title: Polycomb erasers BAP1 and UTX are dispensable for rapid bivalent gene activation but essential for enhancer establishment [RNA-seq]

status: Public on Apr 29 2026

city: Tianjin

first: Meihan

last: Gong

address: Qixiangtai Road

country: China

institute: Tianjin Medical University

type: Expression profiling by high throughput sequencing

summary: Polycomb group (PcG) proteins safeguard cell identity by maintaining target genes in a transcriptionally repressed state through depositing two histone marks, H2A lysine-119 ubiquitination (H2AK119ub1) and H3 lysine-27 trimethylation (H3K27me3). BAP1 and UTX are thought to erase these marks during transcription activation, but their exact roles remain unclear. Here we observe a rapid loss of H2AK119ub1, followed by a reduction in H3K27me3 levels at promoters upon transcription induction, coinciding with a swift dissociation of PRCs. With an acute degradation system, we show that BAP1 and UTX are dispensable for transcription activation or the dissolution of PcG repressive marks. Instead, they promote enhancer establishment during cell fate transition independent of their eraser enzymatic activity. Therefore, our study provides novel mechanistic insights that the dissolution of PcG-marks is transcription-dependent while UTX and BAP1 primarily function as bridging factors to construct enhancers, rather than as erasers of PcG memory.

overall_design: BAP1-AID or UTX-AID ESCs were treated with retinoic acid (RA) for 0, 3, and 6 hours, under conditions with or without indole-3-acetic acid (IAA), followed by RNA sequencing (RNA-seq) analysis.


title: RNA-seq data of virtual memory T  cells In vitro induced from WT and DUSP2-/- CD8+ T cells

city: Beijing

first: Weixuan

last: Wang

address: No. 38 Xueyuan Road, Haidian District

institute: Peking University

summary: Virtual memory CD8+ T (TVM) cells are a distinct subset of antigen-inexperienced cells with rapid effector potential, but their regulatory checkpoints remain elusive. Here, using bulk RNA sequencing, we found that DUSP2 intrinsically limits the differentiation of highly activated TVM cells, thereby constraining antiviral immunity.

overall_design: Primary CD8⁺ T cells isolated from lymph nodes of WT and Dusp2-/- mice were resuspended in T cell medium. Cells were stimulated with anti-CD3 antibody, anti-CD28 antibody, IFN-α and IL-4 to induce virtual memory T cells in vitro. Cells were harvested 18 hours after activation and sorted into CD44super-high and CD44lo CD8⁺ T cell subsets. Total RNA was extracted and subjected to high-throughput sequencing.

first: Wenyu

last: Tian

first: Yaruo

last: Qiu

first: Dan

last: Lv


title: DNA:RNA ImmunoPrecipitation (DRIP) sequencing data of virtual memory T  cells In vitro induced from WT and Cd4-Cre Rpa1fl/fl CD8+ T cells

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Virtual memory CD8+ T (TVM) cells are a distinct subset of antigen-inexperienced cells with rapid effector potential, but their regulatory checkpoints remain elusive. Here, using DRIP sequencing, we found that loss of RPA1 promotes aberrant R-loop accumulation, leading to enhanced chromatin accessibility and subsequent TVM cell differentiation.

overall_design: Primary CD8⁺ T cells isolated from lymph nodes of WT and Cd4-Cre Rpa1fl/fl mice were resuspended in T cell medium (RPMI-1640 supplemented with 10% FBS, 1 × Pen-Strep, 1 mM sodium pyruvate and 0.05 mM 2-mercaptoethanol). Cells were seeded into 48-well plates at a density of 2 × 10^6 cells/mL and stimulated with anti-CD3/28 antibodies, anti-CD3/28 antibodies+IFN-α+IL-4 or left untreated. Cells were harvested 18 hours after activation and subjected to DRIP-seq to assess the R-loop levels.


title: The PGD2/DP2 axis promotes pro-inflammatory responses but attenuates an antigen-presenting role of human basophils

city: Headington

first: Jian

last: Luo

state: Oxford

address: 69 Headley Way

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

summary: Basophils are distinct blood leukocytes that express immunoglobulin (Ig) E receptor FcR1 and can be activated by IgE. Their roles in asthma, particularly IgE-independent effects, remain incompletely understood. Human basophils highly express the prostaglandin D2 (PGD2) receptor 2 (DP2; also known as chemoattractant receptor homologous molecule expressed on Th2 cells, CRTH2). Here we explore the PGD2/DP2 axis as an alternative pathway for basophil activation. Basophils are enriched in patients with severe eosinophilic asthma, correlating with eosinophil counts but not IgE levels. PGD2/DP2 stimulation promots basophil recruitment, activation, and the production of histamine, leukotrienes, and type 2 cytokines. RNA sequencing and further in vitro experiments reveals that, although PGD2 and IgE share some signalling pathways and functions, they induce distinct gene transcriptional signatures. Interestingly, PGD2 downregulats major histocompatibility complex class I-related gene protein (MR1) and attenuates basophil antigen-presentation to mucosal associated invariant T (MAIT) cells, leading to reduced IFN- production. These findings highlight the PGD2/DP2/basophil axis as a contributor to asthma, particularly in IgE-low conditions, and suggest it as a potential therapeutic target for related diseases.

overall_design: RNA-seq profiling of human basophils treated with media, PGD2, PGD2+QAW039, IgE/anti-IgE.

first: Wentao

last: Chen


title: Polycomb erasers BAP1 and UTX are dispensable for rapid bivalent gene activation but essential for enhancer establishment [ChIP-seq]

overall_design: ChIP-seq was performed for H3K27me3, H2AK119ub1, and EZH2 using BAP1-AID and UTX-AID cells treated with retinoic acid (RA) for 0, 3, 6, and 24 hours, in the presence or absence of indole-3-acetic acid (IAA).ChIP-seq for H3K4me1 was performed using BAP1-AID and UTX-AID cells overexpressing wild-type (WT) or catalytically inactive mutant proteins. Target proteins were degraded by pretreatment with IAA, followed by 24 hours of FA differentiation.


title: The balance between R-loop levels and RNAPII occupancy dictates Transcription-Replication Conflict occurrence

city: Munich

first: Ioannis

last: Tsirkas

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München, GmbH

summary: Maintaining genome integrity requires the precise coordination of replication and transcription. While R-loops are known to cause transcription-replication conflicts (TRCs), the precise nature of the barrier, whether it is the RNA:DNA hybrid itself, the stalled RNA Polymerase II (RNAPII), or a combination of both, remains elusive. Using live-cell imaging to monitor a single R-loop prone locus in real time, we demonstrate that wild-type replisomes traverse R-loops with high efficiency. Conversely, depleting R-loop processing factors, such as Rnase H enzymes or Mph1 and Sen1 helicases triggers replication fork stalling, particularly in head-on orientation. Paradoxically, we discover that R-loops serve a critical regulatory function by suppressing excessive RNAPII occupancy. In an RNAPII mutant with high DNA affinity, the enzymatic removal of R-loops leads to a pile-up of RNAPII molecules, creating a barrier to replication, more severe than the R-loops themselves. Our findings reveal a dual nature of R-loops: while they can be obstacles, they also serve as a physiological buffer that prevents the formation of high-density RNAPII “trains”. These findings establish that the precise regulation of both R-loop levels and RNAPII density is critical for preventing harmful TRCs and maintaining genome stability.

overall_design: ChIP-seq of pSer2-RNAPII in Saccharomyces cerevisiae strains growing in 2% Raffinose and 2% Galactose, expressing the mAIRN R-loop forming sequence under the control of GAL10 promoter (Pgal), and labelled with 14xPP7, in Co-Directional (CoD) or Head-On (HO) orientation relative to the replisome emerging from ARS413, in the absense or presence of endogenous Pgal-RNH1-3HA overexpression.

first: Clare

last: Lee

first: Tobias

last: Straub

first: Amir

last: Aharoni

first: Stephan

last: Hamperl


title: SroA links SigS-dependent stress signaling to repression of nitrate respiration in Staphylococcus aureus

city: Washington, DC

first: Karl

last: Thompson

address: 2201 Georgia Ave, NW

country: USA

institute: Howard University

summary: Analysis of the transcriptome changes in vector control vs. sroA over-expression samples.

overall_design: S. aureus RNA was extracted to determine transcriptome changes upon the over expression of sroA.

first: Shahad

last: Alqahtani

first: Sagar

last: Pasham

first: Jamilah

last: Alsulami

first: Brooke

middle: R

last: Tomlinson

first: Emily

middle: A

last: Felton

first: Lindsey

middle: N

last: Shaw

middle: M


title: RNA-seq analysis of B16F10 cells following p300/CBO knockout

city: Grand Rapids

first: Xiaobing

last: Shi

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

summary: The p300 and CBP (CREB-binding protein) paralogs are essential histone acetyltransferases (HATs) that serve as global transcriptional coactivators. In many cancers, including melanoma, these proteins redundantly regulate key oncogenic and lineage-specific gene programs. To investigate their combined role in melanoma, we generated p300/CBP sinlge and double-knockout (dKO) B16F10 murine melanoma cells using CRISPR/Cas9. We then performed bulk RNA-sequencing to identify genes and biological pathways that are critically dependent on these coactivators. Our results define the shared and unique transcriptional targets of p300/CBP in the B16F10 model and provide a resource for understanding how their loss impacts melanoma cell fitness, invasive potential, and stress responses.

overall_design: RNA-seq profiling was performed on B6F10 control cells, Ep300 KO cells, Crebbp KO cells or Ep300 Crebbp double knockout cells.

first: Hongkuan

last: Wang

first: Yucong

last: Yu

first: Hongwen

last: Xuan


title: DNA:RNA ImmunoPrecipitation (DRIP) sequencing data of virtual memory T  cells In vitro induced from WT and Dusp2-/- CD8+ T cells

first: Weixuan

summary: Virtual memory CD8+ T (TVM) cells are a distinct subset of antigen-inexperienced cells with rapid effector potential, but their regulatory checkpoints remain elusive. Here, using DRIP sequencing, we found that loss of DUSP2 promotes aberrant R-loop accumulation, leading to enhanced chromatin accessibility and subsequent TVM cell differentiation.

overall_design: Primary CD8⁺ T cells isolated from lymph nodes of WT and  Dusp2-/- mice were resuspended in T cell medium (RPMI-1640 supplemented with 10% FBS, 1 × Pen-Strep, 1 mM sodium pyruvate and 0.05 mM 2-mercaptoethanol). Cells were seeded into 48-well plates at a density of 2 × 10^6 cells/mL and stimulated with anti-CD3/28 antibodies, anti-CD3/28 antibodies+IFN-α+IL-4 or left untreated. Cells were harvested 18 hours after activation and subjected to DRIP-seq to assess the R-loop levels.

first: Wenyu

last: Tian

first: Yaruo

last: Qiu

first: Dan

last: Lv


title: RNA-seq profiling of SOX10 knockout A375 melanoma cells

summary: SOX10 is a lineage-defining transcription factor that regulates melanocyte identity and melanoma cell states. To investigate the transcriptional consequences of SOX10 loss, we performed bulk RNA sequencing (RNA-seq) in A375 melanoma cells with SOX10 knockout and matched control cells. This dataset enables analysis of gene expression changes associated with SOX10 depletion and provides a resource for studying the role of SOX10 in regulating melanoma transcriptional programs and cell state transitions.

overall_design: RNA-seq profiling was performed on A375 control cells or SOX10 knockout cells.


