title: A Spheroid Model that Recapitulates the Protective Role of the Lymph Node Microenvironment and Serves as a Platform for Drug Testing in Chronic Lymphocytic Leukemia

city: Milano MI

first: Aurora

last: Maurizio

state: Italy

address: Via Olgettina, 60

department: Center for Omics Sciences (COSR)

institute: IRCCS Ospedale San Raffaele

summary: Chronic lymphocytic leukemia (CLL) B cells are characterized by a propensity to undergo rapid apoptosis when cultured in vitro, underscoring the importance of the tissue microenvironment for disease survival. One of the major limitations in studying the role of the microenvironment in tumor development and drug response is the inadequacy of conventional two-dimensional in vitro assays to physiologically reconstruct the complex spatial organization and interactions of cells in their natural lymphoid niches. To overcome this limitation, we developed a novel in vitro 3D lymph node-like spheroid model of the leukemic microenvironment by culturing human CLL cells with fibroblastic reticular cells (FRCs). FRCs are a key structural component of secondary lymphoid organs and are emerging as crucial players in tissue homeostasis and immune responses. Our results demonstrate that CLL spheroids maintain the physiological cellular ratio between FRCs and leukemic cells over time and protect tumor cells from apoptosis by mimicking the protective effects of the microenvironment. This was further demonstrated by venetoclax treatment that showed reduced apoptosis in 3D compared to 2D setting. Importantly, the spheroids promote a gene expression profile more aligned with that of CLL cells in lymphoid tissues. The spheroid model provides a straightforward, quick-to-use platform for investigating drug efficacy under conditions that better replicate the natural lymph node microenvironment. This 3D lymph node-like spheroid model could serve as a valuable tool for studying tumor biology and the protective effects of the stromal microenvironment, and for testing therapeutic strategies in a more clinically relevant setting.

overall_design: Bulk RNA-Seq of CLL cells from the 3D and 2D models.

first: Elisa

last: Lenti

first: Jose Manuel

last: Garcia-Manteiga

first: Andrea

last: Brendolan


title: Cytoplasmic translocation of tumor suppressor HINT1 and its impact on cell shape during density transition

status: Public on Jul 14 2025

city: Tianjin

first: Xiaofang

last: Zhang

state: Tianjin

address: No. 92 Weijin Road, Nankai District

country: China

institute: Tianjin University

type: Expression profiling by high throughput sequencing

summary: Cells at low density exhibit spreading and migration behaviors with more spread-out morphologies, while high-density cultures show confined, rounded morphologies. During this transition, the actin cytoskeleton rearranges from oriented stress fibers to a cortical actin shell, supporting cell movement and shape maintenance. This transition also halts cell proliferation to prevent uncontrolled growth, as seen in tumors. However, the molecular mechanism behind actin cytoskeleton remodeling by cell density is not well understood. Using proteomics of purified open chromatin, we identified the tumor suppressor HINT1 as a key molecule whose nucleocytoplasmic shuttling depends on cell density. RNA-seq analysis of wild-type (WT) and knock-out (KO) HEK293A cells revealed that HINT1 is involved in morphogensis and  development.

overall_design: To investigate the role of HINT1, we established HINT1-KO HEK293A cells using the CRISPR-Cas9 approach and analyzed expressed mRNA using RNA-seq.

first: Fumihiko

last: Nakamura


title: Fibroblast-derived TGFb1 regulates skin repair and fibrosis

city: Cologne

first: Sebastian

last: Willenborg

state: NRW

address: Kerpener Str. 62

department: Dermatology

country: Germany

institute: University of Cologne

summary: Activation of fibroblasts and formation of myofibroblasts are essential for granulation tissue formation following injury. In fibrotic reactions, excessive deposition of ECM by the activated fibroblasts determines scar formation and functional failure. Although these events critically depend on the activity of a plethora of growth factors and cytokines, TGFβ1 is a unique player controlling the immune response and proliferation of many cell types. Different cell types contribute to its release and activation, which is also regulated by the interaction with the ECM and by mechanical forces. The aim of this study was to elaborate whether fibroblast-derived TGFβ1 plays a critical role during these processes. The data demonstrate a dynamic expression of TGFβ1 during tissue repair. Cell-specific ablation of Tgfb1 in fibroblasts revealed that deletion of TGFβ1 attenuates bleomycin-induced skin fibrosis and delays maturation of granulation tissue in skin wounds. Absence of fibroblast-derived TGFβ1 induced vascular alterations (less vascular density and branching, hemorrhage) in early wound healing, potentially influenced by coincident alterations in the formation of stable ECM structure. This can be explained by paracrine regulation of endothelial cells or pericytes by fibroblast-released TGFβ1 and by impaired expression of pro-angiogenic factors in TGFβ1-deficient fibroblasts. Our findings provide novel mechanistic insights into the central role of fibroblast-derived TGFβ1 for early stages of tissue repair and fibrosis in the skin.

overall_design: To elucidate the effect the molecular mechanisms of cell-specific ablation of Tgfb1 in fibroblasts, fibroblasts were isolated from tamoxifen-fed Tgfb1fl/fl:Col1a2-CreERT (termed TGFβ1FKO) mice and controls, mice expressing the floxed Tgfb1 alleles, but no Cre recombinase. RNA was extracted from isolated fibroblast cultured in serum replacement medium for 72h on fibronectin and then submitted to Novogene (Cambridge, U.K.) for bulk RNA-sequencing.

first: Katrin

last: Schönborn

first: Mugdha

last: Sawant

first: Anna

last: Bornikoel

first: Takumi

last: Yamane

first: Isabel

last: Zeinert

first: Beate

last: Eckes

first: Sabine

middle: A

last: Eming

first: Thomas

last: Krieg


title: Innate Lymphoid Cells Originate from Fetal Liver-Derived Tissue-Resident Progenitors

city: Nanjing

first: Jiarui

last: Li

state: Jiangsu

address: Xianlin road #138

institute: Nanjing University of Chinese Medicine

summary: Committed progenitors with innate lymphoid cell (ILC) developmental potential are present in the fetus and bone marrow (BM). However, how fetal and BM hematopoiesis temporally and spatially contributes to ILC pools remains unclear. Here, we elucidated the distinct origins and developmental pathways of extramedullary and intramedullary ILCs during ontogeny. ILC-restricted hematopoiesis is initiated in the fetal liver (FL) and then FL-derived PD-1+ ILC progenitors (ILCPs) seed fetal lung and intestine. Organ niches determine the commitment of ILCPs to downstream precursors, including bipotent ILC1-ILC3 precursors (ILC1/3Ps) that are preferentially residing in the liver and intestine and ILC2 precursors (ILC2Ps) that show predominance in the lung. These precursors persist in adulthood and contribute to local ILC pools via BM-independent manner. In contrast, intramedullary ILC2Ps and ILC2s rely on BM hematopoiesis. Thus, our study highlights extramedullary and intramedullary ILCs with different origins, providing a comprehensive framework for developmental dynamics of ILCs.

overall_design: Lin−CD45+CD127+Flt3−α4β7+CD25− α4β7-expressing progenitors (αLPs) were sorted from E14.5 fetal liver and adult bone marrow tissues respectively of WT  mice for single-cell RNA sequencing (scRNA-seq).

first: Xianwei

last: Wang

first: Lucas

last: Rebuffet

first: Ming

last: Cheng

first: Boqun

last: Bao

first: Yawen

last: Chen

first: Xiaodong

last: Zheng

first: Yongyan

first: Haoyu

last: Sun

first: Rui

first: Eric

last: Vivier

first: Hui

last: Peng

first: Zhigang

last: Tian


title: Translation Regulation Promotes Stress Adaptation in Candida glabrata

city: Faridabad

first: Anil

last: Thakur

state: Haryana

address: Pali Faridabad

department: Biotechnology

country: India

institute: Regional Centre For Biotechnology

summary: Candida glabrata is an important human fungal pathogen leading cause of non-albicans Candida infections. C. glabrata exhibits resistance to key antifungal drugs, rapidly replicates and divides in host macrophages and withstands highly stressful host conditions. This study explores the molecular mechanisms underlying stress adaptations in C. glabrata that contribute to its pathogenicity. Our findings revealed that C. glabrata survives oxidative stress and amino acid starvation more effectively than S. cerevisiae, C. albicans, and C. auris. We noted that Gcn2 kinase and Gcn4 play critical roles in this adaptation as Gcn2 phosphorylates eIF2α and downregulates the global protein translation, activating GCN4. RNA sequencing of WT and gcn4 mutant revealed that GCN4 activation during stress orchestrates the expression of stress-responsive genes vital for survival during amino acid starvation and oxidative stress. Ultimately assisting in the stress adaptative transcriptome. Thus, this study highlights the critical role of the Gcn2–Gcn4 pathway in stress adaptation in C. glabrata.

overall_design: The WT and gcn4 mutant at log phase O.D. in Simple Dextrose (SD) minimal media were treated with 5 mM 3AT (3-amino triazole) that provided histidine starvation and ultimately amino acid starvation and 10 mM H2O2 (Hydrogen peroxide) as a ROS agent generating oxidative stress. Both treatments were given for 30 minutes keeping the untreated control with three individual replicates. The cells were pelleted, and total RNA was extracted from the untreated and treated samples for both stress and biological replicates. Samples were then sent for transcriptome profiling.

first: Aishwarya

last: Rana


title: An Open-Source QIIME2 and R Pipeline for Multi-Amplicon 16S rRNA Profiling: Validation and Application in Pediatric Microbiome Studies

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary: This study presents a validated, open-source QIIME2- and R-based pipeline for 16S rRNA gene profiling using multi-amplicon sequencing. It aims to overcome the limitations of commercial, closed-source tools by offering a standardized and reproducible workflow. The pipeline was benchmarked against proprietary software using five mock communities and 12 child–caregiver fecal sample pairs, showing nearly identical microbial profiles, greater sequencing depth, and improved taxonomic resolution. High reproducibility (R = 0.99, p < 0.0001) was achieved across all datasets. Application to pediatric cancer samples revealed distinct Bifidobacterium variants in children whose microbiota closely matched their caregivers’. This highlights the pipeline’s utility in studying microbial relationships. Overall, the pipeline supports transparent, adaptable, and accurate microbiome analysis, advancing research in both clinical and experimental settings while promoting open-source solutions for reproducible science.

overall_design: The experimental design included sequencing five mock microbial communities and 12 fecal sample pairs from pediatric cancer patients and their caregivers. A multi-amplicon approach (V2–9) was used with semiconductor-based sequencing. Data were analyzed using both the newly developed open-source pipeline and commercial software for benchmarking and a validation set of fecal specimens from 90 cases.


title: Circulating CD4+ T cells identify DNA methylation diagnostic signatures in heart failure with preserved ejection fraction

city: Stanford

first: Mark

middle: Emile

last: Pepin

state: CA

address: 870 Quarry road

department: Cardiovascular Medicine

country: USA

institute: Stanford University

type: Methylation profiling by high throughput sequencing

overall_design: Peripheral blood was collected from patients with a diagnosis of heart failure with reduced (HFrEF) or preserved (HFpEF) ejection fraction, or no known diagnosis of heart failure (HS).

middle: E

first: Giuditta

last: Benincasa

first: Claudio

last: Napoli


title: Single cell RNA-seq analysis of H3.3K4M WT and Hom brain samples (10X Genomics Multiome)

city: Bethesda

first: Timothy

last: Petros

state: Maryland

address: 35 Convent Drive, Bg 35 Room 3B-1002

institute: NICHD

summary: Methylation of lysine4 on Histone H3 (H3K4) is require for promoter and enhancer activation at gene loci and presents distinct methylation patterns over developmental gene clusters. Disrupting in the writer, eraser and reader of H3K4 methylation is associated with developmental syndromes. However, less studies focus on the role of H3K4 methylation in development of interneuron and hypothalamus. Here, we explore the role of H3K4 methylation in the medial ganglionic eminence (MGE) derive interneuron and hypothalamus by directly mutating the lysine 4 on H3.3 to the methionine in mice.

