title: Longitudinal zone- and cell-type-specific immune responses sustain Arabidopsis roots against pathogen infections

city: Ann arbor

first: Ping

last: He

state: Michigan

address: 1105 N. University Ave

institute: University of Michigan

summary: The immunity is dynamically regulated to balance growth and defense. Roots consisting of diverse cell types across longitudinal developmental zones are vital for plant survival amidst most microbial challenges. Leveraging single-cell transcriptomics and imaging of Arabidopsis roots, here, we reveal that in contrast to microbe-associated molecular patterns (MAMPs), plant-derived phytocytokines elicit robust, coordinated immune responses across various root cell types and zones, ensuring the continuity of growth-defense trade-offs at the organismal level. The intensity of immune responses in different root zones tightly correlates with invasion sites of fungal and bacterial pathogens. Differential expression of receptors and key signaling modules in distinct cell types and zones dictates the response intensity to specific elicitors. Furthermore, motif-informed network inference identifies key transcriptional regulators targeting each root cell type, driving cell identity-based transcriptomic immune responses. Our findings reveal that distinct phytocytokines trigger potent and coordinated cell type- and stage-dependent transcriptional reprogramming. The contrasting availability of convergent signaling components and transcription regulators orchestrate cell-identity immune responses at the organ level.

overall_design: Following different elicitors treatment, root cells from 7-day old root seedings were isolated by enzyme digestion and analyzed using the single-cell RNA-seq data.

first: Lahong

last: Xu

first: Fausto

last: Andres Ortiz Morea

first: Yan

last: Yan

first: Derui

last: Liu

first: Xiangpei

last: Kong

first: Camilla

last: Ferrari

first: Daniel

last: Osorio

first: James

last: J. Cai

first: Klaas

last: Vandepoele

first: Libo

last: Shan


title: Genome-wide methylation analysis of pterygium in Indian population

status: Public on Feb 15 2026

city: Madurai

first: Daipayan

last: Banerjee

state: Tamil Nadu

address: 1, Anna Nagar,

department: Proteomics Department

country: India

institute: Aravind Medical Research Foundation

summary: Pterygium is a highly prevalent, progressive conjunctival eye disease and  is characterized by wing-shaped conjunctival fibrovascular overgrowth. Persistent  sunlight exposure is a causative factor for this ocular surface disease and mostly  affects people working outdoors. Surgical excision remains the only treatment option. Ultraviolet (UV) radiation from sunlight is widely recognized as the primary cause of pterygium. While chronic UV exposure induces epigenetic changes in the skin and contributes to skin cancer, the role of epigenetic alterations in pterygium pathogenesis remains largely unexplored. This study aimed to investigate genome-wide methylation changes in pterygium using the Illumina Infinium Epic v2.0 Methylation array. We identified 1,052 hypermethylated CpGs (499 genes) and 686 hypomethylated CpGs (340 genes) in pterygium tissue compared to control conjunctival tissue from cataract patients (Δβ>|0.1|, P<0.05). Hypomethylated genes were mainly associated with the PI3K-Akt and MAPK pathways, while hypermethylated genes were enriched in pathways related to oxidative stress, autophagy, DNA repair, and Wnt signaling inhibition. These findings suggest that dysregulated DNA methylation may contribute to pterygium pathogenesis by upregulating genes involved in cell proliferation, survival, angiogenesis, fibrosis, and extracellular matrix remodeling, while silencing genes associated with oxidative stress response, autophagy, and DNA damage repair.

overall_design: We aimed to perform genome wide methylation analysis in pterygium using Illumina Infinium Epic v2.0 Methylation array. In this study, pterygium tissue were collected from patients undergoing pterygium excision surgery (n = 9) and the conjunctival tissues were obtained from patients with cataracts undergoing Small Incision Cataract Surgery (SICS) (n = 6), serving as controls.

first: L

last: Mathan

first: Tejaswi

last: Prasad


title: Differences in the characteristics of fibrosis scar formation after spinal cord injury in different segments

city: Nantong

first: Chen

last: Chen

state: Jiangsu Province

address: Qixiu Road,Nantong,226001,Jiangsu,China

country: China

institute: Nantong university

type: Expression profiling by high throughput sequencing

summary: After spinal cord injury, fibrotic scars will form, which affect tissue regeneration and functional recovery in the body. However, the differences in fibrotic scars produced by different segments of the spinal cord are still unclear. Here, we demonstrate that after the same spinal cord hemisection injury, the thoracic spinal cord produces the most scars, while the lumbar and cervical spinal cords have fewer scars, and there are also significant differences in functional recovery after injury in the three segments. By comparing the differences in fibrosis scars produced by cervical spinal cord, thoracic spinal cord, and lumbar spinal cord, as well as the different abilities of fibroblasts to promote fibrosis in vitro, the potential mechanism characteristics of injury repair in different segments of the spinal cord were revealed. This article explores the impact of spinal cord segment differences on fibrosis scar formation and their relationship with behavioral functional recovery, revealing the regional heterogeneity of spinal cord tissue fibrosis scar formation and deepening our understanding of the complexity of CNS scar formation. This provides new ideas for future targeted treatment to improve functional recovery after specific spinal cord injuries.

overall_design: Compare the cellular characteristics of fibroblasts in different segments（C/T/L）


title: Transcriptional readthrough and splicing upon chemotherapy treatment

city: New Haven

first: Paulina

last: Podszywalow-Bartnicka

state: CT

address: 333 Cedar Street

department: Department of Molecular Biophysics and Biochemistry

country: USA

institute: Yale University

summary: The Neugebauer lab has previously shown that splicing occurs co-transcriptionally and is coupled to 3’end cleavage. It is known that stress, such as hyperosmotic shock, affects RNA processing. The cellular stress response is an important component of cancer cell response to chemotherapy that can determine cell survival. Herein, we study how the coupling of the RNA processes in leukemia cells is affected in response to stress and therapeutic agents. We used short- and long-read sequencing to follow RNA processing upon treatment.

overall_design:
To determine level of gene expression and transcriptional readthrough as well as determine changes in alternative splicing we used short-read RNA-seq. We analyzed  polyA selected RNA isolated from whole K562 cells (mRNA) and RNA isolated from the cell nucleuses (nuclear RNA) that was later rRNA-depleted.
Before isolation of total RNA the cells were treated with: - 1uM Imatinib (im) for 1h, 6h and 18h - 5uM JTE-607 (jte) for 1h, 6h and 18h - 110mM KCl (kcl) for 1h and 3h.  Before isolation of nuclear RNA cells were treated with: - im for 1h or 18h - jte for 1h - kcl for 1h  All time points ended at the same time and thus the cells were collected in paralell with the untreated control cells (ctrl).
Each experiment was repeated three times (1, 2, 3)

first: Morgan

last: Shine

first: Jing

last: Lin

first: Karla

middle: M

last: Neugebauer


title: Regulation of cell identity by 3D super-enhancers

city: Memphis

first: Brian

middle: J

last: Abraham

state: TN

address: 262 Danny Thomas Blvd

department: Computational Biology

institute: St. Jude Children's Research Hospital

summary: Gene regulation and genome structure are intimately linked, but accurate predictions of the elements that form topological regulatory assemblies in mammalian genomes remain elusive. To address this challenge, we developed BOUQUET, a graph theory-derived algorithm that uses multiple facets of genome topology to discern and interrogate communities of cis-regulatory elements (CREs). BOUQUET’s unbiased approach reveals otherwise undetectable CRE communities, including those that cross presumed insulating boundaries and comprise different categories of CRE. Critically, some communities, which we term “3D super-enhancers (3D-SEs)”, accrue exceptional amounts of regulatory apparatus. 3D-SEs are associated with cell identity-defining genes across mammalian tissues. Microscopy analyses show co-localization and co-expression of genes from the same 3D-SE community within transcriptional co-factor puncta, resembling microcompartments. Gene pairs within 3D-SE communities are co-expressed, and CREs within 3D-SEs are co-accessible. Overall, our model more accurately represents the architectural complexity of CRE interactions, the coordination between chromatin conformation and gene regulation, and the connection between super-enhancers and cell identity.

overall_design: genome-wide gene expression profiling of wild type and Mir290 enhancer-deleted mESC v6.5 cell line is conducted by performing RNA-seq

first: Jie

last: Lv

first: Kelsey

middle: A

last: Maher

first: Alaguraj

last: Veluchamy

first: Yuna

last: Kim

first: Li

last: Dong

first: Bensheng

last: Ju

first: Virginia

last: Valentine

first: Marc

first: Steven

last: Burden

first: John

last: Easton

first: Stanley

middle: B

last: Pounds


title: Transcriptional readthrough and splicing upon chemotherapy treatment [long-read, nascent RNA]

overall_design:
To determine changes in RNA processing steps such as transcriptional readthrough and co-transcriptinal splicing we used long-read sequencing. We analyzed nascent RNA isolated from chromatin fraction of cells, that was additionally depleted of polyA-RNA and rRNA.
Before isolation of nascent RNA the cells were  treated with:
- 1uM Imatinib (IM) for 1h and 18h
- 5uM JTE-607 (JTE) for 1h
- 110mM KCl (KCL) for 45min.
All time points ended at the same time and thus the cells were collected in paralell with the untreated control cells (CTRL and CTRLim).
Each experiment was repeated three times (1, 2, 3)


title: ChIP-seq analysis for H3K4me3, H3K27ac, H3K27me3, p-STAT3, POU2AF1 and ELL2 in MM.1S cells

city: Kumamoto

first: Hiroto

last: Ohguchi

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

department: IRDA

country: Japan

institute: Kumamoto University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Multiple myeloma (MM) is a plasma cell neoplasm that depends on the bone marrow (BM) microenvironment; however, the underlying mechanisms of epigenetic contribution to the pathogenesis of MM are incompletely understood. Here, we delineate the epigenetic-driven transcriptional and splicing program crucial for MM. We recharacterized transcriptional program induced by IL-6/JAK/STAT3 pathway by ChIP-seq and RNA-seq analyses combined with CRIPSR knockout screening database, and identified B cell lineage factors, POU2AF1 and ELL2, as crucial IL-6/JAK/STAT3 targets that are essential for MM cell growth and survival. Genetic depletion of these factors suppressed MM cell growth in vitro and in the xenograft model of IL-6 humanized mice. Mechanistically, POU2AF1 and ELL2 govern MM-distinct transcriptional program representing immaturity, and IL-6/JAK/STAT3 pathway augments this program through upregulating and recruiting these factors to the MM-signature genes. Furthermore, we showed that IL-6 induces alternative splicing that is partly mediated by POU2AF1. Proteomic study identified novel POU2AF1-associated factors that converge in regulation of RNA, including RNA splicing. Indeed, POU2AF1 is adjacent to multiple splicing factors required for MM cell survival and is involved in the organization of nuclear speckles. Finally, we showed that gapmer antisense oligonucleotides (ASOs) targeting POU2AF1 inhibit its expression and MM cell growth in the presence of soluble BM stromal cell factors, including IL-6. Our data demonstrate that IL-6-driven B cell-lineage factors are the vulnerability of MM cells and may represent novel therapeutic targets for this incurable tumor.

overall_design: MM.1S cells were treated with or without IL-6 (control), and subjected to ChIP-seq analysis for H3K4me3, H3K27ac, H3K27me3, p-STAT3, POU2AF1 and ELL2.

