title: CRISP enables comparisons of image-based spatial transcriptomic segmentation quality across ten organs

city: Atlanta

first: James

middle: Ricahrd

last: Rose

state: GA

address: 1750 Haygood Dr NE

department: Biomedical Engineering

institute: Emory University

summary: This dataset comprises 10x Xenium image-based spatial transcriptomics data from a mouse tissue microarray (TMA) containing ten organs (brain, female reproductive tract, heart, kidney, large intestine, liver, lung, small intestine, spleen, and stomach) collected from C57BL/6J mice treated with lipid nanoparticle-delivered β-Galactosidase mRNA or vehicle control and profiled with a 5,006-gene panel.

overall_design: Two-millimeter cores from ten mouse organs (brain, female reproductive tract, heart, kidney, large intestine, liver, lung, small intestine, spleen, and stomach) were collected from C57BL/6J mice receiving either lipid nanoparticle-delivered β-Galactosidase mRNA or vehicle control, assembled into a tissue microarray, sectioned, and profiled using the 10x Xenium platform with a 5,006-gene panel.

first: Rose

last: James Richard

first: Vanover

last: Daryll

first: Santangelo

last: Philip


title: Ribosome decoding memory directs translational re-coding of codon repeats

status: Public on Apr 20 2026

city: Ithaca

first: Saori

last: Uematsu

state: New York

address: 526 Campus Road, Cornell University

country: USA

institute: Cornell University

summary: During mRNA translation, ribosome dynamics at individual codons critically shape the quality and quantity of protein products. Long runs of consecutive codons are generally thought to impede elongation by depleting cognate tRNAs. However, in Huntington’s disease, ribosomes translate hundreds of consecutive CAG codons without catastrophic stalling. Here, we systematically profile ribosome behavior across repeats of all 20 amino acids encoded in the human genome. For proline and lysine repeats – commonly considered difficult to decode – we find that ribosomes accelerate after an initial phase of slow decoding, a phenomenon we term adaptive decoding. Remarkably, codon-specific decoding memory enables iterative translation of arginine repeats, generating internally expanded protein products. In contrast, acidic amino acid repeats trigger ribosomal bypassing and produce internally truncated proteins. Contrary to prevailing assumptions, decoding inertia acquired during repeat translation constraints frameshifting. Disrupting the decoding memory of CAG repeats by inserting proline codons is beneficial in reducing polyglutamine synthesis and aggregation. These findings uncover an adaptive dimension of ribosome decoding that contributes to the synthesis of physiological and pathological amino acid repeats.

overall_design: Ribo-seq of HEK293 cells transfected with mRNA reporters that contain various homopolymeric repeats; Ribo-seq of HEK293 cells under normal conditions, Arg starvation, and SAMD9 activation


title: Organ injury in systemic autoimmunity is mediated by stem-like CD8 T cells arising from tissue-draining lymph nodes

city: New Haven

first: Yulong

last: Wei

state: CT

address: 295 Congress Avenue

department: Microbial Pathogenesis

institute: Yale University

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

summary: Chronic antigen exposure in cancer and infection generates hypofunctional, stem-like CD8 T cells that replenish tissue effector cells for tumor or pathogen control. CD8 T cells infiltrate kidneys in systemic lupus erythematosus, but their origin, differentiation, and function remain incompletely understood. We identified in lupus-prone mice TCF1⁺ stem-like CD8 T cells in renal-draining lymph nodes that underwent TCR-dependent, antigen-driven expansion with differentiation into cytotoxic kidney-infiltrating cells that promoted tissue injury contingent on CD4 T cell help and IL-21/IL-15 signaling. CD8 T cell differentiation was marked by persistent AP-1 activity and cytotoxic function despite immune checkpoint upregulation. We found a parallel program of CD8 T cell differentiation in kidneys of patients with lupus nephritis, reflecting shared pathogenesis. This T cell differentiation program is analogous to that in chronic infections and cancer, indicating conservation across states of chronic antigen stimulation; however, CD8 T cells in systemic autoimmunity retain effector function despite terminal differentiation.