title: Spatial transcriptomic landscape of the Ciona adult brain: functional zonalisation and cellular composition in a sessile chordate brain and a novel insight into neural gland function

city: Minato-ku

first: Xin

last: Zeng

state: Tokyo

address: 8F General Research Bldg.,4-6-1 Shirokanedai

department: The Institute of Medical Science

country: Japan

institute: The University of Tokyo

summary: The ascidian Ciona provides a key model for understanding the evolutionary origin of the vertebrate brain. While the larval nervous system has been extensively characterized, the molecular and cellular organization of the adult neural complex remains poorly defined. In this stugy, we generated spatial transcriptomic maps of the adult Ciona neural complex using the 10x Visium platform. Clustering-based analysis identified five major tissue domains, including the cerebral ganglion, neural gland, ciliated funnel, neural gland duct/dorsal strand, and body wall muscle. To further refine spatial resolution, we computationally reconstructed super-resolution gene expression maps by integrating transcriptomic measurements with histological image features. The super-resolution maps enabled precise delineation of molecular territories within the neural complex.

overall_design: Spatial transcriptomic maps of the adult neural complex of Ciona intestinalis type A (Ciona robusta) were generated from three individuals, with four serial cryosections per donor, using the 10x Visium platform. Approximately 980 super-resolution gene expression maps were computationally reconstructed by integrating transcriptomic measurements with histological image features.

first: Fuki

last: Gyoja

first: Ayana

last: Maruo

first: Nanako

last: Okawa

first: Ken-ichi

last: Mizutani

first: Yutaka

last: Suzuki

first: Kenta

last: Nakai

first: Takehiro

middle: G

last: Kusakabe


title: HSD17B7 is required for Sensory Hair Cells Function by Regulating Cholesterol Synthesis

city: Nantong City

state: Jiangsu Province

address: No.9, Seyuan Road

institute: Nantong University

summary: Cholesterol homeostasis is fundamental to cellular function, and its disruption underlies a wide range of human diseases. However, the contribution of cholesterol biosynthesis to auditory physiology remains poorly understood. HSD17B7 (17β-Hydroxysteroid dehydrogenase type 7) catalyzes the conversion of zymosterone to zymosterol, a key step in the post-lanosterol cholesterol biosynthetic pathway. Here, we found that Hsd17b7 is highly enriched in sensory hair cells of zebrafish and mice. The deficiency of Hsd17b7 led to reduced intracellular cholesterol levels in HEI-OC1 cells and zebrafish hair cells, resulting in compromised MET and acoustic startle responses. In parallel, we identified a heterozygous nonsense variant in HSD17B7 (c.544G>T; p.E182*) in an individual with bilateral profound hearing loss. Expression of the p.E182* mutation failed to rescue the abnormal MET and acoustic startle response in hsd17b7 mutants. Mechanistically, the p.E182* mutation disrupted the interaction between HSD17B7 and the ER retention receptor RER1, resulting in aberrant subcellular localization and altered cholesterol distribution. Together, our findings suggest a conserved and essential role for HSD17B7-mediated cholesterol biosynthesis in sensory hair cell function and identify HSD17B7 as a candidate gene for sensorineural hearing loss.

overall_design: This submission includes single-cell RNA sequencing samples from zebrafish sensory hair cells under different genetic conditions. Samples were collected from wild-type controls and hsd17b7 mutant larvae at 4dpf. The primary experimental variable is hsd17b7 loss-of-function, allowing comparison of transcriptional profiles between mutant and control hair cells.

first: Yuqian

last: Shen

first: Ziyang

first: Xun

first: Fuping

last: Qian

first: Dong

last: Liu


title: Single-cell transcriptomic analysis of CD8+ T cells from peripheral blood of WT and Dusp2-/- mice

first: Weixuan

last: Wang

summary: Virtual memory CD8+ T (TVM) cells are a distinct subset of antigen-inexperienced cells with rapid effector potential, but their regulatory checkpoints remain elusive. Here, using single-cell transcriptomic profiling, we found that depletion of DUSP2 drives the expansion of CD44super-high TVM subset with heightened effector signatures.

overall_design: Six-week-old male WT or Dusp2-/- mice were infected with VSV at a dose of 2 × 10^7 plaque-forming units (p.f.u.). CD8+ T cells from peripheral blood were isolated 18 hours after infection and subjected to single-cell RNA sequencing (10x Genomics) to investigate the role of DUSP2 in antiviral CD8+ T cell responses.


title: Temporal control of sgRNA library activation unlocks large-scale in vivo CRISPR screens

city: Boston

first: Teng

last: Teng

state: MA

address: 201 Brookline Ave Suite 901

institute: Tango Therapeutics

summary: Functional genomics screens have revealed cancer gene dependencies, but cell culture misses vulnerabilities driven by the tumor microenvironment. We implemented CRISPR-StAR (Stochastic Activation by Recombination), an inducible pooled screening system that activates gene knockout after tumor engraftment and provides matched internal controls for guide-level normalization. Using barcode-embedded sequencing and Bayesian analysis, we screened a 30,000-sgRNA library in A549 xenografts and achieved reproducible dropout and enrichment phenotypes using just ~30 tumors. Across additional xenograft models, single tumors yielded reliable functional annotation for ~1,000 genes leveraging within-tumor normalization. Comparing in vivo and in vitro screens uncovered tumor-suppressor effects detectable only in vivo; for example KMT2C and KMT2D knockouts produced contrasting tumor growth and transcriptional programs. Together with our R analysis package, CRISPR-StAR enables scalable in vivo dependency mapping that complements in vitro resources and reduces animal use up to sevenfold versus conventional dropout screens, improving overall methodological rigor at genome-scale clonal resolution.

overall_design: Cas9-expressing cells were infected with a CRISPR-StAR library containing 29,068 guide RNAs targeting druggable genes (A549 cells) or a minipool validation library (both CRISPR-StAR and CRISPR-UMI format) containing 910 guide RNAs (A549, SW1573 and H460 cells) and subsequently engrafted in NOG mice for in vivo growth period. Terminal tumor samples were collected and extracted for gDNA. Custom PCR amplication were carried out and purified to generate NGS sequencing libraries. Guide enrichment or depletion was determined by NGS sequencing and processed by custom pipeline to generate gRNA and UMI counts.

first: Silvia

last: Fenoglio

first: Yi

last: Yu

first: James

last: Tepper

first: Lauren

last: Grove

first: Alborz

last: Bejnood

first: Samuel

last: Meier

first: Ashley

middle: H

last: Choi

first: Hsin-Jung

last: Wu

first: Annabel

last: Devault

first: Shangtao

first: Binzhang

first: Tenzing

last: Khendu

first: Hannah

last: Stowe

first: Esther

middle: C

last: Uijttewaal

first: Minjie

last: Zhang

first: Brian

middle: B

last: Haines

first: Erik

last: Wilker

first: Alan

last: Huang

first: Daniel

last: Schramek

first: Ulrich

last: Elling

first: Xuewen

last: Pan

first: Jannik

last: Andersen


title: RNA-seq profiling of SOX10 overexpression in TADA2B KO A375 melanoma cells

first: Xiaobing

last: Shi

summary: SOX10 is a key regulator of melanoma lineage identity, and TADA2B is a component of the SAGA histone acetyltransferase complex. To investigate the transcriptional interplay between SOX10 and TADA2B, bulk RNA sequencing (RNA-seq) was performed in control and TADA2B KO A375 melanoma cells with and without SOX10 overexpression. This dataset enables comparative analysis of gene expression programs associated with SOX10 activation, loss of TADA2B, and their combined perturbation, providing a resource to examine how SAGA-dependent epigenetic regulation influences melanoma transcriptional states.

overall_design: RNA-seq profiling was performed on A375 control cells, SOX10-overexpressing cells,  TADA2B knockout cells, and TADA2B knockout cells with SOX10 overexpression.

first: Hongkuan

last: Wang

first: Hongwen

last: Xuan

first: Yucong

last: Yu


title: Single cell RNA sequencing of gp33 tetramer-positive CD8 T cells sorted from the SI-LP and spleen of germ-free and SPF mice 16 days after LCMV Docile infection [scRNA-Seq 10x]

city: Freising

first: Gustavo

middle: P.

last: de Almeida

state: Bavaria

address: Liesel-Beckmann-Str. 1

department: Division of Animal Physiology and Immunology

institute: Technical University of Munich

summary: Prolonged antigen exposure in chronic viral infections reduces the effector capacity of cytotoxic T cells - a phenomenon known as T cell exhaustion. Development of T cell exhaustion is driven by high viral titers, strong TCR stimulation, and high antigen concentrations associated with strong inflammatory signals. A largely unexplored factor has been the influence of the microbiome in these processes. Here, we report that T cell exhaustion progresses independently of the presence or absence of a microbiome in chronic lymphocytic choriomeningitis virus (LCMV) infections. Virus-specific CD8 T cells in germ-free mice showed high expression of the inhibitory receptor PD-1 and decreased cytokine production. Moreover, their global gene expression patterns, as determined by single-cell sequencing, were similar to those of cells in specific pathogen-free mice. In line with this, we observed similar pathogen loads with and without a microbiome. Thus, our study demonstrates that the microbiome is dispensable for the induction of T cell exhaustion and for the limited virus control seen in chronic LCMV infections.

overall_design: Germ-free (GF) and SPF C57BL/6 mice were infected with LCMV Docile and tetramer+ CD8 T cells were sorted 16 days post infection from the spleen and lamina propria of the small intestine in a total of three biological replicates.

first: Miriam

last: Kuhlmann

middle: P

first: Wurmser

last: Christine

first: Dietmar

last: Zehn


title: Successive waves of transcriptional repression and de-repression license the cell cycle progression in an archaeon [RNA-Seq]

city: Qingdao

first: yunfeng

last: yang

address: State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P.R. China

institute: shandong university

summary: Archaea of the order Sulfolobales execute a well-structured cell cycle program similar to that of eukaryotic cells. However, the mechanism of cell cycle regulation remains enigmatic. Here, we show that three essential ribbon-helix-helix domain transcription factors, aCcr1, aCcr2, and aCcr3, play pivotal roles in controlling the cell cycle progression in the thermoacidophilic archaeon Saccharolobus islandicus by licensing the timely transcription of the key genes that define the cell cycle phases. The three transcription factors act as repressors and recognize similar regulatory sequences. However, their expression timing during the cell cycle differs: aCcr1 is expressed immediately after the cell division, aCcr3 during the transition between the G1 and genome replication (S) phase, whereas aCcr2 is expressed throughout the cell cycle. The disengagement of aCcr2 from the recognized promoters prior to the M phase is controlled through its phosphorylation by the cyclically-expressed eukaryotic-like kinase aCcrK (archaea cell cycle regulatory kinase). The synergy between aCcr1, aCcr2, and aCcr3 is also achieved through their differential affinities for the promoters and the levels of protein expression. The global regulation of the Sulfolobales cell cycle may be achieved not through transcriptional activation, but rather by repression of the key genes during strategic moments of the cell cycle. We propose a phosphorylation-assisted braking point model for the cell cycle control in Sulfolobales, which may represent a simple evolutionary intermediate on the way to the more complex cell cycle regulation in eukaryotes.

overall_design: The control group consists of empty plasmid strains, while the experimental group comprises strains overexpressing transcription factors aCcr2 and aCcr3, induced by arabinose.

