title: Spatial transcriptomic mapping of canine osteosarcoma reveals immune microenvironment features linked to survival

city: Gainesville

first: Rebecca

last: Nance

address: 2015 SW 16th Ave

department: Small Animal Clinical Sciences

institute: University of Florida

summary: Osteosarcoma (OSA) is the most common malignant bone tumor in dogs and serves as a translational model for human pediatric OSA due to shared molecular features. This aggressive and metastatic cancer exhibits significant heterogeneity, which has limited therapeutic advances. Spatial transcriptomics offers a powerful method to investigate intratumoral complexity and the tumor microenvironment. In this study, we used the 10x Genomics Visium platform to profile spatial gene expression in 14 fresh-frozen canine OSA (cOSA) tumor samples from 11 dogs, including primary, metastatic, and recurrent tumors. Samples were stratified by survival outcomes (short-, median-, and long-term). Spatially variable genes and conserved transcriptional clusters were identified, and integration with published single-cell cOSA data enabled deconvolution of cell type proportions and spatial co-localization. Analysis of 18,834 tissue spots revealed intra-tumoral subpopulations and spatial clustering patterns. Pathways related to immune clearance were spatially enriched in long-term survivors. Deconvolution uncovered co-localization of immune cells such as mast cells with osteoclasts, and T/NK cells with regulatory dendritic cells. This study maps the spatial transcriptomic landscape of cOSA, highlighting immune microenvironment features and spatial gene expression patterns associated with survival. These findings provide insights into OSA biology and may guide future therapeutic strategies in both canine and human patients.

overall_design: Samples for whole transcriptome spatial profiling were taken from 11 canine osteosarcoma patients and included 11 primary tumor samples, 2 patient-matched metastatic samples, and 1 patient-matched recurrent sample.

last: Nance-Richey

first: Rowan

last: Milner

first: Leah

last: Ackerman


title: Assessing the impact of microplastics in inflammatory liver conditions using spatial single cell transcriptomics

status: Public on Apr 27 2026

city: Oklahoma City

first: Tae

middle: Gyu

last: Oh

state: Oklahoma

address: 940 Stanton L Young Blvd

department: Oncology Science

country: USA

institute: University of Oklahoma Health Science Center

type: Expression profiling by high throughput sequencing

summary: Recent evidence highlights the multisystem effects of microplastics. We investigated the effect of the most common microplastic, polyethylene, on liver conditions. We included 4 experimental groups of mice; chow diet, chow diet and microplastics, high-fat/fructose/cholesterol diet, high-fat/fructose/cholesterol diet and microplastics. Following tissue collection after treatment, bulk RNA sequencing was carried out to profile transcriptomic activity of each group.

overall_design: We included 4 distinct experimental mice groups: 1) Chow Diet (n = 4), 2) Chow Diet and Microplastics (n = 5), 3) High-fat/fructose/cholesterol diet (n = 5), 4) High-fat/fructose/cholesterol diet and Microplastics (n = 5)


title: 20S proteasome-regulated proteostasis in ELVAs is critical for oocyte-to-embryo transition and female fertility

city: Hangzhou

first: Chen

last: Yingyan

address: No. 3 Qingchundong Road

country: China

institute: Zhejiang University

summary: Programmed degradation of maternal proteins is essential for the oocyte-to-embryo transition (OET). While pharmacological inhibition studies have established the importance of proteasomes in ovarian reserve maintenance, oocyte maturation and fertilization, the physiological impact of intrinsic proteasome insufficiency and underlying molecular mechanisms remain poorly understood. In mice, endolysosomal vesicular assemblies (ELVAs), specialized membraneless compartments composed of proteasomes, endolysosomes and autophagosomes, facilitate protein degradation during oocyte maturation and early embryogenesis. In this study, we generated mice with oocyte-specific deletion of the proteasomal core subunit Psma7, to investigate the physiological function of the 20S proteasome and its roles in ELVAs-mediated protein degradation. PSMA7-deficiency destabilized 20S proteasomes and disrupted translocation of ELVAs, leading to pronounced accumulation of ubiquitinated proteins in oocytes and zygotes. Consequently, maternal Psma7 deletion resulted in female infertility, manifested by impaired oocyte maturation and developmental arrest at one- to two-cell stage. Furthermore, we observed reduced proteasome abundance and dysfunction of ELVAs in aged oocytes, providing a mechanistic explanation for the decline in developmental competence associated with oocyte aging. Taken together, our findings elucidate the critical function of proteasome-regulated proteostasis within ELVAs in maintaining oocyte quality during OET and reproductive aging.

overall_design: RNA-seq profiling of oocytes from wildtype and oocyte-specific Psma7 conditional knockout (Zp3-Cre; Psma7 flox/flox, termed Psma7 cKO) mice at different stages of oocyte maturation (germinal vesicle [GV] and metaphase II [MII])

first: Yan

last: Rong

first: Songying

last: Zhang

first: Chao

last: Yu


title: Copper-sensitive SPL9 TF regulates expression of indica rice domestication associated miRNAs and phenotypes [RNA-seq]

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: UAS-GKVK Campus

country: India

institute: National Centre for Biological Sciences - TIFR

summary: Domestication of indica rice has facilitated better harvest and yield, however the molecular mechanisms that drove multitude of phenotypes is not fully understood. A few genetic mechanisms such as sequence variations as well as small (s)RNAs and epigenetics have been attributed to indica rice domestication, but upstream regulators of these variations are unknown. Here we identified a copper (Cu) dependent regulatory module involved in the regulation of a SPL family transcription factor (TF) as well as two classes of RNAs under its direct control. Differential accumulation of Cu-associated micro (mi)RNAs and Cu-associated protein-coding RNAs were a major portion of the differences between wild relative of indica rice (Oryza nivara) and cultivated rice lines. We identified OsSPL9 as an upstream regulator of these changes through genetic and molecular analysis as well as by using Cu limited and excess conditions. OsSPL9 bound to the promoters of these genes through a conserved GTAC enriched motif. OsSPL9, Cu-associated miRNAs and their targets were in a regulatory loop, since mis-expression of SPL9 alone, or any individual Cu-associated miRNA also altered levels of other Cu-associated miRNAs and their cognate targets. OsSPL9 mediated regulation was closely linked to Cu accumulation and metabolism, indicating previously unappreciated roles of metal ions in mediating domestication-associated phenotypes. Our study has the potential to facilitate a better understanding of the crosstalk between genetic and epigenetic regulation that contributed to rice domestication connected to altered environment and growth conditions.

overall_design: We have performed RNA sequencing to understand transcriptomic status of wild, cultivated lines and SPL9 perturbation upon varying copper concentrations

first: Padubidri

middle: V

last: Shivaprasad

first: Raju

last: Steffi


title: Copper-sensitive SPL9 TF regulates expression of indica rice domestication associated miRNAs and phenotypes [ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: We have performed ChIP-seq with N-terminal 3XFlag tagged SPL9 transgenic plants - 21 day whole seedlings under different copper deficient (0mg/l), copper sufficient (0.025 mg/l), copper excess (2.5 mg/l). ChIP was performed using Anti-FLAG M2 Magnetic Beads-M8823.


title: Longitudinal changes in DNA methylation in IDH-mutant glioma fuel disease progression through altered cell state differentiation [scRNA-seq]

city: Charlestown

first: Masashi

last: Nomura

state: MA

address: 149 13th street

department: Pathology

institute: Massachusetts General Hospital

summary: IDH-mutant gliomas are initially slow-growing but invariably progress to fatal disease. Major gaps remain in our understanding of the molecular underpinnings and cellular dynamics that drive IDH-mutant evolution. To address this, we integrated joint-capture multi-omic single-cell profiling of DNA methylation, transcriptome and genotype in a longitudinal cohort of 35 IDH-mutant gliomas. Transcriptional and epigenetic comparisons of cell states during glioma progression revealed increased stem-like states, decreased differentiation and identified potential cell states regulators. Single-cell DNA methylation analysis demonstrated methylation loss in progressed tumors, however global DNA methylation was similar between different malignant cells states within individual tumors. This suggests that lower DNA methylation is not due to a change in cell state composition, but rather that it may alter cell state landscapes. To address whether decreased methylation in progressed tumors affects cellular dynamics, we applied a quantitative framework to directly measure cell state heritability and plasticity based on transcriptional annotation of high-resolution phylogenetic trees in clinical samples. Our analysis suggested that decreased methylation reshapes cellular architecture to increased heritability of stem-like states and decreased differentiation. Our study provides insight into the functional impact of DNA methylation on glioma evolution, integrating transcriptional cancer cell states with epigenetic encoding and cell state transition dynamics during cancer progression.

overall_design:
Nuclei from frozen tumor tissue were isolated. The nuclear suspensions were inspected by microscope, counted using a hemocytometer, and used for 10x Genomics workflow.

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

first: Ramya

last: Ravirum

first: Joshua S.

last: Schiffman

first: Dan A.

last: Landau

first: Mario L.

last: Suvà


title: Longitudinal changes in DNA methylation in IDH-mutant glioma fuel disease progression through altered cell state differentiation

type: Methylation profiling by high throughput sequencing

summary: The progression of IDH-mutant gliomas (IDH-G) from slow-growing tumors to fatal disease is associated with transcriptional and DNA methylation changes that remain poorly understood. Here, we profiled a longitudinal cohort of 36 IDH-G samples from 19 patients by joint-capture multi-omic single-nucleus (sn) DNA methylation and snRNA-seq. We show that IDH-G progression is associated with increase in malignant stem-like states, decreased differentiation and with methylation loss, which marks tumors with worse clinical outcome. Methylation loss was uniformly observed across malignant cells within individual tumors, suggesting that it may underlie rather than result from the increase in stem-like states. Analysis of cell state heritability and plasticity based on high-resolution phylogenetic trees connects DNA methylation loss to alterations in glioma cell states encoding and heritability. Our study offers insights on how DNA methylation loss reshapes cellular transitions and how it may mark clinically more aggressive tumors across IDH-G subsets.

overall_design:
Nuclei from frozen tumor tissue were isolated. Nucleus suspensions were inspected by microscope, counted using a hemocytometer, and sorted into 96 well plates by FACS. The single nucleus plates were processed by dual XRBS and Smart-seq2 protocol.