overall_design:
CITE-seq with TCR: CD4 or CD8 T cells isolated from kidney, spleen, and renal lymph node of lupus-prone MRL/MpJ-Faslpr/J or MRL/MpJ-Faslpr/J.Nur77-eGFP (sorted on eGFP expression) mice were hashtagged (TotalSeq™-C, BioLegend) and pooled. Joint scRNA-seq, TCR, and HTO libraries were prepared using the 10x Genomics platform.
Multiome-seq: Single nuclei were extracted from CD44hi T cells from kidney, spleen and renal lymph node of lupus-prone MRL/MpJ-Faslpr/J mice. Joint scRNA-seq and scATAC-seq libraries were prepared using the 10x Genomics platform.

first: Jafar

last: Al Souz

first: Can

last: Cui

first: Rihao

last: Qu

first: Jin-Young

last: Choi

first: Fang

last: Wang

first: Steven

last: Moioffer

first: Julia

last: Barrett

first: Irene

last: Chernova

first: Manvitha

last: Nadella

first: Emilly

middle: R

last: Siniscalco

first: Gilbert

last: Moeckel

first: Nikhil

middle: S

last: Joshi

first: Ping-Min

last: Chen

first: Arnon

last: Arazi

first: Ya-Chi

last: Ho

first: Joseph

last: Craft


title: KAT6A  is essential for developmental control gene expression in neural stem and progenitor cells

city: Parkville

first: Nishika

last: Ranathunga

state: VIC

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Heterozygous mutations in the MYST family histone acetyltransferase gene, KAT6A (MOZ, MYST3) cause the human congenital disorders characterised by intellectual disability, Arboleda-Tham syndrome (KAT6A syndrome). In this dataset, we used neural stem cells isolated from Kat6a+/+, Kat6a+/– and Kat6a–/– E12.5 mouse embryos cultured under proliferating and differentiating conditions to assess the effects of loss of one or both alleles of Kat6a on neural stem and progenitor proliferation and differentiation.

overall_design: Proliferating and differentiating neural stem and progenitor cells isolated from the dorsal telencephalon of N = 4 Kat6a+/+, 4 Kat6a+/– and 4 Kat6a–/– E12.5 mouse embryos cultured under proliferating and differentiating conditions.

first: Alexandra

middle: L

last: Garnham

first: Ranathunga

last: Nishika

first: Anne

middle: K

last: Voss

first: Tim

last: Thomas


title: Effect of hypoxanthine and pyroglutamic acid on downstream signaling mechanisms in vascular smooth muscle cells and endothelial cells.

city: Beijing

first: Xiaozheng

last: Zhou

state: beijing

address: Anzhen Road, Cao Yang District, Beijing, China, 100029

country: China

institute: Beijing Anzhen Hospital, Capital Medical University

summary: To investigate the impact of hypoxanthine and pyroglutamic acid on downstream signaling mechanisms, we treated human aortic smooth muscle cells (HASMCs) and Human aortic endothelial cells (HAECs) with these metabolites and analyzed pathway activation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for vascular smooth muscle cells and endothelial cells treated with hypoxanthine, pyroglutamic acid, Angiotensin II, and/or the inhibitors U83836E and BCX-1777.

first: Zhiyong

last: Du


title: Cellular Signatures of Melanocortin Pathway Genes Across the Locus Coeruleus [Spatial Transcriptomics]

