title: Research advance on unexpected plasticity in the life cycle of Trypanosoma brucei

city: Würzburg

first: Markus

last: Engstler

address: Am Hubland

department: Cell and Developmental Biology

institute: Universität Würzburg

summary: We have previously shown that the slender form of Trypanosoma (T.) brucei is able to infect teneral tsetse flies, develop to the first fly form, which is the procyclic form, and complete the life cycle in the insect vector (Schuster et al., 2021). Further, analysis of the transmission index (TI; defined as the number of salivary gland infections relative to the number of midgut infections) revealed a higher TI for slender as compared to stumpy forms under laboratory conditions, which included the addition of N-acetyl-glucosamine (NAG) to the infective bloodmeal. These findings challenge the prevailing view of the life cycle, according to which only stumpy forms are considered infective to tsetse flies. Here, we show that slender trypanosomes can infect both male and female tsetse flies, irrespective of their teneral status, in the absence of supplements in the bloodmeal. Additionally, an RNA-sequencing time course was performed on both slender and stumpy cells during their transition into procyclic forms. This analysis revealed that slender and stumpy form trypanosomes remain transcriptionally distinct throughout differentiation into the procyclic form. Furthermore, while the protein associated with differentiation 1 (PAD1) remains essential for the transition, slender cells do not require expression of other hallmark stumpy form traits, such as cell cycle arrest or the shortening of their flagella or microtubule corset. Instead, slender trypanosomes are able to transition directly into procyclic forms.    Taken together, these findings demonstrate that while slender cells of T. brucei follow distinct routes to become the procyclic form, they are capable of infecting both teneral and non-teneral tsetse flies, thereby contributing to the transmission and spread of these African parasites.

overall_design: Bulk RNA-sequencing timecourse following stumpy and slender bloodstream forms of  T. brucei during their in vitro transition into the first fly form, the procyclic form. Samples were harvested 0, 8, 15, 24, and 72 hrs after in vitro initiation of differentiation in biological triplicates.

first: Jaime

middle: N

last: Lisack

first: Anna Sophie

last: Kreis

first: Laura

last: Hauf

first: Johanna

last: Krenzer

first: Fabian

last: Imdahl


title: 3D epigenomic landscape of human retinal pigment epithelium [CUT&Tag]

status: Public on Jul 26 2026

city: Hangzhou

first: tang

middle: dong

last: mei

address: 866 Yuhangtang Road

country: China

institute: Zhejiang University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Retinal pigment epithelium (RPE) serves as a vital guardian of visual function, with its dysfunction driving pathogenesis in various retinal diseases, including age-related macular degeneration and inherited retinal disorders. While ongoing RPE cells transplantation clinical trials worldwide, the absence of standardized quality metrics for stem cell-derived RPE represents a significant gap. In this study, we aim to systematically dissect epigenomic divergence among human primary RPE (hRPE), induced pluripotent stem cell-derived RPE (iPSC-RPE), and immortalized ARPE-19 cells through multi-omic analyses. Our study elucidated the distinct functional characteristics of the three types of RPE and their underlying epigenetic regulatory mechanisms, with a particular focus on the development and functional maturation of iPSC-RPE. We further revealed cell-type-specific regulatory blueprints: hRPE exhibits strong extracellular matrix (ECM) organization capacity through 3D-epigenomic (3D genome folding and epigenomic state) regulation, as exemplified by the enrichment of the RUNX1 motif, whereas iPSC-RPE retains signatures of RPE development and weak ECM function, marked by transcription factors such as Hand1, OTX2, PAX6, and ECM-associated genes. On the other hand, ARPE-19 exhibits greater cell proliferation ability and specifically regulated by transcription factors such as KLF5. Together, our data greatly advance our understanding of RPE biology and provide a robust foundation for optimizing iPSC-RPE differentiation protocols and developing innovative therapeutic strategies for retinal diseases.

overall_design: CUT&Tag of hRPE, ARPE-19, iPSC-RPE and iPSC cells

first: Xiyuan

last: Liu

first: Dongmei

last: Tang

first: Jing

last: Zhang

first: Tong

last: Li

first: Jiaxiang

last: Huang

first: Haoxi

last: Chai


title: 3D epigenomic landscape of human retinal pigment epithelium [ChIA-PET]

overall_design: ChIA-PET of hRPE, ARPE-19 cells


title: 3D epigenomic landscape of human retinal pigment epithelium [ChIATAC]

overall_design: ChIATAC of hRPE, iPSC-RPE and iPSC cells


title: 3D epigenomic landscape of human retinal pigment epithelium [ATAC-seq]

overall_design: ATAC-seq profiling of hRPE,iPSC-RPE, ARPE-19 and iPSC cells


title: 3D epigenomic landscape of human retinal pigment epithelium [RNA-seq]

type: Expression profiling by high throughput sequencing

overall_design: RNA-seq profiling of hRPE,iPSC-RPE and iPSC cells


title: Mitochondrial ROS induces metabolic adaptations and maladaptations that differentially regulate ferroptosis sensitivity of the hepatocytes

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

country: USA

institute: Yerkes National Primate Research Center

summary: Ferroptosis mediates the pathogenesis of a plethora of diseases. Mitochondrial reactive oxygen species (mtROS) plays a critical role in ferroptosis induction, but the precise mechanism by which mtROS promotes lipid peroxidation-dependent ferroptosis remains poorly understood. Herein, we employed hepatocytes and iron-induced ferroptosis as models to identify the specific mtROS-mediated redox and metabolic changes that modulate ferroptosis sensitivity. Iron overload induced the activation of multiple antioxidative mechanisms, including altered transport and metabolism of redox-active metals, small Maf (sMaf)-mediated activation of transcription factor nuclear factor erythroid 2-related factor 2 (NRF2), and an increased potential of glutathione biosynthesis. Iron also induced mtROS-dependent suppression of fatty acid oxidation, the activities of citric acid cycle and mitochondrial respiration, protecting against ferroptosis. We further identified that mtROS signaling potentially impairs the biosynthesis of coenzyme Q10 (CoQ) by attenuating the expression of genes in the mevalonate pathway and CoQ8A, a stabilizer of CoQ complex. Importantly, elevating CoQ8A expression mitigated, whereas silencing CoQ8A expression enhanced, the vulnerability of hepatocytes to ferroptosis. The mtROS-mediated downregulation of CoQ8A was dependent on farnesoid X receptor (FXR) and retinoid X receptors (RXRs). Our study demonstrated, for the first time, that mtROS induces impaired CoQ biosynthesis as a maladaptive change that promotes ferroptosis.

overall_design: 4 sets of mouse hepatocytes with 3 replicates each. On day 2 of culture, one group of cells was pretreated with liproxstatin-1 (a lipid ROS scavenger), and another group with Mito-TEMPO (a mitochondrial ROS scavenger), while two received no pretreatment. The treated groups and one untreated group then received FAC treatment.

first: Somesh

last: Banerjee

first: Matthew

middle: R

last: Smith

first: Yining

middle: I

last: Wang

first: Michael

first: Derrik

last: Gratz

first: Peijian

last: He


title: Human gastric extracellular matrix hydrogels maintain organoid growth and reduce gene expression associated with epithelial-mesenchymal transition and inflammation

city: Bozeman

first: Michelle

last: Cherne

state: Mt

address: 2155 Analysis Drive

department: Microbiology and Cell Biology

institute: Montana State University

summary: The extracellular matrix (ECM) material that organoids are maintained in provides crucial signals to the epithelial cells, regulating their function and growth. We here describe the application of human gastric ECM (hgECM) for human gastric organoid culture. HgECM was prepared from human gastric tissue by decellularization and pepsin digestion. Transcriptional profiles of HGOs grown in hgECM and Matrigel were compared using single cell RNA sequencing (scRNAseq). scRNAseq revealed that cell type composition of HGOs in each ECM was comparable. However, HGOs in hgECM had reduced expression of genes associated with stem cells, epithelial-mesenchymal transition, stress, and inflammation compared to HGOs grown in Matrigel. Conversely, HGO culture in hgECM increased expression of gastric tissue-specific genes and of genes associated with growth and metabolism.

overall_design: Primary human gastric tissue was decellularized, and the remaining material was processed further to generate a purified extracelluilar matrix gel. Paired scRNAseq samples were generated by growing each of four gastric organoid lines in (1) Matrigel and (2) human tissue-derived ECM supplemented with 25% Matrigel. Organoids were retrieved from the ECM conditions and dissociated for single cell library preparation using the 10X Genomics Chromium platform for the comparison of transcriptomic responses to the two ECM conditions.

first: Jasper

middle: L

last: Gattiker

first: Katrina

last: Lyon

first: Daniella

last: Russel

first: Thomsas

middle: A

last: Sebrell

first: Alexis

last: Burcham-Carter

first: Samuel

middle: G

last: Mackintosh

first: Andrew

middle: J

last: Gorzalski

first: Diane

last: Bimczok


title: CD36-mediated lipid-accumulation in reactive microglia drives retinal degeneration through Nlrp3-IL-1β pathway [scRNA-seq]

city: Guangzhou

first: xialin

last: liu

address: Jinsui Road

institute: Zhongshan Opythalmic Center, Sun yat-sen University

summary: Lipid accumulation in microglia through CD36 enhances Nlrp3 inflammasome activation, contributing to retinal neurodegeneration.

overall_design: Single cell profilings of retinal CD11b+ cells were from  NaIO3 induced retinal degeneration mice and PBS treated control mice, using 10X genomics platform.

first: Tian

last: Zhou

first: Ziqi

last: Yang

first: Biyan

last: Ni

first: Hong

first: Yang

first: Jingpeng

last: Li

first: Minglu

last: Ma

first: Huaicheng

first: Peng

last: An

first: Huiyi

last: Xu

first: Xiaojing

last: Lin

first: Shiya

first: Shida

last: Chen

first: Lixia

first: Wei

last: Yi

first: Xialin

last: Liu

first: Chang


title: CD36-mediated lipid-accumulation in reactive microglia drives retinal degeneration through Nlrp3-IL-1β pathway [CD36cko_smart_seq]

first: xialin

overall_design: Smart-seq profilings of CD11bintCD45⁺ cells were from wildtype and CD36 cko mice, and  sequencing was performed on NovaSeq X Plus platform.

first: Tian

last: Wang

last: He


title: Single-allele nanoscale mapping of regulatory variants [RNA-Seq]

city: Oxford

first: Joseph

last: Hamley

address: John Radcliffe Hospital/Headley Way

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

summary: Millions of genetic variants are linked to human disease but identifying underlying mechanisms is challenging because most variants lie within the non-coding genome. We developed a Micro Capture-C variant-to-function platform (MCCv) based on analysis of single-allele chromatin structure. This can identify changes in nanoscale chromatin architecture and link variants in cis-regulatory elements to associated genes. Furthermore, MCCv can phase other heterozygous variants within a locus to link regulatory variants to allelically imbalanced gene expression and directly read out variant effects on chromatin interactions following genome editing. With this approach, we investigated 405 cis-regulatory elements linked to immune-mediated inflammatory disease in CD4+ T cells. We uncover a previously undescribed gain-of-function mechanism, which increases risk of autoimmunity through creation of a neo-CTCF motif that blocks super-enhancer contacts with the SESN3 promoter. We show SESN3 regulates mammalian target of rapamycin (mTOR) by sensing tryptophan and demonstrate its role in autoimmunity using mouse models.

overall_design: Two technical replicates of poly A minus RNA from three healthy donor activated CD4+ T cells.

middle: C

first: James

last: Davies


title: Single-allele nanoscale mapping of regulatory variants  [Micro-C]

overall_design: Micro-C data from activated CD4 T cells from a helathy donor with 3 technical replicates.