first: Yunfeng

last: Yang

first: Shikuan

last: Liang

first: Zixin

last: Geng

first: Miguel V

last: Gomez-Raya-Vilanova

first: Wenying

last: Xia

first: Junfeng

last: Liu

first: Qihong

first: Jinfeng

last: Ni

first: Qunxin

last: She

first: Mart

last: Krupovic

first: Yulong

last: Shen


title: RNA-seq analysis of Tada2b knockout in B16F10 cells

first: Xiaobing

last: Shi

summary: Tada2b (Transcriptional adaptor 2B) is a core component of the SAGA complex, where it serves as a critical adaptor for the histone acetyltransferase Gcn5. While Tada2b is known to facilitate gene activation, its specific role in melanoma and the maintenance of the transcriptome remains poorly defined. In this study, we investigated the global gene expression changes resulting from Tada2b loss in B16F10 murine melanoma cells. We generated Tada2b-knockout (KO) cells using CRISPR/Cas9 and performed bulk RNA-sequencing. Our goal was to identify differentially expressed genes and dysregulated pathways that depend on Tada2b-mediated transcriptional regulation.

overall_design: RNA-seq profiling was performed on B6F10 control cells or Tada2b knockout cells.

first: Hongkuan

last: Wang

first: Yucong

first: Hongwen

last: Xuan


title: Integrating Single-Cell and Macroscopic Transcriptomics to Decode Transcriptional and Immune Microenvironment Remodeling Associated with Extravillous Trophoblast Invasion Arrest in Severe Preeclampsia

city: hangzhou

first: Qihang

last: Zhao

address: hangzhou huansha road 261

institute: Hangzhou First People's Hospital

summary: Preeclampsia is a pregnancy-specific systemic disorder that poses significant threats to maternal and perinatal health. The core pathological features of this condition involve shallow invasion of extravillous trophoblasts and defective vascular remodeling at the maternal-fetal interface during early pregnancy. Despite its clinical importance, the transcriptional reprogramming and dynamic cell-to-cell communication at single-cell resolution in severe preeclampsia remain insufficiently explored. This study aims to delineate the lineage shifts of extravillous trophoblasts and the associated immune microenvironment crosstalk

overall_design: Collect placental samples from three patients with severe eclampsia

first: Xiao

last: Lin

first: Juanmei

last: Gao

first: Linzhen

last: Wu


title: Polycomb erasers BAP1 and UTX are dispensable for rapid bivalent gene activation but essential for enhancer establishment [CUT&Tag]

first: Meihan

last: Gong

summary: Polycomb group (PcG) proteins safeguard cell identity by maintaining target genes in a transcriptionally repressed state through depositing two histone marks, H2A lysine-119 ubiquitination (H2AK119ub1) and H3 lysine-27 trimethylation (H3K27me3). BAP1 and UTX are thought to erase these marks during transcription activation, but their exact roles remain unclear. Here we observe a rapid loss of H2AK119ub1, followed by a reduction in H3K27me3 levels at promoters upon transcription induction, coinciding with a swift dissociation of PRCs. With an acute degradation system, we show that BAP1 and UTX are dispensable for transcription activation or the dissolution of PcG repressive marks. Instead, they promote enhancer establishment during cell fate transition independent of their eraser enzymatic activity. Therefore, our study provides novel mechanistic insights that the dissolution of PcG-marks is transcription-dependent while UTX and BAP1 primarily function as bridging factors to construct enhancers, rather than as erasers of PcG memory.

overall_design: CUT&Tag for MLL4 was performed using BAP1-AID and UTX-AID cells overexpressing wild-type (WT) or catalytically inactive mutant proteins. Target proteins were degraded by pretreatment with indole-3-acetic acid (IAA), followed by 24 hours of FA differentiation.


title: Translesional DNA Polη Bypass of LANA-DNA Crosslinks Ensures KSHV Episome Persistence and Tumor Growth

city: Philadelphia

first: Paul

last: Lieberman

state: Pennsylvania

address: 3601 Spruce Street

institute: The Wistar Institute

summary: The episome maintenance of DNA tumor viruses depend on their viral-encoded sequence-specific DNA binding proteins. We show here that the Kaposi’s Sarcoma- Associated Herpesvirus (KSHV) episome maintenance protein LANA can form DNA- protein crosslinks (DPCs) with the terminal repeat (TR) DNA in a cell cycle dependent manner. Targeted shRNA screening identified translesional repair DNA polymerase Polh as necessary for the stability of KSHV TR DNA and viral episome maintenance. We found that Polh co-immunoprecipitates and co-localizes with LANA nuclear bodies. Inhibiting the enzymatic activity of Polh by small molecule provided selective cell killing of KSHV+ B-cells and inhibited tumor progression in mice xenografts. Mechanistically Polh inhibition results in both single and double strand breaks at the KSHV TR due to unresolved LANA-DNA cross-links and replication fork collapse. These findings reveal a new mechanism of viral episome maintenance by DPC coupled to TLS DNA polymerases and identify Polh as a potential target for inhibition of KSHV latent infection in proliferating tumor cells.

sample_organism:
Homo sapiens
Human gammaherpesvirus 8

platform_organism:
Homo sapiens
Human gammaherpesvirus 8

overall_design: DNA-seq of single and double strand breaks isolated from the genomic DNA of a KSHV infected DLBCL cell line treated with polH inhibitor, PNR-7-02.

first: Jayaraju

last: Dheekollu

first: Coltin

middle: J

last: Albitz

first: Anjali

last: Pathania

first: Frederick

last: Keeney

first: Samantha

middle: S

last: Soldan


title: PolySUMOylation restrains ubiquitination to protect fragile genomic loci during replication stress in fission yeast

city: Wroclaw

first: Karol

last: Kramarz

address: Kanonia 6/8

department: Faculty of Biological Sciences

country: Poland

institute: University of Wrocław

summary: Formation of polymeric SUMO chains, polySUMOylation, is an emerging regulator of genome stability beyond its role in proteasomal targeting. Using Schizosaccharomyces pombe, we show that cells devoid of SUMO chains experience elevated, spontaneous replication stress concentrated at rDNA, accompanied by excessive recruitment of the recombination factor Rad52, independently from PCNA-K164 ubiquitination signaling. PolySUMOylation promotes completion of replication following hydroxyurea-induced stress in the absence of recombination. Loss of SUMO chains leads to a global increase in ubiquitination and a shift in toward K63-linked ubiquitin chains. Proteomic analyses identify shared and distinct targets of Nse2 and Pli1 E3 SUMO ligases, suggesting Pli1 role at specific genomic loci such as rDNA. Chromatin mapping demonstrated enrichment of both ligases at rDNA, centromeres, telomeres, and other fragile genomic regions. We propose that sequential monoSUMOylation and Pli1-dependent SUMO chain formation occur on chromatin to limit excessive ubiquitination, which protects vulnerable genomic loci from replication-associated instability.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for E3 SUMO ligases Pli1-12Pk and Nse2-12Pk from fission yeast Schizosaccharomyces pombe.

first: Dorota

last: Misiorna

first: Aleksandra

last: Bogdańska

first: Katarzyna

last: Markowska

first: Paulina

last: Tomaszewska

first: Michał

last: Tracz

first: Ireneusz

last: Litwin


title: Determine transcriptomic changes in TGF-β–activated CAFs following Ce6@D4-EV–mediated photodynamic therapy (RNA-seq)

city: Wuhan City

first: Chengming

last: Qu

state: Hubei

address: No.299 Bayi Road, Wuchang District

institute: Wuhan University

summary: Solid tumors, including pancreatic ductal adenocarcinoma (PDAC), drive the activation of resident quiescent fibroblasts into cancer-associated fibroblasts (CAFs), fostering the development of dense desmoplastic stroma. This pathological remodeling restricts drug delivery and immune infiltration, exacerbating tumor progression. To disrupt this self-reinforcing cycle, we engineered a multifunctional therapeutic platform based on Midkine (MDK)-targeting nanobody (Nb)-functionalized extracellular vesicles (EVs) for precision photoimmunotherapy (PIT). The system leverages the overexpression of MDK in the tumor microenvironment (TME) to achieve selective targeting. In subcutaneous and orthotopic PDAC models, near-infrared (NIR) imaging confirmed the high tumor-targeting specificity of MDK-D4-EVs. Upon loading the clinically approved second-generation photosensitizer chlorine e6 (Ce6), Ce6@D4-EV mediated targeted photodynamic therapy (PDT) triggered immunogenic cell death (ICD), promoting dsDNA release from dying cancer cells and remodeling the immunosuppressive TME via cGAS-STING pathway activation in tumor-associated macrophages (TAMs). Concurrently, Ce6@D4-EV reprogrammed CAFs to suppress extracellular matrix (ECM) deposition, enhancing tumor vascular perfusion, alleviating hypoxia, and improving therapeutic agent penetration and immune cell infiltration. This dual modulation significantly augmented the efficacy of combined therapies, including immune checkpoint inhibitors (anti-PD-1 and anti-CD47 blockades), adoptive T cell therapy, and gemcitabine (Gem) chemotherapy, leading to marked survival benefits in preclinical models. Collectively, this engineered EV-based PIT platform offers a potent strategy to overcome stromal barriers in desmoplastic tumors and establishes a foundation for clinical translation of photoimmunotherapy strategies.

overall_design: TGF-β–activated CAF-like fibroblasts were established by stimulating murine 10T1/2 cells with TGF-β (5 ng/mL). Cells were then subjected to photodynamic therapy (PDT) using MDK-targeted extracellular vesicles loaded with chlorin e6 (Ce6@D4-EV) followed by light irradiation, while matched controls were processed in parallel. Total RNA was extracted from 10T1/2-derived CAFs after treatment (n = 3 biological replicates per group) and used to construct RNA-seq libraries. Libraries were sequenced on an Illumina platform to generate paired-end reads. Reads were quality-controlled, aligned to the mouse reference genome, and gene-level counts were quantified. Differential expression analysis was performed between Ce6@D4-EV+light and control conditions to identify significantly altered genes. Functional enrichment analyses (e.g., KEGG pathway enrichment) were conducted on differentially expressed genes to characterize pathways associated with CAF activation and extracellular matrix remodeling, including TGF-β signaling and ECM-related programs. The processed expression matrix and metadata for all samples are provided.

first: Zhijie

last: Li

first: Yufeng

last: Yuan


title: Regulation of melanoma cellular plasticity by the Mediator complex drives therapeutic resistance [ChIP-Seq]

first: Xiaobing

last: Shi

summary: Melanoma exhibits profound cellular plasticity that enables adaptive responses to therapeutic pressure and ultimately drives treatment resistance. However, the transcriptional mechanisms governing melanoma cell-state transitions remain incompletely understood. Here, we identify the Mediator complex as a central regulator of melanoma cellular plasticity that promotes resistance to targeted therapy. Using genetic and pharmacological perturbations, we show that disruption of Mediator function induces melanoma cell-state switching, promotes dedifferentiation programs, characterized by loss of lineage-specific transcriptional programs and activation of survival-associated gene expression, and enhances resistance to MAPK pathway inhibition. Mechanistically, Mediator tail depletion rewires transcriptional networks governing cell identity and adaptive signaling, enabling melanoma cells to bypass MAPK pathway blockade. Collectively, our findings identify the Mediator tail module as a key transcriptional safeguard against melanoma dedifferentiation and reveal its unexpected role in suppressing cellular plasticity–driven resistance to targeted therapy.

overall_design: Samples 1-24: ChIP-seq for H3K27ac was performed in A375 control and Mediator knockout (KO) cells treated with either DMSO or 1 μM vemurafenib for 24 h.      Samples 25-54: ChIP-seq for MED23, HDAC3, and H3K27ac were performed in A375 control, MED23 KO, and HDAC3 KO cells.

first: Yucong

last: Yu

first: Hongwen

last: Xuan

first: Hongkuan

last: Wang


title: Regulation of melanoma cellular plasticity by the Mediator complex drives therapeutic resistance [crispr]

overall_design: Screens were performed in A375 Mediator knockout cells using a homemade epigenetic library, or a whole-genome knockout library.

