EED, H3K27ac, H3K27me3, IgG, PHC2, PHC3, RING1B, SMARCA1

first: Stefan

last: Niekamp

first: Sharon

last: Marr

first: Rebecca

last: Sanon

middle: C

first: Radhika

last: Subramanian

first: Robert

middle: E

last: Kingston


title: Bulk RNA-seq of mouse 4T1 cells with FGFR2 KO

status: Public on Mar 27 2026

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

type: Expression profiling by high throughput sequencing

summary: A key problem in cancer biology is understanding the phenotypic characteristics of the aggressive cell states present in macrometastases and their molecular underpinnings. Here we report on the cellular constituents of  breast cancer metastases,  revealing that these malignant cells display a gene-expression profile associated to embryonic development of tubular organs.

overall_design: Control or FGFR2 KO cells are cultured in 3D Collagen I gels and then harvested for RNA-seq

first: Robin

last: Caire

first: Giusy

last: Battilana

first: Francesca

last: Zanconato

first: Oriana

last: Romano

first: Michelangelo

last: Cordenonsi

first: Stefano

last: Piccolo


title: Bulk RNA-seq of mouse 4T1 cells with ETV4 KO [FGF]

overall_design: Control or ETV4 KO cells are cultured in 3D Collagen I gels, with 2% Serum and with or without FGF ligands, and then harvested for RNA-seq


title: Bulk RNA-seq of human MDA cells with ETV4 KO

overall_design: Control or ETV1/4/5 KO cells are cultured in 3D Collagen I gels and then harvested for RNA-seq


title: IL-36γ Armored CAR T Cells Reprogram Neutrophils to Induce Endogenous Antitumor Immunity

city: Buffalo

first: Mark

middle: D

last: Long

state: NY

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

country: USA

institute: Roswell Park Comprehensive Cancer Center

summary: Chimeric antigen receptor (CAR) T cells are ineffective against solid tumors due to obstacles of antigen heterogeneity and the immunosuppressive tumor microenvironment (TME). Previous efforts focused on enhancing cytotoxicity and persistence of CAR T cells, while the feasibility of improving their therapeutic efficacy by leveraging the modulatory effects of CAR T cells on host anti-tumor immunity remains unclear. Here, we report that IL-36γ armored CAR T cells eradicated primary solid tumors and enabled rejection of rechallenged antigen-negative tumors. IL-36γ armored CAR T cells favorably modulated the TME and reprogrammed unique neutrophil subsets with tumoricidal ability and antigen-(cross)presenting functions, resulting in the induction of endogenous T cells recognizing tumor antigens beyond CAR-targeted antigens. Our study demonstrates that neutrophil engagement by CAR T cells is a critical step in the establishment of the cancer-immunity cycle and introduces a broadly applicable method to overcome key barriers to adoptive cell therapies for solid tumors.

overall_design: Spleens were collected from CAR T cell–treated, SCLC tumor-bearing mice, endogenous T cells were purified using the Stemcell T cell isolation kit, and the resulting cells were profiled by TCR-seq (Takara).

first: Yihan

last: Zuo

first: Renier

last: Brentjens


title: Alterations in chromatin architecture promote totipotent-like features in a DUX-dependent manner [CUT&Run]

city: Bethesda

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

institute: NIH/NCI

type: Genome binding/occupancy profiling by high throughput sequencing

summary: 2-cell like cells (2CLC) are a transiently cycling population of cells with totipotent-associated features. Interestingly, CTCF depletion leads to 2CLC conversion in mouse ESC. However, the mechanism underlying this reprogramming or whether totipotent-like conversion depends on chromatin structural alterations or to CTCF-specific effects is unclear. We demonstrate that 2CLC conversion mediated by CTCF loss depends on the transcription factor DUX and correlates with nucleolar integrity. We show that depletion of the cohesin release factor WAPL in ESC also promotes 2CLC reprogramming which is increased by CTCF co-depletion. Single-cell RNAseq/ATACseq analyses in CTCF/WAPL-depleted ESC revealed that chromatin accessibility precedes 2C-associated gene expression. Finally, although distinct transcriptional changes were associated to WAPL or CTCF depletion in human ESC, we did not detect any similarity in their transcriptome with those of early stages of human embryo development suggesting a lack of conservation. Our work revealed an intertwined link between higher-order chromatin organization and totipotency in mice.

overall_design: Cut&Run from human ESC control and ESC-CTCF-FKBP treated with dTAG for 0 and 24 hours.

first: Sergio

last: Ruiz

first: Maria

last: Vega-Sendino

first: Grace I

last: Carey


title: Directed evolution of a genetically encoded photocatalyst for temporally resolved proximity labeling of subcellular RNAs and proteins

city: Beijing

first: Yuxin

last: Fang

state: Beijing

address: Yiheyuan Road No.5

country: China

institute: Peking University

summary: In eukaryotic cells, the precise spatial localization of RNAs and proteins is essential for proper cellular function. Genetically encoded photocatalytic proximity labeling techniques have expanded our ability to map subcellular proteomes and transcriptomes, but their temporal resolution remains limited. Here, we introduce Lantern, an engineered flavoprotein optimized via directed evolution, which enables sub‑minute, spatially resolved labeling of cellular biomolecules. Lantern is targetable to diverse subcellular compartments, including the endoplasmic reticulum, mitochondria, and stress granules (SGs), to map local transcriptomes (CAP-seq) and proteomes (CAP-MS). Using Lantern, we observed that m6A‑enriched RNAs are recruited to SGs within five minutes of stress induction, while ER‑proximal RNAs associate with the SG scaffold protein G3BP1 during early SG assembly. Additionally, Lantern was adapted for cell-surface tagging (CAP-CELL), enabling spatially resolved cell typing and the analysis of cell-cell interactions. Collectively, this study establishes Lantern as a powerful tool that offers unprecedented temporal resolution for investigating the dynamic organization of subcellular molecular networks.

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: RNA-seq profiling of the endoplasmic reticulum membrane (ERM)-proximal transcriptome, outmer mitochondrial membrane (OMM)-proximal transcriptome and G3BP1-proximal transcriptome in HEK293T cells. RNA-seq profiling of the G3BP1-proximal transcriptome in rat cortical neurons. And RNA-seq profiling of migrating MC38 cells.

first: Ziqi

last: Ren

first: Fu

last: Zheng

first: Ruixiang

last: Wang

first: Songrui

last: Zhao

first: Wentao

first: Peng

last: Zou


title: Systemic toxicity in hepatic Propionyl-CoA Carboxylase deficiency

city: Baltimore

first: Michael

middle: J.

last: Wolfgang

address: 855 N Wolfe Street

department: Institute for Basic Biomedical Sciences

institute: The Johns Hopkins University School of Medicine

summary: Inborn errors in Propionyl-CoA Carboxylase (Pcca/b) cause life threatening propionic acidemia.  To understand the contribution of mitochondrial propionyl-CoA metabolism to cellular and systemic metabolic dysfunction, we generated inducible and tissue-specific knockout (KO) mouse models of Pcca. Adult inducible loss of Pcca results in acute metabolic decompensation resembling the inborn error. The liver-specific loss of Pcca largely recapitulates this in a sexually dimorphic manner. Propionate and pyruvate converge in the TCA cycle as major anaplerotic substrates. Paradoxically, the simultaneous KO of Pyruvate Carboxylase (Pcx) rescues the lethality of liver-specific Pcca KO male mice. Most metabolites suspected as deleterious in propionic acidemia are exacerbated in Pcca;Pcx double KO mice with the noted exception of methylcitrate suggesting the centrality of this metabolite to systemic toxicity. These data clarify relevant toxic biomarkers and suggest that rebalancing hepatic TCA cycle metabolism as critical to mitigate the adverse effects of alternative propionyl-CoA metabolism.

overall_design: To determine the effects of Propionyl-CoA Carboxylase A (Pcca) deficiency in various tissues. RNAseq was performed on livers of 9-week-old male mice of the following genotypes: controls with floxed Pcca alleles injected with AAV8-TBG-eGFP, gut-specific Pcca knockouts (Villin-Cre), induced full-body Pcca knockouts (ERT2-Cre) treated with tamoxifen, liver-specific Pcca knockouts (AAV8-TBG-iCre), liver-specific double knockouts for Pcca and Pyruvate Carboxylase (Pcx) (AAV8-TBG-iCre) and holocarboxylase synthetase (HLCS) floxed mice (AAV8-TBG-iCre). Following a 4-hour fast in the light cycle, livers were collected, flash frozen, and sent for RNA-sequencing by Novogene Corporation Inc.

first: Jasmine

middle: L

last: Encarnacion

middle: J


title: Alterations in chromatin architecture promote totipotent-like features in a DUX-dependent manner [ATAC-Seq]

overall_design: ATACseq data from mouse ESC control and ESC-CTCF/WAPL-AID treated with IAA for 0 and 48hour or 0, 6, 12, 24 and 48 hours, respectively.


title: Membrane insertion of mitochondrial-encoded proteins regulates ribosome decoding speed

city: Göttingen

first: Peter

last: Rehling

address: Humboldtallee

department: Cellular Biochmeistry

country: Germany

institute: University medical center Göttingen

summary: The human mitochondrial genome encodes thirteen subunits of the oxidative phosphorylation system essential for energy metabolism to drive cellular activities. Translation of eleven mRNAs by membrane-bound ribosomes is coupled to insertion of the nascent polypeptides into the inner membrane aided by the OXA1L insertase. To this end, the mechanism of membrane insertion of nascent polypeptides and the functional link to the translation process are not understood. Here we applied ribosome profiling to assess translation dynamics in combination with cryo-EM analyses of a COX1 ribosome nascent chain complex to visualize co-translational folding of the nascent chain. We find that the membrane topology of the translation product impacts translation speed and that positioning of amphipathic helices in the ribosome vestibule induces structural changes, correlating with translation stalling events. Thus, our findings reveal a tight link between translation process and folding and membrane insertion of nascent polypeptides at the inner mitochondrial membrane.

overall_design: Ribosome profiling and Cryo-EM analysis of human mitochondrial co-translational insertion machinery

first: Thomas

last: Schöndorf

first: Valentyn

last: Petrychenko

first: Ilgin

last: Kotan

first: Luis Daniel

last: Cruz-Zaragoza

first: Drishan

last: Dahal

first: Cong

first: Tanja

last: Gal

first: Sven

last: Dennerlein

first: Günter

last: Kramer

first: Niels

last: Fischer


title: Evolutionary transcriptomic and cellular specializations within the mammalian striatum

city: Dallas

first: Jane

last: Johnson

state: Texas

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: University of Texas Southwestern Medical Center

summary: In this study we generated and analyzed single-nucleus RNA sequencing (snRNA-seq) of human, chimpanzee, rhesus macaque (this study and GSE167920), marmoset (GSE151761 and GSE165578), bat caudate (CN) and putamen (Pu) separately, ferret caudate (GSE151761), and mouse caudoputamen (C-Pu)(GSE151761) spanning 94 million years of evolution. We identified novel interneuron cell types in bat Pu while uncovering fundamental cellular compositional and transcriptomic differences between primate and non-primate striata.

sample_organism:
Macaca mulatta
Pan troglodytes
Homo sapiens
Phyllostomus discolor

overall_design: Generated single nuclear RNA profiles of human, chimpanzee, rhesus macaque, and bat striatal regions, caudate nucleus and putamen.