first: Nicholas

last: Denny


title: Single-allele nanoscale mapping of regulatory variants  [amplicon-Seq]

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: (1) Amplicon sequencing for CTCF edit in activated primary T cells from one healthy donor, 72hrs post-nucleofection.  (2) Amplicon sequencing of Rosa26 and Sesn3, 24hrs post nucleofection in Mouse HSPCs.


title: Single-allele nanoscale mapping of regulatory variants  [Capture-C]

overall_design: Micro-capture C data from Jurkat cells at gain-of-function enhancers, from Immune-mediated inflammatory disease associated enhancers in primary CD4+ activated T cells in 3 healthy donors and from promoter of SESN3 and FAM76B  in primary CD4+ activated T cells in 3 healthy donors. Additionally, MCC data from 176 control variants (including active and inactive enhancers) and MCC ultra data from 4 representative disease-associated non-coding regions.


title: Large-scale reorganization of DNA methylation and upregulation of extracellular matrix genes in cocaine reward-related hippocampal learning [RRBS]

city: New York

first: Miklos

last: Toth

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

type: Methylation profiling by high throughput sequencing

summary: Cocaine addiction is characterized by compulsive drug use and relapse triggered by drug-related cues and contexts. Though previous research on substance use disorders has primarily focused on the mesolimbic reward pathway, the hippocampus plays an important role in encoding the spatial and contextual features of reward-associated learning. The dorsal dentate gyrus of the hippocampus receives contextual information from the entorhinal cortex and forms the memories of drug-associated contexts in sparse ensembles of dentate granule cells. Since dentate granule cells, unlike other principal hippocampal neurons, express dopamine D1 receptors; they uniquely respond to the extracellular increase of dopamine during cocaine use. Given these inputs, we hypothesized that repeated experience with cocaine during self-administration would produce substantial epigenetic and transcriptional changes in dentate granule cells that, via circuit maladaptation, contributes to the strong and lasting memories of drug experience and to the high incidence of relapse. Here we report DNA methylation changes, biased toward hypomethylation, in dentate granule cells at the unusually high number of ~30,000 small, 100-200 bp genomic regions, while the purely environmental challenge of chronic unpredictable stress produced 10 times fewer differentially methylated regions. Cocaine-sensitive epigenomic regions, in contrast to the rest of the genome, had heterogenous methylation in the otherwise largely homogenous population of mature dentate granule cells, suggesting that their cocaine-induced epigenetic malleability is due to relatively unhindered switching between the methylated and unmethylated states. Further, these regions were overrepresented in enhancers and associated with about half of the expressed genes (~8,000) of diverse gene ontology functions that, however, were not random and had relevance to neuronal plasticity. In contrast, only ~400 genes were upregulated in cocaine self-administration that included a significant number of differentially methylated genes. These genes included many collage genes and were enriched in the functional category of Organization of extracellular matrix (ECM), an extra-neuronal structure involved in neuronal connectivity and plasticity. The DNA methylation and gene expression structure of dentate granule cells suggests a poly/omni-epigenic model of context-driven cocaine seeking, similar to the proposed genetic architecture of omnigenic complex traits with the contribution of large effect variants to extreme trait values. This model involves interaction between a large number of epigenetically modified neuronal genes that have small effect size and a small group of differentially methylated and expressed core genes that have large effect size and direct connection to the neuroplasticity phenotype, driving hippocampal plasticity and acquisition of cocaine self-administration. Overall, our data suggest cocaine-induced epigenetic and transcriptional changes that, via maladaptive hippocampal plasticity, may contribute to reward-related contextual learning in the dentate gyrus of cocaine self-administration in mice.

overall_design: dDG DGC layer was dissected, Cocaine group had 4 mice and Saline group had 4 mice

first: Madelyn

last: Baker

first: Elizabeth

last: Brindley

first: Kyle

last: Windisch

first: Anjali

last: Rajadhyaksha


title: A SPDYA Mutation Causes Meiotic Arrest in Non-Obstructive Azoospermia

city: hangzhou

first: Huimei

last: Zheng

address: yuhangtang roda866

institute: ZheJiang Univerisity

summary: Maturation arrest (MA) is a typical pathologic phenotype in men with Non-obstructive azoospermia (NOA), one of the most severe forms of male infertility. However, relationships between MA and meiosis-associated monogenic alterations remain largely unclear. In this study, we identified a homozygous variant (p.R199H）in SPDYA gene through whole exome sequencing in a NOA patient from a Chinese consanguineous family. SPDYA interacts with CDK2 and SUN1, potentially forming a SUN1 SPDYA CDK2 complex that is essential for the attachment of telomeres to the nuclear envelope. Bioinformatics and co-IP analyses indicated a weakened interaction between the mutant SPDYA and CDK2. Histological and immunostaining analysis indicated that spermatocytes with this mutation were incapable of repairing DNA double-strand breaks, resulting in meiotic arrest at zygotene stage of prophase I. The functional impairment of SPDYA led to significant reductions in SUN1 and CDK2 levels, widespread alterations in gene expression, and disruption of multiple signaling pathways critical for spermatogenesis. Overall, our results identify a potential genetic driver of NOA pathogenesis and highlight the role of the SPDYA protein as a regulator of prophase I progression during human meiosis, offering a potential diagnostic marker for male infertility.

overall_design: RNA-seq profiling of seminiferous tubule tissue from the proband carrying a homozygous SPDYA variant and a pooled reference consisting of five obstructive azoospermia patients

first: Yunbo

first: Xiaohang

last: Yang

first: Fan

last: Jin

first: Yongmei

last: Xi

first: Jingping

last: Li


title: Large-scale reorganization of DNA methylation and upregulation of extracellular matrix genes in cocaine reward-related hippocampal learning [RNA-seq]

overall_design: dDG DGC layer was dissected, Cocaine group had 5 mice and Saline group had 5 mice


title: Synergistic Ultrasound-Activable Artificial Enzyme and Precision Gene Therapy to Suppress Redox Homeostasis and Malignant Phenotypes for Controllably Combacting Hepatocellular Carcinoma

city: chengdu

first: yinghao

last: lv

address: Guoxue Xiang

institute: Sichuan university

summary: Hepatocellular carcinoma (HCC) remains one of the most lethal malignant tumors. Multi-modal therapeutics for HCC have attracted increasing attention. However, designing a nanotherapeutic platform with effective chem-/sono- double-modal HCC therapies is still challenging. Here, we first designed a novel porphyrin-based nanomase (Porzyme) P-Por-Os with nano-sonosensitivity for HCC therapy. Endowed with a large hollow spherical structure of poly porphyrins, which efficiently improved the electron transport capacity of polyporphyrins and exposed the active site of superficial metal atoms, P-Por-Os effectively catalyzed the production of ROS from H2O2. This so-called Chemodynamic Therapy (CDT) was further significantly reinforced by Sonodynamic Therapy (SDT) and achieving this therapeutic ultrasound-controlled anti-tumor effects in HCC. More importantly, we developed an metallothionein-2A (MT2A)-targeted enhancement to reverse the resistance to ROS and suppress cancer progression, which could theoretically be termed Precision Gene Therapy (PGT). Overall, the new therapeutic schedule with the triple-combination of P-Por-Os-based CDT, SDT, and PGT achieved remarkable anti-HCC effectiveness. This study reported an innovative artificial enzyme P-Por-Os with high tumor-killing activity and proposed a new triple-combination with CDT, SDT and PGT treatment strategy for HCC.

overall_design: To investigate the mRNA changes of P-Por-Os and P-Por-Os combined with ultrasound treatment on hepatocellular carcinoma cells, we subjected Hepa1-6 cells treated with PBS, P-Por-Os alone, and P-Por-Os combined with ultrasound to RNA-seq analysis.

first: Yinghao

last: Lyu

first: Qian

first: Sinan

last: Xie

first: Zhenyang

last: Zhao

first: Lang

last: Ma

first: Yunshi

last: Cai

first: Hu

first: Haorong

first: Kunlin

first: Fengwei

last: Gao

first: Ying

first: Pu

last: Wu

first: Kaipeng

first: Xinye

last: Dai

last: Lan

first: Hong

first: Chong

last: Cheng


title: mregDCs induce abnormal T cell functions in endometriosis

city: shanghai

first: yiqin

last: zhang

address: No. 910, Hengshan Rd

institute: International Peace Maternity and Child Health Hospital

summary: Endometriosis has a metastatic implantation biology as malignant tumors and an immunological environment as immune escape. However, the role of dendritic cells (DCs) in endometriosis is still unknown. We applied single-cell RNA sequencing (scRNA-seq) on eutopic endometrium and ectopic lesions to dissect heterogeneity within DCs subsets. ScRNA-seq data in public database was also included in the analysis. Flow cytometry was used to identify the presence of ‘mature DCs enriched in immunoregulatory molecules’ (mregDCs) in patient tissues. Multiplex immunofluorescence tissue staining was adopted to show the presence of mregDCs. To further explore the function of mregDCs in endometriosis, mregDCs and naïve CD4+ T cells were sorted by fluorescence activated cell sorting (FACS) and co-cultured. carboxyfluorescein succinimidyl ester (CFSE) assays and intracellular cytokine staining assays were employed to detect proliferation and differentiation ability of naïve CD4+ T cells in vitro. The proportions of T cell subsets in the ectopic lesions of mice following peritoneal transfusion of mregDCs were measured in vivo in a mouse model for endometriosis. ScRNA-seq data analysis displayed the substantial alterations and heterogeneity of DCs subsets in endometriosis. The proportion of mregDCs were up-regulated in the endometriosis scRNA-seq data. Flow cytometry and immunofluorescence staining confirmed the presence and upregulation of the mregDCs in ectopic lesions. The co-cultured experiment showed that endometriosis-associated mregDCs have the ability to induce naïve CD4+ T cells proliferation and differentiating as Th2 and iTregs. After peritoneal transfusion of mregDCs into endometriosis mouse model, the number of Th2 in ectopic lesion increased  significantly. Our research revealed the heterogeneity of DCs landscape in endometriosis in single cell level. We found the specific mregDC celltype may participate in the abnormal inflammation environment in endometriosis and exert profound immunostimulatory and regulatory changes in T cells function.

overall_design: From June 2019 to November 2023, premenopausal patients with EM and premenopausal patients suffering from uterine leiomyoma without EM were recruited. Endometriosis diagnose was confirmed at the time of laparoscopy according to the revised American Society for Reproductive Medicine guidelines and were reviewed by at least two experienced pathologists. All patients have no history of any inflammatory diseases or cancer.

first: Chuqing

last: He

first: Yiqin

last: Zhang

first: Jian

first: Xiaoya


title: Transcription-dependent heterochromatin at the Xist promoter shapes the random choice of the inactive X chromosome

status: Public on Jul 25 2026

city: Berlin

first: Edda

middle: G.