city: New York

first: Fahrunisa Meryem Betul

last: Erol Gulsen

state: NY

address: 1150 St Nicholas Ave

department: Pediatrics

institute: Columbia University

summary: Obesity and Alzheimer’s disease (AD) are epidemiologically associated. The locus coeruleus (LC) – the brain’s primary and most significant source of norepinephrine – is one of the earliest sites of neurodegeneration in AD. The LC participates in feeding behavior through connections with the hypothalamus. The cellular composition of the LC has been characterized at single-cell resolution. However, the constituent cellular signatures of genes related to energy homeostasis – such as the melanocortin pathway genes – in the LC are unclear. We performed single-nucleus RNA sequencing and spatial transcriptomics (Visium) in the human LC, and HiPlex RNAscope in the LC of mice. The melanocortin pathway gene MRAP2 was expressed in the majority of DBH neurons across the LC. Mrap2 was also co-expressed with AD-associated genes such as App, Psen1, Psen2, and Sorl1. More than 20% of Dbh neurons in the LC were positive for Mrap2, App, Psen1, and Psen2. Mrap2 is expressed in the central nervous system and modulates the trafficking and signaling of all five G-protein coupled receptors (GPCRs) of the melanocortin receptor family: Mc1r, Mc2r, Mc3r, Mc4r, and Mc5r. In mice, among the melanocortin receptors, Mc5r showed the highest co-expression with Mrap2, accounting for 17.9% of Mrap2-positive cells, followed by Mc2r with 10.9% of Mrap2-positive cells. Mc1r, Mc3r, and Mc4r showed very limited co-expression with Mrap2. Our study reveals that many Mrap2-positive cells do not express any melanocortin receptor genes, warranting future studies into metabolically relevant GPCRs downstream of MRAP2 in the LC. In summary, our study characterizes melanocortin molecular substrates in the human and mouse LC and highlights MRAP2 as a potential link between pathways of energy homeostasis and neurodegeneration.

overall_design:
Postmortem human locus coeruleus (LC) tissue from one neurotypical adult female donor (76 years old) was profiled by Visium spatial transcriptomics across four sections (Upper Rostral, Lower Rostral, Upper Caudal, Lower Caudal) to map the spatial distribution of melanocortin pathway genes and co-expression with Alzheimer's disease-associated genes at spot resolution across the LC.

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

last: Basak

first: Fahrünisa Meryem Betül

last: Erol

first: Maria Caterina

last: De Rosa

first: Zhangji

last: Dong

first: Victor

last: Ogbolu

first: Hannah

middle: J

last: Glover

first: Rick

last: Rausch

first: Gunnar

last: Hargus

first: Jordi

last: Creus-Muncunill

first: Heather

last: Buchanan

first: Yu

last: Bai

first: Qi

last: Su

first: Betty

last: Chang

first: Christina

last: Adler

first: Delaney

last: Flaherty

first: Benjamin

last: Ciener

first: Harrison

last: Xiao

first: Hasini

last: Reddy

first: Pascaline

last: Aime-Wilson

first: Christiane

last: Reitz

first: Mark

middle: W

last: Sleeman

first: Judith

middle: Y

last: Altarejos

first: Rudolph

last: Leibel

first: Liang Oscar

last: Qiang

first: Andrew

middle: F

last: Teich

first: Claudia

middle: A

last: Doege


title: RNA-seq profiling of non-muscle invasive bladder cancer (NMIBC) tumors

city: Bothell

first: Joseph

middle: D

last: Dekker

state: Washington

institute: Pfizer

summary: Bulk RNA-seq was performed on fresh-frozen non-muscle invasive bladder cancer (NMIBC) tumor biopsies obtained from commercial biobanks (BioIVT and Proteogenex). These data were generated to characterize the transcriptomic landscape of NMIBC tumors and support preclinical studies of integrin beta-6 (ITGB6)-targeted therapies. RNA was extracted from 25 untreated surgical specimens and sequenced using paired-end Illumina sequencing by Azenta Life Sciences.

overall_design: 25 fresh-frozen NMIBC tumor biopsies were profiled by paired-end RNA-seq. All samples are untreated clinical specimens sourced from BioIVT (n=14) and Proteogenex (n=11). No experimental treatment was applied.

first: Robert

middle: T

last: Lawrence


title: Bavachinin Suppresses Growth and Metastasis of Oral Squamous Cell Carcinoma

city: Taoyuan City

first: Chia-Yu

last: Yang

address: No.259, Wenhua 1st Rd., Guishan Dist.