first: Gozde

last: Buyukkahraman

first: Emre

last: Caglayan

first: Yaqiang

last: Zhang

first: Stephen

last: Hoerpel

first: Carlos

last: Orozco

first: Amber

last: Main

first: Chet

last: Sherwood

first: William

last: Hopkins

first: Todd

last: Roberts

first: Sonja

last: Vernes

first: Genevieve

last: Konopka


title: A rewired myeloid niche in spleen establishes stress erythropoiesis

city: Hangzhou

first: Ting

last: Zhou

state: Zhejiang

address: No. 600 Dunyu Road, Xihu District

department: Immunology and Microbiology

institute: Westlake University

summary: The bone marrow is responsible for steady-state erythropoiesis. However, during emergencies, the erythropoietic function can shift to the spleen. It remains unclear how the spleen, which typically performs erythrocyte recycling, can rapidly switch to become a site for erythropoiesis in stress states. We utilized single-cell sequencing and spatial transcriptomic sequencing to compare changes in myeloid and erythroid cells in the bone marrow and spleen, thereby elucidating the key components of the extramedullary erythropoietic niche. We discovered that inflammation can rewire pre-existing macrophages in the spleen, establishing a novel myeloid microenvironment essential for extramedullary erythropoiesis.

overall_design: For single-cell sequencing of the erythroid lineage cells, spleen and bone marrow samples were collected from mice on day 3 and 5 post IL-18m treatment and PBS-treated controls. To minimize data variation due to individual differences, each sample group consisted of a mixture of three mice. For myeloid cells sequencing, spleen and bone marrow samples were collected and pooled from mice on day 1 post IL-18m treatment and PBS-treated control. Myeloid cells from the spleen and bone marrow were FACS sorted separately and then combined back to their original proportions. Samples from different tissues were labeled separately with BD single-cell multiplex sample tags and subsequently mixed together.


title: Nuclear-specific reductive carboxylation of alpha-ketoglutarate fuels histone acetylation to induce FOXA1-dependent gene activation [MB-231 ATAC]

first: Mark

last: Long

summary: Mitochondria remain at the core of cell metabolism, whereas the nucleus integrates cellular and environmental signals to activate genes. However, the mechanisms that directly link cellular metabolism to gene regulation are not well understood. In this work, we focused on deciphering metabolic pathways in the nucleus that control acetylation of histone proteins, and identified a moonlighting mechanism that directs local abundance of acetyl-CoA pool by nuclear localization of mitochondrial enzymes, aconitase (ACO2), and isocitrate dehydrogenase (IDH2). Metabolic tracing studies in the isolated nucleus identified reductive carboxylation of α-ketoglutarate catalyzed by IDH2 and ACO2 rapidly synthesize citrate to increase the acetyl-CoA pool. Genetic and proteomic analyses revealed nuclear IDH2 and ACO2, form a complex with KAT2A for histone acetylation, which increased chromatin accessibility and recruited pioneering factor FOXA1 to activate proliferative gene MKI67. In multiple mouse models of cancer, increased nuclear expression of ACO2 and IDH2 was sufficient to develop aggressive tumors indicating the tumorigenic potential of IDH2-ACO2-KAT2A axis. Altogether, our work revealed a paradigm coupling a nuclear metabolic pathway with histone acetylation to control of gene expression that accentuates hyperproliferative phenotype in tumors.

overall_design: Human breast cancer cells (MDA-MB-231) with or without shACO2 or shACO2-MTS-NLS were profiled by ATAC-seq

first: Abhisha

last: Sawant Dessai

first: Subhamoy

last: Dasgupta


title: Nuclear-specific reductive carboxylation of alpha-ketoglutarate fuels histone acetylation to induce FOXA1-dependent gene activation [C42_ATAC]

overall_design: Human prostate  cancer cells (LNCaP-C4-2) with or without ACO2-KO were profiled by ATAC-seq


title: Chromatin-associated lncRNA-splicing factor condensates regulate hypoxia responsive RNA processing of genes pre-positioned near nuclear speckles [RNA-seq]

city: Urbana

first: Prasanth

last: Kannanganattu

state: IL

address: 601 S Goodwin Ave

department: Cell and Developmental Biology

institute: University of Illinois at Urbana-Champaign

summary: Hypoxia-induced alternative splicing (AS) controls tumor progression and metastasis. The underlying mechanism specifying hypoxia-responsive AS needs to be determined. We demonstrate the role of nuclear speckle (speckle) nuclear domain (ND) and the long noncoding RNA, MALAT1, in hypoxia-responsive AS. Hypoxia-responsive genes position near speckles, the NDs that enhance splicing efficiency, and their differentially spliced exons harbor features that are characteristic of inefficiently spliced transcripts. Speckle-resident MALAT1, induced in response to hypoxia, boosts hypoxia-responsive AS by regulating the binding of SR-family splicing factor1 (SRSF1) to pre-mRNAs of speckle-associated genes. Mechanistically, MALAT1 facilitates the recruitment of SRSF1 to elongating RNA pol II (RNAP II) by promoting the formation of phase-separated SRSF1 condensates that are preferentially recognized and recruited to pre-mRNA by RNAP II. Our results reveal that MALAT1 boosts hypoxia-induced AS of speckle-associated genes by establishing the threshold concentration of SRSF1 as condensates, thereby promoting RNAP II-mediated recruitment of SRSF1 to pre-mRNAs.

overall_design: MCF7 and HEK293T cells were cultured at 37 degrees Celsius with 5% carbon dioxide and then grown in normoxic or hypoxic (0.2% oxygen) conditions for 24 hours before collection. Knockdown of MALAT1 was done by ASO and knockdown of SRSF1 was done by shRNA. RNA was extracted using Trizol and cleaned up using Qiagen RNeasy column.

first: You

last: Song

first: Min

middle: K

last: Shinn

first: Sushant

last: Bangru

first: Yu

last: Wang

first: Qinyu

last: Sun

last: Hao

first: Pankaj

last: Chaturvedi

first: Susan

middle: M

last: Freier

first: Pablo

last: Perez-Pinera

first: Erik

middle: R

last: Nelson

first: Andrew

middle: S

last: Belmont

first: Mitchell

last: Guttman

first: Supriya

middle: G

last: Prasanth

first: Auinash

last: Kalsotra

first: Rohit

middle: V

last: Pappu

first: Kannanganattu


title: Histone deacetylase enzyme activity is not the universal anti-cancer target of HDAC inhibitors [RNA-seq_MC38]

city: Houston

first: Chaitra

last: Rai

state: TX

address: ABBR 631C, 1 BAYLOR PLAZA

institute: Baylor College of Medicine

summary: As a family of anti-cancer drugs, histone deacetylase inhibitors (HDIs) show efficacies against a wide range of cancers, but their mechanism of action is unclear. Here, we performed unbiased bioinformatics analysis and found that genetic variants or expression levels of HDACs do not correlate with the carcinogenesis of most cancer types and do not predict cancer patient survival. Whole-genome CRISPR library screens did not identify HDACs as genes affecting cellular responses to HDIs such as SAHA or MS-275. Overexpression of dominant-negative, catalytically inactive Class I HDACs (HDAC1, 2, 3, and 8) caused a similar degree of histone hyperacetylation as Class I-specific HDI FK228 in cancer cell lines without similar anti-cancer effects, transcriptomic changes, or cellular responses to FK228. The anti-cancer effects of FK228 can be further dissociated from the histone hyperacetylation in an in-situ liver cancer mouse model. Importantly, chemical manipulations of several pan-HDIs abolished HDAC-inhibiting activity but retained the majority of anti-cancer effects in a mouse xenograft cancer model. These results suggest that HDAC enzyme activity is not a universal de facto target of HDIs for their anti-cancer efficacy. These findings have profound implications for understanding the pharmacodynamics of HDIs and developing next-generation compounds for this promising family of anti-cancer drugs.

overall_design: To investigate the anti-cancer effect of SAHA and SAA on MC38 mouse Xenograft model. The study has three groups control, SAHA and SAA. We performed gene expression profiling analysis using the data obtained from RNA-seq of four different groups.


title: Human ChIP-seq of three metastatic Patient-Derived-Organoid (PDO)

first: Silvio

last: Bicciato

summary: A key problem in cancer biology is understanding the phenotypic characteristics of the aggressive cell states present in macrometastases and their molecular underpinnings. Here we report on the cellular constituents of human breast cancer metastases,  revealing that these malignant cells are invariably locked in a chimeric cell state. Human BC metastatic cells indeed display a gene-expression profile associated to embryonic development of tubular organs, while also retaining the transcriptional features of their original adult mammary luminal lineage.

overall_design: Brain metastatic samples were obtained from Istituto Nazionale dei Tumori, Milan, and Istituto Neurologico “Carlo Besta”, Milan, respectively, following ethical approval from their Institutional Review Boards and acquisition of informed consent from all patients. ChIP-seq for five histone modifications was performed on Patient-Derived-Organoid (PDO), derived starting from these samples.

first: Lorenzo

last: Drufuca

first: Michaela

last: Fakiola

first: Massimiliano

last: Pagani

first: Michelangelo

last: Cordenonsi

first: Stefano

last: Piccolo


title: The potent biodegrading actinomycete Rhodococcus opacus 1CP: Relating aromatic compound metabolism with whole-genome and transcriptome data

city: Bielefeld

first: Christian

last: Ruckert-Reed

address: Sequenz 1

department: Medical School OWL

institute: Bielefeld University

summary: The genus Rhodococcus comprises numerous strains recognized for pollutant degradation, secondary metabolite production including biosurfactant, lignin breakdown, or utilization of volatile organic compounds. Often gene redundancies and evolution of alternative pathways are attributed to such characteristics. Rhodococcus opacus 1CP initially isolated as a chlorophenol degrading strain was found to be a model organism comprising several such features. In this study, we analyzed the genome and transcriptome and demonstrated that the strain 1CP undergo three different routes of ortho, meta, and side chain attack in degrading aromatic compounds. The wild type strain, single or double knock-out mutant of phenol hydroxylases, well compensated the loss and chooses the classical ortho-route to attack substituted phenols, while the triple knock-out mutant takes the meta-pathway to act on p-cresol indicating that this pathway serves as a reserve in strain 1CP. Growth of 1CP in phenol, p-cresol and styrene induces several gene clusters that are associated in lignin metabolization. Catechol, protocatechuate, and phenylacetic acid are major key intermediates that are funneled into central pathways which enable the strain 1CP to degrade acetophenone, benzoate, phenol, 2-phenylethanol, and styrene. Strain 1CP has an alternative option with the modified ortho-cleavage pathway which enables it to degrade 2-chlorophenol. Interestingly, in almost all cases, redundant genes were identified, but only in minor cases as phenol hydroxylases, they were found to be active and simultaneously involved in metabolic activities. The transcriptome and kinetic data showed that the redundant styrene-oxide isomerase is upregulated and involved in styrene degradation.

overall_design: Whole transcriptomes of Rhodococcus opacus 1CP grown on 2mM of different carbon sources (tetradecane, phenol, styrol, and p-cresol) using 4 biological replicates each, pooled in the case of tetradecane.