first: Mengying

last: Huang


title: Successive waves of transcriptional repression and de-repression license the cell cycle progression in an archaeon [ChIP-Seq]

first: yunfeng

last: yang

overall_design: Chromatin immunoprecipitation (ChIP-Seq) was performed according to Takemata et al.(39) with slight modifications. Briefly, the cells were collected 3 hours after synchronization, cross-linked by adding 1% formaldehyde for 15 minutes, and quenched with a final concentration of 125 mM glycine. The cells were pelleted by centrifugation at 5,000 g for 10 minutes and washed with PBS. The cells were then resuspended in TBS-TT buffer (20 mM Tris, 150 mM NaCl, 0.1% Tween-20, 0.1% Triton X-100, pH 7.5) and fragmented by sonication until the DNA fragments were of 200-500 bp. After centrifugation (10,000 g for 15 minutes), a 100 µl aliquot of the DNA-containing supernatant was kept apart to be uses as an input control and the remaining sample was divided into two aliquots. One aliquot was incubated with anti-aCcr2,3 antibody-coated protein A beads (Cytiva) and the other was incubated with pre-immune serum-coated protein A beads, which served as a nonspecific binding control (Mock control). After incubation at 60 °C for 10 hrs, the samples were collected and the captured DNA was purified by using the DNA Cycle-Pure Kit (Omega) according to the manufacturer's instruction. The input samples were treated as above without the addition of antiserum and beads. The purified DNA was used for ChIP-Seq library preparation. The library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system

first: Yunfeng

last: Yang

first: Shikuan

last: Liang

first: Zixin

last: Geng

first: Jinfeng

last: Ni

first: Qunxin

last: She

first: Mart

last: Krupovic

first: Yulong

last: Shen


title: Regulation of melanoma cellular plasticity by the Mediator complex drives therapeutic resistance [ATAC-Seq]

overall_design: ATAC-seq was performed in A375 control and Mediator knockout (KO) cells treated with either DMSO or 1 μM vemurafenib for 24 h.


title: Determine the transcriptional changes induced by Ce6@D4-EV–mediated targeted photodynamic therapy in subcutaneous KPC tumors via RNA-seq

overall_design: RNA-seq was performed to investigate the transcriptional programs and signaling pathways underlying Ce6@D4-EV–mediated targeted photodynamic therapy (PDT) in vivo. Subcutaneous KPC pancreatic tumor–bearing mice were treated with Ce6@D4-EV plus light irradiation or corresponding control conditions. Tumor tissues were harvested after treatment, and total RNA was extracted for bulk RNA sequencing. Differentially expressed genes (DEGs) were identified between PDT-treated and control tumors, followed by KEGG pathway enrichment analysis to characterize immune- and stroma-related pathway alterations. This dataset was generated to define molecular mechanisms associated with PDT-induced tumor microenvironment remodeling, including activation of innate immune pathways such as cytosolic DNA sensing and cGAS–STING signaling.


title: The circadian clock component BMAL1 enhances inflammatory response of macrophages by nuclear translocation of peroxisomal β-oxidation enzyme multi-functional protein 2

city: Fukuoka

first: Akito

last: Tsuruta

department: Pharmaceutics

institute: Kyushu university

summary: This study investigated how the circadian regulators BMAL1 and MFP2 control macrophage inflammatory responses through epigenetic mechanisms. Using H3K27ac ChIP‑seq, we analyzed genome‑wide histone H3 lysine 27 acetylation (H3K27ac) in wild‑type, Bmal1‑deficient, and Mfp2‑deficient RAW264.7 cells, a mouse macrophage‑like cell line. Comparative analyses revealed substantial overlap in H3K27ac regions reduced upon loss of BMAL1 or MFP2, suggesting a coordinated BMAL1–MFP2 axis in the regulation of inflammation‑associated chromatin states.

overall_design: ChIP-seq of th histone modification H3K27ac Naive, Bmal1 knockout, and Mfp2 knockout RAW264.7 cells

first: Nodoka

last: Hirao

first: Megumi

last: Shibata

first: Yuya

last: Yoshida

first: Yoshihiro

last: Izumi

first: Naoya

last: Shindo

first: Yuki

last: Shiiba

first: Kazuhiro

last: Higashi

first: Takuto

last: Inoki

first: Yuichiro

last: Kai

first: Yasuha

last: Hiraoka

first: Tomoaki

last: Yamauchi

first: Akio

last: Ojida

first: Bamba

last: Takeshi

last: Matsunaga

first: Satoru

last: Koyanagi

first: Shigehiro

last: Ohdo


title: Regulation of melanoma cellular plasticity by the Mediator complex drives therapeutic resistance [persister]

first: Xiaobing

last: Shi

overall_design: RNA-seq profiling was performed on A375 parental cells, 8-week trametinib-selected persister cells, and cells collected after 4 weeks of drug withdrawal.

first: Yucong

last: Yu

first: Hongwen

last: Xuan

first: Hongkuan

last: Wang


title: Epigenetic regulation of melanoma phenotypic plasticity and therapeutic resistance

summary: Melanoma progression and treatment failure are driven in part by the ability of tumor cells to undergo dynamic phenotypic state transitions. Here, we identify the SAGA chromatin-modifying complex as a critical epigenetic regulator that constrains melanoma phenotypic plasticity and preserves therapeutic vulnerability. Loss of SAGA-dependent epigenetic regulation disrupts lineage-associated chromatin states, leading to widespread transcriptional reprogramming and enhanced cellular adaptability. As a consequence, SAGA-deficient melanoma cells exhibit increased phenotypic heterogeneity and acquire resistance to targeted therapy. Mechanistically, SAGA loss impairs histone acetylation–dependent control of gene expression programs linked to differentiation and stress responses, enabling the emergence of drug-tolerant cell states. Together, these findings establish SAGA as an epigenetic safeguard against melanoma cell-state plasticity and reveal how disruption of chromatin regulatory complexes promotes therapeutic resistance.

overall_design: RNA-seq profiling was performed on A375 control cells or TADA2BKO cells treated with DMSO, 1 μM vemurafenib, or 20 nM trametinib for 24 hours.


title: DEG analysis according to NarQ overexrpession in E. coli W WT, E. coli W NarQXLP deleted strain

city: Pohang-si

first: Junyeong

middle: Yeol

last: Sung

state: Gyeongsangbuk-do

address: 77, Cheongam-ro, Nam-gu, Pohang-si, Gyeongsangbuk-do, Republic of Korea, POSTECH

country: South Korea

institute: POSTECH

summary: In microbial biochemical production, the intracellular accumulation of target chemicals often reduces growth and productivity. One effective strategy to mitigate this problem is to minimize product reuptake. However, the application of this approach in strain development has been challenged by the limited understanding of import-related genes, especially for non-native products. Here, we developed a workflow to identify genes involved in the import of 3-hydroxypropionic acid (3-HP). We constructed a genome-wide overexpression library and coupled it with a 3-HP–responsive biosensor that converts intracellular 3-HP into fluorescence, enabling high-throughput cell sorting by flow cytometry. Sorted cells exhibited a 3.0-fold increase in fluorescence, which was attributed to the overexpression of narQ. Further analysis revealed that the histidine kinase activity of NarQ was essential for this phenotype, and NarQ enhanced import even in the absence of the canonical Nar two-component system. Transcriptome profiling under NarQ overexpression revealed a distinct set of membrane-associated genes—including acrD, mliC, and pgaABCD—that were transcriptionally upregulated as part of the NarQ regulatory response. Functional tests confirmed that overexpression of these genes enhanced 3-HP import, while their deletion in producing strains increased 3-HP titers by up to 21% compared with the control strain. Together, these results establish NarQ as a regulator of a broader membrane-associated network that indirectly governs 3-HP reuptake. This study also provides a systematic framework for identifying import-related genes directly from genomic DNA, thereby advancing the development of more efficient microbial production platforms.

overall_design: RNA-seq profiling of E. coli W_WT and ΔnarQXLP strains with or without NarQ overexpression to identify NarQ-regulated genes involved in 3-HP import.

first: Seungjin

last: Kim

first: Gyoo-Yeol

last: Jung

first: Hyun-Gyu

last: Lim


title: Epigenetic regulation of melanoma phenotypic plasticity and therapeutic resistance [ChIP-seq]

overall_design: ChIP-seq was performed for HA-tagged TADA2B in A375 cells treated with DMSO or 1 μM vemurafenib for 24 h. ChIP-seq for H3K9ac was conducted in A375 control cells, TADA2B KO cells, and GCN5 PCAF double-knockout cells under DMSO or 1 μM vemurafenib treatment for 24 h. ChIP-seq for GCN5 was performed in A375 control cells and TADA2B knockout cells.


title: Spatial transcriptomics and histopathological analysis reveal selective loss of type 2a fibers in Duchenne muscular dystrophy

city: Leiden

first: Clara

last: Martinez Mir

address: Einthovenweg 20

department: Anatomy and Embryology

country: Netherlands

institute: Leiden University Medical Center

summary: Duchenne muscular dystrophy (DMD) features progressive muscle degeneration with extensive remodeling of fiber type composition and metabolism. To circumvent the lack of regional heterogeneity from bulk or small biopsies studies, we employed spatial transcriptomics, metabolic enzyme profiling, immunohistochemistry, and quantitative fiber-type analysis to map the tibialis anterior (TA) in dystrophic (hDMDdel52/mdx) and control mice. DMD muscles exhibited disrupted metabolic compartmentalization, with reduced central oxidative regions and lower oxidative gene expression. Histology confirmed decreased oxidative enzyme activity and MYH2 expression, the most oxidative type 2 fiber. Analysis across TA, extensor digitorum longus, and soleus muscles revealed consistent MYH2 fiber loss within a mosaic of localized pathological states. Modeling interactions between anatomy and disease highlighted spatially restricted transcriptional programs involving extracellular matrix remodeling, cytoskeletal disruption, and immune infiltration, indicating compartment-specific pathology. This multi-modal, spatially resolved framework advances understanding of muscle remodeling and guides biomarker discovery and therapeutic strategies that account for regional heterogeneity.

overall_design: RNA sequencing data from tissue sections isolated from murine tibialis anterior muscles

first: Paola

last: Pisterzi

first: Isabel

last: De Poorter

first: Jamilla

last: Beek

first: Anna

last: Alemany

first: Fanny

last: Sage

first: Niels

last: Geijsen


title: Regulation of melanoma cellular plasticity by the Mediator complex drives therapeutic resistance

overall_design: RNA-seq profiling was performed on A375 control cells, Mediator- or HDAC3-knockout cells, and SOX10-overexpressing cells, either untreated or treated with DMSO or 1 μM vemurafenib for 24 hours.


title: Analysis of BMDMs with or without apoptotic cell pretreatment [RNA-seq]

city: Hong Kong

first: Alfred Sze-Lok

last: Cheng

address: Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, CUHK

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: Immune-checkpoint blockade (ICB) therapies have transformed the treatment landscapes of solid malignancies, including hepatocellular carcinoma (HCC), which is currently the sixth most common cancer and the third leading cause of cancer death worldwide. Despite unprecedented success in clinical trials, the immunosuppressive tumor microenvironment constructed by tumor cells restricts the responsiveness of ICB therapies to a minority of patients. Triggering receptor expressed on myeloid cells-2 (TREM2) counteracts inflammation and maintains metabolic fitness in myeloid cells. Emerging single-cell RNA sequencing data in different types of tumors have identified the significance of TREM2+ myeloid cells in tumor development and ICB resistance. In this study, we aimed to investigate the potential role of TREM2 in HCC ICB resistance.