department: Department of Microbiology & Immunology, Chang Gung University

country: Taiwan

institute: NGS Genomics Core Lab

summary: We investigated the role of bavachinin in oral squamous cell carcinoma (OSCC) and demonstrated that bavachinin inhibits OSCC cell proliferation and promotes apoptosis mainly through the inhibition of the GSK-3β/β-catenin signaling pathway.

overall_design: experimental design: By integrating in vitro, in silico, and in vivo (CDX/PDX) models, our experiments elucidate the role of bavachinin in oral cancer treatment.


title: Acquired genetic and cell state changes in IDH-mutant glioma progression [coculture experiments]

first: Kevin

middle: C

last: Johnson

address: 333 Cedar Street

department: Neurosurgery

summary: Isocitrate dehydrogenase (IDH)-mutant gliomas are malignant brain tumors that typically arise in early- to mid-adulthood and nearly always recur following treatment. However, the genetic and cellular state changes that drive IDH-mutant glioma progression under treatment remain incompletely understood. Here, we integrated single-nucleus transcriptomic profiles, chromatin accessibility profiles and bulk DNA/RNA sequencing from 75 temporally separated gliomas across 35 patients comprising both the oligodendroglioma and astrocytoma IDH-mutant glioma tumor types. We show that malignant cell states transcriptionally resemble stages of normal glial-neuronal lineage development or a reactive mesenchymal-like state, mirroring states previously described in IDH-wildtype glioblastoma. Malignant cell states displayed distinct chromatin accessibility profiles that were comparable between both IDH-mutant glioma types. The abundance of less differentiated malignant cells increased with grade and with genetic alterations such as PDGFRA amplification. Longitudinal analysis highlighted two major malignant cell state transition patterns. First, reduced lineage differentiation and increased proliferative malignant cells at recurrence were pronounced in gliomas that acquired recurrence-associated genetic events, including treatment-associated hypermutation, increased copy number changes, and cell cycle alterations. Second, increased mesenchymal-like state abundance occurred independently of acquired genetic alterations and instead coincided with heightened macrophage expression. Overall, our findings provide an integrative model that traces the cell-intrinsic and extrinsic factors that shape cellular states during IDH-mutant glioma disease progression.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
MGG152, a human IDH-mutant patient-derived glioma cell line, was profiled by 10x single-cell RNA sequencing  3' v4 (polyA) On-Chip Multiplexing (OCM) across 4 different environmental conditions each with 4 biological replicates. These conditions included MGG152 monoculture, MGG152 monoculture treated with irradiation, MGG152 co-culture with mouse macrophage cells, and MGG152 co-culture with mouse macrophage cells treated with irradiation.

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

first: Linbin

last: Zhang

first: Anna

last: Lasorella

first: Roel

last: Verhaak


title: Acquired genetic and cell state changes in IDH-mutant glioma progression

overall_design:
Two IDH-mutant glioma patient-derived neurosphere cell lines were treated with PDGFRA inhibitors or control. The experimental conditions per cell line were dimethyl sulfoxide (DMSO) control, dasatinib (broad SRC/ABL/PDGFR inhibitor), and CP-673451 (selective PDGFRα/β inhibitor). The doses for the PDGFRA inhibitors were 1µM and 5µM. These samples were profiled with single-cell RNA sequencing (10x Genomics, 3' v4).

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

first: Anuja

last: Lipsa

first: Kamil

last: Grzyb

last: Golebiewska


title: Unique transcriptional profiles of adult human immature neurons in healthy aging, Alzheimer’s disease, and cognitive resilience

city: Amsterdam

first: Dilara

last: Ayyildiz

address: Meibergdreef 47

country: Netherlands

institute: Netherlands Institute For Neuroscience

summary: The existence and putative functional significance of immature neurons in the adult human brain, particularly in the context of neurodegenerative disorders, remains an open question. While rodent studies have highlighted active roles for adult-born immature neurons in the hippocampus under both healthy conditions and in Alzheimer’s disease (AD), evidence from the human brain is limited and lacks detailed molecular characterization. To address this gap, we performed single-nucleus RNA sequencing in aged healthy, AD and dementia-resilient human hippocampus to probe immature neuronal signatures and gene expression alterations associated with AD pathology and resilience. Employing a novel experimental and computational pipeline, we identified persistent populations of immature neurons across all donor groups, with transcriptional profiles reflecting ‘juvenile’ cellular functions, which are compromised in AD. Our findings suggest that the presence of these immature neuronal populations per se may actively contribute to maintaining homeostasis within the aged human hippocampus, and cognitive resilience in AD.