first: Yasuyo

first: Shingo

last: Usuki


title: Define the pattern of YAP1-bound genes in pancreatic cancer spheroids.

city: Manhattan

first: Mohamad

last: Assi

state: NY

address: 550 1st Ave

department: Radiation Oncology

institute: NYU Medical Center

summary: In this study, we investigate the genes that are preferentially bound by YAP1 in pancreatic cancer spheroids.

overall_design: Endogenous YAP1 was pulled-down from PATU8902 spheroids, prior to DNA elution and sequencing. IgG is used as an isotype control.

first: Alec

last: Kimmelman


title: Identify positive and negative regulators of autophagy in pancreatic cancer spheroids.

summary: In this study, we reveal the regulators of autophagy in 3D culture and 2D starvation conditions in pancreatic cancer.

overall_design: PATU8902 cells were transduced with the whole-genome Brunello library and cultured under various conditions, prior to flow sorting, DNA extraction and sequencing.


title: Estrogen receptor β target gene expression reveals novel repressive functions in aggressive breast cancer [RNA-Seq]

city: Houston

first: Christoforos

last: Thomas

state: Texas

address: 6670 Bertner Avenue

department: Department of Medicine

institute: Houston Methodist Research Institute

summary: Inflammatory breast cancer (IBC) is a highly metastatic breast carcinoma with high frequency of estrogen receptor a (ERα) negativity and limited treatment options. We previously explored the second ER subtype, (ERβ) and reported correlation of its tumor expression with reduced metastasis in patients and in preclinical models of the disease. We initially associated the anti-metastatic function of the receptor with the inhibition of actin-based cell migration and the associated Rho GTPase signaling in IBC cells. We have now followed an integrated genomics approach to fully delineate the signaling underlying the anti-metastatic effects of ERβ. Through mapping binding sites in IBC cells that express endogenous and transfected ERβ in the presence of an agonist and interrogating this information with altered expression of protein coding mRNAs and miRNAs we have defined the interaction of a biologically active receptor with the cancer genome that controls metastatic signals. We reveal key  regulatory chromatin binding sites and motifs and identify direct target genes and miRNAs and the associated biological functions. Our new findings implicate the regulation of metabolic pathways and signaling in development and tumor microenvironment in anti-metastatic activity of ERβ. Through a rigorous analysis of target genes in clinical datasets we also associate downstream factors with patient outcomes reporting new molecules with targeting potential and strengthening the relevance of ERβ signaling for the metastatic process in breast cancer. Our findings thus offer an opportunity to validate the tumor repressive role of ERβ through a better understanding of its mechanism of action.

overall_design: Analysis of breast cancer cells with different ERβ levels and after treatment with ERβ agonists. Wild-type KPL4 cells with endogenous ERβ (Control cells) vs. KPL4 cells without ERβ (ERβ knockout cells). KPL4 cells without ERβ (ERβ knockout cells) vs. KPL4 cells with ERβ (ΕRβ knockout cells with transfected ERβ). KPL4 ΕRβ knockout cells with transfected ERβ after treatment with vehicle (DMSO) or the ERβ agonist LY500307 for 24 hours

first: Spyros

last: Tastsoglou

first: Ilias

last: Karagounis

first: Marios

last: Miliotis

first: Harika

last: Nagandla

first: Kristina

last: Zambo

first: Maria

last: Liousia

first: Naoto

last: Ueno

first: Amit

last: Maity

first: Artemis

middle: G

last: Hatzigeorgiou


title: Condensin loop extrusion properties, roadblocks, and role in homology search in S. cerevisiae

status: Public on Feb 16 2026

city: Lyon

first: Aurele

last: Piazza

address: 46 Allee d'Italie

country: France

institute: ENS Lyon

summary: The in vivo mechanism, regulations by cis-acting roadblocks, and biological functions of loop extrusion by eukaryotic SMC complexes are incompletely defined. Here, using Hi-C, we identified two condensin-dependent contact stripes at the Recombination Enhancer (RE) and the rDNA in S. cerevisiae. We show that oriented, unidirectional loop extrusion proceeds from these sites with an estimated processivity ~170 kb and a density ~0.04-0.18 that varies across the cell cycle. Centromeres and highly-transcribed RNA PolII-dependent genes are permeable condensin roadblocks. Other positionally labile elements such as replication forks and Smc5/6 complexes bound to substrates generated in the absence of Top2 also hinder loop extrusion by condensin. Cohesin is not an obstacle for condensin. Finally, a DNA double-strand break at MAT blocks condensin, which results in the rapid establishment of a long-range RE-MAT loop that juxtaposes the recombination machinery with its HML donor target. Hence, all budding yeast SMCs are involved in recombinational DNA repair. We propose a revised model for donor selection during MAT switching that exploits specific properties of loop extrusion by condensin. It can serve as a paradigm for the establishment of other types of selective interactions along chromosomes.

sample_organism:
Saccharomyces cerevisiae
Saccharomyces cerevisiae W303

overall_design:
Hi-C experiments were performed on S. cerevisiae asynchronous cultures or in cells synchronized in G1, S, or mitosis, and upon treatment affecting the structuration of chromosomes.

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************

first: Vinciane

last: Piveteau

first: Agnès

last: Dumont

first: Jérôme

last: Savocco

first: Aurèle

first: Chloé

last: Dupont


title: Effects of Integrin-alpha3 (ITGA3) knockdown on gene expression in pancreatic cancer cells [Scr_siITGA3_RNASeq]

first: Mohamad

last: Assi

summary: In this study, we investigate the role of ITGA3 in regulating autophagy flux in pancreatic cancer.

overall_design: ITGA3 was knocked-down using siRNA in PANC2.03 cells prior to RNA extraction and sequencing. Scramble (Scr) is used as a control.

first: Alec


title: Gene expression profiles in pancreatic cancer cells with high or low baseline autophagy flux levels [Low-Auto_High-Auto_RNASeq]

summary: In this study, we characterize the transcriptional signature of pancreatic cancer cells with different autophagy flux levels.

overall_design: PATU8902 cells were cultured in 3D-Matrigel to form spheroids. Cells with high (High-Auto) or low (Low-Auto) autophagy levels were flow-sorted, prior to RNA extraction and sequencing.

last: Kimmelman


title: Effects of constitutive YAP1 activation on gene expression in pancreatic cancer spheroids [EV_YS6A_RNASeq]

summary: In this study, we investigate the role of YAP1 in regulating autophagy flux in pancreatic cancer spheroids.

overall_design: YAP1S6A constitutively active phosphomutant was expressed in PATU8902 cells, which were then cultured in 3D-Matrigel as spheroids, prior to RNA extraction and sequencing. Empty Vector (EV) is used as a control.


title: Effects of NF2 deletion on gene expression in pancreatic cancer spheroids [sgLUC_sgNF2_RNASeq]

summary: In this study, we investigate the role of NF2 in regulating autophagy flux in pancreatic cancer spheroids.

overall_design: NF2 gene was deleted using CRISPR/Cas9 in PATU8902 cells, which were then cultured in 3D-Matrigel as spheroids, prior to RNA extraction and sequencing. A sgRNA against Luciferase (sgLUC) is used as a control condition.


title: Estrogen receptor β target gene expression reveals novel repressive functions in aggressive breast cancer [sRNA-Seq]

first: Christoforos

last: Thomas

type: Non-coding RNA profiling by high throughput sequencing

overall_design: Analysis of breast cancer cells with different ERβ levels. KPL4 cells without ERβ (ERβ knockout cells) vs. KPL4 cells with ERβ (ΕRβ knockout cells with transfected ERβ)

first: Spyros


title: Alterations of splicing and gene expression in IMR90 Control cells and IMR90 RAS cells upon knockdown of SF3B1.

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

summary: The goal of this study was to analyse changes of splicing and gene expression induced in IMR90 Control and IMR90 RAS (HRASG12V) cells upon knockdown of splicing factor SF3B1.

overall_design: Comparative analysis of splicing and gene expression changes in IMR90 control and IMR90 RAS cells induced by knockdown of SF3B1 by siRNA (siSF3B1) compared to non-targeting siRNA (siNT).

first: Wagner

last: Verena

first: Gil

last: Jesus

first: Khadayate

last: Sanjay

first: Ascensao

middle: F

last: Mariana

first: Barbosa

last: Nuno


title: Topology-informed regulatory element collections coordinate cell identity gene expression programs[scRNA-Seq]

first: Brian

last: Abraham

summary: Cis-regulatory elements (CREs) contact target genes to regulate their transcription, but CRE interactions are complex and predicting their function is difficult. Contemporary approaches to predict CRE targets generally assume one-to-one associations and linear genomic proximity. These methods fail to account for long-range CRE contacts caused by folding of the genome, or for circumstances in which a single CRE regulates multiple genes or, conversely, a single gene is regulated by multiple CREs. To address these challenges and investigate CRE accumulation, we developed BOUQUET, an integrative, graph-theory-based approach that utilizes multiple aspects of genome topology to probe communities of CREs, their bound apparatus, and their target genes. BOUQUET discovers CRE communities that are undetectable by existing unbiased methods, such as those with interactions that span insulating loop boundaries as well as regulatory communities that are comprised of clustered promoter elements. A subset of these communities, which we term “3D super-enhancers” (3D SEs), is consistent with aspects of the super-enhancer model and accrues exceptional amounts of regulatory apparatus at crucial cell identity-defining genes. In single-cell analyses, pairs of genes found within the same community are co-expressed, and pairs of CREs are co-accessible, suggesting that the regulation of both types of elements within a topologically defined community is tightly coordinated. In confocal microscopy experiments, we regularly observe co-localization and co-expression of in-community genes, an occurrence which frequently takes place within transcriptional co-factor condensates. Our collective approaches more accurately reflect the complexity of CRE interaction networks, underscores the need for incorporating spatial organization in the study of enhancer biology, and provides a framework for the reinterpretation of SEs, their condensates, and their target genes through the lens of 3D chromatin structure.

overall_design: Signle cell gene expression profiling of mESC v6.5 cell line is conducted by performing scRNA-seq

first: Jie

last: Lv

first: Kelsey

last: Maher

first: Alaguraj

last: Veluchamy


title: Topology-informed regulatory element collections coordinate cell identity gene expression programs

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

overall_design: Refer to individual Series


title: Topology-informed regulatory element collections coordinate cell identity gene expression programs[scATAC-Seq]

overall_design: Signle cell chromatin profiling of mESC v6.5 cell line is conducted by performing scATAC-seq


title: Estrogen receptor β target gene expression reveals novel repressive functions in aggressive breast cancer [ChIP-Seq]

overall_design: Analysis of breast cancer cells with different ERβ levels and after with treatment with the ERβ agonist. KPL4 cells without ERβ (ERβ knockout cells) vs. KPL4 cells with ERβ (ΕRβ knockout cells with transfected ERβ). Wild-type SUM149 cells with endogenous ERβ (Control cells) vs. SUM149 cells with overexpressed ERβ (Control cells with transfected ERβ). KPL4 ΕRβ knockout cells with transfected ERβ after treatment with vehicle (DMSO) or the ERβ agonist LY500307 for 2 hours

last: Tastsoglou

first: Ilias

last: Karagounis

first: Marios

last: Miliotis

first: Harika

last: Nagandla

first: Kristina

last: Zambo

first: Maria

last: Liousia

first: Naoto

last: Ueno

first: Amit

last: Maity

first: Artemis

last: Hatzigeorgiou


title: Effects of the Chinese herbal medicine Zishen Huoluo formula (ZSHLF) on miRNA expression in spontaneously hypertensive rats (SHRs).