overall_design: RNA-seq of BMDM with (n = 3) or without (n = 3) apoptotic cell pretreatment

first: Zhixian

last: Liang

first: Yiling

last: Zhang

first: Siyun

last: Chen

first: Zhewen

last: Xiong

first: Yalin

last: Tu


title: Transcriptomic profiling of TREM2⁺ and TREM2⁻ TAMs in mouse HCC [RNA-seq]

overall_design: RNA-seq of TREM2+ TAM (n = 3) and TREM2- TAM (n = 3) from mouse HCC


title: Epigenetic regulation of melanoma phenotypic plasticity and therapeutic resistance [CRISPR Screen]

first: Xiaobing

last: Shi

overall_design: Screens were performed in parental A375 cells or TADA2BKO cells using a homemade epigenetic library, a whole-genome knockout library, or a whole-genome activation library.

first: Hongkuan

last: Wang

first: Hongwen

last: Xuan

first: Yucong

last: Yu

first: Mengying

last: Huang


title: Disordered protein LAT encodes relative levels of signaling pathways in T cell activation

city: Cambridge

first: Adam

last: Rubin

state: Massachusetts

address: 415 Main St.

institute: Broad Institute

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

overall_design: Refer to individual Series


title: BRD2 upregulation as a pan-cancer adaptive resistance mechanism to BET inhibition [ChIP-seq]

city: Davis

first: Suyakarn

last: Archasappawat

state: California

address: 241 Briggs Hall

department: Microbiology and Molecular Genetics

institute: University of California, Davis

summary: Bromodomain and extraterminal motif (BET) inhibitors, such as JQ1, are promising cancer therapeutics that target epigenetic regulators, particularly BRD4. However, resistance to BET inhibitors (BETi) limits their clinical utility, necessitating a better understanding of adaptive mechanisms. We identified BRD2 upregulation as a conserved response to BET inhibition across multiple cancer types and hypothesized that BRD2 compensates for BRD4 loss, sustaining essential transcriptional programs during treatment. Consistent with this, BRD2 knockdown sensitized cancer cells to BETi in vitro, and combining BRD2 depletion and JQ1 treatment significantly impaired tumor growth in vivo. At the chromatin level, BRD2 and BRD4 ChIP-seq analysis of pancreatic cancer cells showed consistent BRD4 loss from chromatin after JQ1 treatment, while BRD2 displacement differed by sensitivity. Resistant cells maintained higher BRD2 occupancy than sensitive cells, suggesting a link between BRD2 retention and drug response. To dissect the underlying mechanism of BRD2 upregulation upon BET inhibition, we analyzed co-expression networks and observed that NFYA is co-expressed with BRD2 across diverse tissues and cancer types. Consistently, NFYA binds the BRD2 promoter. NFYA depletion abrogated BRD2 upregulation upon BETi treatment, indicating that NFYA is required for BRD2 induction following BET inhibition. Collectively, our findings establish BRD2 as a critical mediator of adaptive resistance to BETi in pan-cancer and identify NFYA as a novel transcriptional regulator of this process. Co-targeting BRD2 or its regulatory network offers a rational strategy to enhance the durability and efficacy of BET-based therapies.

overall_design: Comparative chromatin immunoprecipitation sequencing (ChIP-seq) of BRD2 and BRD4 across three murine KPC-derived PDAC lines (mT3-2D, mT19-2D, mT23-2D) under DMSO or JQ1 (1 µM, 24 hours).

first: Chang-il

last: Hwang


title: BRD2 upregulation as a pan-cancer adaptive resistance mechanism to BET inhibition [RNA-seq]

overall_design: Comparative RNA-seq profiling across three murine KPC-derived PDAC lines (mT3-2D, mT19-2D, mT23-2D) under DMSO or JQ1 (1 µM, 24 hours).


title: Conserved roles of GATA4 and its target gene TBX2 in regulation of human cardiogenesis

city: Exeter

first: Nick

last: Owens

state: Exeter

address: Barrack Road

institute: University of Exeter Medical School

summary: The transcription factor (TF) GATA4 is a key mediator of cardiogenesis. GATA4 regulates cardiogenesis through the expression of its target genes, only some of which have been identified. We have used a gain of function model based on pluripotent embryonic ectoderm explants from Xenopus embryos expressing GATA4, to identify a set of downstream targets of GATA4 which are also regulated by Nodal, a known cardiogenic signal. GATA4 was shown to be required for the expression of target genes tbx2 and prdm1 in vivo, likely acting in a direct fashion by interacting with their regulatory regions. In addition, tbx2 and prdm1 are shown to have roles of their own in vivo, as downregulation of tbx2, a positive target, and overexpression of prdm1, a negative target, interferes with cardiac development in Xenopus embryos.

overall_design: Gene expression measured with RNA-seq timecourse in X.laevis animal caps with induced GATA4 and Nodal, at 2.5, 5.0, 7.5, and 24h post treatment

first: Branko

last: Latinkic

first: Pavel

last: Kirilenko

first: Ilya

last: Patrushev

first: Michael

last: Gilchrist


title: Paired primary-metastasis patient-derived organoids and mouse models identify phenotypic evolution and druggable dependencies of peritoneal metastasis from appendiceal cancer

city: New York

first: Jura

last: Pintar

email: pintarj1@mskcc.org, ganeshk@mskcc.org

state: NY

address: 1275 York Avenue

department: Molecular Pharmacology Program

country: Canada

institute: Memorial Sloan Kettering Cancer Center

summary: Peritoneal carcinomatosis is a common yet deadly manifestation of gastrointestinal cancers, with few effective treatments. To identify targetable determinants of peritoneal metastasis, we focused on appendiceal adenocarcinoma (AC), a gastrointestinal cancer that metastasizes almost exclusively to the peritoneum. Current treatments are extrapolated from colorectal cancer (CRC), yet AC has distinct genomic alterations, mucinous morphology and peritoneum restricted metastatic pattern. Further, no stable preclinical models of AC exist, limiting drug discovery and representing an unmet clinical need. We establish a first-in-class stable biobank of 16 long-term cultured AC patient-derived organoids (PDOs), including 3 matched primary AC-peritoneal carcinomatosis (AC-PC) pairs. By enriching for cancer cells, AC PDOs enable accurate genomic characterization relative to paucicellular AC tissue. We establish an organoid orthotopic intraperitoneal xenograft model that recapitulates diffuse peritoneal carcinomatosis and show that PC-organoids retain increased metastatic capacity, decreased growth factor dependency and sensitivity to standard of care chemotherapy relative to matched primary AC organoids. Single cell profiling of AC-PC pairs reveals dedifferentiation from mucinous differentiated states in primary AC into intestinal stem cell and fetal progenitor states in PC, with upregulation of oncogenic signaling pathways. Through hypothesis-driven drug testing, we identify RAS inhibitor RMC-7977 and Wnt-targeting tyrosine kinase inhibitor WNTinib as novel, clinically actionable strategies to more effectively target AC-PC.

overall_design: scRNA-seq of 3 matched pairs of primary appendiceal adenocarcinoma (AC) and peritoneal carcinomatosis (PC) patient-derived organoids (PDOs).

first: Ahmed

last: Mahmoud

first: Christine

last: Sukhwa

last: Giarrizzo

first: Philip

last: Choi

first: Henry

last: Walch

last: Zhao

first: Jonathan

last: Bermeo

first: Sebastian

last: Chung

first: Manisha

last: Raghavan

first: Samhita

last: Bapat

first: Qingwen

last: Jiang

first: Julia

last: Meredith

first: Canan

last: Firat

first: Andrea

last: Cercek

last: Foote

first: Nikolaus

last: Schultz

first: Walid

middle: K

last: Chatila

first: Garrett

last: Nash

first: Jinru

last: Shia

first: Francisco

last: Sanchez-Vega

first: Steven

last: Larson

first: Arvin

last: Dar

first: Neal

last: Rosen

first: Georgios

last: Karagkounis

first: Karuna

last: Ganesh


title: Multi-tier signaling and epigenomic reprogramming drive microglial inflammatory states and functions associated with demyelination [RNA-seq]

city: Québec

first: David

last: Gosselin

state: Quebec

address: CRCHUL - 2705 Boulevard Laurier, Bloc T - 2-34

department: Molecular Medicine

institute: Université Laval

summary: The extensive heterogeneity of microglia inflammatory states accompanying neurodegenerative diseases underscores the complex molecular mechanisms that regulate these cells. Here, we report on transcriptional effectors that control microglial inflammatory state polarization associated with brain demyelination in mice. Using flow cytometry, microscopy and RNA-seq, we identified two dominant, functionally distinct states of Clec7a+CD229+ inflammatory microglia, discriminated from one another by CD11c expression. Epigenomic analyses implicated extensive genome-wide nucleosome remodeling to the polarization process, driven by state-associated stimulation of transcription factors that included Pu.1, AP-1, Bhlhe40 and Egr2, as well as re-calibration of homeostatic input provided by Mef2. Notably, a H3K27me3-based epigenetic gatekeeping mechanisms controls transcription of Egr2 and Bhlhe40 genes. Loss-of-function experiments validated the physiological relevance of Trem2, Mef2a and Egr2 to the microglial inflammatory state polarization process in the demyelinating brain. Therefore, distinct configuration of transcriptional input cooperate with epigenetic mechanisms to specify microglial inflammatory states and functions.

overall_design: Microglia subsets from healthy mice and mice undergoing brain demyelination were isolated by FACS for 1) RNA-seq analyses to compare gene expression profiles, 2) ATAC-seq to identify transcriptional regulators, and 3) ChIP-seq targeting H3K27me3 to characterize the role of epigenetic mechanism of transcriptional repression to the control of inflammatory activities of microglia.


title: Characterization of the virus-host RNA-RNA interactome across different RNA viruses

city: Helsingør

first: Niels-Ulrik

last: Frigaard

address: Strandpromenaden 5

department: Department of Biology

country: Denmark

institute: University of Copenhagen

summary: Viruses make extensive use of host cell machinery, however, most systematic studies of virus-host interactions focused on proteins with less attention to nucleic acids. RNA plays important roles in storing, conveying, and regulating genetic information. Our understanding of functional interactions between viral and host RNA is dominated by interactions with micro-RNAs (miRNAs), such as the interaction between hepatitis C virus (HCV) and the liver specific miR-122, critical for viral replication. Methodological developments, however, allow for broader exploration of the RNA interaction landscape beyond that of miRNAs. We here set out to identify virus-host RNA interactions by optimizing RNA antisense purification to systematically map RNA-RNA interactions (RAP-RNA) for viral RNA. After using the HCV/miR-122 interaction for validation, we applied RAP-RNA to determine the RNA interactomes for three important human viruses, HCV, yellow fever virus (YFV) and chikungunya virus (CHIKV). We further performed functional studies for HCV interactors. Comparing virus-host RNA interactomes, we observed patterns of mRNAs encoding factors involved in translation and the proteasome, mitochondrial (mt)RNAs, small nucleolar (sno)RNAs and small nuclear (sn)RNAs, thereby providing a more comprehensive understanding of cellular RNA interactions for RNA viruses. This may guide future research directions, e.g. for the role of snoRNAs and snRNAs in viral RNA regulation, with potential to provide further insight to viral exploitation of host factors.

overall_design: RNA antisense precipitation (RAP)-RNA experiments performed on Huh-7.5 cells infected with hepatits C virus (HCV), yellow fever virus (YFV) or chikungunya virus (CHIKV)

first: Nkerorema

middle: D

last: Damas

first: Stefan

middle: E

last: Seemann

first: Rui

last: Costa

first: Nicolas

last: Fossat

first: Lizandro

last: Rivera-Rangel

first: Ulrik

last: Fahnøe

first: Louise

last: Nielsen

first: Jan

last: Gorodkin

first: Jens

last: Bukh

first: Troels

last: Høyer Scheel


title: Multi-tier signaling and epigenomic reprogramming drive microglial inflammatory states and functions associated with demyelination [ChIP-seq]

overall_design:
Microglia subsets from healthy mice and mice undergoing brain demyelination were isolated by FACS for 1) RNA-seq analyses to compare gene expression profiles, 2) ATAC-seq to identify transcriptional regulators, and 3) ChIP-seq targeting H3K27me3 to characterize the role of epigenetic mechanism of transcriptional repression to the control of inflammatory activities of microglia.