overall_design: The Nkx2.1-Cre;H3.3K4M;Sun1-sfGFP mice were generated to harvest all Nkx2.1-lineage GFP+ nuclei via flow cytometry.  Single nuclei from embryonic and adult samples from each genotype were prepared to analyze transcriptome using 10X Genomics Multiome pipeline. Samples: E13.5 MGE and hypothalamus as well as P60 cortex and hypothalamus of H3.3K4M WT and Hom. In addition, one replicate for male and female for each condition.

middle: J


title: Stochasticity in cancer immunotherapy stems from rare but functionally-critical Spark T cells

city: PARIS

first: Joshua

last: Waterfall

state: Please select:

address: 26 rue d'Ulm

department: Department of Translational Research and Inserm U830

country: France

institute: Institut Curie

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Cancer immunotherapies trigger highly variable responses in patients and in genetically identical mice models. To assess the intrinsic stochasticity of these therapies, we performed thousands of well-controlled ex vivo immunoassays. We show that leukocyte responses and tumor cytotoxicity are highly variable at the macroscopic level and statistically distributed as a shifted Poisson process. Stochastic activation of a rare subpopulation of T cells (so-called Spark T cells) coupled to a paracrine IFN-γ- driven positive feedback account for this measured “noise” in immunotherapeutic reactions. We integrated these quantitative insights in a custom-designed machinelearning pipeline to analyze immune reactions with single-cell resolution; this led us to phenotypically and functionally identify the Spark T cells in murine naïve T cells, and in human T cell blasts, as prepared for adoptive T cell therapy. We then demonstrate their relevance in explaining variable outcomes in cancer immunotherapies.

overall_design: scATACseq : Nuclei of sorted CD5lowCD11ahigh and CD5highCD11alow T cell subpopulations from OT-1 Rag1-/- mice were isolated following the nuclei isolation protocol for Single Cell ATAC Sequencing (Low Cell Input) provided from 10x Genomics.

first: Emmanuel

last: Salazar-Cavazos

first: Yoann

last: Missolo-Koussou

first: Gregoire

last: Altan-Bonnet


title: Innate Lymphoid Cells Originate from Fetal Liver-Derived Tissue-Resident Progenitors II

first: Jiarui

last: Li

overall_design: CLP (Lin–CD45+CD127+Flt3+CD25– live cells), ILCP (Lin–CD45+CD127+Flt3–α4β7+CD25–PD-1+CD94– live cells) and ILC1/3P (Lin–CD45+CD127+Flt3–α4β7+CD25–PD-1–CD94+ live cells) were sorted from the fetal liver of WT B6 mice.

first: Xianwei

last: Wang

first: Lucas

last: Rebuffet

first: Ming

last: Cheng

first: Boqun

last: Bao

first: Yawen

last: Chen

first: Xiaodong

first: Yongyan


title: Super-enhancer-driven lncRNA HCG20 regulates pulmonary endothelial cell dysfunction through U2AF2-mediated pre-mRNA alternative splicing

city: Daqing

first: Jian

last: Mei

state: Heilongjiang Province

address: 39 Xinyang Road

department: Daqing campus

institute: Harbin Medical university

summary: Background: Pulmonary artery endothelial cell (PAEC) dysfunction is a pathological hallmark of pulmonary hypertension (PH). Yet, the roles of long noncoding RNAs (lncRNAs) driven by super-enhancers (SE-lncRNAs) in PAECs are not well understood. In this study, we focused on the PAEC-specific SE-lncRNA HCG20 and to elucidate its role and underlying mechanisms in the progression of PH. Methods: ChIP-qPCR, 3C-PCR, CRISPR/Cas9, and dual luciferase reporter assays were employed to identify dysregulated SE-lncRNAs in PAECs and to investigate the pathological role of HCG20. The role of HCG20 in pathological processes was validated in rodent models of PH induced by SU5416/hypoxia (SuHx), monocrotaline (MCT) or hypoxia alone, through adeno-associated virus (AAV)-mediated endothelial-specific HCG20 overexpression or knockdown of HCG20. RNA pull-down, mass spectrometry, RNA immunoprecipitation and RNA-seq were employed to elucidate the underlying mechanisms of HCG20-mediated PAEC dysfunction. Results: We identified the SE-LncRNA HCG20 from H3K27ac and H3K4me1 ChIP-seq data derived from PAEC of patients with PH. A significant upregulation of the HCG20 was found in hypoxia-induced hPAECs, lung tissues and the plasma of patients with PH. Antisense oligonucleotide (ASO) and CRISPR/Cas9, which respectively target HCG20 and its SE, alleviate hypoxia-induced pyroptosis and subsequent endothelial-to-mesenchymal transition (EndMT). Human pulmonary artery smooth muscle cells (hPASMCs) internalize hPAECs-derived exosomes containing HCG20, inducing their excessive proliferation. Targeted delivery of HCG20 into the pulmonary vascular endothelium induced pulmonary vasculature remodeling and increased pulmonary artery systolic blood pressure in rodents. Mechanistically, HCG20 directly bound and stabilized the U2 small nuclear RNA auxiliary factor 2 (U2AF2) protein, thereby facilitating its impact on the alternative splicing of Eukaryotic translation initiation factor 2 alpha kinase 2 (EIF2AK2). Furthermore, we identified a novel mouse ortholog gene, 4833427F10Rik (named Hcg20), of HCG20 for the first time. Our study demonstrated that specific interference with Hcg20 in the pulmonary vascular intima has been shown to ameliorate hypoxia-induced PH. Conclusions: Collectively, our data suggest that HCG20, driven by SE, contributes to PAEC dysfunction through U2AF2-mediated alternative splicing of EIF2AK2. Our work underscores the potential of using HCG20 as a novel biomarker and a promising target for the treatment of PH. Keywords: Super-enhancer, HCG20, Pulmonary artery endothelial cell, Pulmonary hypertension, Alternative splicing

overall_design: RNA-seq analysis of primary pulmonary artery endothelial cells transfected with U2AF2 overexpression plasmid and control NC plasmid.

first: Wei

last: Huang

first: Zi-Tong

last: Meng

first: Shi-Qing

last: Wen

first: Lang-Lin

last: Ou

first: Jun-E

last: Bai

first: Xiao-Ying

first: Hao

last: Yuan

first: Yan-Yu

first: Li-Xin

last: Zhang

first: Yu-Wei

last: You

first: Ying-Li

first: Xiao-Dong

last: Zheng

first: Fei

first: Song

first: Xiang-Rui

last: Zhu

first: Zhao-Si

first: Dang-Ling

first: Xiao-Wei

last: Nie

first: Cui

last: Ma


title: Single cell 10X Genomics Multiome Analysis of H3.3K4M Mutant Brain Samples

first: Timothy

last: Petros

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

overall_design: Refer to individual Series


title: Transcriptome analysis of triple-negative breast cancer cells HCC1937 and MDA-MB-231 treated with Kalanchoe pinnata (Bryophyllum pinnata) reveals regulation of migration and invasion by downregulation of genes JAK2, ROCK1, ROCK2 and PIK3CA.

city: Puebla

first: Marta

middle: Elena

last: Hernandez-Caballero

state: Puebla

address: 13 sur 2702 Colonia Volcanes, Puebla, Mexico

department: Facultad de Medicina

country: Mexico

institute: Benemerita Universidad Autonoma de Puebla

summary: Triple-negative breast cancer (TNBC) is one breast cancer with high mortality due to aggressive tumor behavior and limited treatment options. Natural products are studied for their potential to be an alternative to combining with cancer drugs to improve treatment efficacy. Plant phytoconstituents can regulate cellular processes such as proliferation, differentiation, invasion, angiogenesis, or migration. Kalanchoe pinnata has been used in traditional medicine, it contains flavonoids, phenols, alkaloids, glycosides, bufadienolides, and tannins among others. In the present investigation, we evaluated the effect of aqueous extract and underlying molecular mechanisms on two breast cancer cell lines, HCC1937 and MDA-MB-231, focusing on cellular migration. The cytotoxic activity revealed that HCC1937 cells exhibit more sensitivity than MDA-MB-231 cells. Cell migration was affected in HCC1937 cells after 24h of treatment compared to 48h in MDA-MB-231 cells. The extract had more anti-invasion properties on HCC1937 cells (37.7%, p<0.01) than MDA-MB-231 cells (47%, p<0.05). RNAseq assay showed 1850 differentially expressed genes (DEGs) in HCC1937 cells versus 1534 in MDA-MB-231 cells. The Webgestalt analysis revealed the downregulation of genes involved in cell-cell adhesion, ruffle organization, cell-substrate junction with more downregulated genes in HCC1937 cells. The downregulated genes analyzed with KOBAS-i showed association with MAPK signaling, Focal adhesion, PI3K-Akt signaling, Regulation of actin cytoskeleton, and ECM-receptor interaction pathway. In addition, IPA network analysis revealed the inhibition of signaling pathways RHO GTPase cycle, RHOA signaling, JAK/STAT signaling, Actin cytoskeleton signaling, and Integrin signaling. Data for the docking study indicated the binding potential of Quercetin-3-O-arabinoside, Kaempferol, Quercetin, Ferulic acid, alpha-L-rhamnopyranoside, and Apigenin with JAK2, ROCK1, ROCK2, and PIK3CA proteins. Thus, our results demonstrate that K. pinnata inhibits the proliferation and invasion of TNBC cells by targeting genes involved in these important processes, so it has the potential to be used in combination with chemotherapeutic drugs for cancer treatment.

overall_design: This study analyzed RNA sequencing (RNA-seq) data from MDA-MB-231 and HCC1937 breast cancer cells treated with K. pinnata aqueous extract. We then assessed the DEGs to understand molecular mechanisms involved in cellular migration.

first: Alvizo-Rodriguez

last: Carlos

first: Carrasco-Carballo

last: Alan

first: López-Vazquez

last: Uriel

first: Hernández-Montes

last: Georgina

first: Hernández-Caballero

last: Marta Elena


title: scRNAseq and TCRseq of tumor infiltrating CD8 T cells from samples

city: Shanghai

first: Feixiang

last: Wang

state: Shanghai

address: Chongqing South Road 280

institute: Shanghai Jiaotong University School of Medicine

summary:
The goal of this study is to investigate the role of ageing on tumor infiltrating CD8 T cells
Ageing is a major risk factor for various cancers, and patients aged 65 years or older represent up to 60% of newly diagnosed cancer patients. Ageing results in remodeling of T cell immunity, causing poor clinical outcomes in patients with cancer. During ageing, T cells undergo age-dependent changes and gradually lose their physiological function. Numerous studies have revealed that T cells mediate the surveillance and elimination of tumors, and substantial therapeutic strategies have been developed to improve tumor-specific T cell responses. However, these experimental studies were almost exclusively conducted in young but not old individuals. Therefore, how age-associated T cell dysfunction impacts antitumor immunity requires further investigation.

overall_design:
Fresh cancer patient tissues were collected and isolated into single cell for scRNAseq and TCRseq