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


title: A viral noncoding RNA functions as master regulator of gene expression in latently infected cells

city: Salt Lake City

first: Demian

middle: E

last: Cazalla

state: UT

address: 15 N Medical Drive East, Rm 4100

department: Biochemistry

institute: University of Utah

summary: HSUR1 is a viral small nuclear noncoding RNA of the Sm class that is abundantly expressed by the oncogenic Herpesvirus saimiri. HSUR1 binds a host microRNA, miR-142-3p, and AU-rich element-binding proteins (ARE-BPs). The functional significance of these interactions, and how HSUR1 functions as an Sm-class RNA, remain unclear. Here we show that HSUR1 is a master regulatory noncoding RNA that interacts through base pairing with hundreds of host mRNAs in latently infected cells. HSUR1 target mRNAs that encode proteins with roles in several gene expression processes, T cell differentiation and apoptosis. Consistently, HSUR1 expression changes the transcriptomic profile and identity of the infected T cell and inhibits apoptosis. Mechanistically, we show that HSUR1 recruits miR-142-3p and ARE-BPs to the 3¢ untranslated regions of target mRNAs to destabilize them. These results describe an indirect mechanism by which microRNAs and ARE-BPs can regulate gene expression.

overall_design: For iRICC experiments (experiment 15955R), polyadenylated (polyA+) RNA was selected and hybridized to an antisense DNA oligonucleotide complementary to full-length HSUR1 (anti-H1 DNA) followed by limited single-strand S1 endonuclease digestion to fragment polyA+ RNA while maintaining HSUR1 integrity. After removal of anti-H1 DNA by DNAse I digestion, samples were split into two samples and hybridization with anti-H1 DNA was repeated in one (Control) sample, followed by digestion of both samples with RNAse H, which resulted in removal of HSUR1 only from the Control sample. Following a second digestion with DNAse I, HSUR1 and crosslinked RNAs were purified in both samples under stringent conditions with a biotinylated RNA oligonucleotide antisense to HSUR1. High-throughput sequencing libraries were prepared for both samples using random primers. HSUR1 target mRNAs were identified by comparison of pull downs from HSUR1 samples with Control samples in three independent replicate experiments. For RNA-seq experiment of cj38637-WT and cj38637-deltaHSUR1 cells (experiment 22466R), libraries were prepared from total RNA of these cell lines with NEBNext Ultra II Directional RNA Library Prep with poly(A) mRNA Isolation.

first: Demián

first: Carlos

last: Gorbea

first: Xavier

last: Roca

first: Donald Yuhui

last: Sim


title: Progressive intestinal tumor cell plasticity, Myc activation and loss of Lgr5+ tumor stem cell lineage commitment upon Wnt depletion

city: Helsinki

first: Marika

last: Lassila

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

summary: ScRNA-seq and ATAC-seq was used to investigate the role of Tcf7 and Lef1 in intestinal adenomas

overall_design: Tumors from the small intestines of Apc flox mice were dissociated into single-cells and subjected to scRNA-seq and ATAC-seq.

first: Fatemeh

last: Seyednasrollah

first: Cinzia

last: Bessone

first: Maritta

last: Räisänen

first: Inkeri

last: Vuori

first: Davide

middle: G

last: Berta

first: Johanna

last: Aspholm

first: Tatiana

last: Petrova

first: Lauri

middle: A

last: Aaltonen

first: Pauliina

last: Kallio

first: Kari

last: Alitalo


title: Age- and Tissue-dependent Diversity of Human Plasmacytoid Dendritic Cells Uncovers a Cycling Subset Dominant in Early Life and Cancer

city: Saint Louis

first: Alina

last: Ulezko Antonova

state: MO

address: 660 S. Euclid Ave

department: Path/Immuno

institute: WUSM

summary: Plasmacytoid dendritic cells (pDCs) are innate sentinels that produce type I interferons (IFN-I) during infection. Here, we asked how developmental stage and tissue context shape human pDC transcriptional states. Single-cell RNA sequencing of pDCs from blood, thymus, lymph nodes, and tonsils across fetal, infant, and pediatric stages revealed tissue-enriched programs, including IFN-I-imprinted pDCs in the thymus, NFκB-imprinted pDCs in tonsils, and resting pDCs in blood and lymph nodes. Across tissues, we identified a pDC subset characterized by prostaglandin D2 production and dopamine responsiveness, indicating a potential neuromodulatory axis. Cycling pDCs were abundant in fetal and infant lymphoid tissues and declined with age, while remaining enriched in bone marrow (BM) throughout life. Blastic pDC neoplasm associated with enrichment of cycling, mutation-bearing pDCs in the BM, suggesting that this niche serves as a reservoir for malignant pDCs. Thus, early in life, various lymphoid tissues can generate pDCs. This tissue-specific hematopoiesis may result in distinct cellular and functional outputs.

overall_design: Plasmacytoid dendritic cells were isolated via magnet assisted cell sorting (MACS) and flow assisted cell sorting (FACS) from tonsil, thymus, perithymic lymph node and blood of children (n=21) and adults (n=2).

first: Marco

last: Colonna


title: Undernutrition during late gestation disrupts placental metabolism, transport, and immune function in a sheep model

city: Hefei

first: weibin

last: wu

address: Changjiang Western Road 130

institute: Anhui Agricultural University

summary: In the current study, five late gestation multiparous ewes were restricted to a 30% feeding level to create a model of malnutrition, while five other ewes were fed normally as controls. All ewes were sacrificed and placental samples were collected for transcriptome sequencing to study metabolic changes.

overall_design: Compare the differences in transcriptome profiles between the placental sample from CON and TR ovis aries.

first: Weibin

last: Wu

first: Pengpeng

last: Liu

first: Huizhen

last: Lu

first: Yanfeng

last: Xue


title: Cell autonomous control of CAR signaling and receptor shedding via ADAM17-mediated proteolysis

status: Public on Apr 26 2026

city: san francisco

first: Jeremy

last: Bjelajac

state: CA

address: 2190 grove st

department: Pediatrics

institute: Stanford University

summary: We sought to endow T cell autonomous regulation of cell surface protein expression by exploiting the conditional proteolytic activity of ADAM17 following T cell activation.  Screening of canonical ADAM17 substrates yielded a minimal 15-aa CD62L-derived motif that confers rapid and reversible cleavage of a receptor following T cell activation—termed Activation-Induced Release (AIR). Embedding AIR into tonic-signaling CARs reduced basal CAR expression proportional to the degree of tonic signaling induced, curtailing exhaustion and improving antitumor potency. In non-tonic signaling CARs, AIR decreased activation-induced cell death and enhanced T cell expansion after stimulation. AIR’s modularity supports higher-order logic-gating; AIR-regulated peptide masks enable antigen-dependent unmasking of an EGFR-targeting CAR. Finally, CRISPR knock-in of AIR into endogenous FAS or TGFBR2 endowed them with activation-induced shedding, which enhanced tumor clearance, while preserving signaling in non-activating conditions. AIR is a compact switch that provides fast, autonomous regulation of surface proteins for next-generation cell therapies.

overall_design: RNAseq profiling the transcriptomic differences between HA-GD2 CAR v. AIR-HA-GD2 CAR v. Mock T cells made from 3 different healthy donors following treatment with either DMSO or Dasatinib

middle: R

first: Adrià

middle: C

last: Socias

first: Preeti

last: Nehra

first: Kevin

last: Reynolds

first: Meena

last: Malipatlolla

first: Naiara

last: Martinez-Velez

first: Diane

last: Manjarrez

first: Katie

last: Ho

first: Peng

last: Xu

first: Jennifer

middle: L

last: Hamad

first: Sean

last: Yamada-Hunter

first: Louai

last: Labanieh

first: Elena

last: Sotillo

first: Crystal

last: Mackall


title: Aging restricts maturation of CXCL13+ T follicular helper cells in human immunity

city: Calgary

first: Nathan

last: Bracey

state: Alberta

address: 3330 Hospital Drive

country: Canada

institute: University of Calgary

summary: Secondary lymphoid organs are concentrated sites of adaptive immune responses, but how these structures change over the lifespan is unclear. Recent work has revealed unique alterations to T follicular helper (Tfh) cells in older individuals. However, the gene-regulatory control of Tfh cell development in the context of aging has not been explored. Here, we characterized Tfh cells from human tonsil tissue, finding impaired B cell help, reduced tissue organizational cues, and restricted development with age. Maturation of Tfh cells in older adults was limited by gene-expression programs acquired during early differentiation of naïve CD4T cell precursors, including targets of critical transcriptional regulators like TCF7 and LEF1. Collectively, these results suggest that the transcriptional control of naïve CD4T cell differentiation has a lasting impact on subsequent Tfh maturation. Therefore, the state of the naïve CD4T cell pool during human aging can impair the ability to mount a protective adaptive immune response.

overall_design: Cryopreserved tonsil and PBMC single-cell suspensionsn from human donors were thawed and CD3+ T cells were magnetically enriched. Cells were stained with TotalSeqC antibodies against CD3, CD4, and CD8, along with either a tonsil- or PBMC-specific antibody barcode. Labeled tonsil and PBMC samples for each donor were then combined, and Individual gene expression (GEX), Antibody Dependent Tag (ADT), and T Cell Receptor (TCR) libraries were prepared and sequenced.

first: Casey

last: Beppler

first: Tatjana

last: Bilich

first: Mark

middle: M

last: Davis


title: Image Tracing of Inflammatory Intestinal Organoids via Computational Clearing

city: Daegu

first: Pacian

middle: Sung-Wook

last: Nam

state: Daegu

address: 90 Chilgokjoongangdaero-136-gil

department: School of Medicine

country: South Korea

institute: Kyungpook National University

summary: Gene expression of dextran sulfate sodium (DSS)-treated mouse intestinal organoids (mIOs) was examined by RNA-seq to characterize the inflammatory response. Gene set enrichment analysis (GSEA) revealed the upregulation of inflammatory pathways, including TNF-α signaling via NF-κB and IL-6/JAK/STAT3 signaling, alongside the downregulation of stem cell maintenance and proliferation pathways, including WNT/β-catenin signaling and PI3K/AKT/mTOR signaling.

overall_design: Mouse intestinal crypts were embedded in Matrigel and cultured in EGF, Noggin, and R-spondin (ENR) medium to induce mIOs. The mIOs were treated with dextran sulfate sodium (DSS) to induce inflammation in vitro.


title: Stromal and Endothelial Transcriptional Changes during Progression from MGUS to Myeloma and after Treatment Response [scRNA-seq]

city: Pamplona

first: Itziar

last: Cenzano

state: Navarra

address: Avenida de Pio XII, 55

country: Spain

institute: CIMA Universidad de Navarra

summary: The role of the non-immune bone marrow microenvironment (BME) in the transition from monoclonal gammopathy of undetermined significance (MGUS) into clinically active multiple myeloma (MM) remains incompletely defined. To address this, we transcriptionally profiled endothelial cells (EC), mesenchymal stem cells (MSC), and MM cells at single-cell resolution from genetically engineered mouse models (BIc1 and MIc1) that recapitulate MGUS to MM progression. Our analysis of the BIc1 model revealed distinct transcriptional alterations in EC and MSC, uncovering stage-specific BME-PC interactions shaping disease progression. Interestingly, we identified an interferon (IFN)-related myeloma signature in both EC and MSC that was reversed after treatment with bortezomib (Velcade), lenalidomide (Revlimid), and dexamethasone (VRd).

overall_design: We performed single-cell RNA sequencing (scRNA-seq) on FACS-sorted non-hematopoietic bone marrow cells and GFP+ plasma cells (PC) from BIcγ1 and MIcγ1 murine models that recapitulate human MGUS and MM, with YFPcγ1 mice as controls. In BIcγ1 mice carrying humanized CRBN, a VRd treatment arm (bortezomib, lenalidomide, dexamethasone; oral gavage, 20 weeks) was included to assess therapy-induced BME remodeling. For each experiment, bone marrow cells from 4–6 mice were pooled, and ~15,000 cells per sample were processed using the 10x Genomics Single Cell 3′ v3.1 workflow. Libraries were sequenced on an Illumina NextSeq 2000.

first: Felipe

last: Prosper


title: Stromal and Endothelial Transcriptional Changes during Progression from MGUS to Myeloma and after Treatment Response [RNA-Seq]

overall_design:
We performed bulk RNA-seq on prospectively isolated BM mesenchymal stem cells (MSC) from healthy donors (HD; n=8, bone marrow samples from orthopedic surgery, 50–80 years), MGUS (n=5), SMM (n=2), and MM (n=10) patients. Samples from both sexes were collected with informed consent and ethic approval. Total RNA was extracted, and full-length cDNA libraries were prepared with SMART-Seq v4 plus (Takara), enzymatically fragmented, indexed with unique dual indexes, and sequenced on an Illumina NextSeq 2000 using paired-end.
HR stands for High risk.