first: Selvapravin

last: Kumaran

first: Thomas

last: Heine

first: Janosch

middle: A

last: Gröning

first: Tobias

last: Busche

first: Jörn

last: Kalinowski

last: Rückert-Reed

first: Michael

last: Schlömann

first: Dirk

last: Tischler


title: Age-related gene expression alteration responding to mechanical force and TGFβ signaling [ATAC-seq]

city: Villigen

last: Shivashankar

state: Aargau

address: Forschungsstrasse 111

department: LNB

country: Switzerland

institute: Paul Scherrer Institute

summary: The aging process significantly alters the biomechanical properties of fibroblasts, impacting their cytoskeletal and chromatin organization. These changes are pivotal in modulating cellular responses to mechanical and biochemical stimuli. This study investigates the hypothesis that aging leads to fibroblasts’ divergent adaptation mechanisms to external stimuli. Herein, fibroblasts from young and old cohorts were embedded in 3D collagen gels and subjected to tension and Transforming Growth Factor beta (TGFb) stimulation. The study revealed that mechanical forces and aging exert profound effects on chromatin architecture. Young cells adapted more rapidly to mechanical stress and showed a heightened responsiveness to TGFβ compared to older cells. The identification of key transcription factors implicated in age-dependent responses was further examined, assessing their potential in cellular rejuvenation.

overall_design: ATAC-seq profiling of primary dermal fibroblasts from two age groups (old: 75 years old; young: 10 years old) seeded in 3D collagen gel exposed to tension force and TGFβ stimulation

first: Yawen

last: Liao

first: Luezhen

last: Yuan

first: Trinadha

last: Sornapudi

first: G


title: Single-cell fixed RNAseq of liver fibrosis progression and regression

city: Osaka

first: Thuy

middle: Thi Thanh

last: Le

state: Osaka

address: 1-4-3 Asahimachi, Abeno-ku

department: Department of Global Education and Medical Sciences

country: Japan

institute: Osaka Metropolitan University Graduate School of Medicine

summary: Liver fibrosis regression is a dynamic process involving a variety of hepatic and immune cell populations. Using single-cell fixed RNA profiling (FLEX) on mouse livers from control, TAA-induced cirrhotic, and regression phases, we analyzed 38,136 cells across 10 major cell types. Regression was characterized by the emergence of pericentral hepatocytes enriched in detoxification and antioxidant genes (e.g., Cyp2e1, Txn1), which secreted RARRES2 to modulate hepatic stellate cells (HSCs). Recovered liver sinusoidal endothelial cells (LSECs) expressed scar-resolving genes (Mmp14, Ctsl) and restored fenestrae structure. Kupffer cells regained anti-inflammatory phenotypes, while SEMA4D, produced by monocyte-derived macrophages, activated HSCs; blockade of SEMA4D reduced fibrosis in vivo. Fibrogenic cholangiocyte subsets and LMCD1⁺ HSCs were diminished during regression, with LMCD1 identified as a novel marker of HSC activation. Additionally, NK/T cells, B cells, and neutrophils displayed recovery-associated transcriptional signatures. This single-cell atlas uncovers key transcriptional programs and intercellular interactions driving fibrosis resolution and highlights potential therapeutic targets for chronic liver disease.

overall_design: Advanced fibrosis liver disease was induced by TAA treatment in mice for 10 weeks. For liver fibrosis recovery, mice were recovered for additional two weeks without TAA treatment.

first: Duc

last: Pham

middle: T

first: Norifumi

last: Kawada


title: Bulk RNA-seq of mouse metastatic Breast Cancer cells

first: Silvio

last: Bicciato

overall_design: Control or ETV4 KO cells are cultured as 2D monlayers or in 3D Collagen I gels and then harvested for RNA-seq

first: Robin

last: Caire

first: Giusy

last: Battilana

first: Francesca

last: Zanconato

first: Oriana

last: Romano

first: Michelangelo

last: Cordenonsi

last: Piccolo


title: Single-cell RNA sequencing identifies a unique population of macrophages in the Aristolochic acid I (AAI)-induced AKI-to-CKD transition murine model

city: Shanghai

first: Xiangchen

last: Gu

address: 110 Ganhe Rd, Hongkou  Distrcit

department: Department of Nephrology

institute: Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine

summary: Acute Kidney Injury (AKI) often progresses to Chronic Kidney Disease (CKD), resulting in significant morbidity and mortality. The transition from AKI to CKD is driven by complex cellular mechanisms that are not yet fully understood. In this study, we used an Aristolochic Acid I (AAI)-induced murine model to investigate these mechanisms, performing single-cell RNA sequencing (scRNA-seq) to comprehensively profile kidney immune cells during the AKI to CKD transition. Our analysis revealed significant changes in immune cell populations, particularly macrophages and T lymphocytes. We identified a novel subpopulation of macrophages characterized by the expression of Ctsk, Mmp9, and Acp5, which emerged during the CKD phase. These macrophages were found to interact with T cells, injured proximal tubules, and fibroblasts, suggesting their involvement in chronic inflammation and fibrosis. Targeting this specific macrophage subpopulation may represent a potential therapeutic approach to prevent CKD progression. Additionally, T lymphocytes underwent a transition from effector to exhausted phenotypes, indicating chronic immune activation and sustained inflammation in CKD. Our findings provide new insights into the immune landscape of kidney injury and highlight potential targets for therapeutic intervention in preventing the progression from AKI to CKD.

overall_design: Male C57BL/6 mice, aged 8 to 10 weeks, were used in this study; acute kidney injury (AKI) was induced by intraperitoneal injections of aristolochic acid I (AAI) at a dose of 3 mg/kg administered every three days over a two-week period, followed by a two-week cessation to allow for chronic kidney disease (CKD) development; control mice received equivalent volumes of vehicle solution; all animal procedures were approved by the Institutional Animal Care and Use Committee (IACUC) and conducted following institutional guidelines. The sample sizes were as follows: control group (n=1), AKI phase (n=2), CKD phase (n=2).

first: Chenxi

last: Wang

first: Lin

last: Xie

first: Yaodong

first: Min

last: Chen


title: Transcriptome of napM-deleted strain in Mycobacterium smegmatis mc2 155

city: Wrocław

first: Kornel

last: Milcarz

address: Fryderyka Joliot-curie 14a

department: Faculty of Biotechnology

country: Poland

institute: University of Wrocław

summary: RNA-Seq results for M. smegmatis wild type and napM-deleted strain, deprived of one of the nucleoid-associated proteins - NapM.

overall_design: Three replicates of wild type and napM deleted strains of M. smegmatis mc2 155 were grown in 7H9 + 10%ADC + 0,05% Tween 80 medium in 37 degrees, to logarythmic phase.


title: Spatially organizing million callus cells identify the core-network enable tomato shoot regeneration [RNA-Seq]

city: weifang

first: yongqi

last: liu

state: shandong

address: 699 Binhu Road, Xiashan District

institute: Peking University Institute of Advanced Agricultural Sciences

summary: Plants can regenerate entire organs from somatic cells, offering a powerful system to uncover fundamental principles of cellular reprogramming and self-organization. Unlike animals, depending on pre-existing stem cell niches, plants re-establish pluripotency de novo. Although current understanding emphasizes hormonal control and external environmental cues, a unifying framework that explains how millions of cells coordinate fate decisions across space and time remains elusive. Here, we construct a million-cell spatial transcriptomic atlas of plant regeneration, achieving mesoscale resolution observation for all stages of tomato callus development. This atlas reveals a tripartite stem cell niche architecture: an outer signaling layer, intermediate plastic zone, and a quiescent core, features reminiscent of animal regenerative niches. We uncover a fundamental Inducer-Maintainer-Trigger (IMT) triad model, wherein PI-2 (Inducer) establishes a stem cell activating microenvironment, DCL2/22-nt siRNAs (Maintainer) safeguard pluripotency through post-transcriptional regulation, and EPFL8 (Trigger) initiates stem cell niche establishment. This triad model unifies niche signaling, small RNA-mediated plasticity, and metabolic-state-dependent activation, drawing parallels between plant and animal regeneration. Beyond resolving key questions in plant biology, our findings highlight deep evolutionary convergence in regenerative logic across multicellular life, offering new blueprints for engineering regeneration in synthetic biology, crop science, and tissue engineering.

overall_design: This study utilized HCT116 human colon cancer cells and HepG2 human hepatocellular carcinoma cells. Treatments included IL-6 (50 ng/mL), TNF-α (100 ng/mL), IL-10 (50 ng/mL), Torin1 (1 μM), and negative control (NC), with exposure durations of 3h and 6h. For Torin1, an additional group (3h treatment followed by 3h recovery in drug-free medium) was included. Each condition had 3 biological replicates, totaling 60 RNA samples. RNA was extracted for bulk transcriptome sequencing (Jinshan) and qPCR validation (Yani, Shanshan), focusing on expression changes of TIMP1/2, MMPs, and EGF.

first: Shaoman

last: Zhang

first: Xiehai

last: Song

first: Zhiliang

last: Yue

first: Yongqi

last: Liu


title: Molecular characterisation of the metastatic cell state in Breast Cancer

first: Silvio

last: Bicciato

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Mo90Ce10 exhibits anti-inflammatory properties by attenuating the type 1 IFN response in keratinocytes

first: Lian

last: Cui

state: China

address: 1278 Baode Road

institute: Shanghai Skin Disease Hospital

summary: We performed RNA-seq analysis on HaCaT cells (an immortalized human keratinocyte cell line) under both non-inflammatory and inflammatory conditions (stimulated with 50ng/mL TNF-α), with or without treatment using Mo90Ce10. The principal objective of this study was to elucidate the molecular mechanisms governing the influence of Mo90Ce10 on keratinocytes.

overall_design: HaCaT cells were pre-treated with Mo90Ce10 for 18 hours prior to exposure to either TNF-α or phosphate-buffered solution (PBS) for 6 hours. Each experimental condition was replicated three times to ensure consistency.

first: Hengli

last: Lu

first: Jiangluyi

last: Cai

first: Ying

last: Li

first: Yuling

last: Shi


title: A molecular atlas of brain neurovascular interactions reveals a spatiotemporal requirement of TGFβ signaling in brain angiogenesis

city: Montréal

first: Gael

middle: Louis Max

last: Cagnone

state: QC

address: 3175 Chemin de la Côte-Sainte-Catherine

department: The Montreal single-cell Academy

country: Canada

institute: CHU Sainte Justine


title: Alterations in chromatin architecture promote totipotent-like features in a DUX-dependent manner [RNA-Seq]

first: Desiree

last: Tillo

summary: 2-cell like cells (2CLC) are a transiently cycling population of cells with totipotent-associated features. Interestingly, CTCF depletion leads to 2CLC conversion in mouse ESC. However, the mechanism underlying this reprogramming or whether totipotent-like conversion depends on chromatin structural alterations or to CTCF-specific effects is unclear. We demonstrate that 2CLC conversion mediated by CTCF loss depends on the transcription factor DUX and correlates with nucleolar integrity. We show that depletion of the cohesin release factor WAPL in ESC also promotes 2CLC reprogramming which is increased by CTCF co-depletion. Single-cell RNAseq/ATACseq analyses in CTCF/WAPL-depleted ESC revealed that chromatin accessibility precedes 2C-associated gene expression. Finally, although distinct transcriptional changes were associated to WAPL or CTCF depletion in human ESC, we did not detect any similarity in their transcriptome with those of early stages of human embryo development suggesting a lack of conservation. Our work revealed an intertwined link between higher-order chromatin organization and totipotency in mice.