city: Jinan

first: Xiaolin

last: Wu

address: No. 4655, Daxue Road, Changqing District, Jinan, Shandong Province

institute: Shandong University of Traditional Chinese Medicine

summary: To investigate the changes of miRNA expression in SHRs by the Chinese herbal medicine Zishen Huoluo formula intervention.

overall_design: miRNA-seq analysis of left ventricular in rats. The treatment assignments were as follows: 5 male Wistar-Kyoto Rats were used as a blank control group (WKY), and 10 male SHRs were divided into SHR control group (SHR) and ZSHLF intervention group (ZSHLF). Both WKY anf SHR groups were treated by normal saline. The treatment lasted for 4 weeks.

first: Tong

last: Wang

first: Huayun

last: Yu

first: Xiaotong

last: Song

first: Lin

last: Gao

first: Yue

last: Zhao

first: Qian

last: Chen

first: Haijun

first: Yuan

first: Zhichun


title: Transcriptional profile and TCR sequences from tumor and adjacent normal human colorectal samples

city: Chicago

first: Erin

last: Adams

state: IL

institute: University of Chicago

summary: We focus on characterizing mucosal-resident γδ T cells for determination of their effector profile, characterization of their paired TCR repertoire, and understanding of antigen reactivity towards CD1 molecules through single cell RNA analyses.

overall_design: Intestinal epithelial lymphocytes (IEL) from tumor or adjacent normal tissue from human colon were isolated. Gamma delta T cells were sorted from whole IEL using Vd1 and Vd2 antibodies and/or tetramers of CD1d or MR1. Four 10x Genomics libraries were then made from each sample: gene expression, surface (CITE-seq), alpha beta TCR, and gamma delta TCR.

first: Caitlin

middle: D

last: Castro

first: Mayuri

last: Viswanathan

first: Augusta

last: Broughton


title: SMARCA4 Promotes Lineage Plasticity and Enzalutamide Resistance in Prostate Cancer by Regulating PROX1 via H3K27 Acetylation

status: Public on Feb 14 2026

city: guagnzhou

first: Chenwei

address: 南方医科大学高层学生公寓1635

institute: 南方医科大学

summary: Enzalutamide resistance is a dynamic process often culminating in the aggressive progression to neuroendocrine prostate cancer (NEPC). This lineage plasticity is hypothesized to be driven by underlying epigenetic alterations, yet the core molecular drivers remain unclear. Elucidating these factors is of significant clinical importance for overcoming resistance. To model this transition, we established a dynamic gradient-resistant cell model simulating the clinical response to enzalutamide, and found robust upregulation of the chromatin remodeling factor SMARCA4 in resistant cells. Both in vitro and in vivo experimental results demonstrated that inhibiting SMARCA4 effectively suppresses tumor progression and reverses neuroendocrine transformation. Mechanistically, integrated multi-omics analysis, correlation studies, and protein interaction experiments revealed the transcription factor PROX1 as a crucial downstream target of SMARCA4, where its inhibition alone was sufficient to reverse the aggressive malignancy and neuroendocrine characteristics of resistant cells. We further demonstrated that SMARCA4 enhances H3K27ac levels and chromatin accessibility at the PROX1 locus to regulate its expression. Importantly, the tumor-suppressive effect of SMARCA4 knockdown could be rescued by histone deacetylase inhibitors (HDACi), achieving a level of recovery comparable to PROX1 overexpression. In summary, this study defines a core epigenetic pathway, showing that increased SMARCA4 activity promotes luminal-to-neuroendocrine transformation by enhancing histone acetylation and chromatin accessibility at the PROX1 locus. Targeting the SMARCA4-PROX1 axis provides a valuable therapeutic strategy for combating enzalutamide resistance and NEPC progression.

overall_design: Expression profiling by high throughput sequencing. Genome binding/occupancy profiling by high throughput sequencing

first: Mayao

last: Luo

first: Shidong

last: Lv

first: Qiang

last: Wei


title: Association between blood parameters, whole-blood transcriptomic profiles, and immune-related adverse events in metastatic renal cell carcinoma during nivolumab plus ipilimumab

city: tsukuba

first: Satoka

last: Kinase

address: tenoudai 1-1-1

institute: University of tsukuba

summary: Pretreatment immune profiles associated with immune-related adverse events (irAEs) may inform individualized management strategies, including enhanced monitoring and early toxicity intervention, in patients with metastatic renal cell carcinoma (mRCC) treated with nivolumab plus ipilimumab. In this cohort (n = 51), we analyzed pretreatment peripheral blood parameters and whole-blood transcriptomic profiles. Higher lymphocyte and monocyte counts (odds ratios [ORs] 14.36 and 9.90, respectively) were significantly associated with an increased risk of irAEs, whereas higher neutrophil counts and C-reactive protein levels (ORs 0.08 and 0.27, respectively) were associated with a decreased risk. To characterize immune pathways associated with irAE development, we performed whole-blood transcriptomic analyses. Gene set enrichment analysis revealed upregulation of lymphocyte- and humoral immunity-related pathways and downregulation of neutrophil- and inflammatory-related pathways in patients who developed irAEs. CIBERSORTx demonstrated reduced neutrophil fractions and increased proportions of CD8⁺ T cells and activated memory CD4⁺ T cells, indicating an adaptive immune-dominant profile. Exploratory analysis identified five candidate genes (ANAPC1, CDK4, MCM6, GRAP2, and BST2) that may contribute to the immune features associated with irAE development. Collectively, these findings suggest that irAE development is associated with a distinct systemic immune profile characterized by enhanced lymphocyte-related and reduced neutrophil-related immune activity.

overall_design:
Whole-blood RNA sequencing was performed on pretreatment peripheral blood samples from 51 patients with metastatic renal cell carcinoma treated with nivolumab plus ipilimumab. Patients were stratified according to the development of immune-related adverse events (irAEs). Differential expression analysis, gene set enrichment analysis (GSEA), and immune cell deconvolution (CIBERSORTx) were conducted to characterize transcriptomic differences between irAE-positive and irAE-negative groups.Peripheral whole blood samples were collected in PAXgene Blood RNA tubes (PreAnalytiX) and processed according to the manufacturer’s protocol prior to RNA extraction and library preparation.

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

first: Yoshiyuki

last: Nagumo

first: Bunpei

last: Isoda

first: Hiromichi

last: Sakurai

first: Reo

last: Takahashi

first: Shuhei

last: Suzuki

first: Akane

last: Yamaguchi

first: Ryota

last: Yanagihashi

first: Kozaburo

last: Tanuma

first: Satoshi

last: Nitta

first: Masanobu

last: Shiga

first: Kosuke

last: Kojo

first: Atsushi

last: Ikeda

first: Takashi

last: Kawahara

first: Akio

last: Hoshi

first: Shuya

last: Kandori

first: Bryan

last: Mathis

first: Hiroyuki

last: Nishiyama


title: Enzyme-mediated methylation and alkynylation enables transcriptome-wide identification of pseudouridine modifications

first: Chuan

last: He

state: Illinois

address: 929 E 57th St

department: Chemistry

summary: Pseudouridine (Ψ) is one of the most abundant chemical modifications and plays important roles in RNA function. Advances in our understanding of Ψ have been hindered by a limit of robust methods to precisely and sensitively map their distributions in cellular RNAs. Here, we present ELAP-seq (Enzymatic Labeling and Pull-down for Sequencing) for Ψ detection, which leverages a naturally occurring N1-methyl pseudouridine methyltransferase from Methanocaldococcus jannaschii (Mj1640). This enzyme promiscuously converts Ψ to N1-methyl-Ψ (m1Ψ) or installs a propargyl group at the same location in vitro under a mild condition, exhibiting high sensitivity and specificity, and is also functional inside cells. ELAP-seq enriches Ψ-containing RNA fragments and enables single-nucleotide-resolution Ψ detection with markedly enhanced signal-to-noise ratio and reduced sequencing and computational demands. Using ELAP-seq, we identify thousands of candidate Ψ sites in human HeLa and HEK 293T transcriptomes, validating many previously identified sites as well as reporting new ones. This versatile enzymatic platform expands the toolkit for sensitive labeling and detection of Ψ, advancing the study of RNA modification biology.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: We developed a method named ELAP-seq to detect pseudouridine modification in the whole transcriptome. In this method, poly-A RNA is isolated and fragmented, after which pseudouridine is specifically labeled by methyltransferase Mj1640 with a propargyl group. Further clicking on a biotin molecule enables enrichment of RNA fragments containing pseudouridine for sequencing. Pseudouridine causes stop signature during reverse transcription thus can be detected at single base resolution. Input libraries are built without enzymatic labeling and is for decreasing false positives which also generate stop signatures in the input samples. The input samples are also used for semi-quantitative evaluation of pull-down enrichment levels for each modification site. Two different reverse transcriptases, Superscript IV (corresponing to samples with letter "IV" in their names) and Superscript III (corresponding to samples with letter "III" in their names), were used when constructing the sequencing libraries. We first applied ELAP-seq to synthesic oligos to evaluate the enzyme's sequence preference and performed two replicates using only superscript IV (samples with names starting with 'oligo' mean synthetic probes containing NNΨNN motif and samples with names starting with "spikein" means synthetic probes containing NNUNN motif). We further performed three biological replicates for HeLa and HEK293T cell lines (HeLa-rep1 to 3 and HEK rep1 to 3) to identify candidate modification sites in each cell line.  To identify sites that are responsive to DKC1 knockdown, we treated HEK293T cells with negative control siRNA (sictrl) or DKC1 siRNA (siDKC1) and prepared two biological replicates for each condition using only superscript IV. We also employed a recently established in vitro transcribed RNA (IVT RNA) library from HEK293T transcriptome as a negative control and performed two replicates (sample names start with 'IVT').

first: Yuru

last: Wang

first: Kinga

last: Pajdzik

first: Yutao

last: Zhao

first: Chang

last: Ye

first: Talbot

last: Stone

first: Lisheng

last: Zhang

first: Wen

first: Mahdi

last: Assari

first: Wenxin

first: Caraline

last: Sepich-Poore

first: Qing

last: Dai

first: Ke

first: Minkui

last: Luo

first: Tao

last: Pan


title: Serum tsRNA-Gly-5-0006 in breast cancer: Differential expression and effects on cancer cell biology

city: Nanjing

first: Jianjiang

last: Shen

state: Jiangsu

address: HanZhong load 155#

institute: Jiangsu Province Hospital of Chinese Medicine

summary: Breast cancer (BC) is a leading cause of female mortality worldwide, largely due to metastatic progression and the absence of reliable non-invasive biomarkers for early detection. This study investigates the potential of tRNA-derived small RNA fragments (tRFs) as novel diagnostic and functional molecules in BC. Through high-throughput sequencing and subsequent validation in clinical cohorts, we identified tsRNA-Gly-5-0006 as significantly downregulated in both BC tissues and patient serum compared to adjacent normal tissues, mastitis samples, and healthy controls.