title: Elongin B orchestrates chromatin and transcriptional programs in H3K27M‑mutant diffuse midline glioma [XIII_ELOB_CUTandRUN]

city: Houston

first: Jamie

middle: N.

last: Anastas

state: TX

address: 1 Baylor Plaza

department: Neurosurgery

institute: Baylor College of Medicine

summary: Recurrent driver mutations in genes encoding histone H3 (H3.3K27M and H3.1K27M) are observed in ~80% of diffuse midline gliomas (DMG), which lead to aberrant gene regulation, yet the specific RNA polymerase 2 (Pol2) regulators inducing aberrant DMG transcription are not fully defined. We identified multiple regulators of Pol2 elongation as DMG genetic dependencies in a chromatin-focused CRISPR screen. Additional studies confirm that knockout (KO) of the Pol2 SIII complex gene Elongin B (ELOB) inhibits DMG cell proliferation in tissue culture and tumor growth in xenograft models. Further genomic analyses reveal that ELOB binding sites are enriched in H3K27M oncohistones and that ELOB knockout alters H3K27me3 and H3K27M incorporation at thousands of genomic regions, suggesting a role for ELOB in maintaining dysfunctional chromatin states in DMG. Correspondingly, ELOB loss disrupts Pol2 transcriptional activity and alters the expression of transcripts involved in metabolism, proliferation, and brain development. These findings suggest that Pol2 elongation factors cooperate with H3K27M oncohistones to maintain the epigenetic and transcriptional landscape driving DMG malignancy.

overall_design: For CUT&RUN, a single cell suspension of control or H3K27MKO SU-DIPGXIII+Cas9 cells were immobilized on ConA beads, permeabilized with 0.01% Digitonin, incubated with primary antibodies, and then cut with pAG-MNase to release DNA fragments as previously described. The following antibodies were used in CUT&RUN analyses: ELOB (cat#ab45297, Abcam), ELOA (cat#, Abcam), H3K27M (cat# ABE419, Millipore Sigma),  H3K27me3 (cat#07-449, ActiveMotif). Yeast spike-in DNA (S. cerevisiae; Cell Signaling Technology) was added at 0.5% to each reaction following chromatin digestion.

first: Alan

last: Jiao

middle: N


title: Epigenomic-transcriptional network during neural crest cell differentiation [gene expression]

city: Saitama

first: Kyosuke

last: Mukae

state: Kitaadachi-gun

address: 818, Komuro, Ina-machi

department: Research Institute for Clinical Oncology

country: Japan

institute: Saitama Cancer Center

summary: Neural crest cells (NCCs) originate from the neural tube during early embryogenesis, and they are a pivotal cell population involved in vertebrate development. NCCs are mainly divided into cranial NCCs (cNCCs) and trunk NCCs (tNCCs), which subsequently differentiate into diverse tissues and organs. Proper differentiation and fate determination into NCCs are essential for normal development and survival of individuals, and abnormal differentiation of NCCs can lead to various diseases such as cardiac disorders and tumors. Epigenetic mechanisms, including histone modification and DNA methylation, are crucial for regulating NCC differentiation. However, the specific mechanisms of DNA methylation underlying the differentiation of cNCCs and tNCCs remain poorly understood. This study aimed to address this knowledge gap by comparing the differentiation mechanisms of cranial and trunk NCCs derived from human induced pluripotent stem cells. Through integrated analysis of the transcriptome and DNA methylome data, we found that along with differentiation, DNA demethylation upstream of the transcription start sites of myocyte enhancer factor 2C (MEF2C) in cNCCs and thyroid hormone receptor alpha-2 (THRA2) in tNCCs led to increased expression of these genes. Furthermore, MEF2C and THRA2 were found to potentially regulate NCC markers. Our findings contribute to a detailed understanding of regulatory mechanisms of DNA methylation in normal NCC differentiation and may provide insights into the pathogenesis of NCC-related diseases such as neuroblastoma.

overall_design: Total RNA was extracted from iPSCs, cNCCs and tNCCs, and a microarray analysis was performed using the Agilent platform of 8x60 K design ID G4851B (Agilent Single Color. 39494, Agilent Technologies). Two hundred nanograms of total RNA was labeled with Cyanine3 using a Low Input Quick-Amp Labeling Kit (one color, Agilent Technologies) according to the manufacturer’s instructions. Purified labeled total RNA was hybridized to the expression microarray. Hybridization, the scanning of microarrays, and data extraction from scanned images were conducted according to Agilent protocol version 6.9.

first: Takehiko

last: Kamijo

first: Mik

last: Ohira


title: Tumor-Suppressing Multi-Enterobacteria enhance the anti-PD-1/PD-L1 efficacy in microsatellite stable colorectal cancer

city: Wuhan

first: xiaoting

last: Su

state: Hubei

address: Tongji Hospital, No. 1995, Jiefang Avenue, Wuhan, Hubei

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Gut microbiome significantly influences immunotherapy responses in colorectal cancer (CRC) treatment. While individual enterobacteria have been identified as enhancers of anti-PD-1/anti-PD-L1 therapy, the synergistic effects of multiple enterobacteria remain underexplored. To fill the gap, we introduced Tumor-Suppressing Multi-Enterobacteria (TSME), a consortium of nine beneficial intestinal probiotic strains, and investigated its impact on the anti-PD-1/anti-PD-L1 therapy for microsatellite stable (MSS) CRC. Using a tumor-bearing mouse model and genomic sequencing techniques, our research demonstrated that TSME significantly improved therapy efficacy by optimizing tumor immune microenvironment. Specifically, the addition of TSME notably increased CD8+ T infiltration, modulated cytokine profiles, and up-regulated crucial immune-related pathways, including TNF and JAK-STAT. Additionally, TSME altered intestinal microbial composition, enriching beneficial bacteria such as Akkermansia and Alistipes. These findings suggest that the well-engineered multi-enterobacteria could significantly enhance the effectiveness of immunotherapy for MSS CRC by synergistically modulating the immune and microbial landscapes.

overall_design:
To explore the synergistic effect of tumor suppressing multi-enterobacteria (TSME) in enhancing the anti-PD-1/PD-L1 efficacy in microsatellite stable colorectal cancer (MSS CRC), we developed a a murine model by inoculating mice with CT26 cells.
To assess the changes in gene expression linked to the treatment, we performed RNA sequencing on mouse tumor tissues from various treatment groups.
To examine alterations in the gut microbiota resulting from the combined administration of αPD-L1 and TSME in CT26 tumor-bearing mice, we isolated DNA from the fecal samples of these mice and conducted 16S rDNA sequencing analysis.

first: Xiaoting

first: Mingsheng

last: Zhang

first: Zhou

last: Li

first: Fang


title: TCF7L2 Promotes Abdominal Aortic Aneurysm through Smooth Muscle Cell-Mediated Extracellular Matrix Remodeling [ChIP-Seq]

status: Public on Apr 25 2026

city: Ann arbor

first: Yongjie

last: Deng

address: 2800 Plymouth Rd. NCRC blg26, Rm355s

institute: University of Michigan

summary: Abdominal aortic aneurysm (AAA) lacks effective pharmacological therapies. Here, we investigate transcription factor 7-like 2 (TCF7L2), a genetic locus associated with both thoracic and abdominal aortic aneurysms, to elucidate its role in AAA pathogenesis. Integrating summary-data-based Mendelian randomization (SMR) with single-cell RNA sequencing (scRNA-seq) of human and mouse aortas, we identify TCF7L2 as a gene enriched in vascular smooth muscle cells (VSMCs) and causally linked to AAA development. Smooth muscle cell-specific TCF7L2 knockout significantly attenuates AAA formation across three distinct murine models (Ang II infusion-, BAPN/Ang II co-administration-, and elastase-induced AAA), independent of systemic blood pressure or lipid levels. Mechanistic studies reveal that TCF7L2 directly upregulates MMP14 and downregulates TIMP3 expression, driving MMP2-mediated extracellular matrix (ECM) degradation. Concurrently, TCF7L2 represses integrin β1 (ITGB1) expression, reducing VSMC adhesion to the ECM. Collectively, these findings identify TCF7L2 as a key driver of pathological vascular remodeling in AAA, suggesting that targeting TCF7L2 may offer a novel therapeutic strategy for limiting AAA progression.

overall_design: ChIP-seq analysis of TCF7L2 occupancy in human aortic smooth muscle cells with matched IgG controls.

first: Yaozhong

last: Liu

first: Yang

last: Zhao

first: Hongyu

first: Guizhen

first: Zhenguo

last: Wang

first: Xu

first: Chao

last: Xue

first: Wei

last: Huang

first: Tianqing

last: Zhu

first: Haocheng

last: Lu

first: Yanhong

last: Guo

first: Lin

last: Chang

first: Ida

last: Surakka

first: Eugene

last: Chen

first: Jifeng


title: TCF7L2 Promotes Abdominal Aortic Aneurysm through Smooth Muscle Cell-Mediated Extracellular Matrix Remodeling [RNA-seq]

overall_design: RNA-seq profiling of human aortic smooth muscle cells (HASMCs) transfected with control siRNA or TCF7L2-targeting siRNA under vehicle-treated conditions, with 4 biological replicates per group.


title: Loss of the E3 ubiquitin ligase MARCHF6 alters hepatic lipid metabolism and drives spontaneous hepatosteatosis

city: Amsterdam

first: Sebastian

last: Hendrix

address: Meibergdreef 15

department: Medical Biochemistry

country: Netherlands

institute: UMC Amsterdam location AMC

summary: Metabolic dysfunction-associated steatotic liver disease (MASLD) and its progressive form, steatohepatitis (MASH), feature excessive hepatic fat accumulation, yet the relative contributions of dietary vs. endogenous fats and their interactions has remained enigmatic. Here, we identify the endoplasmic reticulum–associated E3 ubiquitin ligase MARCHF6 as a pivotal regulator of hepatic lipid metabolism. Global or hepatocyte-specific deletion of Marchf6 induced spontaneous accumulation of triglycerides and cholesteryl esters under chow-fed conditions, revealing a cell-autonomous hepatic defect independent of caloric excess. Mechanistically, loss of MARCHF6 stabilized its substrate squalene epoxidase (SQLE), enhancing sterol pathway flux while concomitantly activating the SREBP1-driven lipogenic transcriptional program and increasing lipoprotein clearance. Accordingly, lipidomic analyses demonstrated remodeling of the hepatic lipidome towards polyunsaturated, long-chain neutral lipids, consistent with increased lipogenesis-driven NADPH consumption. In line with this, pharmacological inhibition of the oxidative pentose phosphate pathway reduced lipid accumulation in MARCHF6-deficient human hepatocytes. Congruently, transcriptomic data from human MASLD/MASH patients revealed reduced hepatic MARCHF6 expression alongside an increase in that of the lipogenic genes SREBF1, FASN, and SCD1. Overall, these data establish MARCHF6 as a multifaceted gatekeeper that integrates sterol turnover, NADPH usage, and lipogenesis to maintain hepatic lipid homeostasis

overall_design: RNA seq profiling of total liver tissue of 10 week old WT C57Bl/6J mice and C57Bl/6J mice with liver specific knockout of Marchf6 (deletion of Exon2). Mice were kept on standard chow diet.