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The table below lists GEO accessions reused/reanalyzed for this study.
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title: Single cell ATACseq of primary bronchial epithelial cells from healthy, ex-smoker COPD and current smoker COPD patients cultured in ALI conditions

city: Tokyo

first: Keiko

last: Kan-O

address: Kawadacho 8-1, Shinjuku-ku

department: Department of Respiratory Medicine

institute: Tokyo Women's Medical University

overall_design: Using ALI system, we cultured  primary bronchial epithelial cells from healthy, ex-smoker COPD and current smoker COPD patients for 4 weeks. Single cells were prepared and sujected to scATAC-seq analysis.

first: Ayaka

last: Shiota

last: Kan-o

first: Yumiko

last: Ishii

first: Tomoaki

last: Koga


title: Multi-tier signaling and epigenomic reprogramming drive microglial inflammatory states and functions associated with demyelination [ATAC-seq]

last: Gosselin


title: Transcriptome analysis of primary bronchial epithelial cells from healthy, ex-smoker COPD and current smoker COPD patients cultured in ALI conditions

overall_design: Using ALI system, we cultured  primary bronchial epithelial cells from healthy, ex-smoker COPD and current smoker COPD patients for 4 weeks. We extracted total RNA and sujected to RNA-sesq analysis.


title: Single-cell profiling of limbic excitatory neurons reveals dysregulation of metabolic pathways in Parkinson’s disease

city: South San Francisco

first: Mitchell

last: Rezzonico

state: CA

address: 1 DNA Way

institute: Genentech

summary: Parkinson’s disease (PD) is a common age-related neurodegenerative disorder that is pathologically characterized by the presence of Lewy bodies within neurons across several brain regions. Although the severe, selective degeneration of pigmented dopaminergic neurons in the midbrain results in a characteristic constellation of motor symptoms, how additional neuronal populations are affected in disease and contribute to neuropsychiatric symptoms remains unclear. The amygdala is one of the most frequent brain regions to harbor Lewy bodies in both PD and Alzheimer’s disease with co-existing alpha-synuclein pathology. To understand how neurons and glial cells are altered in this subcortical limbic area in PD, we performed single-nucleus RNA-sequencing (snRNA-seq) of patients and age-matched controls that yielded 168,270 transcriptomes following quality control measures. Through stringent differential gene expression analysis, we found transcriptional perturbations of genes linked to metabolic pathways in excitatory neurons, including upregulation of TFEB, but not inhibitory neurons or neural precursors. Additionally, we observed increased microglia with shifts towards activated states. Through bioinformatic integration of snRNA-seq with genetics studies, our findings suggest that PD risk factors act in cell-autonomous processes through both limbic excitatory neurons and midbrain dopaminergic neurons. Our findings define the selective vulnerability of excitatory neurons in the amygdala and may have implications for the understanding and treatment of non-movement symptoms in PD.

overall_design:
Characterization and annotation of single-nuclei transcriptomes of the amygdala from post-mortem late-onset PD (n=15) and age-matched control (n=8) brains.

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

last: Glock

first: Taylor

last: Watanabe

first: Joel

last: Smith

first: Brad

last: Friedman

first: Daniel

last: Mordes


title: ATAC-seq analysis of primary bronchial epithelial cells from healthy, ex-smoker COPD and current smoker COPD patients cultured in ALI conditions

overall_design: Using ALI system, we cultured  primary bronchial epithelial cells from healthy, ex-smoker COPD and current smoker COPD patients for 4 weeks.


title: Single cell RNAseq of primary bronchial epithelial cells from healthy, ex-smoker COPD and current smoker COPD patients cultured in ALI conditions

overall_design: Using ALI system, we cultured  primary bronchial epithelial cells from healthy, ex-smoker COPD and current smoker COPD patients for 4 weeks. We extracted total RNA and sujected to RNA-seq analysis.


title: RNA-Seq Profiling of Kidney Responses in Wild-Type and Angpt2 Knockout Mice Following a 3-Week Adenine Diet

city: Taipei

first: An Jie

last: Luo

department: Graduate Institute of Physiology

country: Taiwan

institute: National Taiwan University College of Medicine

summary:
Chronic kidney disease (CKD) is characterized by progressive
tubulointerstitial injury, which plays a critical role in renal dysfunction.
Angiopoietin-2 (Angpt2) is implicated in vascular and inflammatory
processes, but its role in CKD remains unclear. In this study,
we performed RNA-seq to analyze gene expression differences
in the kidneys of wild-type  and Angpt2 knockout mice after a 3-week
adenine diet, a well-established model of tubulointerstitial injury.

overall_design:
RNA-seq profiling of the kidney in wild-type and Angpt2 knockout mice
after a 3-week adenine diet.

first: Fan-chi

last: Chang

first: Shuei-Liong

last: Lin


title: Spatial transcriptome for barley development and germination

city: Bundoora

first: Marta

last: Peirats Llobet

state: Victoria

address: 5 Ring road

country: Australia

institute: La Trobe University

overall_design: Barley (cv La Trobe) caryopsis from development (3, 6, 12 and 20 days after pollination) and germination (0, 1, 3, 6 and 24 hours after imbibition) were collected, snap-frozen and cryosectioned. The sections were processed using Visium (10x Genomics) and sequenced using Illumina.


title: Single-cell RNA-Seq data from preeclamptic and healthy placentas

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

summary: To characterize the cellular composition and transcriptomic alterations in placentas affected by preeclampsia, we performed single-cell RNA sequencing on placental tissue with chorioamniotic membranes from three healthy donors and eight individuals with preeclampsia.

overall_design: Immediately following delivery, whole-thickness placental samples and chorioamniotic membranes were digested with to obtain single-cell suspension for sequencing at the University of Michigan Advanced Genomics Core. Cell viability was confirmed to be above 80% for all samples. Libraries were constructed on the 10X Chromium system with chemistry v3 and sequenced on the Illumina NovaSeq 6000 sequencer to generate 150 bp paired-end reads. I'm not sure if we need to add something about data analysis here, depending on the form the submitted data is in.

first: Johann

last: Gudjonsson

first: Lam

last: Tsoi


title: CTCF regulates chromatin accessibility of the HBAD gene promoter during erythroid differentiation

city: Mexico City

first: Gustavo

last: Tapia

state: CDMX

address: Cto. Exterior s/n

department: Molecular Genetics

country: Mexico

institute: IFC-UNAM

summary: Chromatin structure undergoes dynamic rearrangements during cell differentiation. The architectural protein CTCF plays diverse roles in this process. Here, we demonstrate that a subset of gene promoters alters their chromatin accessibility profiles upon CTCF binding during differentiation of the chicken erythroblast cell line HD3. Furthermore, we show that CTCF contributes to establishing a specific 3D chromatin architecture in the α-globin multigenic domain prior to differentiation in HD3 cells.

overall_design: To characterize CTCF's role during in vitro chicken erythroid differentiation, we performed CTCF ChIP-seq in both uninduced HD3 cells and HD3 cells induced for 24 hours. We then generated a promoter-specific mutant lacking the CTCF binding site in the HBAD globin gene and analyzed resulting changes using ATAC-seq, to assess chromatin accessibility, and UMI-4C, to evaluate local chromatin interactions.

last: Tapia Urzúa

first: Hober

last: Núñez Martínez

first: Martin

last: Franke

first: Sylvia

last: Garza Manero

first: Ángel

last: Cerecedo Castillo

first: Carlos

last: Peralta Álvarez

first: Georgina

last: Guerrero

first: José

middle: L

last: Gómez Skarmeta

first: Félix

last: Recillas


title: CTCF regulates chromatin accessibility of the HBAD gene promoter during erythroid differentiation [UMI-4C]


title: Effect of Mettl3 overexpression on gene expression in the livers of mice subjected to chronic-plus-binge ethanol feeding

city: Hefei

first: Jinghao

last: Yao

state: Anhui

address: NO. 218 Jixi Road

department: Oncology

institute: First Affiliated Hospital of Anhui Medical University

summary: Alcohol-associated steatohepatitis (ASH), a severe form of alcohol-associated liver disease (ALD), is characterized by pronounced steatosis and immune cells infiltration. As an inflammatory disease, ASH still lacks effective immunotherapies, and the mechanisms underlying alcohol-induced immune imbalance in the liver microenvironment remain elusive. RNA modifications are known to maintain hepatic homeostasis during physiological and pathological processes. This study aimed to investigate the alteration of RNA modification in ASH and its specific roles in regulating immune homeostasis. Our study found that the level of RNA N6-methyladenosine (m6A) modification and its key writer, METTL3, are markedly reduced in mouse liver during ASH. Hepatocyte-specific Mettl3 overexpression alleviated ASH by improving liver steatosis and inhibiting neutrophils infiltration and inflammatory cytokines production.

overall_design: Adeno-associated viruses (AAVs, AAV8-TBG-MCS-3×FLAG-WPRE, AAV8-TBG-Mettl3-3×FLAG-WPRE) were delivered into the livers of wild-type mice through tail vein injection. After 3 weeks, mice were fed with either control or ethanol-containing diet for 10 days, followed by a single binge of maltose (control) or ethanol .

first: Pei

last: Liu

first: Xinkun

last: Teng

first: Dejie

last: Kong

first: Hua

last: Wang


title: Clinical cure of chronic hepatitis B is dependent on activation and perpetuation of a robust CD4+ T cell response

city: San Francisco

first: Ravi

last: Patel

address: 513 Parnassus Ave

department: CoLabs

institute: University of California San Francisco

summary: Hepatitis B virus (HBV) is a major global pathogen that often leads to immune-mediated progressive liver injury and liver cancer. While seroclearance of the surface antigen (HBsAg) defines clinical cure and reduces disease-associated risks, HBsAg clearance is rarely observed and remains therapeutically elusive. Here we overcome some of the challenges to studying immune mechanisms of HBsAg clearance in chronic hepatitis B (CHB) using our mouse model of age-dependent HBsAg clearance and persistence, and samples from our BeNEG-DO trial that provided longitudinal PBMCs from patients who either cleared HBsAg or retained stable HBsAg levels after stopping nucleos(t)ide analog therapy. We show that young mice fail to clear HBsAg and have an impaired ability to efficiently initiate and sustain an HBV-specific CD4+ T cell response. We also demonstrate a role for CD4+ T cells in hepatic leukocyte organization, HBV-specific CD8+ T cell cytotoxicity, and ultimately HBsAg clearance. Upstream of the CD4+ T cell response, we reveal that hepatic dendritic cells, particularly cDC2s, direct effective CD4+ T cell activation and differentiation. Studies in CHB patients identified immune features of HBsAg clearance that overlap with the mouse model, including Th1 and cytotoxic CD4+ T cell activation and CD8+ T cell cytotoxic effector function. These findings identify an important role for potent CD4+ T cell activation in the clinical cure of CHB, and illuminate potential immunotherapeutic targets for enhancing CD4+ T cell responses to achieve greater HBsAg clearance rates.

overall_design:
PBMC samples were collected from HBeAg-negative CHB patients prior stopping long-term antiviral therapy (AVT) - baseline and at the follow up visits after stopping AVT. Surface protein and gene expresssion was analyzed using CITE-seq. Patients were grouped into two groups:  HBsAg clearance or persistence based on the status of HBsAg after 48 months of follow up post end of treatment .