overall_design: RNAseq from human ESC control, ESC-CTCF-FKBP and ESC-WAPL-FKBP treated with dTAG for 24 and 48 hours or 24 and 72 hours, respectively. RNAseq from mouse ESC-WAPL/CTCF-AID cells containing a DOX inducible cassette expressing ARID3A.

first: Sergio

last: Ruiz

first: Maria

last: Vega-Sendino

first: Grace I

last: Carey


title: A molecular atlas of brain neurovascular interactions reveals a spatiotemporal requirement of TGFβ signaling in brain angiogenesis [scRNA-seq]

summary: Neurovascular interactions (NVIs) are critical in establishing vascular patterning, barrier function, and in regulating cerebral blood flow, thereby maintaining neuronal homeostasis and brain health. While developmental programs and neuronal activity play a central role in cerebral cortex angiogenesis during a critical postnatal period, whether cellular heterogeneity causes region-specific angiogenic regulation remains unknown. Here, we combine spatial and endothelial single-cell RNAseq (scRNAseq) transcriptomic analysis to establish a molecular atlas of developing brain regions and a comprehensive list of spatiotemporal-specific NVIs. We find that the thalamic area has a higher vascular density than the other brain regions and our atlas identifies transforming growth factor β (Tgfβ) and Vegfc ligands enrichment in this area during a critical postnatal period. Neonatal endothelial Tgfβr1 deletion (Tgfβr1iEKO) induces vascular malformations and hemorrhages, primarily in the thalamic area. Mechanistically, we show that loss of endothelial TGFβ signaling increases VEGFC-induced AKT/mTOR signaling in vitro and in vivo, and that mTOR inhibitor Rapamycin efficiently inhibits intracerebral bleeding and vascular defects in Tgfβr1iEKO mice. Altogether, our data suggest that spatiotemporal-specific NVIs control brain vascular heterogeneity, which extends our knowledge of region-specific cerebrovascular development and will benefit our understanding of neurovascular disorders.

overall_design: Endothelial cell enriched scRNA-seq profiles of the mouse brain in healthy and Alk5iEKO P12 mice

first: Alexandre

last: Dubrac


title: Whole-genome combinatorial gene fusions generate novel genes for advanced microbial trait development

status: Public on Mar 26 2026

city: San Diego

first: Helge

last: Zieler

address: 10790 Roselle St

institute: Primrose Bio

summary: Translational fusion of two separate genes into a compound sequence encoding a fusion protein is a key evolutionary mechanism which underpins the emergence of new protein activities, families and architectures. In biotechnology, gene fusion is a valuable molecular evolution tool for tagging proteins of interest and for combining or altering protein activities. To broadly demonstrate and harness the gain-of-function capabilities of fusion genes in a whole-genome approach, we constructed a “Function Generator™” fusion gene library containing pairwise combinations of 5019 protein-coding sequences in the Saccharomyces cerevisiae genome. The open reading frames (ORFs) were PCR amplified from the S288C yeast genome and cloned into a centromeric expression vector, with each ORF represented in the 5’ and the 3’ positions of the resulting gene fusions. To illustrate the ability of fusion genes in the library to confer complex phenotypes, a population of yeast library transformants was screened for resistance to four toxic heavy metal ions (Cd+2, Co+2, Cu+2 and Ni+2). Active fusion genes were cloned, validated and sequenced, revealing a multitude of biological functions represented in these genes, including proteins involved in transcription, translation, metal ion binding & transport and cell cycle control, as well as unknown functions. The gain-of-function principle of gene fusions was confirmed by comparing the activity of selected fusion genes to their constituent single ORFs expressed either individually or in non-fused pairs. Function Generator™ represents a novel and powerful way to approach phenotypic diversity in the laboratory and to bypass a key evolutionary bottleneck for accelerated strain development. The data provided here is from the RNAseq experiment conducted to compare transcriptomic profiles for yeast strains transformed with one of each of the 22 Gain-Of-Function Fusion (GOFF) genes.

overall_design: To analyze the transcriptomes of the 22 selected combinatorial fusion gene clones, triplicate BY4742 transformants of each fusion gene plus the empty vector control were grown in SDCGal-Ura to mid-logarithmic phases of growth, cells harvested and pelleted, then frozen at -80°C and shipped to GeneWiz/Azenta for RNA extraction and Illumina RNAseq mRNA sequencing. RNA was extracted using the Qiagen RNeasy Mini Kit and sequencing libraries were prepared using the New England Biolabs NEBNext Ultra™ II RNA Library Prep Kit for Illumina with the Twist Bioscience UMI Adapter System. Sequencing was performed on the Illumina HiSeq with 150 bp paired-end sequencing, resulting in 17–29 million reads per sample. Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using fastp v.0.23.1. UMI-based deduplication was performed using fastp v.0.23.1 simultaneously. Trimmed and deduplicated reads were then mapped to the S. cerevisiae S288C reference genome (GCF_000146045.2_R64, downloaded from ncbi.nlm.nih.gov) using STAR aligner v.2.5.2b. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.

first: Christopher

last: Schvarcz

first: Melody

last: McNay

first: Sabrina

last: Baffert


title: Dextran-coated Iron Oxide Nanoparticles impairs cardiac function in zebrafish larvae

city: Ribeirão Preto

first: William

last: Lautert Dutra

state: SP

address: Av. Bandeirantes, 3900

department: Genetics Department

country: Brazil

institute: Universidade de São Paulo

summary: Iron Oxide Nanoparticles (IONPs) with no doubt are the next platform for theragnostic in the biomedical field. Cardiovascular pathologies take immense advantage from the use of these nanoparticles in vascular imaging, detection of inflammatory and atherosclerotic lesions and magnetic therapies. However, the potential toxicity caused by the iron ions released from the IONPs core and its underlying mechanism is still unclear. Iron overload in the heart is known to cause disruption in calcium, sodium, and potassium ion channels, arrhythmias, and diastolic and systolic dysfunction. In this study, we employed a toxicity protocol to examine the developmental toxicity and cardiac effects of exposure on a zebrafish larva to Dextran coated IONPs. RNAseq analysis was conducted to establish the mechanisms of toxicity in Tg(fli:EGFP) fish. We validate the results using a series of embryonic cardiovascular function and a vascular development assay. Our results showed a developmental delay in the Dx-IONPs group, pronounced specially in vascular growth, visible in Tg(fli:EGFP) fish. Cardiac function analysis allowed to establish a correlation between Dx-IONP group and Iron salt exposed group from RNAseq. This work brings to light not only phenotypical, but also molecular basis for a better understanding of IONPs toxicity.

first: Giovanna

last: Oliveira

first: Talita

last: Pereira

first: Fernanda

last: Trindade

last: Lautert-Dutra

first: Maurício

last: Bogo

first: Calum

last: MacRae


title: A molecular atlas of brain neurovascular interactions reveals a spatiotemporal requirement of TGFβ signaling in brain angiogenesis [Visium]

last: Cagnone

summary: Neurovascular unit (NVU) communications guide vascular patterning, BBB maturation, and neuronal homeostasis, yet whether these interactions differ across brain regions during development remains unclear. Here, we combine spatial transcriptomics with region-resolved endothelial single-cell RNA sequencing to map cortical and thalamic NVU communication dynamics. We uncover spatiotemporal divergence of endothelial programs and show that neuronal and glial maturation parallels region-specific angiogenic trajectories. We identify neuronal–endothelial TGFβ2 signaling as an essential regulator of thalamic vascularization during a critical postnatal period. Loss of endothelial TGFβR1 signaling leads to mTOR hyperactivation and thalamus-predominant vascular malformations and hemorrhage within this developmental window, and these defects are rescued by mTOR inhibition. Together, these findings show that circuit maturation and region-specific NVU communication programs coordinate postnatal angiogenesis and vascular maturation, providing a framework for understanding regional vulnerability in neurovascular disorders.

overall_design: Spatial transcriptomics of the developing mouse brain - duplicate of coronal sections from P6, P12 and P60 mouse brain.

first: Mathilde

last: Bizou

first: Joel

last: Howard


title: Chromatin-associated lncRNA-splicing factor condensates regulate hypoxia responsive RNA processing of genes pre-positioned near nuclear speckles [TSA-seq]

first: Prasanth

last: Kannanganattu

overall_design: MCF7 cells were cultured at 37 degrees Celsius with 5% carbon dioxide and then grown in normoxic or hypoxic (0.2% oxygen) conditions for 24 hours before collection. Knockdown of MALAT1 was done by ASO. TSA-DNA-seq was performed with SON antibody HPA023535 from Sigma.

first: You

last: Song

first: Min

last: Shinn

first: Sushant

last: Bangru

first: Yu

last: Wang

first: Qinyu

last: Sun

last: Hao

first: Pankaj

last: Chaturvedi

first: Susan

last: Freier

first: Pablo

last: Perez-Pinera

first: Erik

last: Nelson

first: Andrew

last: Belmont

first: Mitchell

last: Guttman

first: Supriya

last: Prasanth

first: Auinash

last: Kalsotra

first: Rohit

last: Pappu

first: Kannanganattu


title: MAF converts metabolic state into superenhancer architecture and dependency in myeloma [RPMI8226 p300 ChIP-seq]

city: Singapore

first: Phyllis SY

last: Chong

address: 14 Medical Drive

country: Singapore

institute: NUS Medicine/CSI Singapore

summary: Lineage-specific transcription factors govern superenhancer assemblies that impose extreme transcriptional output, but how metabolic capacity sustains these regulatory hubs remains unresolved. By integrating metabolomic, epigenomic and chromatin architecture analyses, we identify a previously unrecognized role for MAF in metabolically driven histone acetylation, including the superenhancer-defining mark H3K27ac, through enhanced acetyl-CoA availability derived from rewired glutamine anaplerosis. The channeling of acetylation donors to high-demand enhancer microdomains is facilitated by nucleus-localizing metabolic enzyme citrate synthase, thereby alleviating metabolically constrained chromatin states. This process is further reinforced by MAF-dependent transcriptional regulation of the rate-limiting acetyltransferase p300, culminating in a globally elevated yet spatially precise hyperacetylated chromatin landscape that drives expression of core myeloma oncogenes. Yet, this metaboloepigenetic coupling comes at the cost of conditional vulnerability, unmasking superenhancers as liabilities that can be selectively destabilized with dietary nutrient restriction, as exemplified by the superenhancer-encoded dependency ZC3H3. Our study thus highlights an underappreciated dimension of superenhancer biology, positioning MAF as a metabolic gatekeeper of enhancer function.

overall_design: ChIPseq of p300 in RPMI8226 cells

first: Phyllis

first: Julia

last: Lim

first: Wee-Joo

last: Chng


title: small-RNA sequencing after controlled cortical impact model of repeated mild traumatic brain injury in male rats

city: Philadelphia

first: Stephanie

last: Daws

state: PA

address: 3500 N Broad St

institute: Temple University

type: Non-coding RNA profiling by high throughput sequencing

summary: We report the miRNAs differentially expressed in the orbitofrontal cortex of adult male rats 5 weeks after a controlled cortical injury model of traumatic brain injury (TBI). Animals underwent 3 repeated mild injuries on days 1, 4 and 7. Tissue was collected on day 42.