first: Vinay

last: Sachdev

first: Nienke

last: van Loon

first: Jenina

last: Kingma

first: Roelof

last: Ottenhoff

first: Josephine

last: Tan

first: Marlene

last: van den Berg

first: Suzanne

last: Duijst

first: Aldo

last: Jongejan

first: Johannes

last: Levels

first: Patrick

last: Rensen

first: Sander

last: Kooijman

first: Jan-Freark

last: de Boer

first: Folkert

last: Kuipers

first: Katharina

middle: B

last: Kuentzel

first: Dagmar

last: Kratky

first: Yun

last: Kwon

first: Anja

last: Zeigerer

first: Noam

last: Zelcer


title: Detachment-induced gene expression changes in four lung adenocarcinoma cell lines, H2009, LC-2/ad, H2228, and HCC4006.

city: Shimotsuke

first: Toshiro

last: Niki

state: Tochigi

department: Department of Pathology

institute: Jichi Medical University

summary: The aims of the study was to analyze gene expression changes induced by detachment from culture plate. Of the genes upregulated in detached state, we focused on MUC21, a membrane-anchored mucin, that was previously shown to exhibit anti-adhesive property. Using MUC21-KO cells, we demonstrated that MUC21 play a critical role in the growth and survival of lung adenocarcinoma cells both in attached and detached state.

overall_design: Lung adenocarcinoma cell line, H2009, LC-2/ad, H2228, and HCC4006, were plated onto ultra-low attachment culture plate and RNA was extracted at day 1 and day 7 using the RNeasy Mini Kit. RNA exrtracted from cells in standard cultured condition (in attched state) was used as controls. The RNA samples were then subjected to RNA sequencing. There were no replicates for each sample (n=1).

first: Ryotaro

last: Sakio

first: Daisuke

last: Komura

first: Shumpei

last: Ishikawa


title: mRNA profile of 6 lung adenocarcinoma cell lines

summary: To obatain mRNA profiles of 6 lung adenocarcinoma cell lines

overall_design:
Cell were cultures under standard culture conditions and total RNA was extracted using the RNeasy Mini Kit. There were no replicate samples (n=1).
*** Submitters state that raw data CEL files have been lost and therefore are not included***


title: RNA-seq data of MV4-11, Kasumi-1, and KG-1 cells treated with HDAC8 inhibitor 22d 10 μM and control

city: MONROVIA

first: Yahuei

last: Kuo

address: 1218 S 5TH AVE

department: Hem Malignancies Trans Sci

institute: City of Hope National Medical Center

summary: We performed RNA sequencing on MV4-11, Kasumi-1, and KG-1 leukemia cell lines treated with HDAC8 inhibitor 22d at 10 μM and their respective control groups. The sequencing reads were processed to generate gene-level count matrices. This dataset provides processed count data for downstream gene expression analysis and comparison between treated and control conditions.

overall_design: Three human leukemia cell lines (MV4-11, Kasumi-1, and KG-1) were cultured under standard conditions. Cells were treated with HDAC8 inhibitor 22d at 10 μM for 12 hours, with untreated cells serving as controls. Each condition included three biological replicates.  Total RNA was extracted from each sample using standard protocols, and RNA quality was assessed by Bioanalyzer. Sequencing libraries were prepared using the Illumina TruSeq RNA Library Prep Kit and sequenced on an Illumina NovaSeq 6000 platform to generate paired-end reads of 150 bp.  Raw reads were aligned to the human reference genome (GRCh38) using STAR aligner. Gene-level counts were generated using featureCounts.  The dataset includes processed gene-level count matrices for all samples, which are suitable for downstream differential expression analysis and gene expression profiling.

first: Wancheng

last: Guo

first: Lianjun

last: Zhang

first: Yu-Hsuan

last: Fu

first: Ya-Huei


title: Transcriptional activation of the PKLR gene by novel erythroid-specific regulatory elements [ChIP-Seq]

city: Busan

first: AeRi

last: Kim

address: 2, Busandaehak-ro 63beon-gil, Geumjeong-gu

institute: Pusan national university

summary: We proposed that newly identified transcription regulatory elements act as enhancers for the PKLR gene transcription in erythroid cells.

overall_design: Histone H3K27ac ChIP-seq was performed in control, GATA1 or TAL1-depleted (GAi or TAi) cells

first: Yew Woon


title: Wnt signaling restores evolutionary loss of robust foot regeneration rates in Hydra

city: Davis

first: Sergio

middle: Esteban

last: Campos

address: One Shields Ave

department: Molecular and Cellular Biology

institute: University of California Davis

summary: The regenerative potential of animals varies widely, even among closely-related species. In a comparative study of regeneration across the Hydra genus, we found that while most species exhibit robust whole-body regeneration, Hydra oligactis and other members of the Oligactis clade consistently fail to regenerate their feet. To investigate the mechanisms underlying this deficiency, we analyzed transcriptional responses during head and foot regeneration in H. oligactis. Our analysis revealed that the general injury response in H. oligactis lacks activation of Wnt signaling, a pathway essential for Hydra vulgaris foot regeneration. Notably, transient treatment with a Wnt agonist in H. oligactis triggered a foot-specific transcriptional program, successfully rescuing foot regeneration. Our transcriptional profiling also revealed dlx2 as a likely high-level regulator of foot regeneration, dependent on Wnt signaling activation. Our study establishes a comparative framework for understanding the molecular basis of regeneration and its evolutionary loss in closely-related species.

overall_design: The experimental design of this study included transcriptional profiling of H. oligactis head and foot regeneration, all timepoints, tissues and treatment included at least 3 biological samples each composed of tissue extracted from ~30 animals. A first batch of Illumina sequencing was comprised of 4 biological replicates of homeostatic head and foot tissue and 3 biological replicates of head and foot regenerating tissue at 0, 3, 12 and 48 hours after a transverse bisection at the midpoint of the body column. Regenerating tissue was collected by cutting 1/3 of the body column adjacent to the wound site. Homeostatic heads and feet and 0 hpa head and foot regenerating tissue were treated for 30 seconds with 0.05% DMSO, while 3, 12 and 48 hpa samples were left in 0.5% DMSO for 3 hours before washing. In addition, this first sequencing batch included at least 3 biological replicates of foot regenerating tissue treated with Alsterpaullone 5 uM for 3 hours after amputation and collected at 3, 12 and 48 hours hpa. A second RNA-sequencing batch was comprised of 2 biological replicates of homeostatic head and foot tissue and 3 biological replicates of head and foot regenerating tissue collected at 0 and 24 hpa after 0.05% DMSO treatment and foot regenerating tissue collected at 24 hpa after treatment a 3 hours treatment with 5uM Alsterpaullone. In total this dataset is comprised of 60 RNA-seq samples.

first: Celina

last: Juliano


title: STING dampens the unfolded protein response to enable the presentation of self-antigens on MHC-I during inflammation

status: Public on Apr 24 2026

city: Montréal

first: Lilia

last: Rodriguez

state: Québec

address: 2900, boul. Édouard-Montpetit

institute: University of Montreal

summary: A growing body of evidence supports the contribution of the long-lasting adaptive immune system in Parkinson's disease (PD). We showed that the PD-associated protein PINK1 negatively regulates the presentation of mitochondrial antigens (MitAP) on MHC-I molecules. In vivo evidence indicated that MitAP activation in mice, in the absence of PINK1, led to cytotoxic CD8+ T cell stimulation and severe motor impairments, reversible by L-DOPA. We show here that following TLR4 activation, MitAP is engaged through a pathway involving cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING), which acts as a rheostat to dampen the unfolded protein response (UPR). Without STING, the stress response is amplified, leading to a translational attenuation that inhibits the expression of XBP1s, a transcription factor required for MitAP. STING activity also regulates the repertoire of peptides displayed at the cell surface during inflammation, highlighting a potential role in immunosurveillance. These findings establish STING and the UPR as key immune regulators targetable for therapeutic intervention during autoimmune diseases and PD.

overall_design: RNA-seq profiling of mouse RAW cells treated with LPS or not (control) for 6 hours.

first: Michel

last: Desjardins

first: Ahmed

last: Fahmy

first: Ali

last: Ahmadi

first: Joël

last: Lanoix

first: Tyler

last: Cannon

first: Moustafa

last: Elemeery

first: Camberly

last: Hernandez Paredes

first: Benoit

last: Barrette

first: Eric

last: Bonneil

first: Yong

last: Zhong Xu

first: Maha

last: Ibrahim

first: Guillermo

last: Arango-Duque

middle: O

last: Audemard

first: Sébastien

last: Lemieux

last: Chevet

first: Erwin

last: Schur

first: Philippe

last: Pierre

first: Samantha

last: Gruenheid

first: Pierre

last: Thibault

first: Heidi

last: McBride


title: The DUTRENEO trial: bulk prospective biomarker-guided therapy selection and spatial transcriptomic dissection of immunotherapy response in muscle-invasive bladder cancer

city: Madrid

first: Jaime

last: Martinez de Villarreal

state: Madrid

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

institute: CNIO

summary: Predictive biomarkers for immune checkpoint inhibitors (ICI) have largely been identified retrospectively, but their clinical utility remains unproven in prospective settings. Here, we report the results of DUTRENEO, a prospective, randomized phase 2 trial testing whether a retrospective, well-validated, 18-gene tumor inflammation signature (TIS) could guide neoadjuvant ICI therapy in muscle-invasive bladder cancer. The trial failed to meet its primary endpoint, demonstrating that bulk gene expression stratification does not sufficiently enrich for responders in this setting. To understand the biological determinants of this failure, we generated a single-cell spatial transcriptomics dataset profiling 377 genes in ~5.4 million cells across large tissue areas. This high-resolution profiling revealed that response to ICI is governed by spatial architectures invisible to bulk assays, specifically the proximity of CD8⁺ T cells to cancer cells and the localized co-expression of checkpoints within epithelial-rich neighborhoods. Furthermore, we identified fibroblast-rich communities as a key feature of immune exclusion in non-responders. We derived a quantitative framework for the design of future clinical trials incorporating spatial analyses, demonstrating that reducing the annotation panel to ≥77 genes and sampling ≥3 mm tissue diameter preserves predictive spatial signal while enabling scalable throughput. These findings elucidate the architectural constraints that limit bulk biomarkers and provide a quantitative framework to embed spatial profiling into clinical studies.

overall_design: Transurethral Resection of Bladder Tumor (TURBT) FFPE samples. Patients’ tumours were classified as immune-hot (hot, for simplicity) or immune-cold (cold, for simplicity) based on the score of the TIS signature. Patients with hot tumours were randomized to receive ICI or NAC whereas patients with cold tumours received standard NAC.

first: Francisco

middle: X

last: Real

first: Mustafa

last: Sibai

first: Eduard

last: Porta-Pardo

first: Enrique

last: Grande


title: Archetype analysis of lung adenocarcinoma premalignancy links heterogeneity in premalignant lesions to diverging features of invasive disease

city: Boston

first: Adam

last: Gower

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

summary: Lung adenocarcinoma (LUAD), the most common form of lung cancer, is a heterogeneous disease with highly variable histopathologic features and clinical outcomes. LUAD premalignant lesions (PMLs) are localized proliferative lesions of atypical pneumocytes that proliferate along the alveolar walls. In this study, we characterized the molecular heterogeneity across PMLs, regardless of histologic designation, and identified four unique groups or “archetypes” of PMLs using bulk RNA and exome sequencing data from laser captured microdissected PMLs, normal, and tumor tissue from LUAD resection cases. The archetypes were defined based on expression of recurrent gene co-expression modules discovered using the LUAD PMLs we profiled and three publicly available datasets. One PML archetype, termed “proliferation”, was associated with increased expression of genes involved in cell proliferation, a pro-tumor immune environment, and enrichment for EGFR driver mutations. Another archetype, termed “normal-like”, was associated with similar features to normal tissue, an anti-tumor immune response, and lacked enrichment for driver mutations compared to other archetypes. We projected the PML archetypes into independent gene expression datasets profiling LUAD and found that tumors closest to the proliferation archetype were enriched for multiple features of aggressive LUAD, including high tumor grade and lymph node invasion, and had significantly lower disease-free survival. Proliferation archetype PMLs may represent a subset of lesions with more aggressive features that could improve patient stratification and suggest novel targets for lung cancer interception.

overall_design:
Tissue blocks were obtained from a retrospective cohort of patients. RNA and DNA from multiple lesions (PML or tumor) and normal tissue were isolated from fixed tissue and subjected to bulk RNA sequencing.