overall_design: The tsRNA-Gly-5-0006 is significantly low in breast cancer tissue, and the difference in tsRNA-Gly-5-0006 expression between breast cancer patients and the normal control group is counted. Overexpression of tsRNA-Gly-5-0006 in breast cancer cell line MDA-MB-231, observation of cell phenotype


title: Early adjunct anti-PD-L1 therapy improves outcomes and reverses immune paralysis in murine pulmonary mucormycosis

first: Sebastian

last: Wurster

address: 6565 MD Anderson Blvd

institute: The University of Texas MD Anderson Cancer Center

summary: Invasive pulmonary mucormycosis (IPM) is a severe opportunistic mold infection whose outcome is predominantly host driven. Preclinical proof-of-concept studies and clinical case reports in salvage therapy settings suggested a benefit of immune checkpoint inhibitors (ICIs) in IPM management. However, the kinetics of infection-induced immune paralysis and optimal timing of ICI therapy remain poorly understood. Here, we performed sequential nCounter-based transcriptomics on lung tissue of cyclophosphamide-immunosuppressed mice with IPM (Rhizopus arrhizus infection) to dynamically study the pulmonary immune environment. Within 7 days after infection, lungs of mice with IPM showed reversal of early proinflammatory signaling, impaired T-cell signaling, and upregulation of exhaustion markers. Similar immune paralysis signatures were seen in mice with invasive pulmonary aspergillosis and fusariosis. For therapeutic studies, Mucorales-active antifungal therapy with isavuconazonium sulfate (ISAV) was initiated on day 3 after IPM infection, along with anti-PD-L1 or a non-targeting isotype antibody (control) given either on days 3+5 (early) or days 6+8 (late). Both early and late adjunct anti-PD-L1 therapy were well-tolerated and significantly improved morbidity/mortality outcomes compared to ISAV + isotype. Notably, early adjunct anti-PD-L1 therapy promoted significantly stronger innate immune cell activation, upregulation of key cytokine pathways, reinvigoration of T-helper-cell signaling, and reversal of IPM-induced exhaustion signals than both late adjunct anti-PD-L1 and isotype control. These findings indicate that combined antifungal and early immunomodulatory therapy may be an important strategy to intercept immune paralysis and improve outcomes in immunocompromised hosts with IPM, inviting further preclinical and clinical exploration of early host-directed interventions to treat deadly mold pneumonias.

overall_design: Eight-week-old female BALB/c mice were immunosuppressed with cyclophosphamide (Long Grove Pharmaceuticals; 250 mg/kg on day -4, 150 mg/kg on day -1, and 100 mg/kg twice weekly thereafter). On day 0, mice were infected intranasally with 50,000 spores of Rhizopus arrhizus (clinical isolate Ra-749), 50,000 conidia of Aspergillus fumigatus (reference strain Af-293), or 150,000 spores of Fusarium solani (clinical isolate Fs-001). For therapeutic studies in the IPM model, treatment with ISAV was initiated on day 3 post-infection (64 mg/kg by oral gavage twice daily for 5 days), when the mice had developed significant infection-induced distress. Additionally, mice received 0.25 mg/kg α-PD-L1 (Leinco Technologies, #P371) or the corresponding IgG2b isotype antibody (Leinco Technologies, #I-1034) intraperitoneally either on days 3+5 (early) or days 6+8 (late).

first: Dimitrios

middle: P

last: Kontoyiannis

first: Jezreel

last: Pantaleón García


title: Multiple Factors Contribute to Guaiacol Production by Alicyclobacillus acidoterrestris and Alicyclobacillus suci in Apple Juice, as revealed by Transcriptomic and Phenotypic Analyses

city: ITHACA

first: Katerina

last: Roth

state: New York

address: 411 Tower rd

institute: Cornell University

summary: Alicyclobacillus acidoterrestris and Alicyclobacillus suci are both guaiacol producers that can cause spoilage in products like juices. To study the genetic underpinnings of guaiacol production, transcriptomics was performed on multiple strains of A. suci and A. acidoterrestris under guaiacol production conditions in apple juice. While guaiacol production was consistently higher by A. acidoterrestris than by A. suci, the gene expression levels associated with guaiacol production (e.g., vdcC, vdcB, vdcD) showed significant variability across strains of both species, suggesting that other factors beyond vdcC transcription influence the amount of guaiacol produced. This research provides insights for beverage producers in assessing spoilage risks and developing more informed mitigation strategies.

sample_organism:
Alicyclobacillus acidoterrestris
Alicyclobacillus suci

overall_design: six strains were grown overnight before being inoculated into 50 mL of apple juice at a final concentration of approximately 104 CFU/mL. The Simply Apple brand juice was purchased from a local supermarket. The samples were incubated at 30°C and  sampled on day 3


title: RNA-seq of CT26 cells and tumors treated with or without Midostaurin

city: Shanghai

first: Zhengzhen

last: Wu

address: No. 500 Dongchuan Road, Minhang District

institute: East China Normal University

summary: Immune checkpoint inhibitor therapy has demonstrated efficacy in a variety of tumors. However, due to the high heterogeneity of colorectal cancer, the clinical efficacy of ICB in the treatment of this disease remains quite limited. Activating mutations of KRAS are detected in 35%–50% of colorectal cancer tissues in clinical. Colorectal cancers with these activating mutations are characterized by an immune desert phenotype and aberrant immune-inflammatory microenvironment. Studies have indicated that oncogene addiction in tumorigenesis (such as KRAS mutation) and non-genetic mechanisms, particularly epigenetic regulation, can synergistically modulate multiple types of plasticity of the tumor microenvironment and tumor cells, but how epigenetic regulators function in the immunosuppressive microenvironment specific to KRAS-mutant colorectal cancer is barely known. In this study, we identify that PHF8 functions as a MHC-I suppressor that limits anti-tumor immunity in KRAS-mutant colorectal cancer. We also find a FDA-approved drug, Midostaurin, which can mimic the phenotype of PHF8 depletion and add to the efficacy of ICB treatment and KRAS inhibition.

overall_design: RNA-seq profiling of CT26 cells with or without Midostaurin treatment for 48 h and CT26 subcutaneous tumors treated with or without Midostaurin for 2 weeks

first: Xiufeng

last: Pang


title: An unimolecular GIPR:GLP-1R:PPAR𝛼,𝛾,𝛿 quintuple agonist eliminates obesity and insulin resistance in mice.

city: Neuherberg

first: Robert

middle: Michael

last: Gutgesell

state: Bavaria

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

country: Germany

institute: Helmholtz Center Munich

summary: Drugs to improve obesity-linked metabolic dysfunction are on the rise, with GLP-1:GIP co-agonism being effective in the management of obesity and type 2 diabetes, and with Lanifibranor (Lani), a nuclear acting small molecule triple agonist at the peroxisome proliferator-activated receptors alpha, gamma and delta (PPAR𝛼,𝛾,𝛿) being in phase 3 development for the treatment of metabolic dysfunction-associated steatohepatitis. Seeking to further improve the metabolic efficacy of GLP-1:GIP co-agonism, we here report the design and preclinical evaluation of an unimolecular quintuple agonist, which synergistically combines the body weight and blood glucose lowering effects of GLP-1:GIP co-agonism with the insulin sensitizing effects of Lani through its targeted delivery into only cells that express the receptor for either GIP or GLP-1. In vitro, GLP-1:GIP:Lani is indistinguishable from its GLP-1:GIP backbone in GIPR and GLP-1R signaling and equally stimulates insulin secretion in isolated murine islets. In vivo, however, GLP-1:GIP:Lani is much superior to GLP-1:GIP co-agonism or Semaglutide to decrease body weight, food intake, and hyperglycemia in obese and insulin resistant mice through synergistic incretin and PPAR action in key glucoregulatory tissues. The superior metabolic action of GLP-1:GIP:Lani is demonstrated in mice with genetic (db/db) and diet-induced obesity (DIO), is accelerated in DIO mice with adipose-specific overexpression of GIPR and is absent in DIO double-incretin receptor knock-out mice. Collectively, our data suggest that this novel quintuple polyagonist holds unprecedented therapeutic value to treat obesity and type 2 diabetes.

overall_design: C57BL/6J mice fed a high fat diet were treated daily with either vhcl, a GLP-1:GIP receptor dual agonist, or a GLP-1:GIP:Lani conjucate for 7 days. Tissues  were collected 24 hours after the last injection.

first: Daniela

last: Liskiewicz

first: Ahmed

last: Khalil

first: Seun

last: Akindehin

first: Jon

middle: E

last: Campbell

first: Russel

last: Castelino

first: Callum

last: Coupland

first: Jonathan

last: Douros

first: Annette

last: Feuchtinger

first: Brian

last: Finan

first: Cristina

last: Garcia-Caceres

first: Gerald

last: Grandl

first: Daniel

last: Hass

first: Ezgi

last: Karaoglu

first: Pamela

last: Kakimoto

first: Christine

last: Kusminski

first: Danielle

last: Leander

first: Arkadiusz

first: Xue

last: Liu

first: Gandhari

last: Maity-Kumar

first: Sara

last: Martinez Martinez

first: Stephany

last: Mowery

first: Ruben

last: Nogueiras

first: Marshall

last: Paisley

first: Diego

last: Perez-Tilve

first: Sneha

last: Prakasch

first: Alberto

last: Cebrian-Serrano

first: Monica

last: Tost

first: Jordan

last: Wean

first: Philipp

last: Scherer

first: Randy

last: Seeley

first: Richard

last: DiMarchi

first: Matthias

middle: H

last: Tschöp

first: Natalie

last: Krahmer

first: Patrick

last: Knerr

first: Timo

last: Müller


title: RNA-seq of TCR-stimulated CD4⁺ T cells from SKG mice treated with the Nr4a1 agonist Cytosporone B

city: Kyoto

first: Yoichi

last: Nakayama

state: Kyoto

address: 54, Kawahara-cho, Shogoin

institute: Kyoto University

summary: Rheumatoid arthritis (RA) is a chronic autoimmune disease in which CD4⁺ T cells and T helper 17 (Th17) cells play central roles in driving synovial inflammation. Nr4a1 is an orphan nuclear receptor that acts as a negative regulator of T cell activation. Cytosporone B (CsnB) is a small-molecule Nr4a1 agonist with immunomodulatory properties, but its impact on T cell responses in autoimmune arthritis remains unclear. In this study, we used SKG mice, a T cell–driven model of chronic autoimmune arthritis, to investigate how pharmacologic Nr4a1 activation influences pathogenic T cell responses. CD4⁺ T cells isolated from SKG mice were stimulated through the T cell receptor in vitro in the presence or absence of CsnB, and transcriptomic profiling was performed by RNA sequencing. The resulting dataset provides genome-wide information on CsnB-induced changes in gene expression in activated CD4⁺ T cells, and supports mechanistic analyses of how Nr4a1 activation modulates T cell activation and Th17-related pathways in autoimmune arthritis.

overall_design: Total CD4⁺ T cells were isolated from spleens and lymph nodes of SKG mice using magnetic-activated cell sorting. Purified CD4⁺ T cells were stimulated in vitro on plates coated with anti-CD3 and anti-CD28 antibodies in the presence or absence of the Nr4a1 agonist Cytosporone B (CsnB) for 2 hours.