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


title: The Effect of Senolytic (BI01) Administration on DNA Methylation Clock Age and the Methylome in Aged and Regenerated Skeletal Muscle

city: Lexington

first: Yuan

last: Wen

state: Kentucky

address: 760 Press Ave

institute: University of Kentucky

type: Genome binding/occupancy profiling by genome tiling array

summary: Background: Senescence cells emerge with aging and injury. The contribution of senescent cells to DNA methylation age (DNAmAGE) in vivo is uncertain. Furthermore, stem cell therapy can mediate “rejuvenation”, but how tissue regeneration controlled by resident stem cells affects whole tissue DNAmAGE is unclear. Methods: We assessed DNAmAGE with or without senolytics (BI01) in aged male mice (24-25 months) 35 days following muscle healing (BaCl2-induced regeneration versus non-injured). Young injured mice (5-6 months) without senolytics were comparators.Results: DNAmAGE was decelerated by up to 68% after injury in aged muscle. DNAmAGE was modestly but further significantly decelerated by injury recovery with senolytics. ~1/4 of measured CpGs were altered by injury then recovery regardless of senolytics in aged muscle. Specific methylation changes caused by senolytics included differential regulation of Col, Hdac, Hox, and Wnt genes, which likely contributed to improved regeneration. Altered extracellular matrix remodeling using histological analysis aligned to the methylomic findings with senolytics. Without senolytics, regeneration had a contrasting effect in young mice and tended not to influence or modestly accelerate DNAmAGE. Comparing young to old injury recovery without senolytics using methylome-transcriptome integration, we found a more coordinated molecular profile in young and differential regulation of genes implicated in muscle stem cell performance: Axin2, Egr1, Fzd4, Meg3, and Spry1. Conclusions: Muscle injury and senescent cells affect DNAmAGE and aging influences the transcriptomic-methylomic landscape after resident stem cell-driven tissue reformation. Our data have implications for understanding muscle plasticity with aging and developing therapies aimed at collagen remodeling and senescence.

platform_organism:
Macaca mulatta
Homo sapiens
Mus musculus
Rattus

overall_design: We aimed to profile changes in DNA methylation age (DNAmAGE) and global methylation 35 days after induced chemical injury in the skeletal muscle of young and old C57BL/6J mice. Furthermore, old mice underwent an additional condition in which one group received oral administeration of a senolytic compound and one group served as a vehicle control. To determine DNAmAGE and global methylation, we utilized the Horvath 320k methylation assay. This custom mammalian array combines a prior custom mammalian array with the 285k Illumina Mouse Methylation BeadChip. This was completed on a cohort of 20 old mice (24-25 months) and 5-6 young mice (5-6 months). .

first: Toby

middle: L

last: Chambers

first: Cory

middle: M

last: Dungan

first: Kevin

last: Murach


title: Id2 acts as a metabolic checkpoint underpinning Th17 cell fate decision [scRNA-seq]

status: Public on Jul 13 2025

city: Nanning

first: Wang

last: Xi

state: Guangxi

address: 100 University East Road, Nanning City, Guangxi

department: School of Medicine

institute: Guangxi University

summary: T helper 17 (Th17) cells protect barrier tissues but also trigger autoimmunity.  The precise mechanisms control these opposing processes remain unclear. We identify Id2 as a key factor for pathogenic Th17 cells. Id2 expression is markedly elevated in Myelin-reactive T cells from multiple sclerosis (MS) patients and autoimmune mice. Mice lacking Id2 in Th17 cells completely fail to develop neuroinflammation and do not generate neuron-pathogenic Th17 subset.

overall_design: Single Cell analysis of CD4+YFP+ cells from spleen in Id2 deficient and wild type cells.

first: Xiaojuan

last: Han

first: Xi

first: Yanling

first: Xiangwen

last: Liu

first: Yuchen

last: Kang

first: Chao

last: Li

first: Ping

last: Gao

first: Xiaoyu

last: Zhai

first: Baoqian

last: Jia

first: Baidong

last: Hou

first: Xuyu

last: Zhou

first: Jian

last: Song

first: Fuping

last: Zhang


title: Tumor-targeting oncolytic viruses engineered for glioblastoma immunotherapy

city: Boston

first: Zhaorong

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

summary: We report the development of an oncolytic virus engineered for enhanced targeting of tumor cells, increased safety, and greater antitumor efficacy through the expression of multiple transgenes that remodel the immunosuppressive GBM tumor microenvironment

overall_design: GBM-bearing mice (C57BL/6) were treated with an engineered oncolytic virus or a control virus at day 7 post tumor implantation. At day 20, mice were sacrificed for analysis.

first: Federico

last: Giovannoni

first: Francisco

last: Quintana


title: SF3B1 mutation accelerates the development of CLL via activation of the mTOR pathway

city: Monrovia

first: Lili

last: Wang

state: California

address: 1218 South fifth avenue

department: Systems Biology

institute: City of Hope

summary: RNA splicing factor SF3B1 is among the most recurrently mutated genes in chronic lymphocytic leukemia (CLL); these mutations frequently co-occur with chromosome 13q deletion (del(13q)). The presence of SF3B1 mutation and del(13q) is predictive of poorer prognosis in CLL, suggesting that these two lesions impact the aggressiveness of CLL. While del(13q) in murine B cells (Mdr mice), but not expression of Sf3b1-K700E, drives the initiation of CLL, we hypothesize that SF3B1 mutation accelerates CLL progression. In this study, we crossed mice with a B-cell-specific Sf3b1-K700E allele with Mdr mice to determine the impact of Sf3b1 mutation on CLL progression. We found that the co-occurrence of these two lesions in murine B cells indeed causes acceleration of CLL. We showed that Sf3b1-K700E impacts alternative RNA splicing of Nfatc1 and activates mTOR signaling and the MYC pathway, contributing to CLL acceleration. Moreover, concurrent inhibition of RNA splicing and mTOR pathways leads to cell death in vitro and in vivo in murine CLL cells with SF3B1 mutation and del(13q). Our results thus suggest that SF3B1 mutation contributes to the aggressiveness of CLL through the activation of the mTOR pathway, likely mediated by alternative splicing of Nfatc1, providing a rationale for targeting mTOR and RNA splicing in the subset of CLL patients with both SF3B1 mutations and del(13q).

overall_design: Normal splenic B cells or CLL B cells were first enriched by a pan-B cell selection kit (Miltenyi Biotec, Germany), and total RNA was isolated from these cells using a Nucleospin RNA plus kit (Machery Nagel, Allentown, PA). Libraries for RNA-seq were constructed using the Stranded Total RNA Prep with Ribo-Zero Plus Kit (Illumina) and sequenced on the Novaseq S4 platform using paired-end 150 bp mode. The fastq sequence files exported by the sequencer were checked using FastQC (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc). Adaptors and low-quality bases were removed from the sequencing reads using Trimmomatic. The remaining reads were aligned to the mouse reference genome (mm10) using STAR(20) with default parameters. Adaptor trimming and mapping quality reports were generated using MultiQC. The DESeq2 R package performed differential expression mRNA analyses. mRNAs with absolute log2FC more than 1 and FDR less than 0.05 were identified as significantly dysregulated genes. RNA splicing analysis was performed using our previously established pipeline (24, 46). In brief, we integrated StringTie, LeafCutter , and rMATs to maximally improve the power of detection of splicing dysregulation. We assembled de novo transcripts using StringTie with default parameters. LeafCutter was used to detect additional novel exon boundaries. Together with the isoform annotation file downloaded from GENCODE (release 26), we merged all isoform information to generate a comprehensive isoform annotation file using a custom R script as a reference file for rMATs. Percent spliced-in (PSI) value was calculated using rMATs. For differential splicing analysis, we adopted the differential splicing analysis statistical model from rMATs with an absolute IncLevelDifference value of more than 0.1 and FDR less than 0.05 as significant cutoff.


title: Profiling the spatial architecture of multiple myeloma in human bone marrow trephines with spatial transcriptomics

city: Parkville

first: Yunshun

last: Chen

state: VIC

address: 1G Royal Parade

department: ACRF Cancer Biology and Stem Cells

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: LINC00365 suppresses breast tumor growth and metastasis by inhibiting the HIF-1α-mediated Warburg effect

city: changchun

first: long

last: xu

address: xinmin road

institute: jilin university

summary: To investigate the LINC00365 plays an important role in inhibiting BC proliferation and provided insight into how the HIF-1α/LINC00365 axis is involved in the Warburg effect.We then performed gene expression profiling analysis using data obtained from RNA-seq in MCF-7 cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MCF-7 cells.

first: Buhan

first: Xianzhi

last: Qu

first: Jiang

first: Long

last: Xu


title: CCR5-targeted allogeneic gamma-delta CD19 CAR T cells for HIV-associated B cell malignancy immunotherapy

city: Philadelphia

first: Gregory

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Immune-based cell therapy offers a promising approach to cancer treatment. While autologous chimeric antigen receptor (CAR) T cells have shown success, production is time-consuming, costly, and patient-specific. Gamma-delta (γδ) T cells are promising for ‘off-the-shelf’ CAR T cell therapy. However, clinical translation of γδ CAR T cells is hampered by low frequency, resistance to genetic manipulation, and advanced differentiation after expansion, limiting therapeutic feasibility. Here, we demonstrate a method for in vitro activation and expansion of peripheral blood γδ T cells, facilitating high rates of gene editing and efficient CAR integration. Using artificial antigen-presenting cells, we produce minimally differentiated, highly functional γδ CAR T cells. By targeting an FDA-approved CD19 CAR to the CCR5 locus, we generate CCR5-deficient γδ CD19 CAR-T cells (γδ CCR5KI-CAR19), which demonstrated resistant to HIV-mediated depletion and robust antitumor responses against B cell lymphoma and leukemia. γδ CCR5KI-CAR19 T cells enable the immunotherapy of HIV-associated B cell malignancies. These studies provide preclinical evidence supporting large-scale development of potent allogeneic γδ CAR T cells for diverse immunotherapies.

overall_design: Single-cell RNA-Seq analysis of gamma-delta CAR T cells manufactured with or without feeder cells. Single-cell RNA-Seq was performed using the Chromium GEM-X Single Cell 3' kit. Libraries were constructed with Chromium Connect. Sequencing was performed using a NextSeq 2000. FASTQ files were aligned and summarized as feature-barcode matrices by cellranger v8.8.0 with the GRCh38-2024-A reference. Feature-barcode matrices were analyzed with Seurat v5.0.3 and integrated using the FindIntegrationAnchors and IntegrateData functions with 50 dimensions. UMAP was performed in the top 15 principal components, and cell cycle scoring was performed using Seurat.

first: Angel

last: Ramirez-Fernandez

first: Alexander

last: Dimitri

first: Joseph

last: Fraietta


title: DNA hypermethylation of MED1 and MED23 as early diagnostic biomarkers for unsolved issues in atrial fibrillation

first: Mark

last: Pepin

summary: Although evidence supports that aberrant DNA methylation exists in the hearts of patients with atrial fibrillation (AF), epigenetic phenomena underlying the onset and progression of AF are not yet fully understood. We therefore investigated DNA methylome changes in circulating CD4+ T cells isolated from AF patients and healthy subjects (HS), enrolled in the ongoing DIANA clinical trial (NCT04371809), by using reduced-representation bisulfite sequencing (RRBS). Network analysis was applied to investigate differential DNA methylation profiles and functional effects.  An atrial-specific PPI network revealed 18 hub differentially methylated genes (DMGs). ROC curve analysis revealed that DNA methylation levels of CDK5R1 (AUC = 0.755; P = 0.049), HSPG2 (AUC = 0.768; P = 0.038), WDFY3 (AUC = 0.782; P = 0.029), USP49 (AUC = 0.755; P = 0.049) and GSE1 (AUC = 0.755; P = 0.049), AIFM1 (AUC = 0.764; P = 0.041), CDK5RAP2 (AUC = 0.809; P = 0.017), COL4A1 (AUC = 0.864; P<0.001), SEPT8 (AUC = 0.900; P<0.001), PFDN1 (AUC = 0.900; P<0.01), and ACOT7 (AUC = 0.777; P = 0.032) provided a good performance on predicting the presence AF. Transcriptional profiling of the hub DMGs provided a significant overexpression of PSDM6 (P=0.004), TFRC (P=0.01), CDK5R1 (P<0.001), HSPG2 (P=0.01), WDFY3 (P<0.001), USP49 (P=0.004), and GSE1 (P=0.021) in AF patients vs HS. CDK5R1, GSE1, HSPG2, and WDFY3 resulted the best discriminatory genes both at methylation and gene expression level. Our results provide putative diagnostic biomarkers with the potential to advance precision medicine in AF.