***************************************************************
Data are being uploaded without FASTQ files to protect patient privacy.
***************************************************************

first: Kelley

last: Anderson

first: Linh

last: Tran

first: Kostyantyn

last: Krysan

first: Yohana

last: Kefella

first: Lingge

last: Yu

first: Gregory

last: Fishbein

first: Erika

last: Rodriguez

first: Maryam

last: Shabihkhani

first: Daniel

middle: P

last: Stefanko

first: Emily

last: Green

first: Gang

last: Liu

first: Hanqiao

first: Sherry

last: Zhang

first: Erin

last: Kane

first: Mitra

last: Mehrad

first: Avrum

last: Spira

first: Steven

last: Dubinett

middle: J

last: Burks

first: Sarah

last: Mazzilli

first: Marc

last: Lenburg

first: Jennifer

last: Beane


title: Co-targeting neurotransmitter signaling and CDK9 to treat diffuse midline glioma [RNA-seq]

first: Rebecca

middle: Lauren

last: Murdaugh

state: Texas

address: One Baylor Plaza

summary: Aberrant neurotransmitter signaling and transcriptional dysregulation are hallmarks of glioma and represent potential therapeutic targets. In this study, we uncover mechanisms of crosstalk between monoamine neurotransmitter signaling and transcriptional regulation in diffuse midline glioma (DMG) that can be co-targeted with CDK9 inhibitors (CDK9i) and neuropsychiatric drugs as a potential treatment strategy for DMG. We identified compounds that synergize with CDK9i in DMG using targeted drug screens, then assessed DMG response to CDK9i and neurotransmitter-targeting drugs in cell culture and in orthotopic xenograft mouse models. We then used a multi-omic approach combining proteomic, transcriptomic, and chromatin profiling with phospho-proteomics, RNA-seq, CUT&RUN, and ATAC-seq in DMG cells to characterize mechanisms of synergy between CDK9i and neuropsychiatric drugs. We observe differential expression of neuronal signaling genes in both CDK9i-resistant DMG xenograft tumors and CDK9-low pediatric high grade glioma patient tumors. Additional studies reveal that drugs that modify monoamine neurotransmitter signaling, including neurotransmitter reuptake inhibitors (SSRI/SNRI) and both metabotropic neurotransmitter receptor agonists and antagonists, strongly synergize with CDK9i to reduce DMG cell viability. Co-treating DMG with CDK9i+SSRI/SNRI triggered negative feedback inhibition of autocrine neurotransmitter receptor signaling and reversed a CAMKII-dependent mechanism of CDK9i resistance. Finally, we find that CDK9i+SSRI resulted in altered histone dopaminylation at neurodevelopmental genes associated with CDK9i-resistance. These findings identify neurotransmitter signaling pathways as novel points of vulnerability in CDK9i-resistant DMG that can be targeted with FDA-approved psychiatric drugs to modulate CAMKII signaling and histone dopaminylation in pediatric brain tumors.

overall_design: Tumor samples were isolated from xenograft NSG mice bearing SU-DIPGXIIIP*+ZsGreen/luciferase tumors treated for 3 weeks with vehicle or 15 mg/kg zotiraciclib 3 times per week by dissociating whole brains, depleting mouse cells, and using the human cell fraction for bulk RNA-seq. SU-DIPGXIII samples were treated in vitro for 24 hours with DMSO, 5 𝛍M sertraline, 20 nM zotiraciclib, 6 nM AZD4573, 20 nM zotiraciclib + 5 𝛍M sertraline, or 6 nM AZD4573 + 5 𝛍M sertraline in biological triplicates, dissociated, washed, and processed for bulk RNA-seq (250,000 cells/sample).

first: Brittany

last: Eberl

first: Rosemary

middle: U

last: Richard

first: Ena

middle: I

last: Campos-Hensley

first: Adanze

last: Nnyagu

first: William

last: Elam

first: Nikko

last: Tsao

first: Ruiying

last: Ma

first: Jack

last: Tremblay

first: Alfred

middle: K

last: Dei-Ampeh

first: Kieu

last: Pham

last: Kraushaar

first: Akdes

last: Serin-Harmanci

first: Kwanha

first: Calla

last: Olson

first: Benjamin

last: Deneen

first: Jamie

last: Anastas


title: Co-targeting neurotransmitter signaling and CDK9 to treat diffuse midline glioma [CUT&RUN]

overall_design: SU-DIPGXIII cells were treated for 24 hours with DMSO or 20 nM zotiraciclib + 5 𝛍M sertraline in biological duplicates, dissociated, washed, and used for CUT&RUN.

middle: R

middle: A

first: Daniel

last: Yu


title: Co-targeting neurotransmitter signaling and CDK9 to treat diffuse midline glioma [ATAC-Seq]

first: Rebecca

last: Murdaugh

overall_design: SU-DIPGXIII cells were treated for 24 hours with DMSO or 20 nM zotiraciclib + 5 𝛍M sertraline in biological triplicates, dissociated, washed, and processed for bulk ATAC-seq (1 million cells/sample).

middle: L

middle: C


title: Macrophage-fibroblast crosstalk shapes wound repair signaling in vitro

city: Irvine

first: Wendy

middle: F

last: Liu

email: wendy.liu@uci.edu, enriqud2@uci.edu

state: California

address: 419 S. Circle View Drive

department: Biomedical Engineering

institute: University of California Irvine

summary: Wound healing requires coordinated interactions between macrophages and fibroblasts, yet how contact-dependent signaling integrates with paracrine pathways to regulate their reciprocal behavior is not well defined. Here, we investigated macrophage-fibroblast communication using complementary 2D and 3D in vitro wound healing models combined with live-cell calcium imaging and single-cell RNA sequencing (scRNA-seq). We show that bone marrow-derived macrophages (BMDMs) promote fibroblast scratch closure in a contact-dependent manner independent of connexins, whereas fibroblasts reciprocally regulate macrophage cytokine secretion through distinct mechanisms. Direct cell-cell contact with fibroblasts enhanced macrophage IL10 production via connexin 43 (Cx43)-dependent signaling, whereas TNFα secretion was suppressed through paracrine interactions. We further demonstrate that fibroblast-macrophage contact induces connexin-dependent intermittent calcium signals selectively in macrophages. ScRNA-seq revealed that wounding reshapes macrophage and fibroblast populations, uncovering dynamic regulation of cell adhesion molecules (CAMs) and intercellular signaling pathways. Together, these findings reveal the integration of contact-dependent calcium and connexin signaling with transcriptional remodeling to coordinate macrophage-fibroblast behavior during healing.

overall_design: RNA-seq profiling of cocultured bone marrow-derived macrophages (BMDMs) and NIH/3T3 fibroblasts in a collagen gel, comparing intact gels to those with a 0.2 mm puncture to model in vitro wounding.

first: Maksim

middle: V

last: Plikus

first: Daniela

last: Enriquez-Ochoa

first: Raji

last: Nagalla

first: Yingzi

first: Christian

last: Guerrero-Juarez


title: Epithelial chemokine CCL25 integrates T cell development and intestinal homeostasis

city: Bethesda

first: Michael

last: Kelly

state: MD

address: 41 Center Drive

department: Center for Cancer Research

institute: NCI

summary: The chemokine receptor CCR9 regulates thymic colonization of T-progenitors and intestinal accumulation of TCRgd+ intraepithelial cells (IELs). CCR9-ligand chemokine CCL25 is expressed predominantly in the thymus and the small intestine. By engineering tissue-specific CCL25-deficient mice, we demonstrate that CCL25 locally produced by thymic and intestinal epithelial cells individually supports developing T cell localization in the thymus and TCRgd+ IEL accumulation in the small intestine, respectively. More interestingly, our results reveal that thymic epithelial CCL25 facilitates T-cell positive selection in the thymic cortex. We further find that intestinal epithelial CCL25 promotes nutrient sensing in the small intestine. These results indicate that epithelial CCL25 directs thymic T-cell development and intestinal homeostasis in a tissue-specific paracrine manner.

overall_design: Single cells from dissociated thymus of wildtype mice and Ccl25 conditional knockout (Foxn1-Cre) mice were depleted for CD45+ hematopeotic cells and analyzed by scRNA-Seq to determine the cell-specific expression of Ccl25 and to examine the effect of knocking out Ccl25 on cell populations in the thymus.

first: Yousuke

last: Takahama

first: Jie

last: Li

first: Mei-Ting

last: Yang

first: Mami

last: Matsuda-Lennikov

first: Felix

last: Kalle-Youngoue

first: Aya

last: Ushio

first: Kenta

last: Kondo

first: Meleca

last: Gluckman

first: Kana

last: Bando

first: Takaya

last: Abe

first: Kensuke

last: Takada

first: Felipe

last: Martinez

first: Chuan

last: Wu


title: Stress granule phase separation in stress-responsive cytosolic extract-in-oil droplets

city: Heidelberg

first: Alessia

last: Ruggieri

address: Im Neuenheimer Feld 344

department: Dpt. of Infectious Diseases, Molecular Virology

country: Germany

institute: Heidelberg University

summary: Stress granules (SGs) are biomolecular condensates that form transiently in the cytosol of mammalian cells in response to stress. Dysregulation of their assembly or disassembly is implicated in human age-related diseases. While phase separation is the key process underlying SG assembly, understanding of their function, composition and regulation in response to physiological stimuli is limited. This knowledge gap reflects the challenge of gaining comprehensive and quantitative insights into the dynamic regulation of the complex composition of SGs at the single-cell level. Here we present an emulsion-based microfluidics method to overcome this limitation. "Cytosolic extracts-in-oil droplets” (CEODs) recreate a confined active cytosolic milieu that undergoes phase separation and SG formation in response to stress under physiological conditions. This approach led to the discovery of six novel SG components involved in signalling pathways. CEODs provide a versatile and cost-effective screening platform for future mechanistic and therapeutic studies.

overall_design: RNAseq profiling of mock(untreated)-, dsRNA-, Silvestrol-, and PEG-induced condensates from U2OS cytosolic extracts compared to U2OS cytosolic input.