last: Schulz

state: Berlin

address: Ihnestrasse 63

department: Otto-Warburg-Laboratory

country: Germany

institute: Max Planck Institute for Molecular Genetics

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

overall_design: Refer to individual Series


title: Transcriptomic profiling of ATP6AP1 knockdown in activated human hepatic stellate LX-2 cells

city: Anhui,

first: HanLin

last: Bai

address: Bengbu Medical University

department: Department of Anesthesiology

institute: The First Affiliated Hospital of Bengbu Medical University

summary: Hepatic stellate cell activation is a major driver of extracellular matrix deposition during liver fibrosis. This study investigated the transcriptional changes induced by ATP6AP1 depletion in human hepatic stellate LX-2 cells. LX-2 cells were transfected with ATP6AP1-targeting siRNA or non-targeting control siRNA, with three independent biological replicates per condition. Total RNA was extracted and subjected to RNA sequencing. Sequencing reads were aligned to the human reference genome GRCh38.p10, and differential gene-expression analysis was performed using DESeq2. The dataset was generated to identify the cellular pathways regulated by ATP6AP1 depletion, with particular emphasis on hepatic stellate cell activation, cellular senescence, cell-cycle arrest and Notch signaling

first: Hanlin


title: Unleashed condensation by recurrent mutations of an epigenetic regulator promotes cancer

city: Changsha

first: Jiazheng

last: Lin

address: No. 27 Tianma Road

institute: Hunan university

summary: The pathological mechanisms and significance for the prevalent hotspot mutations in disordered protein regions are poorly understood. ASXL1 is an obligate co-factor for BAP1 in H2AK119 deubiquitination. ASXL1 mutations are very frequent in myeloid malignancies, and are mostly C-terminal truncating mutations concentrated in a specific disordered region of ASXL1. ASXL1 truncations are gain-of-function mutations that promote myeloid malignancies, but the underlying mechanisms remain poorly understood. Here we show that the frequently truncated mutants of ASXL1 possess an intrinsic property of forming phase-separated biomolecular condensates, and this property is normally suppressed by the frequently deleted regions. A disease-mutant of the endogenous ASXL1 in leukemia cells forms dynamic nuclear co-condensates with other endogenous factors important for gene activation. The ASXL1 disease mutants can greatly enhance H2A deubiquitination activity of BAP1 in cells and in vitro reconstituted system, enhance myeloid leukemia cell growth, and promote leukemogenesis in a mouse transplant model by turning on myeloid leukemogenic transcriptional programs. However, substitution of residues important for condensation disrupted or impaired all these abilities, suggesting that the condensation property is crucially important for the ASXL1 mutants in promoting cancer. Moreover, we discover that the conserved negative charges in the highly disordered and frequently deleted region on ASXL1 suppress the condensation of the wild type ASXL1. Charge-neutralizing mutations in this region restores condensation of the full-length ASXL1, and are sufficient to turn ASXL1 into a leukemogenic protein. Biochemical, biophysical, and simulation analyses suggest the intramolecular interactions normally mask the N-terminal region in engaging intermolecular interactions required for phase separation, and disease truncations escape from the regulatory interactions and unleash the phase separation property to form nuclear hubs to promote expression of tumorigenic gene programs. Finally, by showing a striking correlation of the mutation frequencies with the condensation properties and leukemogenesis activity for a series of human patient mutations, we suggest that dysregulation of condensation is a central mechanism for ASXL1 mutations in promoting myeloid malignancies. This suggests that dysregulation of condensation may be a key mechanism for some of the prevalent hotspot disease mutations in the disordered proteomes.

overall_design: Chromatin profiling was performed to examine how ASXL1 truncation and condensation-related mutations affect BAP1 chromatin occupancy, ASXL1 chromatin occupancy, and H2AK119ub chromatin signals. The ChIP-seq datasets include anti-HA ChIP-seq for HA-BAP1 and HA-ASXL1 under ASXL1 (1-590) and ASXL1 (1-590) 10RA conditions. The CUT&RUN datasets include H2AK119ub profiling under ASXL1 (1-590), ASXL1 (1-590) 10RA, ASXL1 (1-590) 25RA, vector control matched to ASXL1 (1-590), ASXL1 (1-1067), ASXL1 (1-1067) 34DN, ASXL1 (1-1067) 36EQ, and vector control matched to ASXL1 (1-1067) conditions. Raw data are provided as paired-end FASTQ files, and processed data are provided as mm39 peak calls in narrowPeak format.

first: Yansu

last: Song

first: Yi

last: Hao

first: Maria

last: Latacz

first: Marta

last: Cykowiak

first: Hao

last: Jiang


title: Physiological YAP activation alleviate ER stress to mitigate alcohol-induced liver damage by promoting ATF6 transcriptional activation

city: Boston

first: Yuchen

last: Liu

state: Massachusetts

address: 188 Longwood Avenue, REB 514B

institute: Harvard school of dental medicine

summary: Alcohol-associated liver disease (ALD) is a major global health concern driven by chronic metabolic stress. Alcohol-induced ER stress is an early event in hepatocytes, which disrupts lipid metabolism and contributes to hepatic steatosis and inflammation, driving liver damage during the progression of ALD and other liver disorders. Here, we report that in a mouse chronic alcohol feeding model, YAP activity in the liver is reduced at early stages of alcohol exposure, primarily by ER stress-induced Unfolded Protein Response (UPR), independently of canonical Hippo kinase activities. We further found that YAP activity is reduced, with elevated ER stress in human ALD.  We demonstrated that genetic deletion of Yap in hepatocytes exacerbates ALD, while overexpression or pharmacological activation of the wild-type (WT) YAP alleviates ALD and ER stress. The protective role of physiological YAP activation in reducing ER-stress-induced hepatic damage is further demonstrated by a substantial rescue of liver function and viability severely compromised by acetaminophen overdose. This is in sharp contrast to pathological YAP hyperactivation that occurs later in alcohol exposure, which exacerbates disease progression in alcoholic hepatitis (AH). Mechanistically, we show that transcriptional activation of Activating Transcription Factor 6 (ATF6), a key transmembrane ER stress sensor that also serves as a transcription factor after ER stress-induced cleavage. We found that ATF6 transcription activity is both necessary and sufficient to mediate the protective role of YAP in ER stress and alcohol induced liver injury, through its target genes Manf and Hspa5 (Grp78). YAP potentiates the ATF6 transcription activity in a TEAD-dependent manner. Our study identifies an ATF6-dependent protective role of YAP in maintaining ER homeostasis, which can be leveraged to prevent or treat ALD and other liver diseases.

overall_design:
Liver tissues for RNA-seq were collected from control mice, hepatocyte-specific Yap knockout mice, and hepatocyte-specific YAP-overexpressing mice after 4 weeks of feeding with either the Lieber–DeCarli control liquid diet (pair-fed) or the Lieber–DeCarli ethanol liquid diet (EtOH-fed).

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Submitter states that missing raw files are due to file loss.
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first: Xiaohui

last: Wang

first: Yingzi

last: Yang


title: Medin-Induced Pro-inflammatory and Prothrombotic Activation of Coronary Artery Endothelial Cells: A Potential Novel Mediator Linking Aging and Atherosclerosis

city: Phoenix

first: Ming

last: Li

state: AZ

address: 650 E Indian School Road

institute: Phoenix VA Health Care System

summary: Background: Age is the most important risk factor for coronary artery disease (CAD) independent of traditional risk factors.  Aging induces classic pro-inflammatory and prothrombotic vascular phenotypic changes whose molecular mediators remain poorly understood.  Medin is a common cleavage product protein that accumulates in vasculature with aging and shown to cause endothelial dysfunction. Its role in CAD is unknown.  The study aimed to evaluate the effects of medin on human coronary artery endothelial cell (HCAEC) pro-inflammatory and prothrombotic activation and establish the relationship between medin and coronary atherosclerosis in human decedents. Methods: HCAECs were exposed to physiologic dose of medin (5 µM) for 20 hours and ribonucleic acid sequencing (RNAseq) with signaling pathway analyses and reverse transcription polymerase chain reaction of select pro-inflammatory and prothrombotic genes performed.  Corresponding protein expression was measured by Western blot or enzyme linked immunosorbent assay in HCAECs exposed to medin (5 µM) without or with nuclear factor-κB (NFκB) inhibitor RO106-9920 (10 µM).  Coronary arteries from 40 deceased individuals underwent immunohistochemistry and medin and plaque burden were quantified and their relationship evaluated. Results: RNAseq showed predominant pro-inflammatory gene expression changes induced by medin.  HCAECs treated with medin showed increased phosphorylated NFκB, elevated protein expression of interleukin (IL)-6, IL-8, monocyte chemotactic protein (MCP)-1, intercellular adhesion molecule (ICAM)-1, vascular cell adhesion molecule (VCAM)-1 and plasminogen activator inhibitor (PAI)-1 and reduced protein expression of thrombomodulin; these changes were reversed by RO106-9920 co-treatment. In human tissues, coronary artery medin strongly correlated with plaque burden (R=0.76, p<0.0001) and coronary macrophage content (R=0.72, p<0.0001). Coronary arteries from decedents with myocardial infarction had higher medin than those without (5.53±2.67% versus 0.02±0.02%, p=0.0005). Conclusions: Medin induced NFκB-mediated endothelial cell pro-inflammatory and prothrombotic activation and was strongly associated with coronary plaque burden and inflammation.  Medin is a novel candidate mediator linking aging and coronary atherosclerosis.

overall_design: human coronary artery endothelial cell (HCAECs) were exposed to medin (5 µM) versus vehicle for 20 hours and subjected to RNAseq profiling

first: Kaleb

last: Morrow

first: Nina

last: Karamanova

first: Randy

last: Woltjer

first: Victoria

last: Krajbich

first: Jingmin

last: Shu

first: Chengyun

last: Tang

first: Alana

last: Maerivoet

first: Jillian

last: Madine

first: Yabing

last: Chen

first: Raymond

middle: Q

last: Migrino


title: An Injectable ROS-Responsive Nanozyme Hydrogel Regulates the Uterine Microenvironment to Reverse Intrauterine Adhesions

city: Guangzhouo

first: Peixian

last: Cheng

address: No. 63 Duobao Road, Liwan District, Guangzhou, Guangdong Province, China.

institute: The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China

summary: Intrauterine injury can induce a self-reinforcing vicious cycle involving inflammation, oxidative stress, and fibrosis, ultimately leading to intrauterine adhesions (IUA), which severely impair women’s reproductive health. Current treatments, such as hysteroscopic adhesiolysis combined with hormonal therapy or physical barriers, still show high recurrence rates and are unable to simultaneously regulate the interconnected pathological processes of inflammation, oxidative stress, and fibrosis. In this study, we developed an injectable ROS-responsive hydrogel (CeTA@GPP) loaded with cerium–tannic acid nanoenzymes (CeTA). Unlike passive physical barriers, this hydrogel system remains stable under physiological conditions but can be selectively cleaved in ROS-enriched inflammatory microenvironments, thereby enabling on-demand, lesion-localized CeTA delivery. This system exhibits superoxide dismutase (SOD)- and catalase (CAT)-mimetic activities, allowing it to scavenge excessive ROS, alleviate oxidative stress, restore mitochondrial membrane potential, promote macrophage polarization from the pro-inflammatory M1 phenotype toward the anti-inflammatory M2 phenotype, and reverse TGF-β1-induced fibrosis in endometrial stromal cells. In a rat model of IUA, CeTA@GPP hydrogel restored uterine antioxidant enzyme activity, promoted macrophage polarization toward the anti-inflammatory M2 phenotype, suppressed TGF-β1 expression and myofibroblast activation, and enhanced cell proliferation and angiogenesis. Transcriptomic analysis further showed that CeTA@GPP hydrogel coordinately downregulated inflammation, oxidative stress, and fibrosis related signaling pathways. Ultimately, CeTA@GPP hydrogel promoted structural and functional regeneration of the endometrium and improved endometrial receptivity. By integrating minimally invasive injectability, physical barrier protection, and intelligent ROS-responsive multi-target bioactivity, CeTA@GPP provides a promising strategy for IUA.