overall_design: Peripheral blood was collected from patients with a diagnosis of atrial fibrillation or no known diagnosis of cardiac dysrhythmia.

first: Teresa

last: Infante

first: Claudio

last: Napoli


title: Generation of iPSC-derived CD4+ Th1 cells enhancing chimeric antigen receptor-T cell cytotoxicity

city: Bunkyo

first: Miki

last: Ando

state: Tokyo

address: Hongo 2-1-1

department: Hematology

country: Japan

institute: Juntendo University

summary: CD4+ T cells are anticipated to enhance the overall immune response, including the anti-tumor activity of chimeric antigen receptor (CAR)-T cell therapy. In the past, we established a culture system to generate CD8+ T cells from iPS cells (iPSCs); however, it was challenging to generate CD4+ T cells. Drawing inspiration from the observation that adult T cell leukemia (ATL) cells are consistently CD4+ and possess Treg characteristics, we successfully generated CD4+ Treg cells by reprogramming ATL cells into iPSCs and then differentiating them into T cells. Gene expression analysis of this generation system suggested that RUNX3 serves as a key regulator in T cell differentiation within the ex vivo generation system. By knocking out RUNX3, we demonstrated the generation of antigen-specific CD4+ Th1 cells via the iPSC route, thereby enhancing the activity of CD8+ CAR-T cells against GD2-expressing lymphoma. These technologies hold significant promise for contributing to “off-the-shelf” immunotherapies against malignant tumors, including solid tumors.

overall_design: Expression profiling by high throughput sequencing

first: Yoshiki

last: Furukawa


title: ATRX Condensates Formed by Liquid-Liquid Phase Separation Regulate Neural Progenitor Cell Identity (ChIP)

city: Shinjuku-ku

first: Tsukasa

last: Sanosaka

address: 35 Shinanomachi

department: Department of Physiology

institute: Keio University School of Medicine

summary: Alpha-thalassemia X-linked intellectual disability syndrome (ATR-X) is caused by mutations in the ATRX gene, which plays a pivotal role in heterochromatin integrity.  In this study, we uncover a novel mechanism by which ATRX influences fate of human neural progenitor cells (hNPCs) through the formation of liquid-liquid phase separation (LLPS)-driven condensates. We discovered that the intrinsically disordered region (IDR) of ATRX is essential for driving LLPS, enabling ATRX to form dynamic condensates within the nucleus. The IDR region can autonomously form phase-separated droplets and recruit co-activators. In addition, formation of these condensates was crucial for the localization of ATRX at super-enhancers (SEs) in hNPCs, directly linking ATRX condensate dynamics to the regulation of gene expression critical for neural differentiation.   Disruption of ATRX condensates leads to impaired neuronal differentiation, emphasizing the functional significance of ATRX in human neural development. Our findings provide new insights into the molecular function of ATRX beyond its established roles in chromatin structure, and suggest that LLPS is a key regulatory mechanism through which ATRX supports neurodevelopment. This study opens avenues for further exploration of how dysregulation of ATRX and its phase-separation ability may contribute to the pathogenesis of ATR-X syndrome and related neurodevelopmental disorders.

overall_design: To evaluate LLPS-dependent genome occupancy and distribution of ATRX in human neural progenitor cells, we performed CUT&RUN about LLPS inhibitor 1,6-Hexanediol treated or untreated cultured human neural progenitors with two ATRX antibodies. We also carried out ChIP-seq about H3K9me3 with same cells to generate chromatin landscapes.


title: In Vitro Validation of DNA-Diffusion and Control Sequences within the AXIN2 Locus [nanopore_plasmid]

first: Gue-ho

last: Hwang

state: MA

address: 300 Longwood Ave

institute: Boston Children's hospital

summary: DNA-Diffusion is a novel generative approach leveraging diffusion probabilistic models for the design of cell type-specific DNA regulatory sequences.  To evaluate the capacity of DNA-Diffusion sequences to endogenously alter AXIN2 transcription, we employed a novel MPRA-like system that utilizes CRE-recombinase mediated cassette exchange and long-read sequencing to measure the gene’s transcriptional output in response to enhancer sequences several kilobases away. We evaluated a total of 100 sequences using the AXIN2 endogenous replacement experiment using the following sequence groups: GM12878 DNA-Diffusion, GM12878 Positive Controls, GM12878 Negative Controls, K562 DNA-Diffusion, HepG2 DNA-Diffusion, and shuffled GM12878 DNA-Diffusion. Our findings demonstrate the potential of DNA-Diffusion to design sequences with therapeutic potential, showing their effectiveness in an endogenous setting.

overall_design: The library was constructed with artificial enhancer and barcode combination flanked with a LoxP/Lox2272 pair. The enhancer and barcode combinations were sequenced using Nanopore seuqencing

first: L

middle: F

last: DaSilva

first: Simon

last: Senan

first: J

last: Kribelbauer

first: GueHo

first: Deplanke

last: Bart

first: Pinello

last: Luca


title: Repurposing Zafirlukast Confers Renal Protection in Ischemia-Reperfusion Injury via Suppressing Macrophage METosis

city: wenzhou

first: Longwei

last: Zhao

address: University-Town, Wenzhou, Zhejiang, P.R.China

institute: Wenzhou Medical university

summary: Tacrolimus is widely used to prevent post-transplant acute kidney injury (AKI) but causes severe toxicities (e.g., nephrotoxicity, hyperglycemia). We repurposed zafirlukast (ZFK), an FDA-approved asthma drug, to address this limitation. In a murine kidney ischemia-reperfusion injury (KIRI) model, ZFK significantly attenuated renal dysfunction, reducing serum creatinine and blood urea nitrogen (BUN) to levels comparable to tacrolimus, without inducing metabolic adverse effects. RNA sequencing revealed that ZFK recapitulated tacrolimus’ anti-inflammatory gene signatures while uniquely suppressing macrophage extracellular trap formation (METosis). Mechanistically, ZFK inhibited METosis by downregulating PAD4 and CitH3 expression, confirmed by immunofluorescence and flow cytometry. Single-cell transcriptomics (Tabula Muris and GEO database) identified macrophages as the primary target via CysLT1R antagonism. This study provides the first evidence that ZFK protects against KIRI by targeting METosis, a key driver of sterile inflammation. Given its established safety profile, ZFK could bypass Phase I trials, accelerating clinical translation as a safer alternative to calcineurin inhibitors. Our findings also highlight the broader potential of ZFK in METosis-related diseases (e.g., sepsis, atherosclerosis) and underscore drug repurposing as a strategic approach for rapid therapeutic development.

overall_design: Male C57BL/6J mice were randomly assigned to two main experimental groups (6 mice per group) as follows: (i) I/R group: received daily oral administration of 0.9% saline for 1 consecutive days, followed by partial bilateral kidney ischemia for 30 minutes, and then a 24-hour reperfusion period; (ii) Zafirlukast + I/R group: received Zafirlukast (10 mg/kg/day, p.o.) or tacrolimus (1 mg/kg/day, p.o.) via oral gavage for 1 consecutive days, followed by laparotomy with bilateral kidneys occlusion for 30 minutes and then a 24-hour reperfusion period. Animals were anesthetized using an intraperitoneal injection of pentobarbital sodium (0.5%, 0.01 mL/g) At the conclusion of the experimental period, the animals were humanely sacrificed by decapitation. Blood was collected via cardiac puncture and centrifuged at 4,000 × g for 10 minutes. The resulting sera were isolated and stored at -80°C for biochemical assessments. The kidneys were excised and divided into three portions. The first portion was homogenized in phosphate-buffered saline, then centrifuged, and the supernatant was stored at -80°C for RNA sequencing assays. The second portion was rapidly frozen in liquid nitrogen and stored at -80°C for Western blot analysis and quantitative PCR. The third portion was immersed in 4% paraformaldehyde for histopathological and immunohistochemical investigations.

first: Xiaochun

last: Ye

first: Meiyun

last: Wen

first: Yumei

last: Huang

first: Ruofang

last: Zheng

first: Ping

last: Wang

first: Ran

last: Chen


title: Stress leads to rapid, genome-wide changes to nucleosome positions and RNA polymerase II occupancy

city: Cambridge

first: Harry

last: Fischl

address: Babraham Research Campus

country: United Kingdom

institute: Storm Therapeutics

summary: Switching cells from growth in glucose containing media to galactose containing media causes rapid changes to nucleosome positions and RNA polymerase II occupancy

overall_design: NETseq, RNA-seq and MNASE-seq to profile changes to Pol2 occupancy, transcript levels and nucleosome positions, respectively, following the switch from exponential growth in glucose (YPD) containing media to galactose containing media (YPG)

first: Jane

last: Mellor


title: Differential expression of circRNAs in virus infection

city: beijing

first: ao

last: zhang

address: Peking University, No.5 Yiheyuan Road Haidina District, Beijing, P.R.China 10087

institute: peking university

summary: There is increasing evidence showing that aberrant expressions of circRNAs are implicated in various physiological or pathological processes. Yet, their roles in antiviral innate immunity remain unknown. To reveal the implications of circRNAs in antiviral innate immunity, we used Human circRNA Array v2.0 microarrays to measure the expression profiles of circRNAs in HEK293 cells infected with or without Sendai virus(SeV). We found 82 up-regulated and 20 down-regulated circRNAs(fold change >2; P <0.05) in HEK293 cells after SeV infection. Upregulation of circRNA hsa_circ_0006916 was established using Real-time quantitative PCR. These results showed abrrant expression profiles of circRNAs in HEK293 cells after SeV infection and revealed their potential roles in antiviral innate immunity.

overall_design: In this study, we determined expression profile of circRNAs in HEK293 cells infected with sendai virus (T293_1P, T293_2P, T293_3P) and without sendai virus (T293_1_, T293_2_, T293_3_) using Human circRNA Array v2.0 microarray (8×15K, Arraystar).

first: Jun

last: Zhang

first: Ao

first: Ranran

last: Yao


title: Id2 acts as a metabolic checkpoint underpinning Th17 cell fate decision [CUT&Tag]

first: Wang

last: Xi

overall_design: CUT & Tag analysis of CD4+YFP+ cells from spleen in Il17CreR26YFP, Il17CreR26YFP Id2f/f and Il17CreR26YFP Id2f/f E2Af/f HEBf/f mice; or CD4+YFP+SLAMF6+ and CD4+YFP+CXCR6+ cells from Il17CreR26YFP mice.