first: Ryosuke

last: Hiwa


title: Development and Characterization of an Inducible Tensin1 Deficient Transgenic Murine Model

city: Madison

first: Nathan

last: Sandbo

state: WI

address: 600 Highland Avenue

institute: University of Wisconsin-Madison

summary: Tensin1 (TNS1) is a key component of focal and fibrillar adhesions, mediating fibrillogenesis, as well as the transduction of mechanical cues and adhesive signaling. To enable further TNS1 characterization, we have developed a novel transgenic mouse that allows for temporally controlled and lineage specific knockout of TNS1. We found no differentially observed effects of TNS1 knockout on mouse health, breeding capacity, or vital organ histopathology. In contrast, RNA sequencing analysis identified 171 differentially expressed genes with Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrating differential expression in osteoclast differentiation and a number of pathways involved in host immune response. Furthermore, STRING pathway analysis showed differential regulation of genes involved in B-cell and myeloid-related signaling pathways, a number of which were validated by reverse transcription-quantitative polymerase chain reaction (RT qPCR). These findings were corroborated by impaired function of TNS1 siRNA monocytes and increased detection of lymphocytes in the bronchoalveolar lavage within days following TNS1 knockout. This study provides a novel understanding of the phenotypic and genotypic changes that occur following knockout of TNS1 that may lead to subsequent understanding of its role in disease.

overall_design: RNA sequencing profiling of TNS1 expressing (TNS1+/+) and inducible, conditional deletion TNS1 knockout mice (TNS1-/-) whole lung lysates. All animals were given tamoxifen for 7 days, and the left lung from each animal was flash frozen, lysated and processed for RNA sequencing 14 days after the completion of tamoxifen treatment.

first: Ksenija

last: Bernau

first: Kelsey

last: Holbert

first: Ivy S.

last: McDermott

first: Babita

last: Rahar

first: Kade W.

last: Coulter

first: Madalyn A.

last: Osterhaus

first: Thomas J.

last: Harr

first: Carson

last: Gehl

first: Angie T.

last: Oler

first: Christopher

last: Huffman

first: Beth

last: Gray

first: Trevor S.

last: Langel

first: Kenneth M.

last: Chan

first: Amir

last: Forati

first: Sandra

last: Splinter BonDurant

first: Mark

last: Berres

first: Kathy J.

last: Krentz

first: C. Dustin

last: Rubinstein

first: Andres F.

last: Mejia


title: PKM2 lactylation promotes colorectal cancer vasculogenic mimicry and resistance to bevacizumab treatment by facilitating FOSL1 super-enhancer formation [RNA-Seq]

city: Guangzhou

first: Weihao

last: Li

address: 651 Dongfeng Road east

institute: Sun yat-sen university cancer center

summary: Despite the clinical utility of bevacizumab in advanced colorectal cancer (CRC), resistance remains a major challenge. Here, we unveiled a lactate-mediated mechanism driving vasculogenic mimicry (VM) and bevacizumab resistance through PKM2 lactylation. PKM2 lactylation at K206 by AARS1 promoted PKM2 nuclear translocation and interaction with FOSL1. PKM2 binding facilitated FOSL1-dependent super-enhancer formation and target gene transcription, which contributed to CRC cell VM. Genetic or pharmacological inhibition of PKM2 lactylation disrupted VM and synergized with bevacizumab in patient-derived pre-clinical models, significantly improving therapeutic efficacy. Together, this study reveals lactylation as a metabolic switch linking cancer glycolytic reprogramming to transcriptional rewiring and proposes targeting PKM2 lactylation to enhance the anti-tumor activity of bevacizumab in CRC.

overall_design: RNA-seq profiling of PKM2 wildtype (WT) HCT116 cells and their PKM2 K206R mutant cells.

first: Jianhong

last: Peng

first: Jiahua

last: He

first: Zhizhong

last: Pan

first: Chi

last: Zhou

first: Junzhong

last: Lin


title: Transcriptomics of different forms of senescence

first: LMS

last: Bioinformatics Core

summary: The goal of this study was to compare the transcriptomics of different forms of senescence with each other and to normal growing and quiescent IMR90 cells.Senescence was induced in IMR90 cells by different stimuli. Therapy-induced senescence was induced by treatment with doxorubicin, irradiation, etoposide and palbociclib. Oncogene-induced senescence was induced by addition of tamoxifen (4OHT) to IMR90 ER:RAS cells.

overall_design: 8 samples in total, 4 replicates each: IMR90 growing, IMR90 quiescent, IMR90 senescent (doxrubicin), IMR90 senescent (irradiation), IMR90 senescent (palbociclib), IMR90 senescent (etoposide), IMR90 ER:RAS non-induced (growing), IMR90 ER:RAS induced (Ras-induced senescence)

first: Verena

last: Wagner

first: Jesus

last: Gil

first: Gopuraja

last: Dharmalingam

first: Sanjay

last: Khadayate


title: Repeat-rich RNA Clusters Repetitive Genomic Elements into Biomolecular Condensates for Heterochromatin Organization and Muscle Integrity

city: Suwon-si

first: Jinmi

last: Choi

state: Gyeonggi-do

address: Seoburo 2066, Jangan-gu

country: South Korea

institute: Sungkyunkwan University

summary: Biomolecular condensation is a pivotal mechanism in chromatin organization and nuclear compartmentalization. However, the molecular mechanism that drives heterochromatin organization and selectively partitions heterochromatin components in muscle cells remains unclear. Furthermore, its pathological implications remain unexplored. Here, we demonstrate that ChRO1, a muscle-specific RNA enriched with simple dinucleotide repeats, is associated with static heterochromatin foci containing similar repetitive elements in C2C12 mouse muscle cells. Through its CU-repeat-rich region, ChRO1 promotes heterochromatin clustering and facilitates the selective partitioning of heterochromatin proteins, as shown in vitro and in cells. Consequently, chromatin interaction stablized at ChRO1-bound regions, reinforcing TAD boundaries and promoting inactive chromatin states. The enhanced intra- and interchromosomal interactions secure the heterochromatinization of non-muscle genes, highlighting ChRO1’s role in establishing chromatin interaction hubs. Disruption of ChRO1 or perturbation of condensate organization induces chromocenter disintegration and muscle atrophic phenotypes, underscoring the importance of these processes in maintaining muscle integrity. Notably, ChRO1 mitigates chromocenter disintegration and atrophic phenotypes in chemically induced atrophy models, emphasizing its protective role. These findings reveal a novel repeat-rich RNA-based mechanism of repetitive DNA condensation that safeguards heterochromatin organization and muscle integrity, providing mechanistic insight and therapeutic implications for muscle-related disorders.

overall_design: HiChIP experiments performed with an anti-H3K9me3 antibody (Abcam, ab8898) in C2C12 WT and ChRO1 KO cells, differentiated for 4 days.

first: Eun-Jung

last: Cho


title: PKM2 lactylation promotes colorectal cancer vasculogenic mimicry and resistance to bevacizumab treatment by facilitating FOSL1 super-enhancer formation [CUT&Tag]

overall_design: CUT&Tag sequencing of anti-H3K27ac in PKM2 wildtype (WT) HCT116 cells and their PKM2 K206R mutant cells; CUT&Tag sequencing of anti-FOSL1 and PKM2 in PKM2 WT HCT116 cells


title: Trimetazidine delays autoimmune diabetes in mice by transiently suppressing CD8⁺ T-cell fatty-acid oxidation

city: Vienna

first: Manuel

last: Salzmann

address: Lazarettgasse 14

department: Department of Medicine II, Division of Cardiology

country: Austria

institute: Medical University of Vienna

summary: Type 1 Diabetes Mellitus (T1D) is an organ specific autoimmune disease, which is characterized by persistent hyperglycemia due to immune-mediated destruction of pancreatic islet β cells. Shifting immune cell metabolism is an emerging therapeutic concept. Therefore, we tested whether the fatty acid oxidation (FAO) inhibitor trimetazidine (TMZ) can restrain autoreactive immunity and delay T1D in a non-obese diabetic mouse model. Of note, TMZ is one of only three approved drugs directly targeting cellular metabolism. TMZ acutely increased mitochondrial membrane potential, suppressed FAO and curtailed activation and proliferation of human CD8⁺ T cells. In dysglycemic NOD mice, a clinically approved dose of TMZ delayed progression to T1D, lowered mean glycaemia and reduced islet CD4⁺/CD8⁺ infiltration. scRNA-seq revealed depletion of FAO-high, stress-responsive secretory cells and mitochondrially active stromal cells, indicating improved pancreatic health. However, prolonged exposure elicited compensatory up-regulation of carnitine-palmitoyl-transferase-1A in CD8⁺ subsets, normalized T-cell infiltration and nullified protection. We conclude that TMZ delivers a dampening of initial T-cell pressure and pancreatic stress. Adaptive upregulation of FAO within cells counteracted observed benefits thereby only transiently delaying disease onset. Our work demonstrates that drugs targeting cellular metabolism needs to retain sufficient potency to not be outpaced by immune cells upscaling metabolic pathways.

overall_design:
Pancreatic tissue was collected from five control mice and five TMZ-treated mice after one week of treatment, initiated when fasting blood glucose reached 150-180 mg/dL.
Pancreatic heads were dissected, snap-frozen, and stored in liquid nitrogen until processing. Tissue dissociation and fixation were performed using the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (PN-1000414, 10x Genomics, Pleasanton, CA, USA). Nuclei and single cells were isolated following the protocol “Tissue Fixation & Dissociation for Chromium Fixed RNA Profiling” (CG000553). Samples from each group (control and TMZ-treated) were pooled and assigned one barcode per group for multiplexed analysis.
Library preparation was performed using the “Chromium Fixed RNA Profiling for Multiplexed Samples” protocol (CG000527, protocol version F), with the Chromium Fixed RNA Profiling Kit - Mouse Transcriptome (4 reactions × 4 barcodes, PN-1000496), Hybridization & Library Kit (PN-1000415), and the Chromium Next GEM Chip Q Single Cell Kit (16 reactions, PN-1000422), all from 10x Genomics. Sequencing was performed on an Illumina NextSeq 2000 instrument using a NextSeq 2000 P4 flow cell (100 cycles, PN-20100994, Lot #20879630, Illumina, San Diego, CA, USA).
Sequencing data were demultiplexed and aligned using Cell Ranger software version 8.0.1 (10x Genomics), with the Mus musculus mm10 (Ensembl 98). Cell Ranger Loupe Browser output files were imported into R (version 4.4.1) for downstream processing. Nuclei with >45% mitochondrial transcript content, nFeature_RNA ≤ 500, or nCount_RNA ≥ 500 were excluded from analysis. Filtered data were normalized, log-transformed, and the resulting matrix was used for all downstream analyses.
Data integration was performed using RPCA-based batch correction implemented in Seurat v5 (https://satijalab.org/seurat/articles/seurat5_integration). Principal component analysis was conducted using the first 20 components, and clustering was performed with a resolution of 0.1. The final annotated dataset was exported as a cloupe file and reloaded into the Loupe Browser (10x Genomics) for visualization and manual inspection of clusters.
Pseudo-bulk differential expression analysis was performed using the DElegate package (https://github.com/cancerbits/DElegate).