overall_design: Female Sprague-Dawley rats (180–220 g, 6–8 weeks old) were selected for this experiment. The animals were housed in a pathogen-free environment with free access to food and water and maintained under a 12 h light/dark cycle. The IUA rat models were established using a combined mechanical injury and infection method. All experiments were conducted under aseptic conditions and in strict accordance with the Animal Research: Reporting of In Vivo Experiments (ARRIVE) guidelines. Briefly, a total of 20 female Sprague-Dawley rats were randomly divided into four groups (5 rats per group): sham surgery group (Sham), IUA model group (IUA), IUA + GPP group (GPP), and IUA + CeTA@GPP group (CeTA@GPP). After anesthesia, the lower abdomen was sterilized and incised with a 3 cm longitudinal incision to expose both sides of the uterus. A 2 mm incision was made near the cervix on both sides of the uterus. A uterine curette was inserted through the incision into the uterine cavity and used to scrape the endometrium until it became noticeably congested and roughened. Subsequently, a 1-0 surgical suture pre-soaked in a 6 mg/L LPS solution at 4 °C for 24 h was implanted into the uterine cavity. The suture tail was led through the abdominal wall and secured to the skin surface for removal 48 h post-surgery. After placement of the LPS-containing suture, 100 μL of GPP or CeTA@GPP hydrogel was injected into the uterine cavity using a syringe through the uterine incision, whereas the IUA group did not receive any injection. Subsequently, the uterus and abdomen were sutured layer by layer. After the operation, the rats were placed in a warm cage to maintain their body temperature until they regained consciousness. All rats received penicillin injections (50,000 units per day) for 3 consecutive days after the operation. The rats were sacrificed 2 weeks after the operation, and uterine tissue samples were collected from the four groups for RNA-seq analysis.

first: Xuemin

first: Xuetao

last: Shi

first: Yong

last: Fan


title: Genome-wide PBX1 binding profiling by CUT&Tag in HUCCT1 and RBE cells

city: DaLian

first: Luo

last: Kai

state: Liaoning Province

address: No. 467, Zhongshan Road, Shahekou District, Dalian 116011, China

institute: The Second Hospital of Dalian Medical University

summary: CUT&Tag was performed to profile PBX1 genomic binding landscapes in untreated HUCCT1 and RBE human cholangiocarcinoma cell lines. Three biological replicates were analyzed for each cell line using an anti-PBX1 antibody.

overall_design: PBX1 CUT&Tag profiling in two human cholangiocarcinoma cell lines (HUCCT1 and RBE), with three biological replicates per cell line.


title: PBX1 knockdown RNA-seq in HUCCT1 and RBE cells

summary: RNA-seq was performed to profile transcriptomic changes after siRNA-mediated PBX1 knockdown in HUCCT1 and RBE human cell lines. Each cell line includes siNC and siPBX1 groups with three biological replicates per group.

overall_design: Bulk RNA-seq analysis of two human cell lines (HUCCT1 and RBE), two treatments (negative control siRNA and siPBX1), and three biological replicates per condition.


title: RNA-seq transcriptomic profiling reveals renoprotective mechanism of novel Psidium meroterpenoid derivatives (d)-G8 and (d)-G4 against cisplatin-induced acute kidney injury in human HK2 tubular epithelial cells

city: Beijing

first: sijia

last: liu

address: Xiannongtan Street, Xicheng District

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: Cisplatin is a first-line chemotherapeutic agent for multiple solid tumors, but its severe nephrotoxicity severely limits clinical application and frequently induces acute kidney injury (AKI), which may further progress to chronic kidney disease. Psidium meroterpenoids from guava possess multiple pharmacological activities, and our previous study synthesized a series of novel Psidium meroterpenoid analogs with renoprotective potential. In this work, we systematically investigated the molecular mechanism of two lead chiral compounds (d)-G8 and (d)-G4 in alleviating cisplatin-induced renal injury via transcriptome sequencing. Human renal proximal tubular HK2 cells were used as the in vitro model, with 6 experimental groups (3 biological replicates per group, total 18 samples): untreated control group, 15 μM cisplatin injury model group, cisplatin + 2.5 μM (d)-G8 group, cisplatin + 10 μM (d)-G8 group, cisplatin + 2.5 μM (d)-G4 group, and cisplatin + 10 μM (d)-G4 group. Total RNA was extracted from all samples for paired-end RNA-seq on Illumina NovaSeq 6000 platform. Differential expressed genes (DEGs) were screened, followed by principal component analysis (PCA), Venn diagram analysis, heatmap clustering, GO and KEGG functional enrichment, as well as gene set enrichment analysis (GSEA). Transcriptomic results demonstrated that both (d)-G8 and (d)-G4 exerted significant renoprotective effects by upregulating copper efflux transporters ATP7A/ATP7B, activating AMPK-mediated autophagy pathway, improving mitochondrial homeostasis, and suppressing multiple inflammatory signaling cascades, with (d)-G8 showing more potent efficacy than (d)-G4. This RNA-seq dataset provides comprehensive transcriptional evidence for the anti-AKI activity of the two meroterpenoid derivatives, and identifies key gene targets and signaling pathways for the development of novel nephroprotective agents.

overall_design: This transcriptome study adopted human renal proximal tubular HK2 cell model to explore the transcriptional regulatory effects of two chiral meroterpenoid compounds (d)-G8 and (d)-G4 against cisplatin-induced acute kidney injury. A total of 6 experimental groups were set up, with 3 biological replicates per group.Total RNA was extracted from each sample, mRNA enrichment, library construction and paired-end RNA-seq (150 bp read length) were performed on Illumina NovaSeq 6000 platform. Group comparisons were conducted between Model vs Control, compound treatment groups vs Model, to screen differentially expressed genes responding to (d)-G8 and (d)-G4 intervention under cisplatin stimulation.

first: Ying-Da

last: Zang

first: Hai-Jie

last: Wu

first: Xin-Yi

first: Zhi-Ling

last: Ma

first: Chuang-Jun

first: Jie

first: Xiao-Guang

first: Li

last: Sheng

first: Sen

last: Zhang

first: Dong-Ming


title: RNA-seq transcriptome profiling of HK-2 human renal tubular epithelial cells upon gene knockdown mediated by sgRNA

summary: Renal tubular epithelial injury plays a critical role in the progression of renal interstitial fibrosis. In this study, bulk RNA-seq was performed to investigate transcriptomic alterations in human HK-2 proximal tubular epithelial cells following target gene knockdown via sgRNA. Cells transfected with non-targeting sgRNA were used as negative control. Three biological replicates were included for each group. This dataset provides transcriptome resources to uncover molecular events regulated by the target gene in renal tubular epithelial cells.

overall_design: Human renal proximal tubular epithelial HK-2 cells were divided into two experimental groups: sgRNA-mediated gene knockdown group (sg) and non-targeting negative control group (NC). Three independent biological replicates were set for each group. Total RNA was extracted from cells for mRNA transcriptome sequencing.

first: Xukun

last: Liu


title: Transcription-dependent heterochromatin at the Xist promoter shapes the random choice of the inactive X chromosome [Xist-Tsix-perturbations_Amplicon_Bisulfite_Seq]

first: Edda

last: Schulz

summary: In female mammals, Xist, the master regulator of X-chromosome inactivation (XCI), is expressed monoallelically. This pattern is established during early embryonic development, when the active Xist allele is chosen at random in each cell. How this choice is made remains incompletely understood. Here we identify a role for the repressive chromatin mark H3K9me3 in the initiation of XCI by combining knock-down and overexpression strategies in differentiating mouse embryonic stem cells, which recapitulate the onset of random XCI. We show that H3K9me3 accumulates at the promoter-proximal region of the silent Xist allele in female cells at the same time when the monoallelic Xist expression is established. Unexpectedly, we find that H3K9me3 accumulation requires prior transcription of Xist itself. This is likely to occur during the initial phase of Xist upregulation, when Xist is frequently transcribed also in male cells and from both X chromosomes in females. A repressive function of Xist-dependent H3K9me3 accumulation is supported by our finding that premature, transient Xist overexpression primes an allele for future silencing and thereby skews the choice of the inactive X. Xist-dependent H3K9me3 recruitment does not require transcription of its antisense transcript Tsix, which can however enhance subsequent maintenance of the mark. In addition, the X-linked Xist activator RNF12 counteracts H3K9me3 formation at the locus independently of its known target REX1. Our results thus suggest an important role of facultative heterochromatin formation in the choice process at the onset of XCI. Activation and repression mechanisms are intertwined, to ensure the silencing of one Xist allele and the activation of the other within each female cell.

overall_design: To investigate the role of Xist and Tsix transcription in DNA methylation at the Xist promoter region, we perturbed them by knockdown or overexpression in mouse embryonic stem cells and differentiating cells. Subsequently, we measured the effect on DNA methylation by amplicon bisulfite sequencing. Knockdown was performed with CasTuner, and Xist overexpression with Doxycycline addition to the cell culture medium, as the Xist promoter of the B6 allele in TX1072 is Dox-inducible. The five amplicons cover the CpG island (chrX:103,482,019-103,482,381 mm10) and the nearby YY1 motifs (chrX:103,481,727-103,482,006) in the promoter-proximal regulatory element of Xist RE57, the promoter of Xist (chrX:103,483,289-103,483,491 and chrX:103,483,101-103,483,344), and Major Satellite Repeats (primers fwd: AAATCTAGAAATGTTTATTGTAGGA - rev: TTCGGATCCTAAAATATATATTTCTCAT). Three replicates per condition.

first: Eleni

last: Kanata

first: Ingrid

last: Pelaez-Conde

first: Gemma

last: Noviello

first: Ilona

last: Dunkel

first: Lena

last: Milanowska

first: Till

last: Schwämmle

first: Melissa

last: Bothe

first: Rutger

last: Gjaltema


title: Transcription-dependent heterochromatin at the Xist promoter shapes the random choice of the inactive X chromosome [Regulators_KD_Amplicon_Bisulfite_Seq]

overall_design: Xist regulators were knocked down (KD) in female ESCs (TX1072) with CasTuner or Split dCas9-KRAB, and the effect on DNA methylation upon differentiation (day 2 and day 4) was measured by amplicon bisulfite sequencing. The role of RNF12 and REX1 on DNA methylation was also investigated in differentiating female ESC lines, either carrying a homozygous deletion of Rnf12 (RNF12-/- , in short Rnf12 KO), or a double deletion of Rnf12 and Rex1 (RNF12-/-REX1-/-, in short DKO) (Gontan et al, 2018). The five amplicons cover the CpG island (chrX:103,482,019-103,482,381 mm10) and the nearby YY1 motifs (chrX:103,481,727-103,482,006) in the promoter-proximal regulatory element of Xist RE57, the promoter of Xist (chrX:103,483,289-103,483,491 and chrX:103,483,101-103,483,344), and Major Satellite Repeats (primers fwd: AAATCTAGAAATGTTTATTGTAGGA - rev: TTCGGATCCTAAAATATATATTTCTCAT). Three biological replicates per condition.


title: Transcription-dependent heterochromatin at the Xist promoter shapes the random choice of the inactive X chromosome [Timecourse_Amplicon_Bisulfite_Seq]

overall_design: Amplicon bisulfite sequencing in TX1072 XX and XO cells during the first 96 hours of 2i/LIF-withdrawal. The five amplicons cover the CpG island (chrX:103,482,019-103,482,381 mm10) and the nearby YY1 motifs (chrX:103,481,727-103,482,006) in the promoter-proximal regulatory element of Xist RE57, the promoter of Xist (chrX:103,483,289-103,483,491 and chrX:103,483,101-103,483,344), and Major Satellite Repeats (primers fwd: AAATCTAGAAATGTTTATTGTAGGA - rev: TTCGGATCCTAAAATATATATTTCTCAT). Three replicates per timepoint and cell line. RNA-seq of the samples is available at GEO: GSE273071.