overall_design: Fresh frozen adult human hippocampal tissue blocks were sectioned into 300 μm thick slices using a cryostat. Sections were maintained on dry ice, and SGZ and GCL, extending from the molecular layer to the hilus were isolated under a stereomicroscope using a 0.5 mm-diameter biopsy puncher.Adjacent sections were stained with hematoxylin to facilitate the accurate identification of the dentate gyrus. Punched tissue samples were stored at -80°C until further processing. For the fetal samples, the region of the tissue containing the DG was identified by hematoxylin staining and sectioned into 50 μm-thick slices using a cryostat. Isolated nuclei samples were further processed for GEM generation, with targeted nuclei recovery of 10000 nuclei/sample by using 10x Genomics Single Cell 3` Reagent Kit (v3.1) according to manufacturer’s protocols (10x Genomics, CG000204_Rev_A).

first: Giorgia

last: Tosoni

first: Sarah

last: Snoeck

first: Elena P.

last: Moreno-Jiménez

first: Amber

last: Penning

first: Estibaliz

last: Santiago-Mujika

first: Olmo

last: Ruiz Ormaechea

first: Hyunah

last: Lee

first: Suresh

last: Poovathingal

first: Kristofer

last: Davie

first: Julien

last: Bryois

first: Will

last: Macnair

first: Jasper

last: Anink

first: Luuk E.

last: De Vries

first: Sahand

last: Farmand

first: Erik

last: Nutma

first: Dick F.

last: Swaab

first: Eleonora

last: Aronica

first: Jinte

last: Middeldorp

first: Sandrine

last: Thuret

first: Laurent

last: Roybon

first: Onur

last: Basak

first: Carlos P.

last: Fitzsimons

first: Paul J.

last: Lucassen

first: Evgenia

last: Salta


title: Spatial transcriptomics dissects mechanism of action of the PD-1 targeted IL15-mutein in B16-F10-OVA tumor-bearing mice

city: Cambridge

last: Tessier

state: MA

address: 350 Water Street

institute: Sanofi US

summary: KD050 is an anti-PD-1/IL-15 bi-functional antibody with strong PD-1 antagonist function, but lower lymphocyte stimulation enabled by a novel mutation on the IL-15. Here, we spatially characterized at RNA level the effect of mKD050 surrogate I in B16-OVA (melanoma) mouse model, in comparison with anti-mPD1 and mouse non-targetKD050 (mntKD050).

overall_design: A total of 20 B16-F10-OVA tumors were characterized, with 5 samples per treatment groups (Isotype Control, anti-mPD-1, mIgG-mutmIL15 and anti-mPD-1-mutmIL15). For each tumor, we defined 3 compartments (“Leading Edge”, “Tumor” and “Necrosis”) based on morphological markers and H&E staining. For each compartment, we then harvested 8 circular (250μm in diameter) ROIs, so a total of 24 per tumor (23 ROIs per tumor for the isotype control group as the first well on each collection plate was dedicated to the no-template control). ROI placement for each compartment was done within the tumor boundaries, including for the “Leading Edge” one

first: Tessier

last: Julien

first: Lee

last: Joon Sang


title: DNA-PK Mediated CRTC2 Phosphorylation Promotes CRTC2 Relocation from Transcription to Repair Complexes Enhancing NHEJ and Suppressing Abscopal Effect