overall_design: miRNA profiles in orbitofrontal cortex of injured or sham adult male Sprague dawley rats

last: Sillivan


title: Chromatin-associated lncRNA-splicing factor condensates regulate hypoxia responsive RNA processing of genes pre-positioned near nuclear speckles [eCLIP-seq]

first: Prasanth

last: Kannanganattu

summary: Hypoxia-induced alternative splicing (AS) controls tumor progression and metastasis. The underlying mechanism specifying hypoxia-responsive AS needs to be determined. We demonstrate the role of nuclear speckle (speckle) nuclear domain (ND) and the long noncoding RNA, MALAT1, in hypoxia-responsive AS. Hypoxia-responsive genes position near speckles, the NDs that enhance splicing efficiency, and their differentially spliced exons harbor features that are characteristic of inefficiently spliced transcripts. Speckle-resident MALAT1, induced in response to hypoxia, boosts hypoxia-responsive AS by regulating the binding of SR-family splicing factor1 (SRSF1) to pre-mRNAs of speckle-associated genes. Mechanistically, MALAT1 facilitates the recruitment of SRSF1 to elongating RNA pol II (RNAP II) by promoting the formation of phase-separated SRSF1 condensates that are preferentially recognized and recruited to pre-mRNA by RNAP II. Our results reveal that MALAT1 boosts hypoxia-induced AS of speckle-associated genes by establishing the threshold concentration of SRSF1 as condensates, thereby promoting RNAP II-mediated recruitment of SRSF1 to pre-mRNAs.

overall_design: MCF7 and HEK293T cells were cultured at 37 degrees Celsius with 5% carbon dioxide and then grown in normoxic or hypoxic (0.2% oxygen) conditions for 24 hours before collection. Knockdown of MALAT1 was done by ASO. SRSF1 eCLIP was performed using SRSF1 antibody (Bethyl Labs A302-052A) coupled to sheep anti-rabbit IgG Dynabeads. After pulldown, the RNA was extracted using Trizol.

first: You

last: Song

first: Min

last: Shinn

first: Sushant

last: Bangru

first: Yu

last: Wang


title: Single-cell transcriptome atlas of human embryos after gastrulation

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

summary: The comprehensive spatiotemporal atlas of gene expression during early human embryonic development is critical for insights into embryogenesis, organogenesis, and disease origins. Leveraging Stereo-seq technology, we generated spatial transcriptomic profiles across 77 sagittal sections of 13 whole human embryos ranging from Carnegie stage 12 to 23, integrated with single-nucleus RNA-seq to elucidate gene expression patterns within defined cellular contexts, revealing the cellular heterogeneity that drives organ-specific differentiation. Our study has established a regulatory profile for the development of 50 organs and 198 substructures, and identified potential tissue-identity regulators. Notably, it uncovered previously uncharacterized gene functions in cardiac and brain development. The atlas not only substantiates and refines current understanding of human organ development but also highlights key organs susceptible to viral infections and genetic disorders. Furthermore, we characterized the allelic gene expression within specific organs at different developmental stages. This work presents a groundbreaking compilation of genome-wide gene expression profiles for each spatially defined cell population, which can be visualized as a spatial display of the embryonic transcriptional landscape. These results offer the most thorough delineation to data of the spatiotemporal transcriptomic dynamics of human organogenesis.

first: Jiexue

last: Pan

first: Yuejiao

last: Li

first: Zhongliang

last: Lin

first: Qing

last: Lan

first: Ying

last: Zhang

first: Huixi

last: Chen

first: Shengwei

last: Sui

first: Man

last: Zhai

first: Lijian

last: Zhao

first: Hongbo

last: Yang

first: Ya

last: Gao

first: Guolian

last: Ding

first: Xun

last: Xu

first: Hefeng

last: Huang


title: Human scRNA-seq of three primary and five metastatic breast cancers

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

institute: University of Padova

summary: A key problem in cancer biology is understanding the phenotypic characteristics of the aggressive cell states present in macrometastases and their molecular underpinnings. Here we report on the cellular constituents of human breast cancer metastases,  revealing that these malignant cells are invariably locked in a chimeric cell state. Human BC metastatic cells indeed display a gene-expression profile associated to embryonic development of tubular organs, while also retaining the transcriptional features of the primary tumor subtype.

overall_design: Primary breast cancer samples and the brain metastatic samples were obtained from Istituto Nazionale dei Tumori, Milan, and Istituto Neurologico “Carlo Besta”, Milan, respectively, following ethical approval from their Institutional Review Boards and acquisition of informed consent from all patients.

first: Roberta

last: Bordo

first: Ramona

last: Bason

first: Massimiliano

last: Pagani

first: Michelangelo

last: Cordenonsi

first: Stefano

last: Piccolo


title: MAF converts metabolic state into superenhancer architecture and dependency in myeloma [RPMI8226 ChIP-Seq]

first: Phyllis SY

last: Chong

overall_design: ChIPseq of H3K4me1 in RPMI8226 cells

first: Phyllis

first: Julia

last: Lim

first: Wee-Joo

last: Chng


title: scRNA-seq of primary tumors and lung metastases from mouse models of metastatic breast cancer

summary: A key problem in cancer biology is understanding the phenotypic characteristics of the aggressive cell states present in macrometastases and their molecular underpinnings. Here we report on the cellular constituents of  breast cancer metastases,  revealing that these malignant cells display a gene-expression profile associated to embryonic development of tubular organs.

overall_design: Primary tumors were dissected from 3 months-old MMTV-PyVT female mice, and from 6 months-old MMTV-Neu female mice. For each sample, tumors from 2 donors were pooled and processed together. Metastasis-containing lungs were harvested from 3 months-old MMTV-PyVT female mice, and from 7-8 months-old MMTV-Neu female mice; lungs were processed after confirming the presence of visible macroscopic metastases; extrapulmonary primary bronchi and mediastinal lymph nodes were discarded; for each sample, lungs from two mice were pooled and processed together.

first: Francesca

last: Zanconato

first: Tito

last: Panciera

first: Paolo

last: Contessotto

first: Oriana

last: Romano


title: Human scRNA-seq of three breast cancer metastases and three normal mammary glands

summary: A key problem in cancer biology is understanding the phenotypic characteristics of the aggressive cell states present in macrometastases and their molecular underpinnings. Here we report on the cellular constituents of human breast cancer metastases,  revealing that these malignant cells are invariably locked in a chimeric cell state. Human BC metastatic cells indeed display a gene-expression profile associated to embryonic development of tubular organs, while also retaining the transcriptional features of their original adult mammary luminal lineage.

overall_design: Discard tissues from three anonymized healthy women undergoing reduction mastoplasty surgery and one surgical metastatic BC sample (BBM5) were collected from Azienda Ospedaliera di Padova, with informed consent according to University of Padua’s institutional guidelines and the Azienda Ospedaliera di Padova Ethics Committee (CESC). Two other metastatic samples (BBM0 and BSM1) were collected from anonymized women with informed consent, as approved by the ethics committee and institutional review board of Regina Elena National Cancer Institute (Rome).

first: Matteo

last: Marchionni

first: Mattia

last: Forcato

first: Sara

last: Donzelli

first: Giovanni

last: Blandino


title: Depletion of Canonical Histones Enhances Direct Reprogramming of Scavenger Cells in vivo

city: Hamburg

first: Baris

last: Tursun

address: Martin-Luther-King-Platz 3

institute: Universität Hamburg

summary:
Direct reprogramming is a procedure that converts the identity of differentiated cells, which can be triggered by defined transcription factors (TFs). Cellular reprogramming offers a promising approach for replacing damaged cells and repairing diseased tissues. In this context, understanding the implications of diverse molecular pathways that regulate cell fate conversion in vivo is necessary to ensure the safety and efficacy of reprogrammed cell therapy.
The nematode C. elegans is a powerful model organism for dissecting molecular processes in vivo and has previously been used to identify reprogramming barriers that are conserved in mammals. Here, we describe the discovery of an unprecedented TF-induced direct reprogramming instance that allows the conversion of mesodermal scavenger cells with hepatic function, known as coelomocytes (CCs) in C. elegans. Direct reprogramming of CCs into neuron-like cells results in the acquisition of neuronal characteristics with corresponding gene expression. Moreover, CCs can also be directly reprogrammed into intestinal cells. This conversion is accompanied by striking morphological changes, including the formation of a single-cell lumen and the development of microvilli, which underlines the acquisition of an intestinal cell fate.
Using reverse genetics by RNAi, we demonstrate that direct reprogramming of CCs can be enhanced upon depletion of specific chromatin-related factors. Notably, knocking down canonical histones substantially enhanced reprogramming. Reducing histone levels is expected to affect chromatin states and gene expression, while improved cell fate conversion upon histone depletion has not been previously reported.

overall_design: Mixed populations of C. elegans strains carrying the temperature-sensitive glp-4(bn2) allele were synchronized by bleaching and grown at restrictive temperature to obtain germline-deficient L3 stage animals. Coelomocytes were labeled using an unc-122 promoter-driven GFP reporter. Experimental animals carried the barIs115 transgene, enabling ectopic expression of CHE-1, while control animals lacked this transgene. Worms were dissociated enzymatically and mechanically, and GFP-positive coelomocytes were isolated by fluorescence-activated cell sorting. RNA was extracted from sorted cells, and poly(A)-selected, strand-specific RNA-seq libraries were prepared and sequenced using paired-end reads on an Illumina NextSeq 500 platform. Samples were grouped into control (WT_CC_L3) and CHE-1-expressing (Repro_CC_L3) conditions for downstream analysis, including differential gene expression using DESeq2.

first: Ismail

last: Özcan

first: Anna

last: Reid

first: Gizem

last: Köse

first: Alexander

last: Blume


title: In situ single-cell profiling of lung metastases from the MMTV-PyMT mouse model of metastatic breast cancer

first: Silvio

last: Bicciato

overall_design: CosMxTM technology [CosMxTM Human Universal Cell Characterization RNA Panel (1000-plex); Nanostring, USA] was applied on a section mouse lung, freshly-harvested from a female MMTV-PyMT C57BL/6J mouse at 5.5 months of age, resulting 18 fields of view (FoVs). The following cell surface markers were used for morphology visualization: B2M/CD298, PanCK, CD45, CD3 antibodies and DAPI.