first: Laura

last: Boccuni

first: Philipp

last: Hohensinner


title: PKM2 lactylation promotes colorectal cancer vasculogenic mimicry and resistance to bevacizumab treatment by facilitating FOSL1 super-enhancer formation [ATAC-seq]

overall_design: ATAC-seq of anti-H3K27ac in PKM2 wildtype (WT) HCT116 cells and their PKM2 K206R mutant cells


title: Follicular mural granulosa cells stockpile glycogen to fuel corpus luteum pre-vascularization

city: Wuhan

first: changjiu

last: he

state: Hubei

address: 1 Shizishan street, Hongshan District

department: College of Animal Science and Technology

institute: Huazhong Agricultural University

summary: The differentiation of follicular mural granulosa cells (fGCs) into luteal cells involves a rapid progesterone synthesis surge and the vascular network development. However, progesterone elevation occurs before vascularization, leaving luteinizing fGCs temporarily devoid of blood supply. The mechanism of how fGCs fuel increased progesterone synthesis during this avascular phase remains unclear. Our research, utilizing single-cell RNAseq and in vivo/ex vivo experiments, revealed that upon receiving the ovulatory/luteinization signal, fGCs transition to a low-energy state, reducing metabolic activity and storing glucose as glycogen.

overall_design: Ovaries were collected at 0 (H0), 1 (H1), and 6 hours (H6) post-hCG injection for single-cell RNA-seq.

first: Changjiu

first: Jianning

last: Liao


title: Mouse models of Alazami syndrome reveal a developmental window of vulnerability in the hippocampal dentate gyrus to transcriptional dysregulation

city: Chengdu

first: T

last: Q

state: Sichuan Province

address: No.17, Section 3, Renmin South Road

institute: West China Second University Hospital

summary: Enhanced P-TEFb activity is thought to promote cell proliferation by increasing the transcriptional output of RNA polymerase II, and normally most cellular P-TEFb is inhibited by 7SK snRNP containing LARP7 and HEXIM1.  Paradoxically, instead of causing overgrowth syndromes, loss-of-function mutations of LARP7 are linked to Alazami syndrome, a human neurodevelopmental disorder characterized by growth restriction and cognitive impairment.  Here, we generate genetically engineered mouse models to investigate the etiology underlying Larp7 deficiency.  Conditional knockout of either Larp7 or Hexim1 in the brain results in similar developmental defects as in human patients.  Notably, the size and the function of the hippocampal dentate gyrus are markedly reduced.  Multi-omics analyses and functional assays reveal that a heightened P-TEFb activity enhances the self-renewal transcriptional programs in Emx1+ neural progenitor cells to limit neurogenesis at the neonatal stage, resulting in dentate gyrus hypoplasia.  These results demonstrate that dysregulated subtissular stem cell dynamics reconcile increased P-TEFb activity and cell proliferation with reduced organismal sizes.  Because neonatal and adult dentate gyrus neurogenesis are highly alike, clinical-grade P-TEFb inhibitors, originally developed for treating cancer, may present a translational opportunity to ameliorate the adverse effects of several medical conditions on dentate gyrus size and function.

overall_design: To identify differentially regulated pathways during neurosphere differentiation, RNA-seq profiling of wild-type and larp7 knockout neurosphere after 2 days differentiation.   ATAC-seq profiling of wild-type and larp7 knockout neurosphere.  CUT&Tag of RNA polymerase II, Pol II-Ser2 and Pol II-Ser5 in wild-type and larp7 knockout neurosphere. Single-cell RNA-seq was used to analyze cell compositions and functional states of the dentate gyrus, obtained from micro-dissected wild-type, Larp7f/f;Emx1-Cre, and Larp7f/f;nestin-Cre mutant mice at P7, respectively.  To obtain enough materials, 3-4 dentate gyri from littermates were combined for each genotype.


title: Long-term chronic exposure of mice to sodium fluoride and a mixture of endocrine disruptors lead to easily observable tooth enamel and retina abnormalities underlying changes in hepatic metabolism

city: PARIS

first: Guido

last: Kroemer

address: 15 rue de L'école de médecine

institute: Centre de Recherche des Cordeliers

summary: Background: Long-term exposure to environmental pollutants contributes to multiple health disorders diagnosed after years when pathologies are established. Early markers are urgently needed. Objectives: To identify early new markers of exposure to low-dose toxicants widely present in daily environment. To achieve this objective, we set up realistic models of environmental exposure and analyzed, in addition to the liver, the most studied xenobiotic target organ, two easily accessible sensitive organs, eyes and teeth, as good potential candidates to be original markers of environmental exposures. Methods: C57BL/6 mice were chronically exposed in drinking water to either 1 mM sodium fluoride (NaF), or a mixture of 15 widely present substances with endocrine-disrupting activities, or both, from the conception to 1 or 10 months after birth. Most doses of the components in the mixture were below the tolerated dose intakes. Eyes, livers and teeth were analyzed at the histological, biochemical and functional levels.Results: All mice in test groups presented lower weight gain than controls with the most significant differences observed in females 30 days after birth (PND 30). Whereas histological analyses showed no significant defects in liver despite metabolic disruptions highlighted by molecular metabolomic and RNAseq analyses, eye retina and tooth enamel presented disorders detected as soon as 3 months of age that considerably worsened in all 10-months old animals. Discussion: Despite clear molecular hepatic metabolic disorders occurring in all test groups, the most evident histological and clinical signs were reported in eyes and teeth. These easily accessible defects may be used as early markers of low-dose exposure to environmental toxicants.

overall_design: RNA-seq profiling of C57BL/6 mice exposed to NaF (1mM), a mixture of 15 endocrines disruptors and the combinaiton of both.

first: Emilie

last: Picard

first: Fatima Domenica Elisa

last: De Palma

first: Sophia

last: Loiodoce

first: Vincent

last: Carbonnier

first: Seiki

last: Achiedo

first: Noor

last: Mimoun

first: Diluxe

last: Mutale

first: Sophie

last: Doublier

first: Sylvère

last: Durand

first: Mélanie

last: Bourgin

first: Fanny

last: Aprohamian

first: Pierre

last: Cordier

first: Louise

last: Gutter

first: Katia

last: Jedeon

first: Marie-Christine

last: Naud

first: Philippe

last: Noirez

first: Jean-Marc

last: Ricort

first: Lotfi

last: Slimani

first: Francine

last: Behar-Cohen

first: Maria Chiara

last: Maiuri

first: Sylvie

last: Babajko


title: Multiscale profiling of tyrosine kinase inhibitor cardiotoxicity reveals mechanosensitive ion channel PIEZO1 as cardioprotective

city: Palo Alto

first: Nazish

last: Sayed

state: CA

address: 240 Pasteur Drive, 3500 BMI

institute: Stanford University

summary: Tyrosine kinase inhibitors (TKIs) have transformed cancer therapy but are associated with significant cardiovascular risks, including hypertension and heart failure. Here, we demonstrate that endothelial dysfunction driven by impaired mechanotransduction underlies TKI-induced hypertension and long-term cardiac dysfunction.

overall_design: COs were generated using iPSC-CMs alone or in combination with iPSC-ECs. For co-culture organoids, iPSC-CMs and iPSC-ECs were dissociated using TrypLE Express (Sigma) and mixed at a 70:30 ratio (CM:EC).

first: David

last: Wu


title: Single-Cell Profiling Across Immune Tissues and Organs Reveals Immunosenescence Signatures in Male Rhesus Monkeys

city: Kunming

first: Zhu

last: zhengna

state: YunNan

address: Kunming University of Science and Technology, Wujiaying Street, Chenggong District, Kunming city, Yunnan Province

summary: Single cell sequencing of rhesus monkey immune tissues and organs

overall_design: Four male rhesus monkeys were divided into two groups by age: young rhesus monkeys (Y, n=2) and old rhesus monkeys (O, n=2). Group Y was 7 years old and group O was 23 years old.Bone marrow, mesenteric lymph, peripheral blood and spleen were collected for single cell analysis.

first: Shengnan

last: Wang

first: Zhengna

last: Zhu

first: Hongju

last: Yang

first: Yaping

last: Yan

first: Luyao

last: Ran

first: Naixue

first: Yichao

first: Li

first: Bing

last: Bai

first: Weizhi

last: Ji

first: Wei

last: Si


title: Engineering intrinsically disordered regions (IDRs) for guiding genome navigation

city: Rehovot

first: Naama

last: Barkai

state: --- Select a state ---

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

summary: Profiling denovo IDR sequences fused to different DBDs to reveal the IDR grammar underlying targeting specificity

overall_design: 100s of IDR variants were designed, synthesized and constructed using CRIPSR and profiled ChEC-Seq

first: Jing

last: Liu

first: Divya Krishna

last: Kumar

first: Bohdana

last: Hurieva

first: Felix

last: Jonas


title: An epigenetic switch in vascular phenotype augments anti-tumor immunity [scRNA-seq]

status: Public on Feb 13 2026

city: Charlottesville

first: Andrew

middle: C

last: Dudley

state: VA

address: 1340 Jefferson Park Avenue

department: Dept. of Microbiology, Immunology, and Cancer Biology

institute: University of Virginia

summary: The abnormal tumor vasculature can present a barrier to the infiltration of anti-tumor immune cells, which impairs immune surveillance and response to immunotherapy. Here, we show that targeting the epigenetic factor DNA  methyltransferase 1 in endothelial cells (ECs) results in reduced angiogenesis while imparting profound changes to the tumor immune microenvironment (TIME), including increased proportions of CD4+ memory T-cells and NK cells. Depleting CD4+ T-cells, or blocking lymphocyte egress from the lymph nodes with FTY720, rescues tumor growth in mice with conditional deletion of Dnmt1 in ECs (Dnmt1iECKO) and dramatically shortens overall survival, whereas NK cells are dispensable. Tumors implanted in Dnmt1iECKO mice show reduced vascular branching, elevated expression of Vcam1, increased vessel-associated T-cells, and a shift in vascular specification including increased proportions of immune-permissive post-capillary venules (PCVs) and interferon-stimulated ECs (IFN_x0002_ECs). Deleting Dnmt1 in EC cultures strikingly potentiates responses to combinations of IFNg and TNFa and, notably, up-regulates important T-cell co-stimulatory molecules for memory CD4+ T-cells, including Icosl, Cd40, and Tnfsf4. Finally, immune checkpoint blockade (ICB) administered to Dnmt1iECKO mice with experimental melanoma lung metastasis reduces tumor burden, with some mice showing tumor eradication. Our findings identify endothelial Dnmt1 as a key regulator of vascular-mediated anti-tumor immunity, providing a rationale for integrating epigenetic modulation of the vasculature with cancer immunotherapy regimens.