title: Transcription-dependent heterochromatin at the Xist promoter shapes the random choice of the inactive X chromosome [Regulators_KD_CutnTag]

overall_design: Xist regulators were knocked down (KD) in female ESCs (TX1072) with CasTuner or Split dCas9-KRAB, and the effect on H3K9me3 upon differentiation was measured by CUT&Tag. The role of RNF12 and REX1 on H3K9me3 was also investigated in differentiating female ESC lines, either carrying a homozygous deletion of Rnf12 (RNF12-/- , in short Rnf12 KO), or a double deletion of Rnf12 and Rex1 (RNF12-/-REX1-/-, in short DKO) (Gontan et al, 2018).


title: Transcription-dependent heterochromatin at the Xist promoter shapes the random choice of the inactive X chromosome [Xist-Tsix-perturbations_CutnTag]

overall_design: To investigate the role of Xist and Tsix transcription at H3K9me3 recruitment at the Xist promoter region, we perturbed them by knockdown or overexpression in mouse embryonic stem cells and differentiating cells. Subsequently, we measured the effect on H3K9me3 by CUT&Tag. Knockdown was performed with CasTuner, and Xist overexpression with Doxycycline addition to the cell culture medium, as the Xist promoter of the B6 allele in TX1072 is Dox-inducible.


title: Transcription-dependent heterochromatin at the Xist promoter shapes the random choice of the inactive X chromosome [TX-Maged1-2tag_CutnTag]

overall_design: CUT&Tag for H3K9me3 in unsorted and sorted TX-Maged1-2tag cells at differentiation day 4 (2i/LIF withdrawal). Cells were sorted based on mScarlet-I3 and mStayGold levels, into a population of Xist-Off cells, a population that is expressing Xist from the B6 allele (Xist-B6) and one that is expressing Xist from the Cast allele (Xist-Cast). Three replicates per condition.


title: RNA-seq of CDO1-overexpressing AGS gastric cancer cells

city: Shanghai

first: Fazhi

last: Wang

address: No. 213, Hongkou Road

institute: Shanghai Jiao Tong University

summary: This study investigates transcriptomic changes associated with CDO1 overexpression in human AGS gastric cancer cells. Poly(A)-selected mRNA libraries from CDO1-overexpressing AGS cells and corresponding control cells were sequenced using paired-end 150-bp reads on the DNBSEQ-T7 platform to identify differentially expressed genes and biological pathways regulated by CDO1 overexpression in gastric cancer cells.

overall_design: RNA-seq was performed on six human AGS gastric cancer cell samples: three biological replicates of control cells and three biological replicates of CDO1-overexpressing cells. Total RNA was extracted, poly(A)+ mRNA was enriched, and paired-end 150-bp libraries were sequenced on the DNBSEQ-T7 platform. Gene-level count data will be provided as processed data.


title: The Role of Brucine A in Renal Fibrosis

city: Hefei City, Anhui Province

first: Shuangyu

last: Li

address: 81 Meishan Road

institute: Anhui Medical University

summary: Renal fibrosis is the common pathological basis for the progression of various chronic kidney diseases to end-stage renal disease, which is mainly manifested as renal tissue inflammatory infiltration, oxidative stress imbalance, renal tubular epithelial cell transdifferentiation and excessive extracellular matrix deposition. Currently, there are no effective targeted reversal methods in clinical practice. Brucine A (BA), a natural triterpenoid active ingredient, possesses significant anti-inflammatory, antioxidant and anti-fibrotic pharmacological activities. It can inhibit renal inflammatory responses and oxidative stress damage, reduce the expression of fibrosis-related proteins and matrix accumulation by regulating key signaling pathways such as TGF-beta1 and NF-kB, thereby effectively delaying the progression of renal fibrosis. This study aims to systematically clarify the intervention effect of BA on renal fibrosis and reveal its potential molecular mechanism, so as to provide experimental evidence and theoretical basis for the prevention and treatment of chronic kidney diseases as well as the clinical transformation and application of BA.

overall_design: Renal cortex tissues were harvested from mice 14 days after unilateral renal ischemia-reperfusion (UIR) surgery. Mice received daily intraperitoneal injection of vehicle solution for 14 consecutive days after surgery. Renal cortex tissues were harvested from mice 14 days after unilateral renal ischemia-reperfusion (UIR) surgery. Mice received daily intraperitoneal injection of brucine A (BA) at a dose of 1 mg/kg for 14 consecutive days after surgery.


title: The fungal volatile organic compound 6-pentyl-alpha-pyrone

city: christchurch

first: Jesus

middle: Francisco

last: Echaide Aquino

address: 85084 Ellesmere Junction Road, Lincoln

department: agls

country: New Zealand

institute: lincoln university

summary: Drought stress is a major constraint on crop production. While Trichoderma fungi are widely recognized for enhancing plant tolerance to abiotic stresses, the fungal molecules responsible for these protective effects remain poorly defined. In this study, we investigated the role of 6-pentyl-a-pyrone (6PP), a volatile compound produced by diverse Trichoderma spp., in modulating plant responses to water deficit. Dwarf bean (Phaseolus vulgaris) seedlings grown from seeds coated with a carrier polymer delivering 6PP were significantly more tolerant to drought stress than seedlings from seeds coated with the polymer alone (control), exhibiting increased leaf area, root length, chlorophyll content, and photosynthetic rate. To elucidate the mechanisms induced by this molecule, comparative transcriptome analyses were performed in the presence and absence of 6PP under both wellwatered and drought conditions; only 49 DEGs were detected under wellwatered conditions. In contrast, 476 expressed genes were identified in drought-stressed plants grown from 6PP-coated seeds, indicating substantial transcriptional reprogramming. 6PP treatment reprogrammed stress-responsive gene networks, including pathways associated with photosynthesis, carbohydrate metabolism, phosphorylation-mediated signaling, defense responses, and oxidative stress regulation. In addition, drought-stressed plants treated with 6PP exhibited enhanced MAPK phosphorylation, providing protein-level evidence for activation of phosphorylation-mediated signaling pathways associated with stress tolerance. Functional enrichment analyses further highlight secondary metabolite pathways, including those for phenylpropanoid and flavonoid biosynthesis, suggesting enhanced production of protective compounds and maintenance of photosynthetic activity under drought stress. Several stress-related genes were modulated prior to drought exposure, indicating a possible priming effect. Collectively, our findings identify 6PP as a potential signaling molecule contributing to enhanced drought resilience and provide new insights into the molecular basis of Trichoderma-mediated stress protection.

overall_design: A 2 × 2 factorial experiment was conducted to evaluate transcriptional responses of dwarf bean (Phaseolus vulgaris) to 6-pentyl-α-pyrone (6PP) under well-watered and drought-stress conditions. Seeds were coated either with carrier polymer alone (control) or with polymer containing 114 mM 6PP. Plants were grown under controlled environmental conditions until development of the second trifoliate leaf. Well-watered plants were irrigated throughout the experiment, whereas drought stress was imposed by withholding irrigation until plants reached wilting stage 3. The four experimental conditions were polymer control under well-watered conditions, 6PP treatment under well-watered conditions, polymer control under drought stress, and 6PP treatment under drought stress. Three biological replicates were collected per condition, resulting in 12 RNA-seq samples. Each biological replicate consisted of pooled trifoliate leaf tissue from five randomly selected plants. Leaflets were immediately frozen in liquid nitrogen, ground to a fine powder, and stored at −80 °C until RNA extraction.

first: Echaide-Aquino

last: Jesus Francisco

first: Hampton

last: John

first: Mendoza-Mendoza

last: Artemio


title: KRAS-Mutation Driven RASA2 Promotes Pancreatic Cancer Metastasis via TGFB2-Dependent Non-Canonical Hedgehog/GLI1 Activation [CUT&Tag]

first: taochen

last: he

address: 180 Fenglin Road, Shanghai, China

institute: Zhongshan Hospital Fudan University

summary: KRAS mutations are a major driver of pancreatic ductal adenocarcinoma (PDAC), promoting tumor initiation, progression, and metastasis. RASA2, a Ras GTPase-activating protein, modulates KRAS protein levels in wild-type contexts, yet its role in KRAS-mutant PDAC remains unclear. Here, we systematically investigated the biological function and molecular mechanisms of RASA2 in KRAS-mutant PDAC. Integrative analyses of multiple datasets and patient-derived samples demonstrated that RASA2 is consistently upregulated in KRAS-mutant PDAC and significantly associated with poor prognosis and metastatic progression. Gain- and loss-of-function studies revealed that RASA2 markedly enhances PDAC cell migration and invasion in both KRAS-mutant and KRAS-wild-type models, indicating that its pro-metastatic activity is largely independent of KRAS mutational status. Transcriptomic profiling and mechanistic interrogation uncovered that RASA2 activates GLI1 through a TGFB2-dependent, Sonic Hedgehog–independent non-canonical Hedgehog signaling pathway. Mechanistically, RASA2 directly interacts with the transcriptional regulator RTF1, facilitating H2BK120 ubiquitination at the TGFB2 promoter and thereby augmenting TGFB2 transcription. This epigenetic activation of TGFB2 subsequently drives non-canonical Hedgehog/GLI1 signaling to confer pro-metastatic traits. Pharmacologic inhibition of TGFB2 signaling or genetic silencing of GLI1 effectively abrogated RASA2-driven migratory, invasive, and metastatic phenotypes both in vitro and in vivo. Collectively, our findings identify RASA2 as a critical mediator of PDAC metastasis downstream of oncogenic KRAS and uncover a previously unrecognized RASA2–RTF1–H2BK120ub1–TGFB2–GLI1 signaling axis. KRAS mutation drives RASA2 upregulation, while the pro-metastatic activity of RASA2 is largely independent of KRAS mutational status. These findings reveal a previously unrecognized mechanism by which oncogenic KRAS promotes metastatic progression through RASA2-dependent epigenetic and transcriptional reprogramming and nominate the RASA2–TGFB2–GLI1 axis as a potential therapeutic target in PDAC

overall_design: Genome-wide profiling of H2BK120ub1 occupancy was performed in PANC-1 pancreatic ductal adenocarcinoma cells using CUT&Tag. An IgG sample was included as a negative control to assess background signals.

first: Taochen

last: He

first: Qiangda

last: Chen

first: Yanfei

last: An

first: Zhihang

last: Xu

first: Zhenlai

last: Jiang

first: Jiande

last: Han

first: Yuqi

last: Xie


title: Transcriptional response to enoxolone treatment in larval zebrafish

status: Public on Jul 27 2026

city: Baltimore

first: Daniel

middle: John

last: Kelpsch

email: dkelpsc1@jh.edu, kelpschd@gmail.com

state: MD

address: 3400 N. Charles Street

institute: Johns Hopkins University

summary: Excess apolipoprotein B-containing lipoproteins (B-lps) are a causative factor in cardiovascular disease. Using the LipoGlo reporter, in which NanoLuciferase is fused to the endogenous apoBb.1 locus, we performed a whole-animal phenotypic drug screen in larval zebrafish and identified enoxolone (18-beta-glycyrrhetinic acid), a triterpenoid derived from licorice root, as a B-lp-lowering compound. To define the transcriptional pathways underlying this effect, we treated 3 days post fertilization LipoGlo-expressing larvae with 8 uM enoxolone or vehicle and collected whole-animal RNA after 4, 8, 12, 16, or 24 hours of treatment. Enoxolone induced a transcriptional response detectable by 4 hours that broadened with treatment duration. The early response was enriched for cholesterol and isoprenoid biosynthesis, lipid transport, and coenzyme A metabolism, whereas the late response was enriched for carbohydrate metabolism and signaling pathways. The cholesterol sensor insig1 was upregulated at every duration examined. Enoxolone-responsive genes overlapped substantially with genes differentially expressed in hnf4a knockout zebrafish intestines, but not with hnf4g knockouts, supporting HNF4 alpha as a target of enoxolone.