first: Aline

last: Reuter

first: Nathan

last: Mikhaylenko

first: Oskar

last: Staufer


title: Spatiotemporal regulation of arbuscular mycorrhizal symbiosis at cellular resolution [RNA-seq]

city: Cambridge

first: Gabriel

last: Ferreras-Garrucho

state: Cambridgeshire

address: 93 Lawrence Weaver Rd

department: Crop Science Centre, Department of Plant Sciences

country: United Kingdom

institute: University of Cambridge

summary: Arbuscular mycorrhizal (AM) symbiosis develops through fungal colonization of root epidermal and cortical cells, culminating in the formation of arbuscules, transient, tree-like intracellular hyphal structures for nutrient exchange. To dissect the complexity of AM establishment in rice (Oryza sativa) roots colonized by Rhizophagus irregularis, we conducted spatial transcriptomics of plant and fungal genes at single-cell resolution. This revealed differences in transcriptional activity between fungal structures and reprogramming of plant cell-identity markers upon colonization. Furthermore, cells hosting similarly developed arbuscules showed striking transcriptional heterogeneity, suggesting hidden functional diversity at the individual cell level. For stage-resolved profiling of translation, we used AM-stage specific Translating Ribosome Affinity Purification RNA sequencing (TRAP-seq) with promoters active at discrete stages of symbiosis or arbuscule development. This revealed extensive spatiotemporal changes in the ribosome-bound transcript population, including sets of phosphate, nitrogen, and carbon transporters and regulators with specific enrichment and depletion patterns at different stages of arbuscule development. Rice transcripts encoding cell wall biosynthesis genes and defense markers were present in low abundance at early stages but highly abundant at late stages of the arbuscule lifespan, supporting a host-driven shift toward arbuscule termination. Together, these findings highlight the nuanced dynamic regulation of AM symbiosis at the cellular level, refining our understanding of how nutrient exchange and fungal development are coordinated in space and time.

overall_design: Gene expression profiling analysis by RNA-seq data of rice (Oryza sativa subsp. japonica cv. Nipponbare) roots at 3 weeks post transfer to sand either mock-inoculated (-Ri) or inoculated with Rhizophagus irregularis (+Ri), of total polyA or TRAP (Translating Ribosome Affinity Purification, that is, after polysomal pull-down with specific antibodies for tagged ribosomal proteins) mRNA pools, for a selection of transgenic TRAP lines under different promoters, either p35S as ubiquitous/constitutive control, or AM-inducible promoters active at distinct developmental stages of the interaction: pAM1 as early, pPT11 as mid, and pARK1 as late colonisation marker.

first: Tania

last: Chancellor

first: Garo

last: Akmakjian

first: Héctor

last: Montero

first: Emma

last: Wallington

first: Samik

last: Bhattacharya

first: Christian

last: Korfhage

first: Julia

last: Bailey-Serres

first: Uta

last: Paszkowski


title: Global transcriptional changes across multiple isogenic C9orf72 Patient iPSC-derived neurons

city: Worcester

first: Alberto

last: Brusati

state: MA

address: N Lake Ave 55

department: Neurology

institute: UMass Chan Medical School

summary: Hexanucleotide repeat expansions in C9orf72 are the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD), yet the mechanisms underlying selective neuronal vulnerability remain unclear. A major challenge in identifying consistent transcriptomic changes across C9orf72 patient-derived lines has been due to heterogeneous differentiations, lack of isogenic controls and low sequencing depth. Here, we generated homogeneous cortical neurons (iCNs) from multiple isogenic C9orf72 patient iPSCs pairs and performed deep RNA sequencing. We identified robust and reproducible gene expression and splicing alterations in pathways related to cytoskeletal organization, extracellular matrix adhesion and synaptic signaling. Notably, we observed exon 30 skipping in FLNB, leading to the loss of its hinge domain. This was accompanied by altered FLNB localization, disrupted actin crosslinking and impaired mechano-transduction pathway. These findings reveal convergent transcriptomic and functional disruptions across multiple isogenic C9orf72 patient derived iCNs and offer new insights into ALS/FTD pathogenesis.

overall_design: RNA-seq was performed on i3 cortical neurons derived from multiple isogenic C9orf72 ALS patient iPSC pairs at Day15 of neuronal differentiation

first: Aparna

last: Sreeram

first: Desiree

middle: M

last: Baron

first: Karly

last: Stallworth

first: Victoria

last: Doocy

first: John

middle: E

last: Landers


title: PU.1 is a mediator of the reactive stroma response associated with castration-resistant prostate cancer

city: Bern

first: Panagiotis

last: Chouvardas

address: Murtenstrasse 24

country: Switzerland

institute: University of Bern

summary: Emerging evidence demonstrates the pivotal role played by the tumor microenvironment, particularly cancer-associated fibroblasts, during prostate cancer tumorigenesis and the development of castration-resistant prostate cancer. In this study, we aimed to characterize the stromal gene expression profile of advanced stages of prostate cancer to identify targetable factors associated with castration-resistant prostate cancer progression. Transcriptomic and histological analysis of the mouse stromal component of androgen-sensitive (PNPCa, BM18) and castration-resistant (LAPC9) patient-derived xenograft models representative of advanced prostate cancer was performed. Master regulator analysis of the patient-derived xenograft stromal gene expression profile was performed to identify targetable stromal-associated transcription factors. Patient-derived xenograft collagen-based organoid tumor-fibroblast 3D co-cultures were established to study tumor-fibroblast interactions and to test the effect of an identified fibroblast-targeting compound. Transcriptomic and histological analysis determined the presence of a “reactive” pro-fibrotic stroma in the castration-resistant (LAPC9) versus the castration-sensitive (PNPCa, BM18) xenograft models, characterized by alpha-smooth muscle actin-positive “myofibroblast-like” cancer-associated fibroblasts, high levels of collagen and tenascin C deposition, and upregulation of myofibroblast and inflammatory markers. Intra-tumoral collagen- and tenascin-positive stromal areas specifically correlate with higher tumor invasiveness. Master regulator analysis identified the transcription factor PU.1 as a mediator of the LAPC9 pro-fibrotic phenotype, whose transcriptional activity can be specifically inhibited by a small molecule (DB1976) that prevents its DNA binding. In LAPC9 collagen-based tumor-fibroblast 3D co-cultures, inhibition of stromal PU.1 activity reverted the fibroblast-associated myofibroblast phenotype and, in turn, reduced tumor organoid growth. In this study, we identified the transcription factor PU.1 as a novel targetable molecular player of the pro-fibrotic, cancer-associated fibroblast phenotype in PCa, and we highlighted the applicability of 3D tumor organoid-fibroblast co-cultures as in vitro tools to test the effect of stromal-targeting compounds.

overall_design: The mouse fraction of 3 prostate PDX models was isolated and profiled with BRB-seq (p0 and p2 culture passages).

first: Francesco

last: Bonollo

first: Daniel

last: Hanhart

first: Simone

last: De Brot

first: Wanli

last: Cheng

first: Beat

last: Roth

first: George N.

last: Thalmann

first: Natalie

last: Sampson

first: Marianna

last: Kruithof-de Julio

first: Sofia

last: Karkampouna


title: Phenotypic profiling of neutrophils in acute Clostridioides difficile infection identifies a TNF-induced activation signature associated with epithelial damage.

city: Cincinnati

first: Rajat

last: Madan

state: OH

address: 231 Albert Sabin Way

department: Infectious Disease

institute: University of Cincinnati

summary: We performed single-cell RNA sequencing (scRNA-seq) on enriched neutrophils isolated from murine bone marrow, blood, and colon. This study aimed to investigate neutrophil heterogeneity and plasticity in response to Clostridioides difficile infection (CDI) and to elucidate mechanisms of neutrophil-associated tissue damage.

overall_design: Mice were challenged with C. difficile M7404 spores following antibiotic-induced dysbiosis. Two days post-challenge, bone marrow, blood, and colon tissues were collected from the mouse exhibiting the highest clinical score. Bone marrow and blood samples from an uninfected (naïve) mouse were used as controls. Neutrophils were enriched using negative magnetic selection and processed by scRNA-seq.

first: Huber

last: Alexander

first: Madan

last: Rajat


title: Neuronal microexons modulate arousal via the cAMP-PKA-CREB pathway in zebrafish

city: Barcelona

first: Tahnee

last: Mackensen

address: Dr. Aiguader, 88

institute: Universitat Pompeu Fabra

summary: Proper regulation of arousal maintains the balance of rest and activity and enables appropriate responses to stimuli; its disruption is a hallmark of many neurodevelopmental disorders. While transcriptional mechanisms of arousal control are well-defined, the contribution of post-transcriptional processes such as alternative splicing remains unclear. Here, we identify a critical role for the microexon splicing regulator srrm3 in maintaining arousal homeostasis in zebrafish. srrm3 mutants exhibit persistent hyperarousal characterized by sleep loss, sensory hypersensitivity, and elevated behavioural and neuronal activity. We identify the cAMP-PKA-CREB signaling axis as a central driver of mutant hyperarousal. Specifically, pharmacological inhibition of cAMP signalling rescues mutant hyperactivity and associated transcriptional changes while wild-type cAMP activation phenocopies the mutant. Downregulation of immediate early genes and a reduced CREB phosphorylation further suggest adaptation to sustained neuronal activation. These findings establish srrm3-dependent microexon splicing as a key molecular layer of arousal regulation linking RNA-processing defects to neuromodulatory imbalance.

overall_design: RNA-seq of FACS-sorted GFP⁺ neurons from 5 dpf Tg(elavl3:GFP) transgenic larvae with WT or srrm3∆eMIC backgrounds; 10x Genomics 3' (v3.1) scRNA-seq and ATAC-seq of FACS-sorted GFP⁺ neurons from 6 dpf Tg(elavl3:GFP) enucleated transgenic larvae with WT or srrm3∆eMIC backgrounds; RNA-seq of FACS-sorted GFP⁺ neurons from 6 dpf Tg(elavl3:GFP) enucleated transgenic larvae with WT or srrm3∆eMIC backgrounds either treated with DMSO (control) or ropinirole (ROP), clonidine (CLO), rolipram (ROL), forskolin (FSK), pentylenetetrazol (PTZ), SQ22536 (SQ); RNA-seq of FACS-sorted GFP⁺ neurons from 6 dpf Tg(elavl3:GFP) enucleated transgenic larvae with WT or srrm3^+/∆eMIC or srrm3^∆eMIC.

first: Luis

last: Pedro Iniguez

first: Thomas

last: Soares Mullen

first: Cristina

last: Rodríguez-Marin

first: François

last: Kroll

first: Giulia

last: Zuccarini

first: Jordi

last: Fernandez-Albert

first: Laia

last: Sancho-Vila

first: Jon

last: Permanyer

first: Isaac

last: Bianco

first: Michael

last: Orger

first: Jason

last: Rihel

first: Manuel

last: Irimia


title: Longitudinal changes in DNA methylation in IDH-mutant glioma fuel disease progression through altered cell state differentiation [Smart-seq2]

city: Charlestown

first: Masashi

last: Nomura

address: 149 13th street

department: Pathology

institute: Massachusetts General Hospital

summary: The progression of IDH-mutant gliomas (IDH-G) from slow-growing tumors to fatal disease is associated with transcriptional and DNA methylation changes that remain poorly understood. Here, we profiled a longitudinal cohort of 36 IDH-G samples from 19 patients by joint-capture multi-omic single-nucleus (sn) DNA methylation and snRNA-seq. We show that IDH-G progression is associated with increase in malignant stem-like states, decreased differentiation and with methylation loss, which marks tumors with worse clinical outcome. Methylation loss was uniformly observed across malignant cells within individual tumors, suggesting that it may underlie rather than result from the increase in stem-like states. Analysis of cell state heritability and plasticity based on high-resolution phylogenetic trees connects DNA methylation loss to alterations in glioma cell states encoding and heritability. Our study offers insights on how DNA methylation loss reshapes cellular transitions and how it may mark clinically more aggressive tumors across IDH-G subsets.

overall_design:
Nuclei from frozen tumor tissue were isolated. Nucleus suspensions were inspected by microscope, counted using a hemocytometer, and sorted into 96 well plates by FACS. The single nucleus plates were processed by dual Smart-seq2 and DNA methylation protocol.