first: Michelangelo

last: Cordenonsi

first: Stefano

last: Piccolo


title: Genomic analysis of avoidance learning in addiction

city: La Jolla

first: Daniel

last: Munro

state: CA

address: 9500 Gilman Drive

department: Psychiatry

institute: UC San Diego

summary: Addictions are among the most heritable of human neuropsychiatric disorders, but human genetic studies have been hampered by the extreme complexity of human genetics, as well as the sheer behavioral complexity of the addictive process, with multiple stages at which humans can exhibit addiction vulnerability – e.g. initial drug exposure, escalation, relapse, etc. We address these shortcomings by studying heterogeneous stock (HS) rats, which have extremely well characterized genetic profiles, and with the support of addictionrehabclinics.co.uk, we utilize behavioral models that examine multiple well-defined time periods in the progression of addictive behaviors. Our preliminary findings show that even though addiction is often viewed as aberrant reward learning, much individual variation in addiction propensity is actually due to differences in avoidance learning. For example, in addition to its well-known rewarding properties, cocaine has aversive effects that show greater individual variability than its rewarding effects, and are stronger predictors of cocaine-seeking. Furthermore, we found that rats differ greatly in “punishment resistance”, i.e. propensity to seek rewards despite adverse outcomes, which is one of the defining characteristics of addiction. Both cocaine avoidance and punishment resistance are highly heritable in HS rats (h2 = 0.58 and 0.48, respectively), and both are critically regulated by the rostromedial tegmental nucleus (RMTg), a major GABAergic afferent to midbrain dopamine neurons that plays key roles in avoidance learning. Building on these findings, we seek to identify the genetic differences underlying these two distinct addiction vulnerability phenotypes using a genome-wide association screen (GWAS) to identify candidate genes in HS rats, followed by eQTL analysis on gene expression in the RMTg and afferent circuits that drive these behaviors. With the support of confidential rehab centre this project will identify candidate addiction-related genes using a highly innovative combination of powerful behavioral tests, extensive neural circuitry knowledge, and the Palmer lab’s groundbreaking sequencing and analytical approaches.

overall_design: RNA-seq profiling of the rostromedial tegmental nucleus (RMTg) brain region from a cohort of outbred rats for use in genomic and statistical genetic analyses

first: Thomas

last: Jhou

first: Abraham

last: Palmer

first: Pejman

last: Mohammadi


title: Bulk RNA-seq of human metastatic Breast Cancer cells

overall_design: Control or ETV1/4/5 KO cells are cultured as 2D monlayers or in 3D Collagen I gels and then harvested for RNA-seq

first: Robin

last: Caire

first: Giusy

last: Battilana

first: Francesca

last: Zanconato

first: Oriana

last: Romano


title: Transcriptomic regulation in the NAcc, PL, and pVTA brain regions in heterogeneous stock rats [nucleus accumbens core]

summary: To aid in the investigation of behavioral trait genetic associations, we collected RNA-seq from three brain regions of 200 genotyped outbred heterogeneous stock (HS) rats. We mapped molecular QTLs and conducted transcriptome-wide association study (TWAS) involving a collection of 281 complex traits.

overall_design: RNA-seq profiling of NAcc, PL, and pVTA brain regions from a cohort of outbred rats for use in genomic and statistical genetic analyses

first: Hao

last: Chen


title: In situ single-cell profiling of a brain metastasis from a HER2+ Breast Cancer Patient and 8 primary tumors from TNBC patients.

summary: A key problem in cancer biology is understanding the phenotypic characteristics of the aggressive cell states present in macrometastases and their molecular underpinnings. Here we report on the cellular constituents of  breast cancer metastases,  revealing that these malignant cells display a gene-expression profile associated to embryonic development of tubular organs. Similar properties are found in malignant cells from pro-metastatic primary tumors but not in primary tumors that never metastatize.

overall_design: CosMxTM technology [CosMxTM Human Universal Cell Characterization RNA Panel (1000-plex); Nanostring, USA] was applied on a  5 um FFPE section from archival surgical specimens derived from BC patients in our institution. The following cell surface markers were used for morphology visualization: B2M/CD298, PanCK, CD45, CD3 (metastasis) or CD68 (primary tumors) antibodies and DAPI.

first: Tito

last: Panciera


title: H2O2-induced astrocytic collagen triggers neuronal death in ischemic stroke [ATAC-seq]

city: Daejeon

first: C. Justin

last: Lee

address: 55 Expo-ro

country: South Korea

institute: Institute for Basic Science

summary: Ischemic stroke is a brain injury caused by the occlusion of blood vessels, leading to reduced blood flow, excessive oxidative stress, and the cascade of events, including the formation of the glial barrier, fibrotic scar, neuronal death, and motor impairment. Despite extensive research into stroke etiology, the specific initiation trigger for neuronal death is mainly unknown, severely limiting the development of effective treatments. Here, we demonstrate that excessive H2O2 generation is the initiating factor of ischemic stroke in the photo-thrombosis (PT) mouse and non-human primate (NHP) models, with H2O2-induced astrocytic type I collagen (COL1) playing a crucial role in the cascade of stroke pathology. Treatment with KDS12025, an H2O2-decomposing peroxidase enhancer, significantly alleviates these effects by reducing H2O2-induced COL1 in extremely low doses in mouse and NHP stroke models. In cultured astrocytes, H2O2 stimulates the production of astrocytic COL1 through post-transcriptional up-regulation of Col1 mRNA by decreasing microRNA29, leading to the death of neighboring neurons. Using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI), we observe profound alterations in N-glycan profiles, particularly fucosylated N-glycans, which reverted to normal levels in both the KDS12025 treatment and astrocytic Col1 gene-silencing groups. The gene-silencing of astrocytic Col1 or Fut8, a key enzyme responsible for core fucosylation necessary for COL1 secretion, prevents neuronal death and motor impairment. Our findings reveal that H2O2-induced astrocytic COL1 production is critical to ischemic stroke. These findings propose that targeting H2O2, astrocytic COL1, and FUT8 could be effective therapeutic strategies for ischemic stroke, offering new avenues for treatment.

overall_design: ATAC-sequencing of primary mouse cortical astrocyte isolated from p4 pub. The astrocytes are treated with H2O2 for 3 hours and then harvested after 1 day.

first: In

middle: Y

last: Hwang

first: Jae

middle: H

first: C


title: H2O2-induced astrocytic collagen triggers neuronal death in ischemic stroke [RNA-seq]

overall_design: RNA-sequencing of primary mouse cortical astrocyte isolated from p4 pup. The astrocytes are treated with H2O2 for 3 hours and then harvested after 1 day and 3 days.


title: An optimized protocol for efficient derivation of pancreatic islets from multiple human pluripotent stem cell lines

city: Stockholm

first: Cheng

last: Zhao

state: Stockholm

address: H9 Klinisk vetenskap,171 77 Stockholm

department: Clinical Science

country: Sweden

institute: Karolinska institute

summary: Future success of cell therapy for type 1 diabetes (T1D) relies on robust protocols for the differentiation of stem cells to pancreatic islets. However, currently established protocols generate stem cell-derived pancreatic islets (SC-islets) which contain non-endocrine cell populations and have immature functionality. Herein we report the development of a new protocol for the generation of potent SC-islets enriched in functional endocrine cells from multiple human pluripotent stem cell (hPSC) lines. We show that laminin-521 efficiently supports monolayer differentiation of 8 testes hPSC lines to endocrine progenitor (EP)  stage. The efficiency was further improved by reducing the pancreatic progenitor (PP) stage. Importantly, we find that aggregation of EP reduces unwanted non-endocrine and proliferative cells. Subsequent suspension cultures generate SC-islets with  strong in vitro glucose responsiveness, similar to human islets. Upon transplantation of 300 SC-islets into the anterior chamber of the eye of a diabetic mouse model, the SC-islets undergo further maturation in vivo and re-establish normal glycemic control. The SC-islets before and after transplantation are to a major extent free of non-endocrine cell populations. In conclusion, our robust differentiation protocol results in endocrine enriched and highly functional SC-islets that should be well suited for transplantation into patients with T1D.

overall_design: In vitro differentiation of human pluripotent stem cells into pancreatic islets followed by thier transplantation into the anterior chamber of the eye of diabetic mice

first: Siqin

last: Wu

first: Galyna

last: Bryzgalova

first: Shivam

last: Chandel

first: Paschalis

last: Efstathopoulos

first: Kelly

last: Blust

first: Anna

last: Voznesenskaya

last: Falk

first: My

last: Hedhammar

first: Per-Olof

last: Berggren

first: Fredrik

last: Lanner


title: Transcriptomic regulation in the NAcc, PL, and pVTA brain regions in heterogeneous stock rats [prelimbic cortex]

first: Daniel

last: Munro

first: Abraham

last: Palmer

first: Pejman

last: Mohammadi


title: IL1R2 Identified as a Key Hub Gene Regulating Vascular Endothelial Function in Kawasaki Disease

city: Jinhua

first: Yi

last: Zhan

address: houshan Road 266

institute: Jinhua Maternal and Child Health Care Hospital

summary: Background: Kawasaki disease (KD) is a multisystemic vasculitis of unknown aetiology in children. KD with coronary artery lesion is now the leading acquired heart disease in children. Peripheral blood mononuclear cells (PBMCs) play roles in KD. We identified hub genes based on RNA sequencing data and validated them in PBMCs and human umbilical vein endothelial cells (HUVECs) coculture with PBMCs. Methods: mRNA microarray of PBMCs from 12 acute KD patients and 12 healthy controls was performed to screen differentially expressed mRNAs (DE-mRNAs). We selected 20 KD patients and 20 healthy controls for validation, and established HUVECs coculture with PBMCs. Real time-PCR was finally conducted to confirm the reliability and validity of the expression level of DE-mRNAs from PBMCs and HUVECs coculture. Results: A total of 6039 DE-mRNAs were found (2267 upregulated, 3772 downregulated). Thirty hub genes were selected. KD PBMCs significantly impaired HUVECs viability and migration. IL1R2 was downregulated, FCGR1A, and CD177 mRNAs were upregulated in acute KD. IL1R2 was elevated, FCGR1A and CD177 mRNAs were downregulated in convalescence. And the real-time PCR and ELISA results showed IL1R2 was downregulated in acute KD PBMC-HUVECs co-cultures and elevated in convalescence. Conclusion: These findings may improve our understanding of PBMCs and HUVECs coculture with PBMCs in KD.

overall_design: experimental design RNA-seq profiling of Kawasaki Disease patients and healthy controls

first: Xiaofeng

last: Hong

first: Qianwen

last: Wang

first: Tian

last: Lan

first: Jianxin

last: Xu

first: Jiandong

last: Shi


title: Transcriptomic regulation in the NAcc, PL, and pVTA brain regions in heterogeneous stock rats

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

overall_design: Refer to individual Series


title: Impaired redox adaptation through SLC38A5-dependent glutamine metabolism contributes to melatonin-mediated anoikis sensitivity and metastasis suppression in bone cancer

city: Taichung

first: Chih-Hsin

last: Tang

address: 91 Xueshi

country: Taiwan

institute: China Medical University

summary: Malignant bone cancer, including osteosarcoma and chondrosarcoma as popular subtypes, are aggressive neoplasms which arise from bone tissue and have lung metastasis. Tumor cells evade anoikis through reactive oxygen species (ROS)-mediated redox homeostasis, which modulates signaling cascades that promote proliferation, survival, and metastatic invasion into distant sites. Melatonin, synthesized primarily by the pineal gland, has been implicated in cancer prevention and therapy due to its inhibitory effects on bone cancer growth and progression. Little is known about the mechanisms underlying anoikis resistance in bone cancer cells or whether melatonin can therapeutically modulate this process. We demonstrated that glutamine metabolism is essential for bone cancer cells to maintain anoikis resistance. Melatonin treatment disrupted glutamine metabolism and altered redox homeostasis, as evidenced by increased ROS accumulation and reduced NADPH/NADP⁺ ratios under anchorage-independent conditions. Notably, solute carrier family 38 member 5 (SLC38A5), a glutamine transporter, was identified as a critical regulator of bone cancer progression, with higher SLC38A5 expression correlating with poorer clinical outcomes. Melatonin suppressed SLC38A5 expression and attenuated anoikis resistance through inhibition of the PI3K-Akt signaling pathway. Consistently, reduced SLC38A5 expression was associated with decreased lung metastasis in melatonin-treated groups in an orthotopic mouse model. Collectively, our findings reveal a previously unrecognized role of melatonin in modulating glutamine-dependent redox balance and anoikis resistance in bone cancer. This study highlights SLC38A5-mediated glutamine metabolism as a critical determinant of metastatic potential and supports melatonin and SLC38A5 as promising therapeutic targets for osteosarcoma and chondrosarcoma.