overall_design: LipoGlo-expressing zebrafish larvae [Fus(ApoBb.1-NanoLuciferase); Tg(ubi:mCherry-2A-Firefly Luciferase)] were treated at 3 days post fertilization with either 8 uM enoxolone or vehicle (0.1% DMSO / 50 ppm Tween-20 / E2 embryo medium). Whole animals were collected after 4, 8, 12, 16, or 24 hours of treatment. Each sample is pooled total RNA from five larvae. Biological replicates are independent clutches, collected on three separate occasions (batch 1, 2, 3). Each treatment duration was analyzed as an independent experiment comparing enoxolone to time-matched vehicle.

first: Liyun

last: Zhang

first: James

middle: H

last: Thierer

first: Adrian

last: Rivera Cruz

first: Kobe

last: Koren

first: Urmi

last: Kumar

first: Yuki

last: Lin

first: Monica

last: Hensley

first: Mira

last: Sohn

first: Jun

middle: O

last: Liu

first: Thomas

last: Lectka

first: Jeff

middle: S

last: Mumm

first: Steven

last: Farber


title: Transcription-dependent heterochromatin at the Xist promoter shapes the random choice of the inactive X chromosome [WGBS]

first: Edda

last: Schulz

overall_design: We performed Whole-Genome Bisulfite-Sequencing (WGBS) in differentiating XO mouse embryonic stem cells (TX1072 XO B7 cell line). Samples were collected at days 0, 2 and 4 of 2i/LIF-withdrawal. This experiment was performed in parallel to GSE253792.

first: Eleni

last: Kanata

first: Ingrid

last: Pelaez-Conde

first: Gemma

last: Noviello

first: Ilona

last: Dunkel

first: Lena

last: Milanowska

first: Till

last: Schwämmle

first: Melissa

last: Bothe

first: Rutger

last: Gjaltema


title: Distinct histone 3 lysine methylation states underlie tumor immune surveillance

city: Philadelphia

first: Sharan

last: Venkatesh

state: PA

address: 421 Curie blvd

institute: University of Pennsylvania

summary: Mutations in histone 3 at or near lysine 36 (H3K36) have dominantly acting oncogenic effects in multiple tumor types by limiting H3K36-directed methyltransferases. Paradoxically, we find that expression of the H3K36M oncohistone unexpectedly inhibits tumor formation in KRAS-driven lung adenocarcinoma by inducing a potent immune-mediated tumor clearance. Mechanistically, oncohistone expression derepresses endogenous retroviral element transcription, results in the accumulation of double-stranded RNA (dsRNA), and activates an innate antiviral-like immune response that eradicates tumor growth. Surprisingly, while inactivation of the H3K36 di-methyltransferase NSD2 replicated all effects of oncohistone expression, inactivation of the H3K36 tri-methyltransferase SETD2 abolished element derepression and all associated downstream anti-cancer effects that are induced by oncohistone expression. These observations restructure our understanding of the roles of H3K36 methylation, the consequences of its deregulation in cancer, and shape our expectations for therapeutic interventions targeting H3K36 methyltransferases.

overall_design: RNA was extracted from 3 cell lines per group (KP-Ctrl, KP-Setd2KO, KP-H3K36M-Ctrl, KP-H3K36M-Setd2KO) and subjected to paired-end sequencing. ChIP was peformed for H3K36me2, H3K36me3, and H3K27me3 on lung adenocarcinoma cell lines (2 per group: KP-Ctrl, KP-Setd2KO, KP-H3K36M-Ctrl, KP-H3K36M-Setd2KO). ChIP-seq libraries were generated and sequenced by Genewiz/Azenta Life Sciences. ATAC-seq libraries were generated and sequenced by Genewiz/Azenta Life Sciences from cyropreserved cell lines (3 per group: KP-Ctrl, KP-Setd2KO, KP-H3K36M-Ctrl, KP-H3K36M-Setd2KO).

first: Amy

last: Gladstein

first: David

last: Feldser


title: Single-cell sequencing reveals the immune cell landscape of peripheral blood mononuclear cells in primary membranous nephropathy

city: GuangZhou

first: Li

last: qy

address: Jinan University, No.601, West Huangpu Avenue, Tianhe District, Guangzhou City, Guangdong Province, China

institute: Jinan University

summary: Primary membranous nephropathy (PMN) stands as the predominant pathological subtype of primary nephrotic syndrome in adults. Approximately one-third of patients diagnosed with primary membranous nephropathy will eventually progress to end-stage renal disease (ESRD), carrying a poor prognosis. Our study employed single-cell RNA sequencing to investigate PMN, with the objectives of characterizing immune cell phenotypes, deciphering intercellular interaction patterns, and elucidating the potential mechanisms implicated in PMN pathogenesis.

overall_design: To investigate the potential mechanisms of PMN, we performed single-cell RNA sequencing (scRNA-seq) on peripheral blood mononuclear cells (PBMCs)  from 5 patients with PMN and 3 healthy controls

first: Wenjun

last: Shan

first: Qiyu

last: Li


title: Immune hallmarks of recurrent immune checkpoint inhibitor-mediated inflammatory arthritis

city: Houston

first: Roza

last: Nurieva

state: TX

address: 7455 Fannin St,, Unit 906

department: Immunology

institute: The University of Texas MD Anderson Cancer Center

summary: Immune checkpoint inhibitor (ICI) therapy is often associated with immune-related adverse events including inflammatory arthritis (ICI-IA). However, the mechanisms underlying ICI-IA, especially its recurrence, have not been fully investigated. The purpose of this study is to elucidate mechanisms of recurrent ICI-IA by analyzing longitudinal synovial fluid (SF) samples. SF samples were collected from six ICI-IA patients at the first and second occurrences of ICI-IA and analyzed with single-cell RNA sequencing (scRNAseq) (n=3), scTCRseq (n=3), scBCRseq (n=3), and flow cytometry (n=6). SF samples from cancer-naïve osteoarthritis patients (n=6) were used as negative controls. Analysis revealed that effector CD8+ T cells and PD-1hi CXCL13hi CD4+ T cells were enriched in the SF of ICI-IA patients. Ninety three percent and fifty percent of the top ten expanded clones of effector CD8+ T cells and PD-1hi CXCL13hi CD4+ T cells, respectively, were shared between the first and second ICI-IA flare. These top clones were characterized by the production of pro-inflammatory type 1 cytokines including IFNg, TNFa, and IL-21, especially in the second flare, suggesting immune memory responses to cognate antigen. Cell-cell communication analysis suggests that effector CD8+ T cells and PD-1hi CXCL13hi CD4+ T cells interacted with each other and with myeloid cells and B cells through chemokines (CXCL9/10/11/13, CCL3) and cytokines (MIF, IL-2/7/15/21). Overall, longitudinal SF analysis from ICI-IA patients for the first time revealed the expansion of effector CD8+ T cells and PD-1hi CXCL13hi CD4+ T cells with type 1 cytokine signatures that potentially contribute to development or recurrence of ICI-IA.

overall_design: We performed single cell RNA sequencing, TCR sequencing, and BCR sequencing of synovial fluid cells isolated from three patients with first and second inflammatory arthritis after immune checkpoint inhibitor therapy and three osteoarthritis

first: Synat

last: Keam

first: Yanshuo

last: Chu

first: Sang

last: Taek Kim


title: KRAS mutations reprogram RNA m6A modification to drive CD73-dependent immune evasion in colorectal cancer [RNA-seq]

city: Seoul

first: Seung-Pyo

last: Hong

address: 103 Daehak-ro

country: South Korea

institute: Seoul national university

summary: KRAS mutations, present in about 40% of colorectal cancers (CRCs), are strongly associated with an immunosuppressive tumor microenvironment characterized by restricted immune infiltration and poor responses to immunotherapy. Here, we show that KRAS mutations remodel the m6A epitranscriptome to promote immune evasion. Methylated RNA-immunoprecipitation sequencing of isogenic CRC cells revealed that KRAS-mutant cells exhibit increased N6-methyladenosine (m6A) deposition on CD73 mRNAs, enhancing the stability of the transcripts by promoting interaction with IGF2BP3. This m6A modification was driven by TEAD4-dependent recruitment of the METTL3 methyltransferase complex, identifying TEAD4 as a spatial regulator of m6A deposition. Functionally, METTL3 knockdown in KRAS-mutant syngeneic tumors suppressed tumor growth and restored antitumor immunity by increasing CD8⁺ T-cell and natural killer (NK)–cell infiltration in a CD73-dependent manner. Moreover, METTL3 inhibition synergized with anti-PD-1 therapy and a CD73 inhibitor to reduce tumor burden. Together, these findings demonstrate that KRAS-driven m6A remodeling is a key mechanism of immune suppression in CRC and highlight METTL3 as a promising therapeutic target.

overall_design: RNA-seq of syngeneic tumors (CT26, CT26 with shMettl3 knockdown, with shMettl3 knockdown + Cd73 high expression)

first: Seungjae

last: Shin

first: Jong-Il

last: Kim

first: Sung-Yup

last: Cho


title: Rat thymic epithelium-free areas are specialized medullary niches enriched for mature thymocytes and distinct stromal subsets

city: Shimotuga

first: Yasushi

last: Sawanobori

state: Tochigi

address: Kitakobayashi 880, Mibu

country: Japan

institute: Dokkyo medical university

summary: The rat thymic medulla provides the microenvironment for negative selection, late thymocyte maturation, and thymocyte egress, and is generally characterized by widespread distribution of medullary thymic epithelial cells (mTECs). In contrast, rat thymic medulla contains medullary epithelium-free areas (mEFAs), but the cellular composition and functional significance of these regions remain unclear. Here, we combined spatial transcriptomics, scRNA-seq, and robust cell-type decomposition (RCTD) to characterize mEFAs in Lewis rat thymus. These analyses revealed that mature single-positive thymocytes, including CD4SP, CD8SP, and regulatory T-cell-lineage cells, were preferentially localized in mEFAs, whereas immature SP subsets were enriched in medullary epithelium-containing areas. Rat thymic mesenchymal cell-3 and -4 (TMC3 and TMC4) subsets were also enriched in mEFAs. These subsets were broadly similar to mouse medullary fibroblasts but displayed distinct predicted interactions with SP thymocytes, including costimulatory molecule–receptor, chemokine–receptor, and ECM–integrin axes. In addition, the venous endothelial cells (vECs) expressing portal endothelial cell markers were accumulated in mEFAs. The S1P transporter gene Spns2 was preferentially expressed in both TMC4 and vEC subsets, suggesting increased local concentration in mEFAs. These findings indicate that rat mEFAs are specialized medullary niches linking stromal organization, thymocyte maturation, and thymic egress.

overall_design: Spatial transcriptomics and scRNA-seq datasets were generated from 8-week-old Lewis rat thymi. Rat thymocyte and thymic stromal scRNA-seq datasets were used, together with published mouse reference datasets, to construct reference objects for cell-type annotation. Cell types in the spatial transcriptomics dataset were inferred by robust cell-type decomposition (RCTD). Spatial localization of thymocyte and stromal subsets, as well as cell-type-associated gene expression patterns, were then analyzed.