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

first: Jillian

last: Jespersen

first: Lia

last: Avanesyan

first: Gabriela

last: Fragiadakis

first: Stewart

last: Cooper

first: Jody

last: Baron


title: The mechanism of growth-promoting bacteria Enterobacter sp. CS8-gfp enhancing the degradation of atrazine-thiamethoxam in rice plants

city: Zhoukou

first: Xuejin

state: Henan

address: No. 26 East Renmin Road

department: Department of Gastroenterology

institute: Zhoukou Central Hospital Affiliated to Henan Medical University

summary: Plant-microbe interactions have been applied in the phytoremediation of pesticides to ensure food safety and reduce environmental health risks. However, the plant signaling molecules triggered by microbes to degrade pesticides remain unclear. Herein, we demonstrated that CS8-gfp, a growth-promoting strain, promoted degradation of two pesticides in rice plants. To better understand the the potential mechanisms, we provided the transcriptome of CS8-gfp inoculated/uninoculated rice using RNA sequencing (RNA-seq).

overall_design: Rice seeds were surface sterilized with a 3% H2O2, and cultured in the dark at 28 °C for 2 d. The germinated seeds were transferred to a hydroponic system for cultivation under the following conditions: light intensity, 200 μmol/(m² s); photoperiod, 14 h light/10 h dark; day/night temperature, 30/25 ± 1 °C. After cultivation for 14 d, the rice plants(CS8) were immersed in the CS8-gfp for 6 h, and control plants(UCS8) were treated with sterile water.

first: Liya

last: Ma


title: Effect of myeloid specific Trem2 knockout in hepatocellular carcinoma after anti-PD-1 therapy [ChIP-seq]

first: Alfred Sze-Lok

last: Cheng

overall_design: ChIP-seq (H3K36ac) of liver tumor from LysM-Cre (n = 3) and Trem2-MKO (n = 3) mice after anti-PD-1 treatment

first: Zhixian

last: Liang

first: Yiling

last: Zhang

first: Siyun

last: Chen

first: Zhewen

last: Xiong

first: Yalin

last: Tu


title: Effect of myeloid specific Trem2 knockout in hepatocellular carcinoma after anti-PD-1 therapy [RNA-seq]

overall_design: RNA-seq of liver tumor from LysM-Cre (n = 3) and Trem2-MKO (n = 3) mice after anti-PD-1 treatment


title: Spatial transcriptomics characterization of ecosystems in the immune tumor microenvironment of diffuse large B-cell lymphoma

city: Paris

first: Alba

last: Diaz Herrero

address: 1 Av. Claude Vellefaux, 75010 Paris

country: France

institute: INSERM

summary: This dataset comprises spatial transcriptomic profiles from 10 tissue samples of Diffuse Large B-cell Lymphoma (DLBCL) the most common subtype of non-Hodgkin’s lymphoma and secondary lymphoid organ controls (SLO). The diffuse nature of DLBCL challenges the analysis of cellular organization within the immune tumor microenvironment (TME). We employed spatial transcriptomics to map spatially-resolved gene expression patterns. The analysis led to the identification of six cellular ecosystems (Cell-Eco) that differ in cellular composition, functional patterns, and neighborhood characteristics. The spatially-resolved Cell-Eco signatures provided prognostic scores that stratified patients with different overall survival rates. We also found that C1q+ tumor-associated macrophages are the primary cells interacting with malignant B cells and influencing the spatial architecture of the TME. This resource offers valuable insights into the spatial complexity of the DLBCL microenvironment and its potential prognostic significance.

overall_design: DLBCL FFPE (formalin-fixed paraffin-embedded) samples were collected from eight different patients, including two resections and eight biopsies (n=10 in total); n=6 pre-treatment biopsies from six different patients, n=2 longitudinal biopsies (before and after R-CHOP therapy) from an additional patient, and n=2 different pre-treatment biopsies from another patient.  Samples were obtained from the Pathology Department at Hospital Saint Louis in Paris, France. Additionally, two adjacent sections from a healthy lymph node (LN) and two from a non-metastatic tonsil were collected from individuals undergoing non-cancer-related surgeries at Hospital Bichat and Robert Debré in Paris, France. All the samples were analyzed using Visium spatial transcriptomics (10X Genomics)

first: Pierre

last: Tonnerre


title: Myeloid dickkopf-1 fuels neurovascular and neuroimmune alterations in ischemic stroke

first: David

last: Gosselin

summary: Neurovascular impairments and neuroimmune deregulation contribute to injury progression after ischemic stroke. Dickkopf-1 (DKK1) elevated levels correlates with poor stroke outcomes. DKK1 antagonizes the canonical Wnt pathway that plays a critical role in regulating neurovascular and neuroimmune functions. Herein, we report that DKK1 expression in the normal adult brain is absent, but is de novo expressed at the lesion site after experimental ischemic stroke. Using genetic tools to conditionally induce DKK1 expression in a tissue-specific manner, we reveal that its early induction aggravates neurological deficits and injury severity after stroke, associated with altered neuronal and vascular functions. DKK1 post-stroke induction hinders lesion containment by disorganizing the astroglial scar, leading to a chronic neuroinflammation and increased anxiety-like behaviors. Using chimeric mice, we unravel that DKK1 is released by bone marrow-derived cells (BMDCs) expressing myeloid markers that infiltrate the lesion site. DKK1 restricted induction in BMDCs is sufficient to mediate astroglial scar disorganization. Notably, neutralization of DKK1 limits injury progression and improves neurological recovery after stroke. Our findings indicate that BMDCs-derived DKK1 promotes injury progression after stroke and suggest that neutralizing its biological activity represent a promising therapeutic avenue for ischemic stroke.

overall_design: To investigate the role of DKK1 following ischemic stroke, we induced DKK1 by doxyxycline 3 days after MCAo. We analyzed DKK1/ON and WT/DOX ipsilateral lesioned tissue and contralateral intact tissue of the brain hemispheres 28 days after MCAo.

first: Ayman

last: ElAli


title: DNA repair drives cisplatin-induced neuronal death

status: Public on Apr 28 2026

city: Utrecht

first: Jeroen

last: van den Berg

state: Utrecht

address: Uppsalalaan 8

institute: Hubrecht Institute

summary: Cisplatin and similar alkylating chemotherapy agents are the cornerstone treatments for many types of cancers. While effective, these drugs induce long-term side-effects in post-mitotic tissues including the nervous system. There are no known effective pharmacological interventions for chemotherapy-induced neurotoxicities, in part due to our limited understanding of how neurons and other non-dividing cells respond to DNA damage. Here, we show that nucleotide excision repair (NER) is responsible for cisplatin adduct removal in human neurons. However, contrary to its protective role in dividing cells, NER drives neuronal cell death in response to cisplatin. Through DNA repair synthesis, NER exhausts low levels of deoxynucleoside triphosphate (dNTP) pools found in post-mitotic neurons. dNTP pools are first consumed to resolve transcription blocking lesions through transcription-coupled NER. When dNTPs become exhausted, toxic double-strand breaks accumulate across the genome primarily because of incomplete global-genome NER. Supplementation with deoxynucleosides (dN) or genetic upregulation of dNTP production protects neurons from cisplatin-induced cell death. These results identify low levels of endogenous dNTP pools as a vulnerability of post-mitotic cells to DNA damage and suggest nucleoside supplementation as a strategy to protect patients from chemotherapy-induced neurotoxicity.

overall_design: i3Neurons were treated with 20 µM cisplatin for 24 hours with 20 µM EdU added for the indicated times (either 24 hours or hours 1-7 or 17-24 of cisplatin treatment). Neurons were harvested as single cells by incubating with accutase for 20 minutes and resuspending by repeated pipetting. Cells were washed with PBS, resuspended in 1 mL PBS, and then fixed by dropwise addition of 4 mL ice cold methanol under mild vortexing. Fixed cells were stored overnight at -20°C. The next day, the methanol solution was removed, and cells were resuspended in storage buffer (10% DMSO, 20 mM HEPES pH 7.5, 150 mM NaCl, 2 mM EDTA, EDTA-free protease inhibitors) and kept at -20°C until processing.

first: Willian

last: Nathan

first: Andre

last: Nussenzweig


title: Effect of myeloid specific Trem2 knockout in hepatocellular carcinoma after anti-PD-1 therapy

city: Hong Kong

address: Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, CUHK

institute: The Chinese University of Hong Kong

overall_design: Refer to individual Series


title: Foxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for functional differentiation of Treg cells [RNA-seq]

city: Hongo, Bunkyo-ku

first: Ryuichi

last: Murakami

state: Tokyo

department: Graduate School of Pharmaceutical Sciences

institute: The University of Tokyo

summary: Mechanisms by which diverse transcription factors (TFs), particularly the master regulator Foxp3, shape the heterogeneous transcriptional and epigenetic landscape of regulatory T (Treg) cells remain poorly understood. Here, we discovered that Foxp3 cooperates with BATF to direct cis-regulatory programs and gene expression essential for differentiation of immunosuppressive effector Treg (eTreg) cells. Simultaneous single-cell chromatin accessibility and transcriptome profiling, combined with topic modeling, identified cis-regulatory elements and associated programs jointly regulated by these TFs in eTreg cells. Genome-wide mapping of Treg cell-specific BATF and eTreg cell-specific Foxp3 binding sites revealed their co-binding at some of these cis-elements, synergistically enhancing accessibility and transcription. Furthermore, we provide evidence that Foxp3 interacts with specific TFs to orchestrate diverse cis-regulatory programs among Treg cell differentiation states. Thus, Foxp3 serves as a master, but context-dependent regulator, cooperating with other TFs, including BATF, to shape the heterogeneous cis-regulatory and transcriptional landscape critical for functional Treg cell differentiation.

overall_design: Expression profiling by high throughput sequencing

first: Norihito

last: Hayatsu

first: Zhenan

last: Liu

first: Shohei

last: Hori


title: Psilocybin Elicits a Conserved Glucocorticoid-Responsive Gene Signature Across Five 5-HT2A Receptor-Rich Brain Regions in the Male Rat

city: Tehran

first: Ashkan

last: Veysi

state: Tehran

address: 16 Azar avenue

department: Cell and molecular biology

country: Iran

institute: University of Tehran

summary: psychedelics are a class of substances best known for their extraordinary mind-altering effects, psychoactive properties that give them both opportunities and risks towards people’s mental health. Based on evidence from clinical trials, psilocybin, a widely used psychedelic for research purposes, appears to produce long-lasting therapeutic effects with minimal physical side effects in patients with a range of mood and addictive disorders. However, as psilocybin profoundly impacts perception, emotion, cognition and the sense of self, it is difficult to use it in the same way that ordinary candidate compounds with therapeutic potential are tested in routine daily clinical trials. Preclinical experiments can therefore provide valuable insights into the molecular mechanisms underlying the reported clinical effectiveness of the compound. Several lines of evidence strongly suggest that psilocybin exerts its effects through 5-HT2A receptors located postsynaptically to serotonergic neurons, particularly concentrated in the frontal cortex, parts of the limbic system (i.e., amygdala and hippocampus), and striatum. In an attempt to improve our knowledge of regional patterns of gene expression in the brain induced by psilocybin, we have generated a global map of gene expression in selected regions of adult rat brain (medial prefrontal cortex, cingulate cortex, hippocampus, and striatum; both right and left sides) using 3prime-RNASeq technology. While our findings revealed a few differentially expressed genes (DEGs) to be present in two or more regions, others had a region-specific profile. Additionally, pathways normally activated by glucocorticoids were found to be enriched in all the examined brain regions following psilocybin treatment.