city: tianjin

first: zhanjie

last: xiu

address: HUANHU XI ROAD, TIYUAN BEI, HEXI DISTRICT

institute: TIANJIN MEDICAL UNIVERSITY CANCER INSTITUTE & HOSPITAL

summary: DNA damage repair and transcription are antagonistic cellular processes that require precise spatiotemporal coordination to maintain genomic integrity. Transcriptional silencing at DSB sites is essential for efficient repair, mediated through localized histone modifications and direct inhibition of RNA polymerase II (Pol II). However, the role of transcriptional activators in coordinating DSB repair with transcriptional silencing remains elusive. Here, we identify the transcriptional coactivator CRTC2 as a key coordinator of DNA repair and transcriptional regulation. We demonstrate that CRTC2 promotes canonical non-homologous end joining (c-NHEJ) both in vitro and in vivo. Mechanistically, PARP1 activation recruits CRTC2 to DNA breaks, where it facilitates DNA-PKcs recruitment and assembly of the DNA-PK holoenzyme, thereby driving c-NHEJ. DNA-PK–mediated phosphorylation of CRTC2 at Ser433 dissociates it from transcriptional complexes, suppressing target gene transcription, and promoting its incorporation into DNA repair complexes. Thus, establishing a positive feedback loop that enhances NHEJ efficiency. CRTC2 loss radiosensitizes cancer cells, potentiates irradiation-induced cGAS–STING activation, promotes cytotoxic CD8⁺ T cell infiltration, and enhances the abscopal effect. Furthermore, AAV8-mediated targeting of CRTC2 sensitizes tumors to radioimmunotherapy. Our results reveal CRTC2 as bifunctional nodal effector coupling transcriptional silencing to DNA repair and propose its inhibition as a promising strategy for radioimmunotherapy sensitization in resistant malignancies.

overall_design: The Crtc2+/+ and Crtc2-/- mice were intraperitoneally injected with DEN (25 mg/ kg) at age of 2-weeks old. Mice maintain NASH diet from 8 to 26 week and sacrificed after 26 weeks. Tumors from liver were collected for single-cell RNA sequencing.

first: Fangdi

last: Zou


title: Methylation of the Cg12712415 Locus Suppresses TAK1 Expression to Mediate Immune Paralysis in Severe Pneumonia

city: jinan

first: zhang

middle: jia

last: min

address: 山东省济南市平阴县

institute: jinan central hospital

summary: Severe pneumonia lethality often arises not from excessive inflammation, but from subsequent immune system "paralysis" (immunoparalysis), a clinical challenge lacking specific biomarkers and effective therapies. Our study addressed this by identifying key epigenetic checkpoints driving immunoparalysis. Herein, we identify that DNA methylation at the Cg12712415 locus acts as an epigenetic switch to distinguish and predict secondary immunoparalysis in severe pneumonia patients. Mechanistically, DNMT3A specifically catalyzes this methylation, silencing transcription of the critical kinase TAK1 by blocking RNA polymerase II binding. TAK1 loss impairs monocyte/macrophage functions, disrupts intercellular crosstalk, induces CD8⁺ T cell exhaustion and regulatory T cell expansion, and causes systemic immunosuppression. Importantly, macrophage-derived exosome-mediated TAK1 delivery reversed immunoparalysis and improved survival in animal models. Our findings establish the "DNMT3A–Cg12712415–TAK1" axis as a novel regulatory pathway, provide a new immunoparalysis biomarker, and lay the foundation for an epigenetic-based targeted therapy.

overall_design:
RNA Extraction and Transcriptome Sequencing
Total RNA was extracted from isolated and purified CD14⁺ monocytes using TRIzol reagent. Following ribosomal RNA (rRNA) depletion, sequencing libraries were constructed according to the Illumina library preparation protocol and subsequently sequenced on the Illumina Genome Analyzer II platform.
ATAC‑seq
A total of 1×10⁵ fresh cells were used for each assay. Libraries were constructed using Tn5 transposase treatment and sequenced on an Illumina platform. Raw reads were subjected to quality control using fastp and aligned to the reference genome with Bowtie2. PCR duplicates were removed using Picard, and MACS2 was used for peak calling to identify open chromatin regions (ATAC‑seq peaks). Identified peaks were annotated with HOMER, followed by transcription factor binding motif analysis.
Chromatin Immunoprecipitation (ChIP)
Log-phase cells were washed with PBS, cross-linked with 1% formaldehyde at room temperature for 10 min, and quenched with glycine. After lysis, chromatin was sonicated to 200–500 bp fragments. Chromatin was incubated with anti-RNA polymerase II antibody or control IgG pre-bound to Protein A/G magnetic beads at 4℃ overnight. After washing, elution, cross-link reversal and proteinase K digestion, DNA was purified and analyzed by qPCR for target region enrichment.