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

last: Ravirum

first: Joshua S.

last: Schiffman

first: Dan A.

last: Landau

first: Mario L.

last: Suvà


title: ATF2 phosphorylation is a core transcriptional driver of neuron apoptosis

first: Claire

last: LE PICHON

address: 35A Convent Drive, 2D933

department: NICHD

institute: National Institutes of Health

summary: Apoptotic neuron death is a common feature of many neurodegenerative diseases. Perhaps surprisingly, the exact mechanisms by which neurons undergo apoptosis have yet to be elucidated. We conducted an unbiased whole genome screen in human neurons to discover genes required for apoptotic neuron death and found the kinase MAP3K12 and transcription factors JUN and ATF2 among top hits. JUN is a known downstream target of the injury signaling cascade controlled by the MAP3K12 kinase (dual leucine zipper kinase or DLK), presumably via phosphorylation. Here, we show that JUN upregulation, but not its phosphorylation, is necessary for apoptosis, raising the question of how its upregulation is controlled. We demonstrate that phosphorylation of ATF2 by the kinases MAP3K12 and MAP3K13 is in fact the essential step for transcriptional upregulation of JUN. We identify phospho-ATF2 as the core driver of the pro-apoptotic transcriptional response in neurons and the factor responsible for converting the DLK/LZK kinase signaling cascade into a pro-degenerative transcriptional response. We validate this role of ATF2 in cultured human neurons and in injury models in vivo. Since targeting members of this signaling pathway to block neuronal death has proved difficult, ATF2 offers a promising alternative.

overall_design: 2 RNAseq experiments were performed. Experiment 1: 4 WTC11 iPSC cell lines (wild type, DLK KO, LZK KO and DLK LZK double KO) that each harbored a doxicycline cassette driving NGN2 expression were differentiated into cortical neurons. On day 14, cells were treated with 5 nM vincristine or DMSO vehicle for 16 hours, then RNA was harvested. Experiment 2: WTC11 i3Neurons expressing the CRISPRi machinery were transduced with lentivirus encoding gRNA against ATF2 or JUN, or a scrambled control gRNA. Cells were differentiated into i3Neurons and on day 14 were treated with DMSO or 5 nM vincristine, and RNA was harvested 16 hours later.

last: Le Pichon

first: Jorge

last: Gómez-Deza

first: Matthew

last: Nebiyou

first: Lara

last: El Touny

first: Mor

last: Alkaslasi

first: Zhenyu

last: Zuo

first: Josette

last: Wlaschin

first: Francisco

last: Nadal-Nicolas

first: Stacey

last: Slavutsky

first: Eliza

middle: Y

last: Lloyd

first: Nathan

last: Ashby

first: Mira

last: Sohn

first: Dale

last: Ryan

first: Wei

last: Li

first: Ken

last: Cheng

first: Pedro

last: Rocha


title: Numb-Ifi204 inhibits microglial activation and the hippocampal inflammation induced by LPS.

city: Xi'an

first: Zhang

last: Siyu

state: ShanXi

address: GaoQiao

institute: Xi'an Jiaotong University

summary: This study aimed to identify the mechanisms regulating microglial activation and to explore potential therapeutic targets for neuroinflammation-related cognitive dysfunction disorders. We uncover a novel role for Numb in regulating microglial activation and highlight its interaction with Ifi204 in the LPS-induced TLR4 signaling pathway. We demonstrate that Numb promotes the autophagic degradation of Ifi204, thereby inhibiting the TLR4 signaling pathway and reducing excessive inflammatory responses in microglia. Furthermore, our findings show that Numb-mediated inhibition of microglial inflammation protects hippocampal neurons from synaptic damage, morphological abnormalities, and apoptosis.

overall_design: RNA-seq profilling of scr and shNumb cells


title: A Druggable TGF-β-Mediated Stromal Programming Axis in ATM-Deficient Pancreatic Cancer

city: La Jolla

first: Kyle

last: Gaulton

state: CA

address: 9500 Gilman Dr

department: Pediatrics

institute: University of California, San Diego

summary: The tumor microenvironment (TME) actively contributes to pancreatic ductal adenocarcinoma (PDAC) pathogenesis via a dynamic bidirectional tumor–stroma dialog. Here, we show that homologous recombination-defective (HRD) neoplastic epithelium reprograms its TME in a genotype-specific manner to promote cancer aggressiveness. Autochthonous mouse models, co-culture systems, single-nucleus multiomics investigations and human PDAC specimens revealed that tumoral ATM serine/threonine kinase status impacts cancer-associated fibroblast fate towards αSMA+ myofibroblastic (myCAF) differentiation, independently of P53 loss-of-function. Vice versa, myCAFs foster cancer aggressiveness and specific chemoresistance patterns. Specifically, ATM deficiency is associated with the activation of reactive oxygen species and actomyosin signaling axis, increased contractility, and a greater TGF-β1 release. Pharmacological interference with TGF-β signaling reverts myofibroblast differentiation, chemoresistance, and tumor promotion in various ATM-deficient PDAC models. Overall, our findings demonstrate that both mouse and human HRD-PDACs reprogram their TME towards a cancer-promoting fate, making them suitable for combinatorial therapies targeting intrinsic vulnerabilities and extrinsic tumor–stroma crosstalks.

overall_design: Pancreatic ductal adenocarcinoma tumors were extracted from two female KPC (Atm+/+; Trp53fl/fl; Kras+; p48Cre+) and two female AKPC (Atmfl/fl; Trp53fl/fl; Kras+; p48Cre+) mice after 8-11 weeks of life. Nuclei from both KPC and from both AKPC tumors were pooled together and then two runs (one KPC, one AKPC) of paired snRNA-seq and snATAC-seq were performed.

first: Hannah

last: Mummey

first: Elodie

last: Roger

first: Yun

last: Lee


title: A lineage shared core gene expression network specific to human infants, links human evolution to ASD in oligodendrocytes and Parkinsons disease in neurons

city: Rotterdam

first: Menno

last: Creyghton

address: Doctor Molewaterplein 40

institute: Erasmus MC

summary: Human-specific faculties of neural development at the postnatal stage are largely unknown, as evolutionary comparisons have either relied on adult material, immature cell culture proxies, or comparisons with more distant species. To address this, we performed snRNAseq (10x Genomics) on rare human, chimpanzee, and rhesus macaque prefrontal cortex (PFC) infant samples. This study represents the first to include infant chimpanzee samples in such evolutionary comparisons, providing novel insight into human-specific neural development and its susceptibility to neural disease.

overall_design: Frozen PFC samples were dissociated with tissue punches to include all cortical layers. Intact nuclei were sorted for DAPI+ nuclei to remove debris for 10x genomics snRNAseq.

first: Jonathan

last: Klavert


title: eIF4G2-Mediated Translation Initiation of Histone Modifiers is Essential for Intestinal Stem Cell Maintenance and Differentiation

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: 2-1, Hirosawa

department: Center for Pioneering Research

institute: RIKEN

summary: eIF4G2 (also known as NAT1, p97, or DAP5) is an evolutionally conserved protein homologous to the C-terminal two-thirds portion of eukaryotic translation initiation factor (eIF) 4G. Despite its abundant and ubiquitous expression, the physiological and pathological functions of eIF4G2 are poorly understood. Here, we show that acute inactivation of eIF4G2 in adult mice results in rapid weight loss with abnormalities in multiple organs. Genome-wide ribosome profiling revealed that eIF4G2 is critical for the translation of key histone modification proteins involved in the maintenance and differentiation of intestinal stem cells. Our study underscores the importance of eIF4G2-mediated translation in multicellular organisms.

overall_design: Ribosome profiling and RNA-seq of small intestinal organoids from Eif4g2 KO mice

first: Haruko

last: Kunitomi

first: Aye

last: Khaine

first: Radia

last: Jamee

first: Maricelle

last: Lancerro

first: Eugenea

last: Rauchendeuri

first: Samuel

last: Perli

first: Yoshiko

last: Sato

first: Mio

last: Ruivo

first: Kiichiro

last: Tomoda

first: Mari

last: Mito

first: Yuichi

last: Shichino

first: Shinya

last: Yamanaka


title: Low-input RNA-seq suggests metabolic specialization underlying morphological heterogeneity in a gut commensal bacterium

city: Wurzburg

first: Elise

last: Bornet

address: Josef-Schneider Strasse 2

institute: Helmholtz Insitute

summary: Isogenic bacteria can be phenotypically diverse. This heterogeneity is evident in the Bacteroidota, a predominant phylum of the human gut microbiota. These bacteria adopt diverse morphologies, yet the molecular basis of their morphological heterogeneity is poorly understood. Here, we systematically characterize the variation in cellular morphology of Bacteroides thetaiotaomicron cells during laboratory growth and after isolation from different host niches. We develop a sensitive transcriptomics approach and apply it to B. thetaiotaomicron sorted into sub-populations of varying cell sizes. Differential expression analysis indicates metabolic specialization associated with morphology. Transcriptomic data also reveal morphological marker genes, whose size-dependent expression is validated through fluorescence in situ hybridization. Morphological characterization of deletion and overexpression mutants reveals that specific marker genes causally contribute to B. thetaiotaomicron cell-size determination. Since phenotypic heterogeneity is a common feature of microbial consortia, this study serves as a blueprint for understanding the role of bacterial genes in morphological variation

overall_design: RNA-Seq profiling the different morphotypes of Bacteroides thetaiotaomicron

first: Gianluca

last: Prezza

first: Laura

last: Cecchino

last: Jenniches

first: Jochen

last: Behrends

first: Caroline

last: Tawk

first: Kerwyn Casey

last: Huang

first: Till

last: Strowig

first: Jorg

last: Vogel

first: Lars

last: Barquist

first: Antoine-Emmanuel

last: Saliba

first: Alexander

last: Westermann


title: Gene Regulatory Networks Orchestrating Oocyte Fate Bifurcation in Primordial Follicles Revealed by Single-Cell Transcriptomics

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

summary: The first wave of primordial follicle activation occurs around postnatal day 2.5 (P2.5), with the remaining follicles entering a dormant state to ensure a continuous supply of fertilizable oocytes. However, the molecular mechanisms underlying this critical fate bifurcation remain poorly understood. Here, we employ SMART-seq2 to profile transcriptional dynamics in individual perinatal female mouse germ cells across three developmental stages: cysts at embryonic day 17.5 (E17.5), primordial follicles at P2.5, and primary follicles at P6.5. Unsupervised clustering and trajectory inference reveal two distinct transcriptional states in P2.5 oocytes, corresponding to dormant and activated subpopulations. Activated oocytes exhibit upregulation of genes linked to PI3K-Akt/mTORC1 signaling, extracellular matrix (ECM) disassembly, and oocyte maturation, whereas marker genes of dormant oocytes are enriched in oxidative stress response and DNA repair pathways. Transcriptional regulatory network reconstruction based on SCENIC inference identifies key transcription factors (e.g., Bhlhe41, Tcf3/12) orchestrating the fate bifurcation. Notably, dormant oocytes form a stable transcriptional state distinct from the continuous activation and development trajectory. Our findings provide a comprehensive landscape of gene expression and regulatory networks correlated to fate determination of P2.5 primordial follicles, paving the way for advanced therapeutic strategies for related diseases and improved techniques for in vitro follicle activation.