first: Xiaojuan

last: Han

first: Xi

first: Yanling

first: Xiangwen

last: Liu

first: Yuchen

last: Kang

first: Chao

last: Li

last: Gao

first: Xiaoyu

last: Zhai

first: Baoqian

last: Jia

first: Baidong

last: Hou

first: Xuyu

last: Zhou

first: Jian

last: Song

first: Fuping


title: SARS-COV2 in intestinal organoids

city: Graz

first: Barbara

last: Jelusic

address: Auenbruggerpl. 2

country: Austria

institute: Med Uni Graz

summary: Inflammatory bowel disease (IBD) patients are generally at an increased risk for viral diseases. Viral infections of tissue affected by chronic IBD are insufficiently understood, especially in the context of flare-ups; while some studies have confidently shown aggravation of symptoms in large cohorts, others found no association. Although not considered at an increased risk of Coronavirus Disease 2019 (COVID-19), IBD patients suffer more frequent gastrointestinal symptoms during COVID-19 and a worse outcome has been associated with certain IBD medications and disease activity. For this reason, we generated intestinal epithelial organoids from ileum with Crohn’s disease (CD) and colon with ulcerative colitis (UC) together with healthy controls. Each group included five to six patients. Using RNA sequencing we showed that IBD organoids were not more susceptible to infection. The highest viral load two days after infection was in healthy ileum and is correlated to the expression of SARS-CoV-2 entry receptor ACE2 and proteases CTSL/B. Pathway analyses determined an apparently weaker defense reaction in CD organoids to SARS-CoV-2 which could simply be due to the lower viral load compared to the healthy group. In contrast to CD, there was an activation of viral defense in infected UC colon, especially interferon signaling, resembling highly infected healthy ileum. This was not seen in healthy colon and was unexpected since UC and healthy colon did not differ in viral load. In uninfected IBD organoids compared to healthy, there was an already stronger basal expression of genes implicated in viral defense, for example, of viral sensors OAS1 and OASL in CD and interferon regulatory transcription factor IRF7 in UC. Some were further influenced by SARS-CoV-2 infection with notable differences between CD and UC.  To conclude, infection with SARS-CoV-2 did not lead to higher viral numbers in IBD organoids providing reassurance for patients in remission. Still, we observed a more pronounced epithelial defense reaction to the virus in UC colon, prompting further investigations on whether this could be the reason for stronger gastrointestinal symptoms of COVID-19 seen in IBD patients or if it could lead to a consequent IBD flare.

overall_design: RNA Seq data  of intestinal organoids of patients with and without intestinal inflammatory diseases  was collected without and upon in-vitro SARS-COV2 infection

first: Stefan

middle: T

last: Boerno

first: Gregor

last: Gorkiewicz

first: Alexander

last: Moschen


title: In Vitro Validation of DNA-Diffusion and Control Sequences within the AXIN2 Locus [gRNA]

first: Gue-ho

last: Hwang

overall_design: To validate enhancer sequences in the AXIN2 locus, a cell line (MEC1) was created with a stably integrated CRE recombinase and an RMCE landing pad within the AXIN2 gene and perturbated the RNA expression using a library that includes various enhancer DNAs, barcodes, and LoxP/Lox2272 sites. The mRNA expressions were analyzed from barcode sequences obtained from mRNA and gDNA using NextSeq sequencing.

first: L

last: DaSilva

first: Simon

last: Senan

first: J

last: Kribelbauer

first: GueHo

first: Deplanke

last: Bart

first: Pinello

last: Luca


title: DNA methylation controls unmethylated transcription start sites in the genome in trans

city: Montreal

first: David

last: Cheishvili

state: Quebec

address: 3655 Sir William Osler

country: Canada

institute: McGill

summary: The inverse correlation between DNA methylation and steady state mRNA levels is imperfect; a large number of genes, which are unmethylated in the promoter region, are silenced. We show here that either pharmacological inhibition of DNA methyltransferase (DNMT1) with 5-aza-2'-deoxycytidine (5-azaCdR) or knockdown with shRNA dramatically expands the number of transcription initiation positions in the genome including many unmethylated promoters. Induction of unmethylated promoters in response to inhibition of DNMT1 is a result of activation by demethylation of methylated upstream regulators such as the transcription factor HNF4A. Our results imply that the landscape of genes that are regulated by DNA methylation is more wide-ranging than genes silenced by methylation of their own cis regulatory sequences. We propose a hierarchical model of transcriptional control by DNA methylation whereby regulation of unmethylated promoters is dependent on the methylation state of trans upstream regulators.

overall_design: RNAPII ser 5 ChIP DNA from primary liver culture and SKHep1 cancer adenocarcinoma cells, treated with scrambled control, 1uM of 5azaCdR and ShDNMT1

first: Moshe

last: Szyf


title: Synergistic enhancement of SvLAC-1 gene expression by strong promoter and surfactant: A novel strategy to improve laccase production in Inocutis levis

city: Lanzhou City

first: Lan

middle: Lan

last: Yu

state: Anning District

address: Northwest Normal University, Shi Street, Anning District, Lanzhou City, Gansu Province, China

department: College of Life Sciences

institute: Northwest Normal University

summary: Laccase content was determined under the influence of different concentrations of Triton X-100, and the key enzyme genes  were cloned, and finally the expression of laccase was improve by strong promoter substitution

overall_design: Laccase content of Inocutis levis-zhu4935 was varied using 0 ml, 15 ml of Triton X-100 and three replicates of each data, 0 ml was labeled as CK group and 15 ml was labeled as T group.

first: Yanjun

last: Ma

first: Pengcheng

last: Di

first: Zilu

first: Lanlan


title: ATRX Condensates Formed by Liquid-Liquid Phase Separation Regulate Neural Progenitor Cell Identity

first: Tsukasa

last: Sanosaka

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

overall_design: Refer to individual Series


title: Id2 acts as a metabolic checkpoint underpinning Th17 cell fate decision [RNA-seq]

first: Wang

last: Xi

overall_design: RNA-sequencing of CD4+YFP+ cells from spleen and lymph node in Il17CreR26YFP, Il17CreR26YFP Id2f/f and Il17CreR26YFP Id2f/f E2Af/f HEBf/f mice; or CD4+YFP+SLAMF6+ and CD4+YFP+CXCR6+ cells from Il17CreR26YFP mice.

first: Xiaojuan

last: Han

first: Xi

last: Wang

first: Yanling

last: Wen

first: Xiangwen

last: Liu

first: Yuchen

last: Kang

first: Chao

last: Li

first: Ping

last: Gao

first: Xiaoyu

last: Zhai

first: Baoqian

last: Jia

first: Baidong

last: Hou

first: Xuyu

last: Zhou

first: Jian

last: Song

first: Fuping

last: Zhang


title: ATRX Condensates Formed by Liquid-Liquid Phase Separation Regulate Neural Progenitor Cell Identity (RNA)

overall_design: We examined impact of LLPS inhibiton with 1,6-Hexanediol treatment or mutation in human neural progenitor cells. For the inhibitor assay, we sampled human neural progenitor cells of 1.5% 1,6-Hexanediol treatment for 2 hours with three biological replicates. For the comparison of LLPS-inhibited mutants, we sampled differentiated neural progenitor cells from WT and mutated (ΔEx15) iPSCs with three biological replicates.


first: David

last: Cheishvili

type: Methylation profiling by genome tiling array


title: In Vitro Validation of DNA-Diffusion and Control Sequences within the AXIN2 Locus [mRNA]

first: Gue-ho

last: Hwang

overall_design: To validate enhancer sequences in the AXIN2 locus, a cell line (MEC1) was created with a stably integrated CRE recombinase and an RMCE landing pad within the AXIN2 gene and perturbed the RNA expression using a library that includes various enhancer DNAs, barcodes, and LoxP/Lox2272 sites. The mRNA expressions were analyzed from barcode sequences obtained from mRNA and gDNA using NextSeq sequencing.

first: L

last: DaSilva

first: Simon

last: Senan

first: J

last: Kribelbauer

first: GueHo

first: Deplanke

last: Bart

first: Pinello

last: Luca


title: Mutant GFAP alters lineage commitment of neural organoids [AxDorganoids_bulk_experiment1]

city: Vestec

first: Zuzana

last: Matusova

address: Prumyslova 595

department: Laboratory of Glial Biology and Omics Technologies

country: Czech Republic

institute: Institute of Biotechnology of the Czech Academy of Sciences

summary: Glial fibrillary acidic protein (GFAP) is a type-3 intermediate filament protein mainly expressed in astrocytes in the central nervous system. Mutations in GFAP cause Alexander Disease (AxD), a rare and fatal neurological disorder. How exactly mutant GFAP eventually leads to white and grey matter deterioration in AxD remains unknown. GFAP is also expressed in radial glial cells, which are neural stem cells in the developing brain. Here, we used AxD patient-derived induced pluripotent stem cells (iPSCs) to explore the impact of mutant GFAP during neurodifferentiation. Our results show that GFAP is already expressed in iPSCs. Moreover, we have found that mutations in GFAP can severely affect neural organoid development through altering lineage commitment in embryoid bodies. Together, these results support a key role for GFAP as an early modulator of neurodevelopment.

overall_design: We generated unguided neural organoids from an Alexander Disease patient-derived iPSC line (R239C-AxD-1), as well as from an isogenic control line (R239R-Ctrl) derived from this patient line. We used the AggrewellTM800 plate to generate embryoid bodies. In experiment 1, we performed RNAseq at day 3,5,7 and 9 of differentiaton to investigate the gene expression underlying a morphological phenotype that we observed.

first: Werner

last: Dykstra

first: Rachel

last: Battaglia

first: Pavel

last: Abaffy

first: Nuria

last: Goya-Iglesias

first: Dolores

last: Perez-Sala

first: Henrik

last: Ahlenius

first: Mikael

last: Kubista

first: R

last: Pasterkamp

first: Li

first: Jianfei

last: Chao

first: Yanhong

last: Shi

first: Lukas

last: Valihrach

first: Milos

last: Pekny

first: Elly

last: Hol


title: Mutant GFAP alters lineage commitment of neural organoids [AxDorganoids_bulk_experiment2]

overall_design: We generated unguided neural organoids from an Alexander Disease patient-derived iPSC line (R239C-AxD-1), as well as from an isogenic control line derived from this patient line (R239R-Ctrl). In experiment 2, we used the AggrewellTM800 plate as well as 96-well round bottom ultra low attachment plates to generate embryoid bodies. We performed RNAseq at day 3,5,7 and 9 of differentiaton to investigate how the two different growth protocols influenced organoid development.

last: Li


first: David

last: Cheishvili

overall_design: Total RNA obtained from primary liver cells (NorHep) and cancer HCC cells line (HepG2, SKHep1) isolated from triplicate culture was subjected to expression aray analysis and compared to RNAPolII-Ser5 ChIPseq and Illumina 450K methylation data

first: Moshe

last: Szyf


title: A Liver-to-Skin Neuroimmune Axis Transmits Visceral Distress via Midkine-Driven Alloknesis

status: Public on Jul 12 2025

city: Shanghai

first: Zihan

last: Wang

address: No. 555 Zu Chongzhi Road, Zhangjiang, Pudong, Shanghai

department: Shanghai Institute of Materia Medica

institute: University of Chinese Academy of Sciences

summary: The skin, long considered as a passive barrier and target of external insults, could also function as a sentinel for internal pathology, although the underlying mechanisms remain poorly understood. Here, we identify a neuroimmune circuit linking liver injury to mechanically evoked itch (alloknesis) in the skin. The hepatokine Midkine (MDK) emerges as a critical circulating signal, elevated in liver injury, which activates skin-resident macrophages through LRP1, inducing NGF production and subsequent sensitization of cutaneous pruriceptors. Importantly, elevated serum Midkine levels in liver disease patients strongly correlated with alloknesis severity, highlighting the conserved liver-skin axis. These findings reveal an inter-organ communication pathway that transduces visceral stress into periphery sensory hyperactivity, establishing the skin as a reflective interface of internal organ dysfunction.

overall_design: Dorsal skin CX3CR1+ cells were collected for smart-seq assay using CCl4 or Vehicle-treated Cx3cr1-creER:Ai9 mice in three biological replicates. Hepatocytes were collected for bulk-RNA seq assay using CCl4 or Vehicle-treated C57 mice in three biological replicates.