title: Development and validation of a long-term co-maturation protocol for human stem cell-derived microglia and neuronal networks

city: Nijmegen

first: Klaas

last: Mulder

address: Geert Grooteplein 26

department: Molecular Developmental Biology

country: Netherlands

institute: Radboud University

summary: Microglia-neuron interactions play a key role in a variety of central nervous system disorders. Technologies using human induced pluripotent stem cells (hiPSCs) have been developed to model human brain cells with the goal to understand their function. To effectively study neuro-immune crosstalk and investigate microglial contributions to neuronal network development and function, both microglia and neurons should co-mature allowing for long-term interactions throughout their differentiation. Here, we present a co-maturation protocol that robustly generates glutamatergic neuronal networks containing hiPSC-derived microglia. We validated the long-term co-cultures using single-cell transcriptomics, imaging and neuronal activity readouts. In this protocol, astrocytes were required for long-term survival of microglia and for their integration into neuronal networks. Our co-maturation approach induced the typical ramified microglia morphology and characteristic microglia-neuron interactions. Homeostatic markers like P2RY12 and TMEM119 and neuronal remodeling associated genes were upregulated compared to microglia monocultures, highlighting the necessity of the environment to generate and maintain the context-dependent microglia signature in vitro. Our co-maturation model provides a powerful tool to assess the role of human microglia in modulating neuronal function and development in health and disease.

overall_design: Single-cell RNA-sequencing (10x Genomics Chromium Fixed RNA/Flex assay) was performed on hiPSC-derived microglia (iMG) monocultures and neuron-glia-microglia co-maturation cultures at DIV 28 (day in vitro). Conditions compared include microglia monoculture (M, n = 2) and microglia in co-maturation cultures together with neurons and astrocytes (T, n = 3), profiled across three independent batches/libraries (technical replicates: FLEXLib1-3), each internally multiplexed by 10x Flex probe-barcoding to allow direct comparison of conditions within the same sequencing run. The starting material for the microglia was identifcal for M and T (same vial of HPCs) to rule out confounding effects.

first: Annika

last: Mordelt

middle: W

first: Laura

last: Wingens

first: Nael

last: Nadif Kasri

first: Lot

middle: D

last: de Witte


title: SARS-CoV-2 Defective Viral Genomes from Distinct Genomic Regions Drive Divergent Interferon Responses

city: Rochester

first: Justin

last: Brennan

address: 601 Elmwood Ave.

department: Microbiology & Immunology

institute: University of Rochester Medical Center

summary: Defective viral genomes (DVGs) are naturally generated during genomic replication of many RNA viruses. When produced early in infection or supplemented at the onset of infection, DVGs can attenuate viral pathogenesis by stimulating IFN responses and antagonizing wild type (WT) virus replication, highlighting their potential as antiviral therapeutics. However, during natural infection DVGs can exert both antiviral and proviral effects depending on their generation kinetics, species, and abundance, underscoring the need to better understand their roles in viral pathogenesis. Coronaviruses (CoVs) remain a major global health threat and ubiquitously generate DVGs, yet DVGs’ roles during CoV infection are largely unknown. Using SARS-CoV- 2 as a model, we previously identified DVGs in vitro and in patient samples and discovered two major genomic hotspots (A and B) for their generation. Here, we first showed that overall DVG abundance tended to positively correlate with COVID-19 severity, with approximately 40% of DVGs originating from a specific genomic region designated hotspot B. Analysis of a publicly available single-cell RNA-seq datasets revealed that DVGs from hotspot B, but not hotspot A, were associated with elevated IFN responses, suggesting that DVGs derived from different genomic regions vary in their ability to stimulate innate immunity. To test this directly, we constructed two representative DVGs corresponding to hotspots A and B. Both DVGs suppressed the replication of co-infecting WT virus; however, only DVG-B induced robust IFN responses, exceeding those triggered by WT virus alone. This was further confirmed in human precision-cut lung slices. Mechanistically, DVG-B–derived dsRNA exhibited a distinct subcellular distribution compared with WT virus. Complementation with the nucleocapsid (N) partially restored dsRNA organization but did not alter the IFN response. Together, our findings demonstrate that DVGs arising from distinct genomic hotspots differentially regulate IFN responses, potentially contributing to varied pathogenic outcomes during SARS-CoV-2 infection.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: To determine the impact of SARS-CoV-2 (Hong Kong strain, HK), DVG-B, DVG-A or SARS-CoV-2ΔN infections on the host transcriptome. A549-ACE2 cells were singley infected at MOI=1 with SARS-CoV-2, DVG-B or DVG-A for 24 hours. Alternatively, A549-ACE2 cells were co-infected at with SARS-CoV-2 and DVG-B or DVG-A, respectively, for 24 hours. Note for the co-infections that cells were infected at MOI=1 for both SARS-CoV-2 and DVG-B or DVG-A, yielding a total MOI of 2. Total RNA was extracted with Trizol followed by DNase digestion and RNA-seq.

first: Yan

last: Sun


title: Effect of DBP in LO2 and LX2 cells

city: Jeju

first: Eun Bok

last: Baek

address: 102 Jeju Daehak-ro

institute: Jeju National University

summary: Trasnscriptomic analysis in LO2 and LX2 cells induced by DBP

overall_design: DBP was treated for 24 hours in LO2 and LX2 cells

first: Eun-Bok

last: Beak


title: Lymphotoxin Beta Receptor Activity in Fibroblasts Regulates Collagen Synthesis and is Crucial for Lung Fibrosis

city: La Jolla

first: Michael

last: Croft

state: CA

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

summary: Fibroblast-specific deletion of LTβR in mice exposed to allergen significantly reduces lung collagen deposition and inflammation, despite unchanged fibroblast numbers. LIGHT-LTβR signaling in human pulmonary fibroblasts increases the expression of multiple collagen isoforms, molecules involved in structural rigidity, and molecules controlling cell migration and adhesion, explaining the importance of LTβR in promoting lung fibrosis.

overall_design: Bulk RNA seq. analysis from human pulmonary fibroblasts stimulated with 50 ng/ml LIGHT, 5 ng/ml TGFβ, 25 ng/ml IL-13, and 100 ng/ml IL-17A and in combination of IL13 or IL17A with LIGHT

first: Nandita

last: Ghosh

first: Rinkesh

middle: K

last: Gupta

first: Gurupreet

last: Sethi

first: Kai

last: Fung

first: Jeamin

last: Jung

first: Ann

last: Balancio


title: KRAS mutations reprogram RNA m6A modification to drive CD73-dependent immune evasion in colorectal cancer [ChIP-seq]

first: Seung-Pyo

last: Hong

overall_design: ChIP-seq (with TEAD4 and METTL3 antibody) of SW48 KRAS G12D/+ knock-in, wild type (WT) cell lines (three times replicates).

first: Seungjae

last: Shin

first: Jong-Il

last: Kim

first: Sung-Yup

last: Cho


title: KRAS mutations reprogram RNA m6A modification to drive CD73-dependent immune evasion in colorectal cancer [MeRIP-seq]

overall_design: MeRIP-seq of SW48 wild type, SW48 KRAS G12D/+ and G12V/+ knock-in cell lines.


title: KRAS mutations reprogram RNA m6A modification to drive CD73-dependent immune evasion in colorectal cancer [scRNA-seq]

overall_design: scRNA-seq of syngeneic tumors (CT26, CT26 with shMettl3 knockdown, with shMettl3 knockdown + Cd73 high expression) using 10X Genomics platform


title: Mutation of SCARECROW-LIKE28 or CYTOKININ OXIDASE3/5 suppresses rosette branching in Arabidopsis

city: Auckland

first: Zhiwei

last: Luo

state: Auckland

address: 120 Mt Albert Road

institute: PLANT AND FOOD RESEARCH

summary: Shoot branching is an important trait that influences plant architecture and crop productivity. It is triggered by the perception of developmental and environmental cues and controlled by a complex and interconnected regulatory network. Multiple plant hormones, including strigolactones (SLs), auxin and cytokinin (CK) regulate branching; however, the interplay between them has yet to be fully elucidated.  In this study, novel branching regulators were identified through a series of transcriptomic, functional and genetic studies. Based on expression that was correlated with either bud growth suppression or bud outgrowth in petunia, multiple candidates were selected, and their function in modulating branching were studied using Arabidopsis mutant lines. The scl28 and ckx3 ckx5 mutants showed significant reduction in rosette branching and altered flowering time relative to wild-type (WT) Arabidopsis. Transcriptome comparison between these mutants and WT suggested upregulation of strigolactone (SL) biosynthesis genes in these mutants might contribute to the suppression of rosette branching. This was supported by genetic data indicating that SCL28 and CKX3/5 regulate rosette branching via the SL signalling pathway but regulate flowering independently. These findings add new knowledge to the regulation and connection between SL and other hormones and developmental processes.

overall_design: The tissue containing the axillary meristems (AM) was harvested after bolting, when each plant had a visible bolt that measured less than 1 cm in height. For WT, Atd14-7 and ckx3 ckx5, the AM tissues were harvested at 23 days after sowing while the AM tissues for scl28 were harvested at 25 days after sowing, with all harvesting occurring in the morning, between 9 – 11 am. This was done for each plant by carefully excising the stem portion of the plant using a scalpel, removing leaves, roots, and the apical elongated part of the stem, leaving the lower stem and axillary meristems. The AM tissues were immediately frozen using liquid nitrogen. Two to three AM tissue samples were pooled to form one replicate, and a total of five replicates per genotype were collected for subsequent RNA extraction. Four samples with the highest RNA integrity number (RIN) from each genotype were chosen, resulting in a total of 16 samples that were sent for RNA-seq analysis.

first: Bart

last: Janssen

first: Joanna

last: Putterill

first: Kimberley

last: Snowden


title: RNA-seq of HT and ST14-knockout B-cell lymphoma xenografts

city: Taipei

first: Yi-Lin

last: Chiu

address: No. 161, Sec. 6, Minquan E. Rd., Neihu Dist.

country: Taiwan

institute: National Defense Medical Center

summary: This dataset presents RNA sequencing (RNA-seq) data from human B-cell lymphoma HT wild type and ST14 knockout tumors established in immunodeficient mice. The study aimed to investigate alterations in tumour biology, transcriptomic changes and  gene expression differences induced by ST14 knockout.

overall_design: Human HT B-cell lymphoma cells (1.5 × 10⁷), including wild type and ST14 knockout, were implanted subcutaneously into male CAnN.Cg-Foxn1nu/CrlNarl mice (4 weeks old). Tumor size was monitored twice weekly; mice were euthanized if volumes exceeded 2000 mm³. At the study endpoint, tumors were excised and total RNA was extracted with QIAzol/RNeasy. Strand-specific libraries were prepared by Genewiz and and sequenced on an Illumina NovaSeq 6000 platform using 2×150 bp paired-end mode. FastQC was used for read-quality assessment, adapters and low-quality bases were trimmed, and transcript abundance was quantified against the Ensembl GRCh38 (release 114) transcriptome using Salmon v1.10.0 and kallisto v0.46.1.

first: Xin-Jie

last: Lu

first: Hsing-Fan

last: Lai


title: Decoding Schwann cell activation in pancreatic cancer neural invasion by mimicking nerve injury responses and using spatial transcriptomics

first: Luju

last: Jiang

state: State...

address: Dongchuan Road 800, Minhang, Shanghai, China

institute: Shanghai Jiaotong University

summary: Perineural invasion (PNI) is a critical neuropathic change in pancreatic cancer, driven by cancer-nerve interactions, where Schwann cells (SC) undergo reprogramming similar to nerve injury, promoting tumor spread. Despite this, the molecular mechanisms underlying SC activation and their involvement in extrapancreatic PNI remain poorly understood. In this study, we drew an analogy between the process of PNI and nerve injury, identifying six nerve injury-related genes (ARRDC4, ATF3, CBFB, NAV2, SNTB1, and TOX) that are highly expressed in SC and implicated in PNI. To certify the role of the selected six genes in neural invasion, the expression of these genes in N008 were knockdown by siRNA.After knocking down the expression of these six genes in N008 cells and performing RNA sequencing, it was found that the knockdown of these genes was associated with the activation of neural pathways, such as axon regeneration, Schwann cell differentiation, axonogenesis, and neurogenesis ,suggesting that these genes likely influence the functions of periphery nervous system.