first: Shi

last: Zhang


title: Dual BCL-xL and BCL-2 Inhibition for Advanced Myeloid Neoplasms: A phase 1 dose-escalation study of Navitoclax, Venetoclax, and Decitabine

city: Boston

first: Hayden

last: Bell

state: Massachusetts

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Background: The BCL-2 inhibitor venetoclax in combination with a hypomethylating agent is effective against most acute myeloid leukemia (AML) subtypes, but less so against other high-risk myeloid neoplasms. One resistance mechanism to BCL-2 inhibition is increased dependence on alternate BH3-only anti-apoptotic proteins, such as BCL-xL. Navitoclax is a BCL-2/BCL-xL inhibitor that has been previously studied in hematologic malignancies. Patients and methods: We conducted a Phase 1 study of dose-escalated navitoclax added to venetoclax/decitabine for subjects with 1) secondary (s-AML) or therapy-related AML, 2) accelerated- or blast-phase myelofibrosis (AP/BP-MF), 3) myelodysplastic syndrome (MDS)/myeloproliferative neoplasm (MPN) overlap syndromes with excess blasts, or 4) relapsed/refractory (R/R) MDS with excess blasts.  Results:Sixteen subjects were enrolled.  Dose-escalation for BP-MF and s-AML was not completed due to discontinued navitoclax supply.  Most common grade ≥3 treatment-emergent adverse events included neutropenia (69%), thrombocytopenia (69%), and febrile neutropenia (47%). No clinically significant bleeding was observed. One dose-limiting toxicity of delayed neutrophil recovery occurred. Among 15 evaluable subjects, the overall objective response rate was 60% (9/15). The recommended phase 2 dose was decitabine 20 mg/m2 days 1-5, venetoclax 400 mg/day days 1-14, and navitoclax 50 mg/day days 1-14 for AP-MF, MDS/MPN, and R/R MDS.  Correlative studies indicate preserved immature platelet fractions despite on-target reduction of mature platelets, a reduction in disease-associated aberrant monocytes in subjects with monocytic disease, and higher baseline myeloblast dependence on BCL-2 and BCL-xL as predictive of response.  Conclusion:Navitoclax added to venetoclax/decitabine is safely tolerable and is active in patients with high-risk myeloid malignancies.

overall_design:
Bone marrow aspirate mononuclear cells from patients with chronic myelomonocytic leukemia (CMML), including paired longitudinal samples from two unique study patients, underwent single cell multiome (scRNA-seq + scATAC-seq) sequencing. Patients were participants in a single-center, open-label nonrandomized phase 1 study (NCT05455294) investigating administration of navitoclax, venetoclax, and decitabine. Single nuclei were prepared and processed using the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression workflow. Libraries were sequenced on an Illumina NovaSeq 6000.