first: Yanyong

last: Cheng

first: Zili

last: Xie

first: Ting

first: Yuanyuan

last: Ye

first: Wenbo

last: Jiang

first: Yifei

last: Liu

first: Tianyi

last: Shen

first: Liyan

last: Wu

first: Lei

last: Zhang

first: Liqin

last: Zhou

first: Ximin

last: Hu

first: Hongfei

first: Fengxian

first: Heng

last: Xu

first: Jing

last: Feng


title: Dppa2 synergizes with p53 in promoting DNA damage-induced apoptosis of mouse embryonic stem cells [ChIP-Seq]

city: Guangzhou city

first: Mangmang

state: Guangdong province

address: 1838 N Guangzhou Ave

department: Department of Cell Biology School of Basic Medical Sciences

institute: Southern Medical University

summary: Dppa2 (Developmental pluripotency associated 2), specifically expressed in embryonic stem cells (ESCs) and reactivated in certain cancers, plays important roles in regulating the transition between pluripotency and differentiation. However, its involvement in the DNA damage response (DDR) of mouse ESCs (mESCs) has remained unclear. Here, we identify a surprising pro-apoptotic function for Dppa2 as a novel p53-interacting partner in mESCs. Dppa2 physically interacts with p53 and is transcriptionally repressed by p53 upon DNA damage. By comparing the effects of Dppa2 in p53+/+ and p53-/- mESCs, we find that Dppa2 promotes DNA damage-induced apoptosis (DIA) of mESCs in a p53-dependent manner. RNA-seq and chromatin immunoprecipitation followed by sequencing (ChIP-seq) reveal that Dppa2 and p53 co-repress genes involved in cell cycle regulation and self-renewal, which are highly expressed in ESCs. Mechanistically, Dppa2 recruits p53 to the enhancers of these co-repressed genes. Consequently, Dppa2 depletion significantly compromises p53’s binding intensity and alleviates transcriptional repression. Collectively, our findings uncover a novel mechanism of p53-mediated apoptosis achieved through cooperation with its ESC-specific partner, Dppa2, thereby highlighting a previously unappreciated tumor suppressor identity of Dppa2.

overall_design: To explore Dppa2 binding sites in mESCs upon DNA damage, we performed Dppa2 ChIP-seq on p53+/+ R1E cells, either untreated or treated with Adriamycin for 8 h.

first: Sisi

last: Chen

first: Lu

first: Xiaojun

last: Tan


first: David

last: Cheishvili

overall_design: Bisulphite converted DNA from the samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.2

first: Moshe


title: Coinfection with Fowl Adenovirus Serotypes 1 and 4 (FAdV-1 and -4) Enhances FAdV-4 Replication through FAdV-1-mediated Upregulation of HSPA2 Expression

city: Yangling

first: xiaoxuan

last: Li

state: ShaanXi

address: 3 Taicheng Street

institute: Northwest A & F University

summary: Fowl adenoviruses (FAdVs) are widely distributed in poultry populations around the world, and many diseases are associated with FAdV infection in chickens. This study documented the first characterization of coinfection with fowl adenovirus serotypes 1 and 4 (FAdV-1 and -4) associated with hydropericardium hepatitis syndrome (HHS) in Chinese layer flocks, revealing a novel viral cooperation mechanism. Two novel strains (CH/SX/201805-1 and -4) were identified and isolated, with whole-genome sequencing showing CH/SX/201805-1 clustering with FAdV-1 (99.7% identity to FAdV-A-61/11z), whereas CH/SX/201805-4 displayed characteristic ORF19/27/29 deletions mirroring emergent Chinese FAdV-4 variants. Experimental coinfection in SPF chickens resulted in 87.5% mortality, which was 16.7% greater than that resulting from infection alone, with exacerbated pathology. In vitro coinfection experiments demonstrated concurrent viral replication within same LMH cells, a previously unreported phenomenon, where FAdV-1 increased FAdV-4 replication efficiency 21-fold (P<0.001). Transcriptomic profiling revealed heat shock protein A2 (HSPA2) as the most differentially expressed gene, which was upregulated 2.8-fold during coinfection compared with infection with FAdV-4 alone. Functional validation through HSPA2 knockdown reduced FAdV-4 replication, establishing that FAdV-1 potentiates FAdV-4 through HSPA2-mediated host modulation. These findings provide the first evidence of HSPA2-dependent interserotype synergy in avian adenoviruses and can be used to develop a cellular model for FAdV coinfection studies. These insights redefine the understanding of FAdV pathogenesis and create new avenues for targeted intervention strategies against emerging poultry adenoviral coinfections.

overall_design: LMH cells were seeded in 6-well plates and divided into four groups: the FAdV-1 alone group, the FAdV-4 alone group, the coinfection group and the control group. The cells were inoculated with CH/SX/201805-1 (MOI = 1), CH/SX/201805-4 (MOI = 1), or a mixture of both (MOI = 0.5 each). At 12 hpi, total RNA was extracted via TRIzol (TaKaRa, Tokyo, Japan) and sequenced via a NovaSeq 6000 sequencer (Illumina Inc., San Diego, CA) by Beijing Biotechnology Company Ltd. (Beijing, China). The raw reads were processed via fastp (https://github.com/OpenGene/fastp), and the sequences were mapped to the Gallus gallus genome (NCBI GCF_000002315.6) via HISAT2.2.4. DEGs were identified via edge R with a log2 (fold change) ≥ 1 and P < 0.05.

first: Miao

last: Dan

first: Dongying

first: Binbin

last: Ren

first: Yifan

last: Ge

first: Yayu

first: Julian. A

last: Hiscox

first: James P.

last: Stewart

first: Qin

last: Zhao

first: Mingzhi

last: Liao

first: Yani

last: Sun


title: Identification of Novel DNA Sequence Motifs that Modulate Transcription in T cells

city: VANCOUVER

first: Nicole

last: Knoetze

state: British Columbia

address: 675 west 10th avenue

institute: Canada's Michael Smith Genome Sciences Centre

summary: Considerable progress has been made towards associating transcription factor binding sites (TFBS) with cell-type-specific gene expression, however, the full repertoire of DNA sequence motifs that regulate transcription remains unknown. Improving our understanding of transcriptional regulation is especially important in T cells, given the enormous potential of genetically engineered T cells as an emerging class of therapeutics. Here, we report results from a comprehensive and unbiased survey investigating whether there are novel motifs enriched in regulatory regions of genes with the highest constitutive and selective expression across diverse T-cell subsets. Using computational and experimental methods, we identified 2,036 novel motifs and 629 previously curated TFBS that are enriched, both individually and in specific combinations, in the regulatory regions of genes exhibiting T-cell-specific gene expression. We then used the self-transcribing active regulatory region sequencing (STARR-seq) assay to evaluate all possible three-way combinations of a subset of 18 candidate motifs to test their ability to modulate transcription in immortalized lymphoblastic cell lines of T-cell origin (Jurkat E6) versus myeloid origin (K562). Our results revealed novel motifs that modulate gene transcription in T cells, with some exhibiting stronger regulatory effects than TFBS for TFs with established roles in T cells. The regulatory activity of these novel motifs was influenced by the motif’s orientation, position, and copy number. Overall, these results highlight our incomplete understanding of the relationship between sequence composition and T-cell gene regulation, and indicate that previously annotated TFBS represent only a subset of motifs capable of modulating gene transcription in T cells.

overall_design: STARR-seq was performed following the protocols described in (Felix, Muerdter, et al. Nature Methods 15.2 (2018): 141-149).

first: Scott

middle: D

last: Brown

first: Eric

last: Yung

first: Anthony

last: Bayega

first: Robert

last: Holt


title: Integration of Phospho-Signaling and Transcriptomics in Single Cells Reveals Distinct Th17 Cell Fates

city: Birmingham

first: Rob

last: Welner

state: AL

address: 1824 6th Ave S

department: Medicine - Hem/Onc

institute: University of Alabama at Birmingham

summary: Single-cell RNA sequencing (scRNA-seq) provides the resolution and scale necessary to identify transcriptional programs but fails to capture post-transcriptional information critical to decipher signaling networks and cellular states. We present Vivo-seq, a novel platform that integrates single-cell RNA-seq and intracellular CITE-seq following cellular fixation with a deep eutectic solvent, which preserves multiple domains of biological information beyond RNA transcripts alone. Vivo-seq enables simultaneous capture of both transcriptional and phospho-signaling states in single cells. Applying this platform to developing T-helper 17 (Th17) cells, we find that simultaneous phosphorylation of ERK1/2 and c-FOS leads to maximal IL-2 and IL-17 production. Furthermore, we show that early IL-2 production imprints developing Th17 cells for enhanced maintenance or cytokine-dependent transdifferentiation during subsequent antigenic stimulation. By integrating transcriptional and phospho-signaling information at single-cell resolution, we identify a hyperactivated Th17 cellular state associated with early IL-2 production that has downstream consequences on functional plasticity.

overall_design: Murine naive T cells were isolated from the spleen, split into 3 separate cultures, and polarized under Th17 conditions for 3 days. On day 3, the cultures were split and half were left in basal culture medium (unstimulated) and the other half were treated with PMA/ionomycin for 3 hours (stimulated). The cultures were then fixed in a deep eutectic solvent (DES; VivoPhix) and stored at -80C. On the day of single-cell RNA-seq (scRNA-seq), cultures were transitioned to aqueous buffer, as described in the manuscript, blocked, split in half, and then stained with hashtag antibodies and one of two different intracellular CITE-seq panels. 12 total unique samples were generated (n=3 unstimulated cultures + n=3 stimulated cultures x 2 panels of inCITE-seq antibodies). All samples were hashed into the same well for 10X Genomics 3’ V3 scRNA-seq.

first: Seth

last: Fortmann

middle: S


title: Persistent impact of embryonic temperature on cellular metabolism in the developing Atlantic salmon liver revealed by single nuclei transcriptomics

city: Penicuik

first: Carl

middle: Iain James

last: MILTON

state: Midlothian

address: Flat 8D high street

institute: University of Edinburgh

summary: Environmental temperature influences every biochemical and physiological process in poikilothermic fishes. Embryogenesis is a sensitive period of development where the thermal regime can promote plasticity in phenotypes that persist deep into the life cycle, with potential implications for aquaculture. However, the mechanisms by which embryonic temperature affects phenotypic development later in life remain poorly understood. In this investigation, we investigate the impact of changing embryonic temperature on the transcriptome of thousands of liver cells sampled from farmed Atlantic salmon fry. Three groups of fish were grown at 4, 6 or 8°C solely from fertilization to the eyed-stage of embryogenesis, then reared under a standardised temperature regime until sampling, one-month post start-feeding (seven weeks post temperature treatment). Single nuclei RNA sequencing identified hepatocyte, cholangiocyte, mesenchymal, endothelial and immune cell populations. Seven hepatocyte subpopulations were identified with distinct gene expression programs. Comprehensive analyses identified strong impacts of embryonic temperature on the transcriptome of hepatocytes, implicating diverse metabolic functions, pathways and regulatory genes. This included pervasive changes in the mevalonate and insulin-like growth factor-growth hormone pathways, consistent with alterations in cholesterol/lipid metabolism and endocrine growth regulation. Combined, our results indicate that altering temperature during a short window of embryogenesis regulates the long-term development of metabolic functions in farmed Atlantic salmon.

overall_design: Atlantic salmon were grown under three different temperatures (4,6 and 8°C) from fertilisation to the eyed stage of embryogenesis. Livers were then sampled one month after start feeding for snRNA-seq

first: CIJ

last: Milton

first: RS

last: Taylor

first: J

first: CC

last: Lazado

first: NM

last: Wade

first: E

last: Burgerhout

first: DJ

last: Macqueen


title: Nuclear Pirin promotes HCC by acting as a key inflammation-facilitating factor

city: Xiamen

first: Huanhuan

last: Ma

address: Xiang'an South Road 4221-120

institute: Xiamen University

summary: HCC has a poor response to therapy and a bad prognosis with chronic inflammation be the most common etiologies for HCC progression. Here we report a redox-dependent regulation mechanism of PIR protein nuclear shuttling, leading to liver inflammation and HCC progression.