overall_design:
Tumor Endothelial Cell (TEC) Isolation and Sorting
YUMMER1.7 tumors (~1 cm³) from three control mice and three Dnmt1iECKO mice were harvested, and tumors within each sample were pooled to obtain sufficient EC numbers. Samples were collected in ice-cold low-glucose DMEM (LG-DMEM), washed thoroughly, and minced into fragments <5 mm under sterile conditions. Tissue fragments were transferred to GentleMACS C tubes containing a digestion mix of collagenase II (2 mg/mL, Worthington LS004176), dispase (2.5 U/mL, Worthington LS02104), and DNase I (1 mg/mL, Worthington LS002006). Tumors were digested at 37 °C for 3045 min with agitation (120 rpm) and processed on a GentleMACS Dissociator using program m_imptumor_02 to achieve single-cell suspensions. Digested samples were passed through 100µm strainers, washed with FACS buffer (PBS + 0.5% BSA + 2 mM EDTA), and centrifuged at 1200 rpm for 5 min. Red blood cell lysis was performed using 1× Pharm Lyse B. Cell suspensions were first incubated with Live-or-Dye viability dye (Biotium 32002), followed by Fc block (Miltenyi 130-092-575) for 10 min on ice. Cells were then stained with PE-conjugated CD31 (BD 553373) and APC_x0002_conjugated CD45 (BD 559864) for 30 min on ice.Live CD31⁺CD45⁻ tumor endothelial cells (TECs) were sorted on an Influx cell sorter (Becton Dickinson) into LG-DMEM supplemented with 10% FBS, washed, and resuspended in PBS + 0.04% BSA. Final cell suspensions were adjusted to 500700 cells/µL with >85% viability. Sorted TECs were immediately used for 10x Genomics Chromium Single Cell 3’ v3 library preparation according to the manufacturer’s protocol.
Single-cell RNA-seq Library Preparation and Sequencing
Sorted cells were processed using the 10x Genomics Chromium Single Cell 3′ Gene Expression kit (GEM-X v4) following the manufacturer’s protocol. Libraries were prepared targeting ~10,000 cells per sample and sequenced on an Illumina NextSeq 2000 using the P2 XLEAP-SBS 100-cycle kit (paired-end) at a depth of 20,00025,000 reads per cell.

first: Dae Joong

last: Kim

first: Mitchell

last: McGinty

first: Swetha

last: Anandh

first: Caroline

last: Riedstra

first: Yuvraj

last: Sethi

first: Melanie

last: Rutkowski


title: An epigenetic switch in vascular phenotype augments anti-tumor immunity [bulkRNA-seq]

overall_design: Bulk rnaSequencing: Mouse lung ECs were seeded at 1×105 cells/mL in 6-well plates and cultured overnight at 37 °C in a humidified 5% CO2 incubator. The next day, cells were transfected with either control siRNA or DNMT1-targeting siRNA (BLOCK-iT oligos; Invitrogen) using Lipofectamine RNAiMAX (Thermo Fisher Scientific) in Opti-MEM I Reduced Serum Medium for 4 h, following the manufacturer’s instructions. A BLOCK-iT Alexa Fluor Red fluorescent oligo (Invitrogen) was used in parallel wells to monitor transfection efficiency. After 4 hrs, the transfection medium was replaced with growth medium containing 20% serum, and the cells were cultured for 24 hrs at 37 °C, humidified 5% CO₂. A second siRNA transfection was performed 24 h later to reinforce the knockdown. Cells were then treated with TNFa (10 ng/mL) or IFNg (1,000 U/mL) for 16 hrs. Total RNA was isolated using a column-based RNA extraction kit (Zymo Research) according to the manufacturer’s instructions. Libraries were prepared and sequenced by Novogene for bulk RNA-seq analysis. Experiments were performed with n = 4 biological replicates per condition.


title: Timecourse of Chromium exposure (Bisulfite-Seq)

city: Boston

first: Bernardo

last: Lemos

state: MA

address: 665 Huntington Avenue

institute: Harvard Chan School of Public Health

type: Methylation profiling by high throughput sequencing

summary: Bisulfite DNAseq was performed in a timecourse analysis of responses to Chromium exposure in LCLs

overall_design: The design consist of measurements prior to the onset of exposure and at 3 time points after the onset of exposure.

last: Lin

first: Jianlin

last: Lou


title: Timecourse of Chromium exposure (RNA-Seq)

summary: RNAseq was performed in a timecourse analysis of gene expression responses to Chromium exposure in LCLs

overall_design: The design consist of gene expression measurements RNAseq prior to the onset of exposure and at 3 time points after the onset of exposure

first: Alan

last: Branco


title: Timecourse of Chromium exposure

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

overall_design: Refer to individual Series


title: Patient-derived organoid – immune cell co-culture platform for therapeutics discovery in high-grade endometrial cancer

city: Jammu

first: Santhilal

last: Subhash

state: Jammu and Kashmir

address: Jagti, NH-44, PO Nagrota

department: Biosciences and Bioengineering

institute: Indian Institite of Technology Jammu

summary: We established a biobank of 85 patient-derived organoids (PDOs) generated from 44 individuals, encompassing a broad range of endometrial cancer (EC) subtypes, including a majority of high-grade endometrial cancer (HGEC) PDOs from African American patients. From these same patients, we isolated autologous immune cells, enabling the creation of PDO–immune cell co-cultures that reflect each patient’s unique characteristics without evoking allogeneic immune responses. To dissect the roles of antigen presentation pathways and evaluate proof-of-principle immunotherapeutic interventions, we performed bulk RNA sequencing, flow cytometry, and live-cell imaging.

overall_design: Bulk RNA-seq profiling of endometrial cancer patient-derived organoids (PDOs) and matched normal (CTL).

first: Charlie

last: Chung

first: Brian

last: Yueh

first: Onur

last: Eskiocak

first: Semir

last: Beyaz


title: Transcriptomic Analysis Reveals Differential Gene Expression in the Mouse Medial Habenula During Nicotine Withdrawal

city: Nanjing

first: Yi-Xuan

last: Zhang

state: Jiangsu Sheng

address: Longmian avenue 101

department: Shool of pharmacy

institute: Nanjing Medical University

summary: Negative emotion during smoking cessation is a major obstacle to successful quitting, yet the underlying molecular mechanisms remain poorly understood. Nicotine withdrawal induces profound transcriptional alterations in brain regions associated with affective processing, prompting us to investigate their contribution to withdrawal-induced negative emotional states. Here, by performing transcriptomic sequencing of the ventral medial habenula (MHb) in a mouse model of nicotine withdrawal, we found that calcium channel–related genes were markedly upregulated. Further analysis revealed a concomitant downregulation of the RNA-binding protein Pumilio 1 (Pum1), which acts to suppress calcium channel expression. Together, these findings identify a Pum1–calcium channel regulatory axis that may underlie nicotine withdrawal–induced negative affect.

overall_design: Six wild-type mice were administered nicotine ditartrate (4 mg/kg, intraperitoneally) twice daily for 14 consecutive days. On day 15, nicotine injections were replaced with saline to induce nicotine withdrawal, and these mice were assigned to the experimental group (designated as the nicotine group for transcriptomic analysis). In parallel, four wild-type mice received intraperitoneal injections of saline for 17 consecutive days and served as the control group (designated as the control group). On day 17, medial habenula (MHb) brain tissue was collected from mice in both groups for transcriptomic sequencing, and differential gene expression was analyzed.

first: Zhi-Wei

last: Zheng

first: Feng

last: Han

first: Ying-Mei

last: Lu


title: Phagocytes as Plaque Catalysts: Human Macrophages Generate Seeding-Competent Aβ42 Fibrils with Cross-Seeding Activity

city: Rotselaar

first: Daan

last: Moechars

address: Catharinalaan 43

country: Belgium

institute: KULeuven

summary: The prevailing view frames microglia and macrophages as guardians against amyloid beta (Aβ) accumulation in Alzheimer’s disease (AD). Here, we overturn this paradigm by demonstrating that human phagocytic cells—including differentiated THP-1 macrophages and iPSC-derived microglia—are not merely passive responders but active producers of extracellular, seeding-competent Aβ42 fibrils, the amyloid species most strongly linked to parenchymal plaque formation and neurodegeneration. These cell-generated aggregates differ structurally and functionally from synthetic fibrils, exhibiting heightened seeding activity and the ability to cross-seed tau aggregation, a key driver of AD progression. Notably, Aβ42 fibril formation in this system requires active cellular processes and is exacerbated by loss of TREM2, a major AD risk gene. Transcriptomic profiling reveals an early inflammatory response resembling microglial states observed in human AD models, positioning this system as a tractable, human-relevant platform to dissect the interplay between Aβ aggregation, innate immunity, and genetic susceptibility. Our findings suggest that macrophages and microglia play a dual role in AD, acting both as responders and inadvertent catalysts of pathogenic amyloid formation, with implications for early therapeutic intervention.

overall_design: RNA-seq profiling of THP-1 Macrophages exposed to different levels of Aβ42 peptide

first: Katerina

last: Konstantoulea

first: Meine

last: Ramakers

first: Sarah

last: Borrie

first: Dries

last: T’syen

first: Malgorzata

last: Sliwinska

first: Brajabandhu

last: Pradhan

first: Giulia

last: Albertini

first: Grigoria

last: Tsaka

first: Bert

last: Houben

first: Mark

last: Fiers

first: Maarten

last: Dewilde

first: Dietmar

middle: R

last: Thal

first: Michael

last: Willem

first: Jonas

last: Neher

first: Bart

last: De Strooper

first: Frederic

last: Rousseau

first: Joost

last: Schymkowitz


title: A lymph node-tumor spatiotemporal atlas of exhausted T cell clone evolution

city: shanghai

first: KUN

last: LIU

address: dong an Road

institute: Fudan university

summary: Current surgical guidelines overlook preserving uninvolved lymph nodes (uiLNs) in non-small cell lung cancer, principally stemming from an underappreciation of their critical role in anti-tumor immunity. Here, we discovered a significant immunosuppressive microenvironment in metastatic lymph nodes. In contrast, CD200+ progenitor exhausted T cells (Tpex) markedly expanded within uiLNs following immunotherapy. Effective clonal sharing of exhausted T cells between uiLNs and tumors correlated strongly with complete pathological response. Previously unrecognized tumor-resident C1QA+ dendritic cells secreted CXCL9, facilitating T cell recruitment, whereas fibroblast-enriched neighborhoods in non-responders created immunosuppressive barriers hindering CXCL9 diffusion and CD200+ Tpex migration. Finally, we confirmed that tumor-reactive Tex clones from uiLNs could persist systemically and identified two neoantigen peptides as direct targets of these tumor-reactive Tex cells. Our study unprecedentedly elucidates the spatiotemporal dynamics of immunotherapy-responsive T cell subsets in LN-tumor axis and provides compelling evidence to support selective LN dissection strategies to preserve uiLNs.

overall_design: We generated single-cell and spatial data on 106 matched tumors, lymph nodes, and blood samples from two cohorts including a phase ll neoadjuvant anti-PD-1 (serplulimab) immunotherapy clinical trial (NCT05775796).

first: Yang

last: Zhang

first: Haiquan

last: Chen


title: Identification of target genes and regulatory networks for bone mineral density GWAS loci through systematic targeting and inhibition [hFOB BMD STING-seq]

city: Toronto

first: John

last: Morris

state: Ontario

address: 160 College Street

department: Donnelly Centre for Cellular and Biomolecular Research

country: Canada

institute: University of Toronto

summary: Osteoporosis is characterized by low bone mineral density (BMD) and elevated fracture risk. Most BMD-associated GWAS variants lie in noncoding regions, complicating efforts to identify causal genes and mechanisms. To overcome this variant‑to‑function challenge, we previously developed STING‑seq, a framework integrating biobank‑scale GWAS with single‑cell CRISPR inhibition (CRISPRi) screening to directly connect noncoding cis‑regulatory elements (CREs) to their target genes. Applied to human fetal osteoblast (hFOB) cells across osteogenic differentiation, STING‑seq linked 76 CREs to 75 target genes at BMD loci. Arrayed CRISPRi and activation validated key CRE–gene relationships, including long‑range enhancers regulating CXCL12 (over 500 kb apart). We further uncovered trans‑regulatory networks and characterized the DAP3–YY1AP1 bidirectional promoter, demonstrating a role for DAP3 in mineralization via mitochondrial pathways. Together, these findings provide mechanistic insight into how noncoding GWAS variants shape osteoblast activity and highlight the genes and pathways that mediate genetic effects on BMD.