overall_design: RNA profiling of the human primary Schwann cell HUM-iCELL-N008 after knocking down the expression of these six genes (ARRDC4, ATF3, CBFB, NAV2, SNTB1, and TOX) by siRNA.

first: Shuqi

last: Cai

first: Zheqi

last: Weng

first: Shan

last: Zhang

first: Shu-Heng


title: Ankrd11 deficiency reverses the dysfunction of chronic HBV-specific T-cell [Cut&Tag]

first: Wei

last: Xu

address: No. 3, 1 Beichengxi West Road, Chaoyang District, Beijing 100020, China

institute: Institute of Microbiology, Chinese Academy of Sciences

summary: To investigate the impact of Ankrd11 deficiency on H3K27ac modification in CD8 T cells, we performed H3K27ac CUT&Tag assays comparing H3K27ac modification levels between Ankrd11-knockout and wild-type CD8 T cells.

overall_design: Ankrd11 KO and Control cells were generated by retroviral transduction. sgRNA-positive cells (NGFR+) were sorted 5 days post-transduction with >95% purity for subsequent Cut&Tag assays.

first: Xuyu

last: Zhou


title: Single-Cell RNA-Seq Reveals Immunosuppressive Effects of Triple-Negative Breast Cancer–Derived Exosomes on NK Cell Responses

city: Indiana University

first: Reza

last: Shahbazi

address: 980 W Walnut st

institute: Indiana University

summary: Triple-negative breast cancer (TNBC) is a highly aggressive and immunogenic subtype that lacks effective targeted therapies. Although tumor-derived exosomes are known to influence immune responses, their direct role in shaping human NK cell plasticity remains insufficiently characterized. In this study, we performed an integrative single-cell multiomic analysis of primary human NK cells following exposure to exosomes isolated from 17 genomically distinct TNBC cell lines. By combining single-cell transcriptomics, we identified conserved and subtype-specific immunoregulatory programs elicited by TNBC-derived exosomes.

overall_design: Single-cell RNA profiling were performed on primary NK cells from 17 exosome-treated samples and one untreated control.

first: Samaneh

last: Maleknia

first: Sanam

last: Rezaei Benam


title: Grapevines pre-treated with biocontrol bacteria have an altered transcriptional response to Xylella fastidiosa and a reduction in Pierce’s disease severity

city: Riverside

first: Caroline

last: Roper

address: 900 University avenue

institute: University of California, Riverside

summary: In a previous DNA-based microbiome study of grapevines in areas of Pierce’s Disease (PD) pressure, we determined that taxa belonging to the Pseudomonas and Achromobacter genera negatively associated with PD severity and titer of the causal agent, Xylella fastidiosa, leading us to hypothesize that these taxa suppress PD. Here we tested this hypothesis using two bacterial isolates from the grapevine endosphere, Pseudomonas viridiflava and Achromobacter vitis. We demonstrate that pre-treatment with these two isolates significantly reduced PD symptoms and X. fastidiosa titer, comparable to that of a known PD biocontrol agent, Paraburkholderia phytofirmans PsJN. We monitored early spatial transcriptional responses using genome-wide transcriptional profiling in vines that were pre-treated with the biocontrol strains and then inoculated with X. fastidiosa. We coupled this with phenotyping of internal tylose development and external disease symptoms and bacterial titer and determined that grapevines pre-treated with the biocontrols A. vitis and PsJN developed fewer tyloses and PD symptoms and underwent major transcriptional reprogramming in response to X. fastidiosa. These included up-regulation of genes in auxin- and ethylene-signaling pathways linked to tylose development. In contrast, P. viridiflava pre-treatment also resulted in a reduction of tyloses and PD symptoms but did not induce major transcriptional changes in vines, suggesting it likely has a direct inhibitory effect to X. fastidiosa through antibiosis. Using this data, we propose a model that incorporates timely and effective deployment of tyloses related to induction of ethylene and auxin pathways as a key factor in PD resistance.

overall_design: For all in planta bioassays, V. vinifera cv. Cabernet Sauvignon was used. Grapevine transcriptomes were assessed in plants treated with a given BCA and subsequently inoculated with X. fastidiosa 7 days later. Plants inoculated with 1X PBS buffer at the time of inoculation with the pathogen served as controls for the “BCA only” treatment. Plants inoculated with 1X PBS and challenged with X. fastidiosa 7 days later served as controls for the “pathogen-challenge” treatments. Petioles for the “pathogen-challenge” treatments were harvested at 1-day after inoculation with X. fastidiosa both at the point of inoculation and 10 nodes above the point of inoculation (n=12 plants per treatment per timepoint). Specifically, three petioles were harvested at the POI (nodes 3-6) or 10 nodes above the POI (nodes 10-12) and immediately frozen in liquid nitrogen

first: Elizabeth

last: Deyett

first: Biagio

last: DiSalvo

first: Mélanie

last: Massonnet

first: Vanessa

last: Ashworth

first: Dario

last: Cantu

first: Steve

last: Lindow

first: Philippe

middle: E

last: Rolshausen


title: Induced transcription in a gene desert region advanced replication timing

city: Shenzhen

first: zengqi

last: wen

state: Guangdong

address: No. 66 Gongchang Road, Guangming District

department: Zhongshan School of Medicine

institute: Sun Yat-sen University Shenzhen Campus

summary: This study investigates whether transcription can directly reorganize DNA replication timing. To isolate the effect of transcription from native chromatin context, we established an inducible transcription system within a large late-replicating gene desert on mouse chromosome 2. Using Repli-seq, we found that induced transcription is sufficient to advance replication timing across an approximately 800-kb genomic domain. The induced early-replicating domain displayed an asymmetric replication timing profile relative to the knock-in site, and this asymmetry was independent of transcriptional direction. Genome-wide analysis further showed that pronounced asymmetry is uncommon among native early-replicating domains. These data provide direct evidence that transcription can reshape large-scale replication timing.

overall_design: Repli-seq was performed in engineered mouse embryonic stem cells carrying an inducible Tet-on transcription system inserted into a late-replicating gene desert on mouse chromosome 2. Samples included control and doxycycline-induced conditions across multiple time points, as well as forward- and reverse-oriented knock-in lines. For each condition, BrdU-labeled S-phase cells were sorted into four fractions, S1 to S4, followed by paired-end sequencing. Processed data include normalized Repli-seq signal tracks and replication timing profiles calculated from the S1-S4 fractions.

first: Chaozhang

last: Feng


title: Ankrd11 deficiency reverses the dysfunction of chronic HBV-specific T-cell [RNA-seq]

city: Beijing

summary: To investigate the transcriptomic changes in CD8 T cells upon Ankrd11 deficiency, we performed RNA-seq to analyze alterations in the transcriptome between Ankrd11-knockout and wild-type CD8 T cells.

overall_design: Ankrd11 KO and Control cells were generated by retroviral transduction. sgRNA-positive cells (NGFR+) were sorted 5 days post-transduction with >95% purity for subsequent RNA sequencing.


title: Systematic identification of age-related microbiome metabolites that impact the brain - mouse brain ATAC-seq

status: Public on Jul 24 2026

city: Stanford

first: Meenakshi

last: Chakraborty

address: 269 Campus Drive

institute: Stanford University

summary: These ATAC-seq data were generated from the brains of mice exposed to glycodeoxycholate or the appropriate vehicle control for 2 hours (administration route: intravenous retro-orbital injection). For more details, please see our preprint at https://doi.org/10.1101/2025.10.03.680371.

overall_design: ATAC-seq profiling of right brain hemispheres after mice were exposed to glycodeoxycholate or the appropriate vehicle control

first: Ami

last: Bhatt


title: RNA sequencing for amniotic fluid cells of preeclampsia and control rats

city: Chengdu

first: Jiashuo

last: Zhang

state: Sichuan

address: No. 28, Dianxin South Road

institute: West China Hospital

summary: Previous studies reported maternal preeclampsia could disturb offspring neurodevelopment. Amniotic fluid cells can accurately present the development of the fetus. We obtained and sequenced the amniotic fluid cells of preeclampsia and control pregnant rats to explore the effect of maternal preeclampsia on offspring neurodevelopment.

overall_design: We established preeclampsia and control pregnant rat models. On embryonic day 18.5 (E18.5), we performed total hysterectomy and collected amniotic fluid. Amniotic fluid was centrifuged to obtain amniotic fluid cells. Amniotic fluid cells were cultured. When cells were passaged for the 4th time, cells were collected and sequenced.


title: Systematic identification of age-related microbiome metabolites that impact the brain - mouse brain RNA-seq

summary: These RNA-seq data were generated from the brains of mice exposed to trimethylamine N-oxide, palmitate, glycodeoxycholate, indoleacetate, or appropriate vehicle controls for 2 hours (administration route: intravenous retro-orbital injection). In the naming scheme, S = saline only and SD = saline containing 6% DMSO. For more details, please see our preprint at https://doi.org/10.1101/2025.10.03.680371.

overall_design: RNA-seq profiling of left brain hemispheres after mice were exposed to one of four metabolites or appropriate vehicle controls


title: Lipofected mRNAs are spliced in Human cells

city: Kansas City

first: Ariel

middle: Alejandro

last: Bazzini

state: Missouri

institute: Stowers Institute for Medical Research

summary: Current strategies for therapeutic use of mRNAs and for testing the function of specific mRNA isoforms assumes that transfected mRNAs are not further processed by cellular splicing machinery. Here we show that lipofected mRNAs can be spliced in human cells, utilizing canonical splice donor and acceptor sites and this is suppressed by spliceosome inhibition. This post-transcriptional splicing has important strategic implications for the use of transfected mRNAs in experiments and therapies.

overall_design: RNA-seq profiling of HEK293T cells transfected with IVT mRNA at 24h or 4h post transfection. All 24h samples are without drugs, and 4h samples were treated with DMSO, 20nM PladB or 100nM PladB.

first: Cameron

last: Berry

first: Alejandro

last: Diaz de la Vega Gonzalez


title: Xenium spatial transcriptomics identifies mesenchymal fibroblast expansion and conserved fibrotic ECM programs in keloid

city: Los Angeles

first: Min

last: Deng

address: 650 Charles E. Young Dr. S., CHS-52-139

department: Medicine

institute: University of California, Los Angeles

summary: In this study, we applied single-cell-resolution targeted Xenium spatial transcriptomics (Xenium ST) to define keloid-associated cellular and molecular programs within intact tissue architecture, with a focus on fibroblast populations and conserved pro-fibrotic gene programs linked to ECM remodeling across diverse ancestry.

overall_design: Normal skin from one Asian donor and keloid biopsies from Asian (AN), White non-Hispanic (WNH), and Hispanic/Latino (H/L) donors were collected under UCLA IRB approval with written informed consent and processed as FFPE sections. Xenium ST was performed using the 10x Genomics 260-gene human skin panel plus a 100-gene custom add-on panel enriched for fibrosis, ECM remodeling, growth factor signaling, and inflammatory pathways. After quality control, the dataset included 8,749 cells from normal skin and 41,264, 54,831, and 22,489 cells from AN, WNH, and H/L keloid, respectively, with average and median transcript counts of 167 and 125 per cell. Cells with nCount_RNA >5 were analyzed in Seurat v5.3.05 and Xenium Explorer. Since normal skin was available only from the Asian donor, direct normal–keloid comparisons were restricted to the Asian samples, whereas comparisons across keloid samples were considered exploratory lesion-level observations.