overall_design: Primary Hepatocytes of Tg and Wt mice were isolated and cultured for 24 hours before subjected to RNA extraction.

first: Qinxi

last: Li

first: Tingyan

last: Cao


title: CRISPRi Screening of Enhancers in Human Primary Astrocytes Identifies Regulatory Circuitry Disrupted in Alzheimer’s Disease

city: Sydney

first: Javier

last: Perez Burillo

state: NSW

address: Chancellery Walk

institute: University of NSW

summary: We used CROP-seq to perform a high-throughput, parallel screen of 979 candidate enhancer perturbations in normal human astrocytes (NHAs), a primary cell-line. We identified the target gene(s) for 145 of these candidates, which were enriched for transcription with eRNA, transcription factor footprinting, and superenhancer annotation. Most regulatory interactions were <50kb, targeting the nearest gene in ~50% of cases, but were not typically captured by eQTL or in silico predictions. These data elucidate the regulatory network of an understudied-but-crucial brain cell-type.

overall_design: Genomic DNA was extracted from three different lots of Lonza Normal Human Astrocytes (NHA). Genotype sequencing was then performed on the extracted DNA

first: Nicole

last: Green

first: Gavin

last: Sutton

last: Pérez-Burillo

first: Juli

last: Wang

first: Irina

last: Voineagu


title: Fitness benefits of genetic rescue despite chromosomal differences in an endangered pocket mouse

city: Houston

first: Olga

last: Dudchenko

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: Two thirds of Earth’s species have undergone population declines, leaving many vulnerable to genomic erosion and inbreeding depression. Genetic rescue can boost fitness of small populations, but perceived risks of outbreeding depression can limit its use. We quantified these trade-offs in hundreds of endangered Pacific pocket mice (Perognathus longimembris pacificus), combining whole genome sequences with fitness data. The impacts of genomic erosion in remnant populations were reversed in an admixed breeding program, suggesting potential benefits of genetic rescue. However, differences in chromosome numbers increase the risk of genetic incompatibilities. Fitness analyses suggested that although admixed karyotypes may have reduced fertility, non-admixed mice with low heterozygosity and high genetic load had even lower fitness, pointing to a greater risk of extinction if populations remain isolated.

overall_design: We use Hi-C to characterize large-scale structural variation in the genomes of 17 Pacific pocket mouse individuals from three wild remnant populations.

first: Aryn

middle: P

last: Wilder


title: scRNA-seq data of CSF1R WT/WT, naïve CSF1R WT/I792T and Mr BMT-treated CSF1R WT/I792T (deficient gene replaced by normal gene) mice brain cells.

first: Bo

last: Peng

address: 138 Yixueyuan Road

department: Institute for Translational Brain Research

institute: Fudan University

summary: To further characterize the influence of Mr BMT on the brains of ALSP mouse, we harvested brains from CSF1R WT/WT, naïve CSF1R WT/I792T and Mr BMT-treated CSF1R WT/I792T (deficient gene replaced by normal gene) mice for single-cell RNA-sequencing (scRNA-seq)

overall_design: Briefly,  brain from CSF1R WT/WT, naïve CSF1R WT/I792T and Mr BMT-treated CSF1R WT/I792T (deficient gene replaced by normal gene) mouse was collected and dissolved to single cell, then be sequenced.

first: Xiaoyu

first: Yanxia

last: Rao

first: Li

first: Jingying

last: Wu

first: Yafei


title: RNA-seq: screening key metastasis-related RBP genes of hepatocellular carcinoma

city: Guangzhou

first: Yun

middle: yun

last: Xiao

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

summary: Tumor metastasis is a major factor contributing to high mortality in patients with hepatocellular carcinoma (HCC). RNA binding protein (RBP)-mediated post-transcriptional regulation is involved in the precise control of signal transduction; however, the role of RBPs in HCC metastasis remains to be elucidated. To identify the key RNA binding protein (RBP) genes involved in hepatocellular carcinoma (HCC) metastasis, we conducted an RNA-seq analysis in the human HCC cell lines with high (MHCC97H) and low (MHCC97L) spontaneous metastatic potentials.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MHCC97H and MHCC97L cells.

first: Yunyun

first: Yue

first: Dongni

last: Shi


title: Inhibition of lysine demethylase 6B blocks the development of ASXL1 truncation-mediated myeloid malignancies [RNA-seq]

city: San Antonio

first: Peng

last: Zhang

address: 8403 Floyd Curl Drive

institute: UT Health San Antonio

summary: To investigate the role of KDM6B in the pathogenesis of truncated ASXL1-mediated myeloid malignancies, we purified the Lin-cKit+ cells from bone marrow of WT, Kdm6bΔ/+, Asxl1Y588XTg, and Asxl1Y588XTg;Kdm6bΔ/+ mice and performed the bulk RNA-seq to study the dysregulated genes due to the reduction of Kdm6b in Asxl1 mutant context.

overall_design: RNA-seq for bone marrow Lin-cKit+ cells from WT (n=3), Asxl1Y588XTg (n=3), Kdm6bΔ/+ (n=3) and  Asxl1Y588XTg;Kdm6bΔ/+ (n=3) mice.

first: Pingpin

last: Sui

first: Guo

last: Ge

first: Feng-Chun

last: Yang


title: PHLOWER - Single cell trajectory analysis using Decomposition of the Hodge Laplacian [multiome]

status: Public on Jul 11 2025

city: Aachen

first: Mingbo

last: Cheng

state: North Rhine-Westphal

address: Pauwelsstr. 19

institute: Uniklinik RWTH Aachen

summary: To dissect nephrogenic differentiation trajectories in kidney organoids using the multiome pipeline, organoids were harvested at different time points during culture.

overall_design: The following differentiation stages were processed: day 7 (cells harvested from the 2D cell layer, primitive streak - intermediate mesoderm stage), organoids day 7+5~(day12), day 7+12~(day19) and day 7+18~(day25).

first: Jitske

last: Jansen

first: Christoph

last: Kuppe

first: Rafael

last: Kramann

first: Ivan

middle: G

last: Costa


title: Mutant RIT1 cooperates with YAP to drive an EMT-like lung cancer state

city: Seattle

first: Alice

last: Berger

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

summary: The discovery of oncogene addiction in cancer has led to the development of over a dozen FDA-approved biomarker-driven therapies in lung adenocarcinoma, but many rare driver mutations remain untargeted. Somatic mutations of the “Ras-like in all tissues” (RIT1) gene are non-canonical driver events in lung cancer, occurring in ~2% of lung adenocarcinomas in a mutually exclusive fashion with KRAS and EGFR mutations. Patients with RIT1-mutant lung cancer lack targeted therapy treatment options, and a lack of pre-clinical models has hindered the development of therapeutic strategies for RIT1-mutant lung cancer. Here we report a new mouse model with inducible regulation of the cancer-associated RIT1M90I variant. We show that autochthonous expression of RIT1M90I in the lung weakly promotes cancer alone or in combination with loss of the p53 tumor suppressor. However, potent synergy between RIT1M90I and inactivation of Nf2 and p53 drives an aggressive lung cancer with 100% penetrance and short latency. We show this oncogenic cooperation is driven by synergistic activation of cJUN, a component of the AP-1 complex. Therapeutic inhibition of MEK and YAP/TEAD suppressed RIT1M90I-driven lung cancer in vitro and in vivo. These data identify YAP/TEAD as an important mediator of RIT1’s oncogenic potential and nominate TEAD as an important drug target in RIT1-mutant lung cancer.

overall_design: Data provided is single cell RNA-sequencing generated from 10X Chromium NextGEM 3' and Illumina sequencing. Samples include primary lung tissue specimens from RIT1 M90I/Nf2fl/fl/p53fl/fl mice including (1) tumor cells and (2) cells from adjacent normal lung. Also included are cells from a tumor-derived cell line derived from a tumor of a mouse of the same genotype (3). All cells were from the SPC-Cre cohort described in Rominger et al.

middle: H

first: Saksham

last: Gupta

first: Mary

middle: C

last: Rominger


title: Inhibition of lysine demethylase 6B blocks the development of ASXL1 truncation-mediated myeloid malignancies

overall_design: Refer to individual Series


title: PHLOWER - Single cell trajectory analysis using Decomposition of the Hodge Laplacian [Xenium]

summary: We performed multiplex siRNA knockdown experiments of the identified neuronal lineage defining TFs PAX3, RFX4 and ZIC2 in kidney organoids in iPSC derived kidney organoids during the differentiation process from day 19 onwards.

overall_design: Kidney organoids (at least N=3 per condition per experiment, 2 independent experiments) were transfected using ON-TARGETplus™ SMARTpool siRNA’s ZIC2 (Catnr L-017505-00-0005), RFX4 (catnr L-013577-00-0005) and PAX3 (Catnr L-012399-00-0005, work concentration 25nM, Horizon Discovery, Cambridge, UK) and DharmaFECT Transfection reagent 1 (0.5% v/v) from day 7+5 (intermediate mesoderm stage) onwards until the end of the protocol until day 7+18. Organoids were refreshed every other day.

last: Jasen


title: Pharmacological Manipulation of Nested Oscillations in Human iPSC-Derived 2D Neuronal Networks

city: La Jolla

first: Anne

last: Bang

state: CA

address: 10901 North Torrey Pines Road

department: Prebys Center

institute: Sanford Burnham Prebys Medical Discovery Insititute

summary: Neural networks, formed by synchronized oscillatory bursts of activity across large populations of neurons, are fundamental to human cognition and behavior, and disrupted in neurodevelopmental disorders. Yet, mechanisms driving the emergence of these rhythms, known as oscillogenesis, are not well understood, particularly in the human brain. Using multi-electrode arrays, we investigated oscillogenesis in 2D human induced pluripotent stem cell (hiPSC) cultures at different developmental stages, and under pharmacological challenges, in two models: 1) iCell GlutaNeurons (iGluta) and 2) Neurogenin-2 patterned induced neurons (NGN2-piNs).  iGluta cultures exhibited nested oscillations that were reduced by GABAA receptor blockade and emerged earlier when the proportion of GABAergic neurons was increased. Furthermore, pharmacological manipulations of voltage-gated potassium (Kv) channels and cholinergic receptors modulated the pattern of nested oscillations, demonstrating the assay’s potential for drug screening and modeling network dysfunction. In contrast, NGN2-piNs exhibited only rudimentary nested oscillations that were not affected by GABAA receptor blockade, despite the presence of GABAergic neurons, and showed distinct responses to Kv channel blockade. These results reveal the capacity of these 2D cultures to model oscillogenesis, and underscore the need for their continued refinement, paving the way for linking systems-level neural networks to human cognition and disease.

overall_design: Study of gene expression in iCell GlutaNeurons (iGluta), FujiFilm Cellular Dynamics Inc. after 3 weeks of culture for determining cellular composition of the culture and expression of relevant receptors and channels

first: Alexander

last: Wooten


title: Transcriptome analysis identifies id2b as a blood flow sensitive gene

city: Hangzhou

first: Shuo

last: Chen

address: Yuhang tang Road 866

department: school of medicine

institute: Zhejiang university

summary:
Purpose: To investigate biomechanical cues influencing heart morphogenesis.
Methods:  Approximate 1000 hearts dissected from 96 hpf Tg(myl7:mCherry) and tricaine-treated Tg(myl7:mCherry)  embryos were collected for RNA sequencing.
Results:  2,013 up-regulated and 2,517 down-regulated genes were identified. Enrichment analysis of DEGs encoding TFs affected by perturbing biomechanical forces identified several pathways known to be involved in heart development, including the transforming growth factor beta (TGFβ) signaling and Notch signaling pathways. Further analysis demonstrated id2b expression in embryonic hearts depends on blood flow.
Conclusions: we analyzed embryonic zebrafish hearts without contractility and identified genes that are regulated by biomechanical forces. Specifically, id2b was identified as a blood flow sensitive gene.