overall_design: We isolated mouse ovaries embryonic day 17.5 (E17.5), postnatal day 2.5 (P2.5), and postnatal day 6.5 (P6.5). The ovaries were enzymatically dissociated into single-cells suspensions, and individual germ cells were manually collected for single-cell RNA-sequencing (scRNA-seq).

first: Hanwen

last: Zhang

first: Xingsi

last: He


title: Flavonoid and isoflavonoid biosynthetic gene expression is affected by MYB36 transcription factor deficiency in Lotus japonicus [UV-B_Experiment]

city: Sevilla

first: MARCO

last: BETTI

state: Sevilla

address: C. Prof. García González 1

department: Bioquímica Vegetal y Biología Molecular

institute: Universidad de Sevilla

summary: MYB36 has been identified as a new transcription factor (TF) that may be involved in isoflavonoid metabolism and stress responses in the model legume Lotus japonicus. A series of transcriptomic and metabolomic approaches have been carried out to attempt to identify the specific genes that can be under the control of MYB36 TF in this plant. For this purpose, transcriptomic data were obtained for wild type (WT) and two different lines of homozygous myb36 mutant plants, under two different stress conditions shown to be related with isoflavonoid metabolism: UV-B irradiation and salt stress. Results obtained showed a completely different and almost reciprocal picture of the global transcriptomic of the WT plants under both types of stress situations. Further comparison of up- and down- regulated genes revealed a very similar response of WT and mutant plants under UV-irradiation. In contrast, a completely different response was detected in salt stress between WT and mutant plants. None of the genes modulated by salt stress in myb36 mutants were also modulated by UV-B irradiation. Furthermore, most of the genes modulated by salt stress in the mutants corresponded to genes specifically involved in isoflavonoid but not flavonoid biosynthesis, thus illustrating on the genes that can be under the specific control of MYB36. These results identify for the first time MYB36 as specifical TF in the regulation of (iso)flavonoid biosynthesis, a class of compound specifically produced by legume plants. In addition, the results obtained revealed MYB36 as a crucial TF in the response to salt stress in legume plants.

overall_design: A comparative RNAseq analysis of WT and of Ljmyb36 mutant, KO for the LjMYB36 gene encoding for the MYB36 transcription factor was carried out. WT and mutant plants were subjected to UV-B treatment for 16 h together with the continuous visible-light illumination. Control plants were subjected only with continuous visible-light illumination. WT and mutant tissues were harvested after 4 hours of the beginning of the light period after 30 days of growth.

first: Maria Dolores

last: Monje-Rueda

first: Peter

last: Pal'ove-Balang

first: Antonio

last: Márquez

first: Marco

last: Betti

first: Margarita

last: García-Calderón


title: Flavonoid and isoflavonoid biosynthetic gene expression is affected by MYB36 transcription factor deficiency in Lotus japonicus [Salt_Experiment]

overall_design: A comparative RNAseq analysis of WT and of Ljmyb36 mutant, KO for the LjMYB36 gene encoding for the MYB36 transcription factor was carried out. WT and mutant plants were subjected to a gradual increase of 50 mM NaCl every 4 days in the nutrient solution until reaching the final salt concentration of 100 mM NaCl, after which the plants were harvested (32 days of total growth and 2 days of growth in the presence of 100 mM NaCl). Control plants were watered with ‘Hornum’ nutrient solution for 34 days in absence of NaCl concentration. WT and mutant tissues were harvested after 4 hours of the beginning of the light period after 34 days of growth.


title: PPARγ-Mediated Ferroptosis in Macrophages Enhances Persistent Pulmonary Infction by Mycobacterium tuberculosis

first: Zhiqiang

state: Jiangsu

address: Hankou 22

department: Medical School

institute: Nanjing University

summary: In this study, we found that Mycobacterium tuberculosis (Mtb) uses the PPARγ-GPX4 axis to induce ferroptosis in host cells, promoting persistent infection. Elevated PPARγ levels in macrophages post-Mtb infection, due to direct interactions with Mtb IDH and impaired degradation, lead to suppressed GPX4 expression and increased lipid peroxidation. Deleting PPARγ reduces lung inflammation, Mtb burden, and restores GPX4 expression in infected macrophages. This discovery of Mtb hijacking PPARγ to induce ferroptosis suggests a promising target for tuberculosis treatment.

overall_design: Multi-omics study investigates the epigenetic mechanisms underlying the interaction between Mycobacterium tuberculosis and macrophages, shedding light on the mechanisms of pathogen-host interactions.

first: Wenyuan

last: Pu

first: Hongwei


title: tsRNAs sequencing of FFPE tissues reveals i-tRF-Gly-GCC as a biomarker for colorectal cancer

city: Guangzhou

first: Xiaoyun

state: Guangdong

address: 190 Kaiyuan Avenue, Huangpu

department: Infection and Immunity

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

summary: Colorectal cancer (CRC) remains one of the most prevalent and deadly malignancies worldwide, requiring reliable biomarkers for detection. This study profiled tRNA-derived small RNAs in CRC tissues, identifying 1051 differentially expressed tsRNAs. Notably, i-tRF-Gly-GCC was significantly elevated in CRC tissues and patient sera compared to controls, with ROC analysis yielding an AUC > 0.7, underscoring its diagnostic potential. Weighted Gene Co-expression Network Analysis (WGCNA) revealed that i-tRF-Gly-GCC's target genes, including RAC2, which was downregulated in the COAD and READ datasets, are closely related to CRC. Gene Ontology and KEGG pathway analyses further linked i-tRF-Gly-GCC to cancer-related processes. Functional experiments in HCT-116 cells demonstrated that i-tRF-Gly-GCC enhances cell proliferation and migration. These results highlight i-tRF-Gly-GCC as a novel non-invasive biomarker for CRC detection and a potential therapeutic target, advancing our understanding of tsRNA-mediated regulation in CRC and paving the way for clinical applications.

overall_design: This study included 24 FFPE clinical tissue samples (12 CRC and 12 paracancerous) and 20 clinical serum samples (10 CRC and 10 healthy volunteers). High-throughput sequencing on tissue samples to construct colorectal cancer tsRNAs expression profiles. Use them to identify target genes of tsRNAs,and cellular experiments and analysis of TCGA datasets confirmed their role as biomarkers.

first: Yu

last: Wan

first: Yuting

last: Jiao

first: Anrui

last: Liu


title: scRNA-Seq of CD45+ cells in B16F10 tumor after adoptive cytotoxic T lymphocyte immunotherapy

city: Osaka

first: Koji

last: Nagaoka

address: 377-2 Ohno-Higashi, Osaka-Sayama

department: Department of Immunology

institute: Kindai University Faculty of Medicine

summary: Although adoptive cell transfer (ACT) with tumor-specific CD8⁺ T cells induces initial tumor regression, tumors often relapse due to incomplete eradication and immune evasion. To investigate the mechanisms of tumor regrowth after ACT, we performed single-cell RNA sequencing (scRNA-seq) of tumor-infiltrating immune cells in a murine melanoma model. B16F10 melanoma-bearing C57BL/6 mice were treated with gp100-specific Pmel-1 cytotoxic T lymphocytes (CTLs). Tumors were harvested on days 3, 7, and 14 post-transfer, and CD45⁺ immune cells were isolated for 10x Genomics Chromium-based scRNA-seq. This dataset supports the analysis of immune cell states during tumor progression after ACT.

overall_design: C57BL/6 mice were subcutaneously inoculated with B16F10 melanoma cells. On day 9 after tumor inoculation, mice received intravenous adoptive transfer of in vitro-activated gp100-specific Pmel-1 cytotoxic T lymphocytes (CTLs). Tumors were harvested on days 3, 7, and 14 following ACT. Tumors from individual mice were enzymatically dissociated into single-cell suspensions, and CD45⁺ immune cells were isolated from each sample using magnetic bead-based selection. Equal numbers of CD45⁺ cells from three mice were pooled at each time point and subjected to single-cell RNA sequencing using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index).

first: Kazuhiro

last: Kakimi


title: Epigenomic-transcriptional network during neural crest cell differentiation [DNA methylation]

city: Saitama

first: Kyosuke

last: Mukae

state: Kitaadachi-gun

address: 818, Komuro, Ina-machi

department: Research Institute for Clinical Oncology

institute: Saitama Cancer Center

summary: Neural crest cells (NCCs) originate from the neural tube during early embryogenesis, and they are a pivotal cell population involved in vertebrate development. NCCs are mainly divided into cranial NCCs (cNCCs) and trunk NCCs (tNCCs), which subsequently differentiate into diverse tissues and organs. Proper differentiation and fate determination into NCCs are essential for normal development and survival of individuals, and abnormal differentiation of NCCs can lead to various diseases such as cardiac disorders and tumors. Epigenetic mechanisms, including histone modification and DNA methylation, are crucial for regulating NCC differentiation. However, the specific mechanisms of DNA methylation underlying the differentiation of cNCCs and tNCCs remain poorly understood. This study aimed to address this knowledge gap by comparing the differentiation mechanisms of cranial and trunk NCCs derived from human induced pluripotent stem cells. Through integrated analysis of the transcriptome and DNA methylome data, we found that along with differentiation, DNA demethylation upstream of the transcription start sites of myocyte enhancer factor 2C (MEF2C) in cNCCs and thyroid hormone receptor alpha-2 (THRA2) in tNCCs led to increased expression of these genes. Furthermore, MEF2C and THRA2 were found to potentially regulate NCC markers. Our findings contribute to a detailed understanding of regulatory mechanisms of DNA methylation in normal NCC differentiation and may provide insights into the pathogenesis of NCC-related diseases such as neuroblastoma.

overall_design: Genomic DNA was isolated from iPSCs, cNCCs, and tNCCs of 414C2, 201B7, and 604A3 cells using a proteinase K (FUJIFILM) method with subsequent purification by phenol-chloroform (NIPPON GENE, Tokyo, Japan). After RNase treatment and additional purification, genome-wide DNA methylation analysis was conducted using an Infinium MethylationEPIC BeadChip v.1.0 (Illumina, San Diego, CA, USA). Each sample was analyzed once because of the high analytical reproducibility of this microarray. The microarray assessed the degree of methylation of 862,927 probes with a β-value ranging from 0 (unmethylated) to 1 (fully methylated). To reduce the data size for convenient handling, neighboring probes (CpG sites) were assembled into a genomic block consisting of probes within 500 bp using MACON. A genomic block was annotated based on its relative location from the transcription start site (TSS) and against a CpG island. All 862,927 probes were assembled into 551,478 genomic blocks, and 538,523 blocks on the autosomes were used for methylation analysis. The DNA methylation level of each genomic block was calculated as the mean β value of all probes within the genomic block.

first: Takehiko

last: Kamijo

first: Naoko

last: Hattori

first: Satoshi

last: Yamashita

first: Toshikazu

last: Ushijima