overall_design: We treated 12 male rats each with 2 mg/kg of psilocybin and 12 male rats in control group with saline. In the next step, samples from five regions of the rats brains, including mPFC, cingulate cortex, striatum, amygdala, and hippocampus, were subjected to RNA extraction, library preparation and RNA-sequencing.

first: Daniela

last: Atanasovski

first: Maryam

last: Ardalan

first: Nasrin

last: Motamed

first: Elias

last: Eriksson


title: Queuosine promotes wecB-dependent phage resistance and biofilm formation in marine bacterium Shewanella glacialimarina

city: Helsinki

first: Pavlina

last: Gregorova

address: Viikinkaari 9B

country: Finland

institute: University of Helsinki

summary: Transfer RNA (tRNA) modifications critically fine-tune translational accuracy and efficiency, influencing bacterial adaptation to environmental challenges. Among these, the queuosine (Q) modification has recently emerged as a regulator of biofilm formation, yet its role during phage infection remains unknown. Here, we investigate how Q modification links host translational control to phage infection. We show that phage infection activates the Q biosynthetic pathway, leading to elevated Q levels and enhanced translation of NAT-biased genes. This shift drives two interconnected outcomes, namely increased biofilm formation and enhanced mutagenesis mediated by translesion synthesis polymerases. We further identify conserved, slippage-prone regions within surface-related genes that act as hotspots for adaptive variation. Together, our findings uncover a novel mechanistic link between tRNA modification and phage-driven bacterial diversification.

overall_design: Expression profiling (RNA-seq) of infected and uninfected cells 70 min post infection.

first: Minna-Maria

last: Heinonen

first: Nina

last: Sipari

first: Peter

last: Sarin


title: Vitrification of Culter alburnus Embryos by Laser-Assisted Warming with Gold Nanorods

city: shanghai

first: xiaohui

last: chen

address: No.999, Huchenghuan Rd, Nanhui New City, Shanghai, P.R. China

country: China

institute: Shanghai Ocean University

summary: Cryopreservation of fish embryos is highly challenging, and to date, successful reports of fish embryo cryopreservation remain scarce. In this study, we optimized the vitrification solution and employed gold nanorods (GNRs) in a laser-assisted warming process to improve the hatching rate of Culter alburnus embryos after cryopreservation. With V11 vitrification solution (15% DMSO, 10% EG, 15% PG, and 1 mM MT) and a laser-assisted warming condition (25 μg/mL GNRs with continuous 15 W laser irradiation), we achieved rapid and homogeneous warming, and the mean hatching rate of cryopreserved embryos reached 18.83%. RNA-seq revealed that above cryopreservation procedure led to significant transcriptional changes in calcium signaling pathways and apoptosis-related genes, which may facilitate further optimization of vitrification solution. This study provides a basis for further improving the efficiency of embryo cryopreservation in Culter alburnus and other fish species.

overall_design: Tail-bud stage embryos of Culter alburnus were used to establish a vitrification-based cryopreservation protocol. The toxicity and vitrification performance of different cryoprotectants were first evaluated to identify suitable candidates. Laser-assisted warming conditions, including laser power and gold nanorod (GNR) concentration, were then optimized based on warming rates. Multiple vitrification solutions were screened to determine the optimal formulation. Embryos were subsequently vitrified using the selected solution and rewarmed by either conventional water-bath warming or laser-assisted warming with gold nanorods. Post-warming outcomes were assessed by hatching and malformation rates. Finally, RNA sequencing was performed to analyze transcriptional responses in larvae derived from cryopreserved embryos.

first: Xinqing

last: Cai

first: Yuting

last: Luo

first: Hongkuan

last: Song

first: Jiamin

last: Wang

first: Yipeng

last: Ren

first: Bingshe

last: Han

first: Junfang

last: Zhang


title: Transcriptome sequencing of cavernous fibroblasts cultured on substrates with different stiffness.

city: Zhuhai

first: Biao

last: Liu

address: meihuadong road

institute: The Fifth Affiliated Hospital, Sun Yat-sen University

summary: Fibrotic diseases involve increased mechanical stress due to extracellular matrix deposition, significantly altering cellular metabolism. However, a systematic understanding of how mechanical force regulates lipid metabolism across different molecular layers remains limited. We employed an integrated multi-omics approach, including transcriptomics, Ribo-seq, proteomics, and lipidomics, to comprehensively assess the effects of mechanical stretch on lipid metabolism in human cavernous fibroblasts. Our analysis revealed that while mechanical force elicits complex multi-layered responses, post-translational regulation predominantly drives this lipid metabolic reprogramming. Lipidomics identified a significant reduction in fatty acids and an upregulation of ganglioside. Key genes central to this mechanosensitive metabolic shift were pinpointed. This study demonstrates that mechanical force hierarchically reprograms lipid metabolism. The shift from fatty acids to ganglioside underscores a key metabolic adaptation in fibroblasts. Targeting the identified critical genes may offer a promising therapeutic strategy for fibrosis-related diseases.

overall_design: Primary corpus cavernosum fibroblasts were cultured on the surface of Matrigel-coated dishes with pre-adjusted stiffness. After 48 hours, the samples were collected for subsequent experiments. HD stands for high stiffness, MD for medium stiffness, and SO for low stiffness (soft).

first: Yuzhuo

last: Chen


title: Ribo-seq of cavernous fibroblasts cultured on substrates with different stiffness.


title: Beyond ACE2: DPP4 Engagement Redefines SARS-CoV-2 Receptor Tropism

city: ChongQing

first: Yu

address: Gaotan Street

institute: Army Medical University

summary: The continued evolution of SARS-CoV-2 has produced variants with enhanced transmissibility despite reduced binding affinity to the canonical entry receptor ACE2, suggesting the involvement of additional host factors. Here, we integrate large-scale sequence analysis, structure-informed machine learning, biochemical assays, cell-based entry models, and in vivo infection studies to examine receptor usage diversification in recent SARS-CoV-2 variants. We find that multiple post-Omicron lineages, including XBB-derived variants, exhibit increased functional engagement of dipeptidyl peptidase 4 (DPP4), accompanied by reduced reliance on ACE2-mediated entry in defined experimental contexts. In human DPP4 knock-in mice, representative XBB variants display enhanced replication with limited pulmonary pathology. Together, these findings support a model in which SARS-CoV-2 evolution is characterized by diversification of receptor engagement strategies, highlighting DPP4 as a functionally relevant entry factor that may contribute to viral fitness under immune pressure.

overall_design: RNA-seq profiling of hDPP4-KI mice lung tissues which infected with Delta or XBB.1.9.1 variants at Day0, Day3, Day5 and Day7.

first: Jing

last: Li

first: Yumeng

first: Zhuangzhuang

last: Shi

first: Yunkai

last: Zhu

first: Tiecheng

first: Xiaoyang

last: Zhou

first: Lu

last: Dai

first: Shanshan

last: Yang

first: Ruixuan

first: Peng

last: Xie

first: Mengyao

last: Yu

first: Li

last: Gao

first: Jiaxin

last: Hu

first: Tao

last: Jiang

first: Lin

first: Weiyang

last: Sun

first: Yuzhang

last: Wu

first: Liqun

last: Fang

first: Yuwei

first: Jintao


title: Epigenetic regulation of melanoma phenotypic plasticity and therapeutic resistance [ATAC-seq]

city: Grand Rapids

first: Xiaobing

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

summary: Melanoma progression and treatment failure are driven in part by the ability of tumor cells to undergo dynamic phenotypic state transitions. Here, we identify the SAGA chromatin-modifying complex as a critical epigenetic regulator that constrains melanoma phenotypic plasticity and preserves therapeutic vulnerability. Loss of SAGA-dependent epigenetic regulation disrupts lineage-associated chromatin states, leading to widespread transcriptional reprogramming and enhanced cellular adaptability. As a consequence, SAGA-deficient melanoma cells exhibit increased phenotypic heterogeneity and acquire resistance to targeted therapy. Mechanistically, SAGA loss impairs histone acetylation–dependent control of gene expression programs linked to differentiation and stress responses, enabling the emergence of drug-tolerant cell states. Together, these findings establish SAGA as an epigenetic safeguard against melanoma cell-state plasticity and reveal how disruption of chromatin regulatory complexes promotes therapeutic resistance.

overall_design: ATAC-seq was performed in A375 control cells, TADA2B KO cells, and GCN5 PCAF double-knockout cells under DMSO or 1 μM vemurafenib treatment for 24 h.

first: Hongkuan

last: Wang

first: Hongwen

last: Xuan

first: Yucong


title: Phosphorylated DEK sustains leukemia stem cells by enabling PBX3-driven transcriptional reprogramming [CUT&Tag 2]

city: Chongqing

first: Zhe

last: Chen

address: 1 Yixueyuan Road, Yuzhong District

institute: Chongqing Medical University

summary: Leukemia stem cells (LSCs) drive acute myeloid leukemia (AML) initiation, relapse, and chemoresistance, yet the core post-translational events governing LSC formation and maintenance remain elusive. Here, through phosphoproteomic profiling of normal hematopoietic stem and progenitor cells (HSPCs) versus LSC-enriched population, we identify DEK phosphorylation as a critical modification during leukemogenesis. Functional studies in MLL-AF9- and HOXA9/MEIS1-driven AML mouse models, as well as patient-derived xenografts (PDXs), demonstrate that DEK deficiency impairs LSC maintenance and AML development. Moreover, DEK deletion enhances LSC chemosensitivity to the standard-of-care combination of azacitidine and venetoclax (Aza/Ven), whereas DEK overexpression confers robust chemoresistance. Mechanistically, DEK recruits the transcription factor GABPA to drive overexpression of transcriptional cofactor PBX3, a key oncogenic driver in AML, thereby sustaining a leukemogenic transcriptional program. This DEK-GABPA interaction strictly depends on DEK phosphorylation at Ser301/303/306/307 (the 4S site), which stabilizes the conformation of the DEK-GABPA complex. We demonstrate CK2 as the upstream kinase that directly phosphorylates DEK-4S site. Importantly, inhibition of DEK phosphorylation through 4S site mutations or treatment with a clinical-stage CK2 inhibitor CX-4945 selectively depletes LSCs while sparing normal HSPCs. Furthermore, combining CX-4945 with venetoclax promotes LSC apoptosis and suppresses the PBX3-mediated leukemogenic transcriptional program, exhibiting synergistic anti-AML effects both in vitro and in vivo. Collectively, our findings uncover a previously unrecognized phosphorylation event (DEK-4S phosphorylation) that sustains LSCs and establish the CK2-DEK axis as a promising LSC-specific therapeutic strategy in AML.

overall_design: GFP⁺ MOLM-13 cells expressing shControl, shDEK-1, or shDEK-1 rescued with DEK-4S-A were sorted for DEK and GABPA-CUT-Tag-seq.


title: Phosphorylated DEK sustains leukemia stem cells by enabling PBX3-driven transcriptional reprogramming [ATAC-seq 2]

overall_design: GFP⁺ MOLM-13 cells expressing shControl, shDEK-1, or shDEK-1 rescued with DEK-4S-A were sorted for ATAC-seq.