overall_design: JJ012 and 143B cells were cultured under suspension conditions and treated with melatonin (1 mM, 72 h) or left untreated as controls for RNA-seq analysis.

first: Bao-Tran

last: Nguyen


title: Syncytin-a deficiency compromises murine sperm function by suppressing PRL/PGE2 and PI3K/AKT/mTOR pathway

first: Honglian

last: Yu

address: No. 279, Zhouzhu Highway

institute: Shanghai University of Medicine and Health Sciences

summary: The human endogenous retrovirus W envelope protein syncytin-1 (syncytin-a in mus) can be involved in fetal development and tumorigenesis. The role of syncytin-1 in male infertility has not been identified. To explore the mechanisms of syncytin-1 in male infertility, the prostatic epithelial-specific syncytin-a knockout (syna CKO) mouse model was constructed. Firstly, male infertility, abnormal testicular seminiferous tubule, and prostate gland were discovered in syna CKO mice. Then, irregular sperm motility, morphology, and MMAF-associated gene expression (AKAP3, SPAG6) were detected in syna CKO mice. Increased PGE2 and PRL modulate the lipid metabolism of the testis in syna CKO mice. Syna CKO with inhibitor or activator treatment identified that syna knockout could inhibit the PI3K/AKT/mTOR pathway, Ca²⁺ levels, and elevate caspase 3 expression. Therefore, we propose a hypothesis that syna deficiency exacerbates testicular lipid accumulation and apoptosis by suppressing the PI3K/AKT/mTOR and Ca2+ pathway, ultimately leading to spermatogenic dysfunction and male infertility. The study initially included 3 WT and 3 KO samples. After quality control and exploratory analysis, one control sample (WT1) was identified as a biological outlier and excluded from the final differential expression analysis.

overall_design: We performed RNA-seq on mouse testes from WT and KO groups (n=3 per group).

first: Qianqian

first: Zhenwei

first: Zhenpeng

last: Li

first: Dongle

last: Liu

first: Xiaotong

last: Yan

first: Yan

last: Zhang

first: Ning

last: Chi

first: Qiang

last: Bian

first: Zhankui

last: Zhao


title: Effect of AAV-mediated non-fibrogenic TBX18 expression in mouse hearts

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

summary: Gene therapy-based biological pacemakers have been proposed as an alternative to their hardware-based counterparts. In this context, short-term ectopic expression of the T-box transcription factor 18 (TBX18) in the ventricle reportedly generated potent short-term pacemaker function in various animal models. Here, we investigated the effect of adeno-associated virus (AAV)-mediated long-term expression of TBX18 in mouse hearts. Mice were injected with AAV vectors containing GFP-labeled Nanoluciferase or GFP-labbeled TBX18 at the left ventricular apex. Left ventricular tissues were harvest 2 weeks later. The results suggest that at non-fibrogenic level, TBX18 expression suppress working myocardial genes but does not induce pacemaker phenotype.

overall_design: RNA-seq profiling of mouse left ventricular tissues transduced with AAV-Nluc and AAV-TBX18 vectors.

first: Jianan

first: Karel

last: van Duijvenboden

first: Gerard

last: Boink


title: Human Macrophages Encode Stimulus-Specific Information of Prior Exposures Through Trained Immunity

first: Aoife

last: O'Farrell

address: 415 Curie Blvd

institute: University of Pennsylvania

summary: Trained immunity (a form of innate immune memory), defined in part by heightened responses to pathogen restimulation, can be generated by many different stimuli. However, both the quantitative differences in trained states generated by different stimuli and the downstream consequences of those differences remain unclear. Here, we used primary human monocyte-derived macrophages to demonstrate phenotypic and molecular stimulus specificity of trained immunity six days after initial exposure. Quantification of cytokine production with single-molecule RNA imaging demonstrated stimulus-specific patterns of response to restimulation, with trained cells showed stronger responses to secondary stimuli more similar to their initial stimulation. Differential licensing of inflammatory transcription factors was associated with encoding of specificities in chromatin six days after training, while memory of some, but not all, training stimuli is lost by eleven days post-training in vitro. Overall, our findings demonstrate that different training stimuli can impart specific memories which generate distinct training phenotypes.

overall_design: To assess whether different training stimuli generated distinct epigenetic changes, we assessed chromatin accessibility by ATACseq six days and eleven days after training with various stimuli in primary human monocyte-derived macrophages.

first: Jingxin

first: Arjun

last: Raj


title: Culturomics reveals Fusobacterium-Prevotella mutualism as a hallmark of nasopharyngeal tumor microbiota [Cell RNA-seq]

city: Guangzhou

first: Liu

state: GuangDong

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

summary: To investigate the functional characteristics of NPC cells treated with Fusobacterium or Prevotella

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NPC HK1 Cells with different bacteria treatment

first: Ying-Qi

last: Lu


title: Gene expression in patients with pulmonary hypertension due to valve heart disease

city: Madrid

first: Ana I

last: Fernandez-Avila

state: Madrid

address: C/ Doctor Esquerdo, 46

department: Cardiology

country: Spain

institute: Hospital GU Gregorio Marañon

summary: To delve deeper into the molecular mechanisms underlying pulmonary hypertension secondary to left heart disease (PH-LHD), an essential step toward developing a comprehensive classification, reliable biomarkers and targeted therapies. In this study, we analyzed the whole transcriptome (mRNA) of a unique cohort of patients with persistent PH due to valvular heart disease (PH-VHD) to identify biological pathways associated with disease prognosis. The analysis was performed using the well-characterized SIOVAC (Sildenafil for Improving Outcomes after Valvular Correction) clinical trial cohort. We included 116 patients with demonstrated PH-LHD after valvular correction, and 30 VHD patients with no or mild PH (Control).

first: Jorge

last: Martinez-Solano

first: Javier

last: Bermejo


title: MAF converts metabolic state into superenhancer architecture and dependency in myeloma [shscr ChIP-Seq]

first: Phyllis SY

last: Chong

summary: Lineage-specific transcription factors govern superenhancer assemblies that impose extreme transcriptional output, but how metabolic capacity sustains these regulatory hubs remains unresolved. By integrating metabolomic, epigenomic and chromatin architecture analyses, we identify a previously unrecognized role for MAF in metabolically driven histone acetylation, including the superenhancer-defining mark H3K27ac, through enhanced acetyl-CoA availability derived from rewired glutamine anaplerosis. The channeling of acetylation donors to high-demand enhancer microdomains is facilitated by nucleus-localizing metabolic enzyme citrate synthase, thereby alleviating metabolically constrained chromatin states. This process is further reinforced by MAF-dependent transcriptional regulation of the rate-limiting acetyltransferase p300, culminating in a globally elevated yet spatially precise hyperacetylated chromatin landscape that drives expression of core myeloma oncogenes. Yet, this metaboloepigenetic coupling comes at the cost of conditional vulnerability, unmasking superenhancers as liabilities that can be selectively destabilized with dietary nutrient restriction, as exemplified by the superenhancer-encoded dependency ZC3H3. Our study thus highlights an underappreciated dimension of superenhancer biology, positioning MAF as a metabolic gatekeeper of enhancer function.

overall_design: ChIPseq of MAF in RPMI8226 cells

first: Phyllis

first: Julia

last: Lim

first: Wee-Joo

last: Chng


title: MAF converts metabolic state into superenhancer architecture and dependency in myeloma [ChIP-Seq]

overall_design: ChIPseq of H3K27ac in RPMI8226 control and MAF knockdown cells


title: Gene expression profiling of lung tissue from LPS-induced acute lung injury mice treated with Renshen Baidu Powder

city: Qingdao

first: Peng

last: Chen

address: 308 Ningxia road, Qingdao

institute: Qingdao University

summary: This dataset presents transcriptomic profiles of lung tissue from a murine model of LPS-induced acute lung injury (ALI) following treatment with Renshen Baidu Powder (RSBD). LPS induced a robust inflammatory gene signature, which was significantly reversed by RSBD.

overall_design: C57BL/6 mice were treated with intratracheal LPS to induce ALI, followed by oral administration of RSBD for 5 days. Lung tissues were collected on day 5 post-LPS. Three groups: Control (saline), LPS (vehicle), LPS+RSBD. Each group contained 3 biological replicates. Total RNA was extracted from lung tissues and subjected to strand-specific RNA-seq.

first: Fei

last: Li

first: Shixu

last: Liu

first: Guohu

last: Di


title: Oligodendrocyte subtype imbalance and dysfunction contribute to motor deficits and Purkinje cell axonopathy in SCA1

city: New Haven

first: Changwoo

last: Lee

state: CT

address: 295 Congress

institute: Yale University

summary: Spinocerebellar ataxia type 1 (SCA1) is a neurodegenerative disease marked by progressive motor deficits and Purkinje cell (PC) degeneration, driven by polyglutamine expansion in ataxin-1. While oligodendroglial dysfunction precedes PC loss, its direct contribution toward SCA1 pathogenesis remains unclear. Here, using an oligodendroglia-specific SCA1 conditional knock-in mouse model, we demonstrate that mutant ataxin-1 in oligodendrocytes is sufficient to drive aspects of SCA1-related pathology, including dysregulated myelination, PC axonal shrinkage, and torpedo formation, ultimately impairing motor coordination. Cross-species single-nucleus RNA-sequencing reveals cerebellar oligodendrocyte subtypes with distinct gene expression and abundance dysregulation that contribute to demyelination. This, compounded by a progressive decline in the neuroprotective functions of a cerebellar-specific oligodendrocyte subtype, establishes a critical link between demyelination, axo-myelinic dysfunction, and axonal pathology in SCA1. Upstream transcriptional regulator analysis in oligodendroglia identifies TCF7L2 and HTT as key mediators of oligodendroglial dysfunction in SCA1, suggesting shared pathogenic mechanisms with other polyglutamine diseases. These findings position oligodendroglia as central players in SCA1 pathogenesis and underscore their essential role in supporting PC of axonal integrity.

overall_design: we performed snRNA-seq on the cerebella of OL-SCA1-cKI( SCA1fl/+; NG2-cre) mice and their SCA1fl/+ littermate controls at 30 weeks

first: Janghoo


title: RNA-seq analysis of host responses to Newcastle disease virus infection in HD11 cells

city: Harbin

first: Shi

last: Qiankai

address: No.678 Haping Road

institute: The Chinese Academy of Agricultural Sciences

summary: We performed bulk RNA sequencing to characterize transcriptional responses in HD11 cells under two experimental conditions: Mock and NDV. Each condition included three biological replicates. This study was designed to investigate the effect of Newcastle disease virus infection on host gene expression in chicken macrophage-like HD11 cells. Raw sequencing data and processed expression matrices are included in this submission.