overall_design: 96 hpf Tg(myl7:mCherry) and tricaine-treated Tg(myl7:mCherry) zebrafish hearts were collected for RNA-seq.

first: Jie

last: Yin

first: Pei-dong

last: Han


title: Effect of depletion of id2b on gene expression during zebrafish heart development

summary:
Purpose: To investigate other  possible phenotype of id2b mutant and the mechanism of how id2b fuctions in heart morphogenesis.
Methods:  Approximate 1000 hearts dissected from 120 hpf id2b+/+; Tg(myl7:mCherry) and  id2b-/-; Tg(myl7:mCherry)  embryos were collected for RNA sequencing.
Results:  Enrichment analysis of DEGs demonstrated that the top-ranked anatomical structures affected by id2b deletion included the heart valve, the compact layer of ventricle, and the atrioventricular canal, id2b inactivation also impacted phenotypes such as cardiac muscle contraction and heart contraction.
Conclusions: Zebrafish id2b loss of fuction leads to abnormal heart valve and heart contraction defect. Besides, id2b regulates heart contraction through controlling nrg1 synthesis.

overall_design: 120 hpf id2b+/+; Tg(myl7:mCherry) and  id2b-/-; Tg(myl7:mCherry) zebrafish hearts were collected for RNA-seq.


title: PHGDH Drives 5-FU Chemoresistance in Colorectal Cancer through the Hedgehog signaling

city: Firenze

first: Gianluca

last: Mattei

state: FI

address: Via di S. Marta, 3

institute: Università degli Studi di Firenze

summary: This study investigates the role of phosphoglycerate dehydrogenase (PHGDH) in 5-fluorouracil (5-FU) chemoresistance in colorectal cancer (CRC). The researchers discovered that PHGDH expression is highly variable in tumor tissues and patient-derived CRC organoids, with elevated PHGDH levels correlating with reduced sensitivity to 5-FU treatment. Through transcriptomic analysis, PHGDH was found to promote activation of the Hedgehog (HH) signaling pathway, which plays a key role in chemoresistance. PHGDH silencing reduces HH activation and increases sensitivity to 5-FU, while PHGDH overexpression has the opposite effect. Significantly, combined treatment with 5-FU and HH pathway inhibitors (JC19 or GANT61) synergistically enhances chemosensitivity in high-PHGDH expressing CRC cells, organoids, and xenograft models. This dual-targeting approach effectively limits tumor growth in mice. The findings establish PHGDH as a potential biomarker for predicting response to 5-FU-based chemotherapy and suggest that targeting the PHGDH-HH axis may represent a promising therapeutic strategy to overcome chemoresistance in CRC.

overall_design: RNA-seq profiling of wildtype HCT8 colorectal cancer cells and their PHGDH-silenced clones to investigate transcriptomic changes associated with PHGDH silencing and its impact on 5-FU chemoresistance mechanisms.

first: Caterina

last: Mancini

first: Giulia

last: Lori

first: Marta

last: Iozzo

first: Fabio

last: Cianchi

first: Laura

last: Fortuna

first: Daniela

last: Massi

first: Filippo

last: Ugolini

first: Dayana

last: Desideri

first: Salvatore

last: Piscuoglio

first: Antonio

last: Pezone

first: Francesca

last: Magherini

first: Alessio

last: Biagioni

first: Tiziano

last: Lottini

first: Demetra

last: Zambardino

first: Giuseppina Ivana

last: Truglio

first: Elena

last: Petricci

first: Luisa

last: Maresca

first: Barbara

last: Stecca

first: Erica

last: Pranzini

first: Maria Letizia

last: Taddei


title: Base-resolution profiling of 5-glyceryl-methylcytosine in Chlamydomonas reinhardtii via DEA-sequencing [WGBS]

first: Fanchen

last: Wang

state: Shanghai

address: 1239 Siping Road

institute: Tongji University

summary: 5gmC (5-glyceryl-methylcytosine), a vitamin C-derived hypermodified base, was identified in the genome of Chlamydomonas reinhardtii. Despite its potential involvement in active DNA demethylation, the global distribution of 5gmC and its function as a stable epigenetic mark remain poorly understood. In this study, we employed a commercial DNA deaminase to distinguish 5gmC from 5mC (5-methylcytosine) and C, enabling precise profiling of 5gmC across the entire genome. This DEA-sequencing method demonstrates superior performance compared to the previously proposed approach, which relies on TET dioxygenase-coupled bisulfite treatment. Using both methods, we identified numerous confident 5gmC sites. Unlike 5mC, which predominantly occurs at CpG sites, 5gmC is more evenly distributed across both CpG and non-CpG contexts. Remarkably, 5gmC and 5mC are largely mutually exclusive, with less than 2% of the sites overlapping between the two modifications. Additionally, 5gmC shows significant enrichment at transcriptional start sites (TSS) and transcriptional end sites (TES), contrasting with the more extensive localization of 5mC in intergenic and gene body regions. Importantly, 5gmC levels are positively correlated with transcription, while 5mC typically exhibits an inverse relationship with gene expression. Together, these findings suggest that 5gmC is not only an intermediate in active DNA demethylation but also functions as a stable epigenetic mark, potentially influencing transcriptional regulation independently of 5mC.

overall_design: WGBS of 5mC (BS) and 5gmC (DEA/TET-BS) in the C. reinhardtii strains (CC125 and CC5325).

first: Baodan

last: He

first: Zixin

first: Weiying

last: Meng

first: Yutao

last: Fu

first: Wanyue

last: Zou

first: Shuxia

last: Sun

first: Keyao

last: Zhao

first: Haoming

last: Jiang

first: Zhiyan

first: Jianhuang

last: Xue


title: Base-resolution profiling of 5-glyceryl-methylcytosine in Chlamydomonas reinhardtii via DEA-sequencing [RNA-seq]

overall_design: RNA-seq of C. reinhardtii strains (CC125 and CC5325).


title: Spatial transcriptomics reveals modulation of transcriptional networks across  brain regions after auditory threat conditioning

city: Belmont

first: Joy

last: Otten

state: Massachusetts

address: 115 Mill Street

institute: McLean Hospital

summary: Prior research has demonstrated genome-wide transcriptional changes related to fear and anxiety across species, often focusing on individual brain regions or cell types. However, the extent of gene expression differences across brain regions and how these changes interact at the level of transcriptional connectivity remains unclear. To address this, we performed spatial transcriptomics RNAseq analyses in an auditory threat conditioning paradigm in mice. We generated a spatial transcriptomic atlas of a coronal mouse brain section covering cortical and subcortical regions, corresponding to histologically defined regions. Our finding revealed widespread transcriptional responses across all brain regions examined, particularly in the medial and lateral habenula, and the choroid plexus. Network analyses highlighted altered transcriptional connectivity between cortical and subcortical regions, emphasizing the role of steroidogenic factor 1. These results provide new insights into the transcriptional networks involved in auditory threat conditioning, enhancing our understanding of molecular and neural mechanisms underlying fear and anxiety disorders.

overall_design: We used auditory threat conditioning in 16 mice, 8 tone control mice and 8 auditory threat conditioned mice. Brain slices were taken at a bregma of -1.8 and all samples were analyzed using Visium spatial transcriptomics.

first: Dan

last: Shu

first: Torsten

last: Klengel


title: Inhibition of lysine demethylase 6B blocks the development of ASXL1 truncation-mediated myeloid malignancies [ChIP-seq]

first: Peng

last: Zhang

summary: To investigate the role of KDM6B in the pathogenesis of truncated ASXL1-mediated myeloid malignancies, we purified the Lin-cKit+ cells from bone marrow of WT, Kdm6bΔ/+, Asxl1Y588XTg, and Asxl1Y588XTg;Kdm6bΔ/+ mice and performed ChIP-seq using H3K27me3 to investigate the gene regulation by this specific histone modification.

overall_design: H3K27me3 ChIP-seq for bone marrow Lin-cKit+ cells from WT (n=2), Asxl1Y588XTg (n=2), Kdm6bΔ/+ (n=2) and  Asxl1Y588XTg;Kdm6bΔ/+ (n=2) mice.

first: Pingpin

last: Sui

first: Guo

last: Ge

first: Feng-Chun

last: Yang


title: Molecular Cartography of the Human and Mouse Down Syndrome Brain [Slide-seq]

city: Boston

first: Brian

last: Kalish

address: 220 Longwood Ave

department: Neurobiology

institute: Boston Children's Hospital

summary: To gain molecular insight into the prenatal neurobiology of DS, we performed single-nucleus sequencing, spatial transcriptomics, and proteomics on mid-gestational prenatal human brain tissue. We captured altered expression dynamics of lineage commitment genes in DS neural progenitor cells, which suggest changes to the fate and functionality of neuronal and glial cells.

overall_design: We performed Slide-seq on mid-gestational prenatal human samples (n=3 euploid, n=3 Down Syndrome).

first: Min Yi

last: Feng

first: Wuxinhao

last: Cao

first: Gen

last: Li

first: Bharti

last: Kukreja

first: Nareh

last: Tahmasian

first: Bianca

last: Rusu

first: Ji-Young

last: Youn


title: RNA-sequencing analysis of aneurysmal tissues with or without treatment of targeted nanotherapy.

city: Chongqing

first: hu

last: kaiyao

address: shapingba District of Chongqing

institute: the third military medical university

summary: Our study represents the first detailed analysis of aneurysmal tissues with or without our targeted nanotherapy, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles.

overall_design: Aortic mRNA profiles of rats with or without treatment of targeted nanotherapy  were generated by deep sequencing, in triplicate, using SOAPnuke.

first: Jianxiang

first: Kaiyao

last: Hu


title: PoreMeth2: decoding the evolution of methylome alterations with Nanopore sequencing.

city: Florence

first: Marta

last: Baragli

address: Via di S. Marta 3

department: Department of Information Engineering

institute: University of Florence

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


title: PoreMeth2: decoding the evolution of methylome alterations with Nanopore sequencing. [WGS]

summary: In epigenetic analysis, identifying differentially methylated regions (DMRs) typically involves detecting groups of consecutive CpGs that show a significant change in their average methylation level. However, the methylation state of a genomic region can also be defined by a mixture of patterns (epialleles) with variable frequencies and the relative proportion of such patterns can provide information on its mechanisms of formation. However, traditional methods based on bisulfite conversion and NGS, due to the read size (150 bp), allow epiallele frequency analysis only in high-CpG-density regions, limiting differential methylation studies to only 50% of the entire human methylome. Nanopore sequencing, with its long reads, enables the analysis of epiallele frequency across both high- and low-density CpG regions. We introduce a novel computational approach, PoreMeth2, an R library that integrates epiallelic diversity and methylation frequency changes from Nanopore data to identify DMRs, assess their formation mechanisms and annotate them to genic and regulatory elements. We applied PoreMeth2 to cancer and glial cell datasets, demonstrating its ability to distinguish epigenomic changes with strong effect on gene expression from those with weaker effect on transcriptional activity. PoreMeth2 is publicly available at https://github.com/Lab-CoMBINE/PoreMeth2.

overall_design: Methylation analysis of three AML patients at first diagnosis (tum) and after relapse (rel).

first: Gianluca

last: Mattei

first: Barbara

last: Gega

first: Alessandra

last: Mingrino

first: Martina

last: Chiechia

first: Gianmaria

last: Frigè

first: Luca

last: Mazzarella

first: Francesco

last: De Logu

first: Romina

last: Nassini

first: Pier Giuseppe

last: Pelicci

first: Alberto

last: Magi