overall_design: We generated human fetal osteoblast 1.19 (hFOB) cell lines constitutively expressing a CRISPRi system. We then performed a single-cell pooled CRISPRi screen targeting select noncoding candidate cis-regulatory elements. The experiment was performed first as a pilot study on an undifferentiated hFOB (day 0) and then as a full study on hFOB after osteogenic induction, reading out days 0, 2, and 4. We performed single-cell RNA-seq using 10X Genomics Chromium Next GEM Single Cell 5′ Reagent Kits v2 (dual index) on cells detached from culture plates. We labeled cells from each state with different hashtag antibodies targeting cell surface proteins (BioLegend TotalSeq 394661, 394663, 394665, 394667) following the manufacturer’s recommendations. We then pooled equal numbers of cells from each state into a single sample and aliquoted them into as many reactions as needed to capture approximately 200,000 cells in total. We constructed sequencing libraries for the three different barcoded nucleic acids for each reaction according to 10X Genomics protocols and pooled them disproportionately so that mRNA-derived cDNA libraries represented ~90% of the sample, with gRNA and hashtag libraries comprising the remaining 10%. We sequenced the pooled library to a depth of approximately 20,000 mRNA/cDNA reads per cell on an Illumina NextSeq sequencing platform. We used 2 microfluidics channels for the pilot experiment and 6 channels for the full experiment.


title: Identification of target genes and regulatory networks for bone mineral density GWAS loci through systematic targeting and inhibition


title: RNA-Seq quantitative analysis of the regulatory effects of plasma exosomes from CML patients on CML cell transcriptomes

first: Fei

last: Li

state: Guangdong

address: 135 Xingang West Road, Haizhu District

institute: Sun Yat-sen University

summary: Drug resistance frequently results in treatment failure for leukemia and leads to the progression of chronic myeloid leukemia (CML) into an accelerated or blast phase. Although new tyrosine kinase inhibitors (TKIs) and combined TKI therapies have been developed to address BCR-ABL1 mutation-induced drug resistance in CML patients, an increasing number of primitive CML cases exhibit reduced responsiveness or are unresponsive to TKIs. Herein, we discovered that plasma exosomes from TKI-resistant CML patients(R-Exo) promote drug resistance in CML compared to plasma exosomes from drug-sensitive CML patients (S-Exo). To shed light on the mechanism underlying Exo-induced CML drug resistance, we performed high-throughput RNA-Seq analyses to reveal the differentially expressed genes in CML cells treated with or without plasma exosomes from healthy controls (H-Exo), S-Exo, or R-Exo. We observed a significant upregulation in the expression of drug resistance-related genes and regulatory genes associated with fatty acid metabolism in K562 cells following R-Exo treatment.

overall_design: RNA-seq profiling of K562 control cells, H-Exo-treated K562 cells, S-Exo-treated K562 cells, and the R-Exo-treated K562 cells.

first: Qing


title: Carbohydrate fatty acid monosulfateester enhances the immunogenicity ofinfluenza antigens via TLR4/2-dependent mechanisms

city: Palakkad

first: Jagadeesh

last: Bayry

state: Kerela

address: IIT Palakkad

institute: IIT palakkad

summary: Adjuvants are critical for optimizing the efficacy of influenza subunit vaccines, yet currently approved formulations fail to elicit durable and broad protection. Here, we dissect the immunostimulatory mechanisms of a synthetic carbohydrate fatty acid monosulphate ester (CMS), a key immunogenic component of a squalane-in-water emulsion adjuvant currently in phase I clinical trials. Using human peripheral blood mononuclear cell (PBMC)-based assays, we show that CMS markedly enhances antigen‑specific T cell responses to influenza hemagglutinin (HA) peptides. While recombinant H7N9HA alone poorly activated antigen‑presenting cells, co‑formulation with CMS induced robust dendritic cell (DC) activation, cytokine secretion, and a balanced polyfunctional effector and regulatory T cell response. Bulk RNA sequencing of CMS‑stimulated DC revealed strong induction of toll‑like receptor (TLR)-driven innate inflammatory pathways. Furthermore, functional blockade experiments confirmed that CMS adjuvanticity depends on TLR4 and TLR2 receptors. These results define the molecular basis of CMS‑driven immune activation and highlight this adjuvant as a promising platform for next‑generation influenza vaccines targeting emerging pandemic strains.

overall_design:
We treated  dendritic cells derived from the peripheral blood monocytes of healthy donors with CMS (n=3 donors). Untreated dendritic cells maintained in cell culture medium were used as control  (n=3)

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

middle: V

last: Retnakumar

first: Suraj

last: Singh


title: Bulk RNA sequencing of interfollicular Tfh cells isolated from the palatine tonsils of recurrent tonsillitis and IgA nephropathy.

city: Sapporo

first: Ippei

last: Ikegami

state: Hokkaido

address: S1 W17, Chuo-ku

department: Department of Human Immunology

institute: Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine

summary: Immunoglobulin A nephropathy (IgAN) is a chronic glomerular disease characterized by mesangial IgA deposition, which can progress to end-stage renal failure. Tonsillectomy is used as a therapeutic intervention to slow disease progression and provide early clinical benefit. However, the immune mechanisms within the palatine tonsils that contribute to IgAN pathogenesis remain incompletely understood. To define the tonsillar immune environment that regulates pathological antibody production, we analyzed T cell subsets in relation to renal function. Interfollicular T follicular helper (IF-Tfh) cells (CD3+CD4+CD8-PD-1loCXCR5lo) were significantly expanded in IgAN tonsils compared with disease controls and strongly correlated with clinical markers of renal abnormalities. Transcriptomic analysis of IF-Tfh cells from IgAN tonsils revealed a distinct gene expression profile enriched for effector memory T cell–like features associated with kidney impairment.

overall_design:
We performed bulk RNA sequencing of interfollicular Tfh cells isolated from the palatine tonsils of 4 patients with recurrent tonsillitis (RT) and 4 patients with IgA nephropathy (IgAN). Although informed consent was obtained from all donors, consent for public deposition of the raw sequencing data was not obtained due to ethical and privacy considerations. Accordingly, the raw data are not publicly available.

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

last: Sugaya

first: Shingo

last: Ichimiya


title: miR126-mediated alteration of vascular integrity in Rett syndrome

city: Cambridge

first: Tatsuya

last: Osaki

address: 43 Vassar street, 46-6227

department: Picower Institute for Learning and Memory

institute: Massachusetts Institute of Technology

summary: Rett syndrome (RTT) is a neurodevelopmental disorder caused by mutations in methyl-CpG binding protein 2 (MeCP2). MeCP2 is a non-cell type-specific DNA binding protein, and its mutation influences not only neural cells but also non-neural cells in the brain, including vasculature-associated endothelial cells. Vascular integrity is crucial for maintaining brain homeostasis, and its alteration may be linked to the pathology of neurodegenerative diseases, but a non-neurogenic effect, such as the relationship between vascular alteration and RTT pathogenesis, has not been shown. Here, we developed a microvascular network model using RTT patient-derived induced pluripotent stem (iPS) cells that carry the MeCP2[R306C] or MeCP2[R168X] mutation to investigate early developmental vascular impact. To expedite endothelial cell differentiation, doxycycline-inducible ETV2 expression vectors were inserted into the AAVS1 locus of RTT patient-derived iPS cells and their isogenic controls by CRISPR/Cas9. With these endothelial cells, we established a disease microvascular network and observed higher permeability in RTT microvascular networks than in isogenic controls, indicating that the barrier function is altered by MeCP2 mutation. Furthermore, by microRNA profiling and RNAseq, we found that hyperpermeability is associated with up-regulation of miR126-3p in RTT patient-derived endothelial cells and can be rescued by restoring miR126-3p levels. Overall, our findings point to miR126-3p-mediated vascular impairment in RTT patients and suggest potential therapeutic approaches for restoring function.

overall_design: Total RNA was isolated from the cells from 2D culture using RNAeasy Mini Kit (Qiagen) following manufacture protocol. RNA-sequencing was performed by the Broad Institute Sequencing Platform. 50M paired-end configuration and read-data were mapped to human reference genome GRCh37/hg19.

first: Zhengpeng

last: Wan

first: Koji

last: Haratani

first: Ylliah

last: Jin

first: Marco

last: Campisi

first: David

last: Barbie

first: Roger

last: Kamm

first: Mriganka

last: Sur


title: Microglia TFEB Activation Attenuates Alzheimer’s Disease Pathology by Enhancing Autophagy-Lysosomal Function

city: Incheon

first: Yeji

last: Kim

state: Yeonsu-gu

address: 155 Gaetbeol-ro, Yeonsu-gu

department: Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences & Technology

institute: Gachon University

summary: Alzheimer’s disease (AD) is characterized by amyloid-β (Aβ) accumulation, neuroinflammation, synaptic dysfunction, and cognitive decline. Impairment of microglial autophagy-lysosomal pathway (ALP) is increasingly recognized as a key driver of the disease progression. Transcription factor EB (TFEB), a master regulator of ALP, has emerged as a promising therapeutic target; however, its specific role in microglia remains unclear. Here, we aimed to determine the therapeutic effects of microglial TFEB expression in AD pathogenesis. We established a tamoxifen-inducible, microglia-specific TFEB-overexpressing 5xFAD mouse line (5xTFEB) and conducted behavioural testing, histopathology and biochemical analyses, live-cell imaging of Aβ phagocytosis, and bulk RNA sequencing. Differential gene expressions were analysed, and inflammasome activation was evaluated. Microglial TFEB overexpression restored ALP function, promoted phagolysosomal clearance of oligomeric Aβ, and reduced the amyloid burden in the cortex, hippocampus, and entorhinal cortex of the 5xFAD mice. These changes rescued memory deficits in both male and female 5xTFEB mice. Transcriptomic profiling revealed upregulation of ALP and downregulation of inflammatory signalling. Additionally, inflammasome activation was attenuated in 5xTFEB mice. Targeted TFEB activation in microglia reprograms degradative and immune pathways, enhancing Aβ clearance while alleviating neuroinflammation and cognitive impairment in AD. Overall, microglial TFEB modulation is a promising cell-type–specific therapeutic strategy for AD and related neurodegenerative disorders.

overall_design: To investigate transcriptomic alterations associated with TFEB activation in Alzheimer’s disease, total RNA was extracted from the cortex and hippocampus of 7-month-old WT, 5xFAD, and 5xTFEB mice and subjected to RNA sequencing.

first: Tae-Young

last: Ha

first: Oksana

last: Kondaurova

first: Myung-Shik

last: Lee

first: Keun-A

last: Chang