overall_design: Six RNA-seq libraries were generated from HD11 cells under two experimental conditions: Mock and NDV. Each condition included three biological replicates. This design enables assessment of host transcriptomic responses to Newcastle disease virus infection in HD11 cells.

first: Qiankai

last: Shi

first: Junfeng

last: Sun

first: Shengwang


title: Tet2 deficiency alters CD4+ T-cell function and promotes T-cell lymphoma with a TFH-cell immunophenotype.

city: Omaha

first: Javeed

last: Iqbal

state: Nebraska

address: 601 S 42nd St

institute: University of Nebraska Medical Center

summary: TET2 mutations are frequent in TFH derived lymphomas, but how epigenetic disruption initiates malignant T cell transformation is unclear. We performed CRISPER mediated TET2-knockout in normal human CD4+ T cells and culture them long term.  We perfromed scRNAseq   after 40 or  90 days or long-term culture (>200 days).  ScRNA-seq revealed a persistent proliferative cluster characterized by elevated stem like transcriptional features compared to wild type counterparts

overall_design: sc-RNAseq of WTor CRISPER modified TET2-/- human CD4+ T cells after 40 or  90 days or long-term culture (>200 days).

first: Wing C

last: Chan


title: Hepatic multilineage organoids derived from hypoimmunogenic iPSCs for liver regenerative medicine

city: Milano

first: Arianna

last: Vallerga

address: via Mario Negri 2

department: Experimental Oncology

institute: Mario Negri Institute for Pharmacological Research

summary: Hypoimmunogenic multicellular hepatic organoids were characterised by single-cell RNA sequencing to understand their cellular composition. Lineage cell identity was confirmed by gene and protein expression combined with ultrastructural analysis of cells by electron microscopy. Hepatic functional maturation was demonstrated by the production of liver-specific proteins, as shown by immunoassays. Together with the presence of a highly functional endothelial network, these properties confer therapeutic potential for inherited hepatic plasma protein deficiencies, end-stage liver disease and metabolic disorders.

first: Ariannna

first: Ilaria

last: Craparotta

first: Piera

last: Trionfini

first: Annalina

last: Caroli


title: Single-Cell Transcriptomics Reveals the Characteristics of Bone Marrow Cellular Heterogeneity After Intramedullary Nail Implantation in Osteoporotic Fractures

city: Shanghai

first: Tianle

last: Ma

address: 180 Fenglin Rd

institute: Zhongshan Hospital

summary: After fracture, the femoral bone marrow microenvironment in mice initiates a series of reparative responses. The spatiotemporal coordinated regulation of gene expression not only determines the activation characteristics of hematopoietic and mesenchymal progenitors but also directly regulates the dynamic remodeling of various functional cell populations in the bone marrow microenvironment and the execution of bone repair functions. Historically, studies on the effects of intramedullary implant materials on the bone marrow microenvironment post-fracture have mostly relied on histological analysis of bulk tissues or functional assays of pre-selected isolated cell subsets. These approaches fail to accurately capture the heterogeneous transcriptional programs of individual cells, especially the dynamic transcriptional changes of cells in the bone marrow and on the implant surface after intramedullary nail placement. To systematically characterize the changes in the femoral bone marrow microenvironment after fracture and clarify the heterogeneity and dynamic transcriptional changes of cells in the bone marrow and on the implant surface following intramedullary nail placement, we employed single-cell mRNA sequencing (scRNA-seq) to profile the transcriptional landscapes of femoral bone marrow samples and implant-adherent cells from fracture mice implanted with intramedullary nails of different materials. This technique provides core data support for elucidating the molecular mechanisms underlying material-regulated cell differentiation trajectories and functional remodeling during fracture healing.

overall_design: Femoral bone marrow samples and implant-adherent cells from osteoporotic fracture mice implanted with two types of intramedullary nails, namely magnesium (Mg) intramedullary nails and Mg-TAGelMA intramedullary nails.

first: Guobin

last: Qi

first: Zhe

last: Wang


title: Transcriptomic regulation in the NAcc, PL, and pVTA brain regions in heterogeneous stock rats [posterior ventral tegmental area]

first: Daniel

last: Munro

summary: To aid in the investigation of behavioral trait genetic associations, we collected RNA-seq from three brain regions of 200 genotyped outbred heterogeneous stock (HS) rats. We mapped molecular QTLs and conducted transcriptome-wide association study (TWAS) involving a collection of 281 complex traits.

overall_design: RNA-seq profiling of NAcc, PL, and pVTA brain regions from a cohort of outbred rats for use in genomic and statistical genetic analyses

first: Hao

last: Chen

first: Abraham

last: Palmer

first: Pejman

last: Mohammadi


title: Kinome CRISPR screen for Rhabdomyosarcoma cells in combination with pralatrexate

city: Durham

first: Seth

last: Zimmerman

state: NC

address: 308 Research Dr.

institute: Duke University

summary: We found that pralatrexate causes temporary tumor regression in RH4 cell xenograft model. In order to identify possible therapeutic targets that could be targeted in combination with pralatrexate, we performed a whole Kinome CRISPR loss of function screen in cells dosed with pralatrexate.

overall_design: RH4 cells were infected with lentivirus encoding the Brunello kinome library at 1,000x coverage.  48 hours later, cells were selected with 0.25 µg/ml puromycin for 72 hours.  A portion of the cells were harvested at this point for baseline measurements.  The remaining cells were allowed to recover for 72 hours, and then treated with 1.5 nM pralatrexate or vehicle control and passaged at 4 day intervals for 10 days.  On day 10, 5 x 106 cells were harvested and genomic DNA isolated using an ammonium acetate precipitation method.  The sgRNA sequences from each sample were PCR amplified using primers with Illumina adaptors and indexes for multiplexing as described.  Samples were pooled and sequenced at the Duke Genome Sequencing Core Facility, to an average sequencing depth of 1,200 reads per sgRNA.

middle: P

first: Christopher

last: Counter

first: So Young

last: Kim


title: Characterization of cellular responses of Ptpn6 (SHP-1) cKO in hippocampus by scRNA-seq

city: South San Francisco

first: Xingyue

middle: Monica

last: Ge

address: 1 DNA Way

institute: Genentech

summary: Ptpn6 (SHP-1) is known to impact signaling pathways in immune cells in various different ways, and in many cases, SHP1 opposes immune cell activation by nonreceptor tyrosine kinases such as Syk, Jak or ZAP70. In Alzheimer’s disease, multiple AD risk genes are expressed in microglia and related to microglial regulation and function. SHP-1 interacts with ITIM domains of multiple AD GWAS genes including Siglec-11, LILRB2, PILRA, and CD33 and SHP-1 is also known as a negative regulator of DAP12/Trem2 signaling. To understand cellular pathways of ITIM signaling and delineate benefits and liabilities of ITIM signaling inhibition, here we characterize Ptpn6 cKO (Cohort I) and Ptpn6 cKO crossed with previously characterized AD mouse model TauPS2APP (Cohort II) by single cell RNA-seq. We found that Ptpn6 deletion unleashes disease-like transcriptional changes in vivo. We also discovered distinct microglia activation states associated with protective versus exacerbative Ptpn6 genotypes. Current scRNA-seq results reveal both protective and latent degenerative potential of microglia held in check by Ptpn6.

overall_design: For scRNA-seq study in non-disease background cohort, 5-6 months old Ptpn6 loxp/loxp;Cx3cr1-CreERT2-/- (n=3) or Ptpn6 loxp/loxp;Cx3cr1-CreERT2+/- (n=3) were taken down 2 months after tamoxifen injection. For scRNA-seq in TauPS2APP background, Ptpn6 wt/wt (n=5), wt/loxp (n=4), or loxp/loxp (n=6) were crossed with Cx3cr1-CreERT2+/- and TauPS2APP, and tamoxifen was injected at 5-6 months old age and mice were taken down 2 months afterwards.

first: Seung-Hye

last: Lee

first: Ainhoa

last: Etxeberria

first: Gloriia

last: Novikova

first: Monica

first: Brad

last: Friedman

last: Bohlen


title: CTG clade-specific proteins of the RSC chromatin remodeling complex regulate cell cycle progression of a critical priority fungal pathogen, Candida albicans

city: Hyderabad

first: Amartya

last: Sanyal

state: Telangana

address: Jawahar Nagar, Kapra Mandal, Medchal District

department: Biological Sciences

country: India

institute: BITS Pilani Hyderabad Campus

summary: The RSC (Remodels the Structure of Chromatin) and the homologous chromatin remodeling complexes are known to regulate cell cycle progression in various organisms, including Saccharomyces cerevisiae, Drosophila, and Homo sapiens. In this work, we characterized the role of two novel CTG clade-specific proteins (Nri1 and Nri2) of the RSC complex in the regulation of cell cycle progression in a critical priority fungal pathogen, Candida albicans. We observed that Nri1, alone or along with Nri2, regulates cell cycle progression at multiple stages. The nri1Δ/Δ and nri1Δ/Δ nri2Δ/Δ mutants exhibited transient cell cycle arrest, defective spindle morphology, and cytokinesis. Transcriptomic analysis supported these mutant phenotypes and indicated a broad role of Nri proteins in the cell cycle. From our results, we conclude that Nri proteins are crucial for C. albicans proliferation and fitness.

overall_design: We investigated the functions of Nri1 and Nri2 proteins of C. albicans RSC complex by analyzing the transcriptomic changes in the cells lacking either one or both the proteins. Transcriptomic profiles of the mutants were compared with the wild type C. albicans strain. Three biological replicates were analyzed for each strain.

first: Ankita

last: Joshi

first: Gayatri

last: Brahmandam

first: Santanu

last: Ghosh


title: The polymerized protein response (PPR) is activated by genetic variants that polymerize in the ER and is mediated by NFκBp50

city: Saint Louis

first: Paul

last: Cliften

state: MO

address: 4444 Forest Park Avenue

department: Genetics

institute: Washington University School of Medicine

summary: In previous studies we have shown that accumulation of the polymerogenic variant ATZ that causes α1-antitrypsin deficiency (ATD) activates NFκB DNA binding.  Here we discovered that this response, which we are naming the polymerized protein response (PPR), is characterized by NFκB p50 homodimers, distinct from the p50/p65 heterodimers in the canonical NFκB inflammatory response and the unfolded protein response (UPR).  The PPR is also activated by other disease associated variants that polymerize in the ER whereas disease-associated variants that do not form polymers activate p50/p65 heterodimers and UPR. The PPR elicits a unique gene expression profile, including changes that stabilize p50 homodimers in cytoplasm and nucleus.  The PPR is blocked by specific genetic substitutions within the luminal and cytosolic domains of Derlin-2 providing evidence that the ERAD retrotranslocation complex is a proximal transducer of this signaling mechanism. We hypothesize that the PPR is a proteostasis response pathway complementary to the UPR, designed to protect the cell from the specific proteotoxic effects of polymers that form aberrantly in the ER.

overall_design: RNA-Seq profiling of male WT PBS vs. male PiZ PBS, male WT PBS  vs male WT TNF-alpha, male WT DMSO  vs. male WT tunicamycin, and male PiZ PBS vs. male PiZ PBS p50-KO (-/-)

first: Munanairi

last: Admire

first: Rudnick

last: David A.

first: Huang

last: Jiansheng

first: Perlmutter

last: David H.