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

last: Chen

first: Yiwen

last: Liu

first: Jeremy

last: Ryan

first: Jason

last: Wu

first: Emma-Jayne

last: Minihane

first: Eric

last: Winer

first: Marlise

last: Luskin

first: Daniel

last: Roberts

first: Virginia

last: Volpe

first: Rahul

last: Vedula

first: Maximilian

last: Stahl

first: Matthew

last: Hersch

first: Dylan

last: Wilson

first: Jessica

last: Lee

first: Ilene

last: Galinsky

first: Mary

last: Gerard

first: Donna

last: Neuberg

first: Richard

last: Stone

last: DeAngelo

first: Anthony

last: Letai

first: Andrew

last: Lane

first: Jacqueline

last: Garcia


title: A skin-hypothalamus axis couples heat stress and metabolic dysfunction

city: Changsha

first: Xu

last: Feng

state: Hunan

address: 87# Xiangya Road

department: Department of Endocrinology, Endocrinology Research Center

institute: Xiangya Hospital of Central South University

summary: With the ongoing rise in global temperatures, heat stress is increasingly implicated in chronic metabolic disorders; however, whether a transient high-temperature experience leads to enduring metabolic vulnerability and persistent hypothalamic adaptations remains unclear. To address this question, we established a controlled heat stress (HS) mouse model. Eight-week-old male mice with comparable body weights were assigned to HS or paired-fed (PF) conditions. HS mice were exposed to 37 °C for 6 h during the dark phase for 1 week with ad libitum access to food. PF mice were maintained at room temperature and pair-fed to match the food intake consumed by HS mice during the 6-h exposure window, followed by ad libitum feeding for the remaining 18 h to ensure comparable total daily intake. After HS, mice were returned to room temperature for a 2-week quiescent stage (QS), during which blood glucose and serum corticosterone normalized, indicating recovery from acute stress. Hypothalamic cells were collected from PF, HS, and QS groups for single-cell RNA sequencing to characterize heat stress–associated changes in hypothalamic cellular composition and transcriptional states. We observed a sustained increase in astrocyte abundance after HS that persisted into QS, and identified an expanded astrocyte subpopulation marked by high Lrrc7 expression, providing a foundation for further investigation of persistent hypothalamic responses to heat exposure in the context of metabolic regulation.

overall_design:
To investigate whether HS induces persistent changes in hypothalamic cellular composition and transcriptional states, 8-week-old male mice with comparable body weights were assigned to HS, PF, or RT conditions. Hypothalamic cells were collected from mice in the PF, HS, and QS groups and subjected to scRNA-seq. PF served as an intake-matched control to account for differences in food consumption during HS, whereas HS and QS samples represented the heat-exposed state and the post-exposure recovery state, respectively.

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Submitter states that missing raw files are due to file corruption, for GSM9558485.
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first: Hai-Yan

last: Zhou

first: Xiang-Hang

last: Luo


city: Aichi Prefecture

first: Mamoru

last: Oyabu

address: 7-430 Morioka-cho, Obu-shi

department: Geroscience Research Center

country: Japan

institute: National Center for Geriatrics and Gerontology

summary: Catabolic conditions, such as starvation, inactivity, and cancer cachexia, induce Forkhead box O (FoxO) transcription factor(s) expression and severe muscle atrophy via the induction of ubiquitin–proteasome system-mediated muscle proteolysis, resulting in frailty and poor quality of life. Microarray analysis of quadriceps muscle of fed or 24 h-fasted wild type mice and skeletal muscle-specific FoxO1,3,4 knockout mice identified the potential novel FoxOs-target genes in skeletal muscle including Redd1, Sestrin1, Castor2, Chac1, Depp1, Lat3, as well as Cebpd. This study comprehensively identifies novel potential FoxOs-target genes in skeletal muscle and clarifies the pathophysiological role of FoxOs, master regulators of skeletal muscle atrophy.

overall_design: Microarray profiling of quadriceps muscles of fed or 24 h-fasted male 8-week-old mFoxO1,3,4-/- (skeletal muscle specific FoxO1,3,4 knockout) mice and age-matched wild type (WT) mice. mFoxO1,3,4-/- mice were generated as previously described (PMID: 35061305). Briefly, Cre recombinase was driven by human α-actin (HSA) promoter to specifically delete FoxO1, FoxO3, and FoxO4 in skeletal muscle in mFoxO1,3,4-/- mice.

first: Yasutomi

last: Kamei


title: Intestinal LKB1 loss drives a pre-malignant program along the serrated cancer pathway [bulkRNA-seq]

city: Utrecht

first: Jelte

last: van der Vaart

address: Universiteitsweg 100

department: Center for Molecular Medicine

institute: University Medical Center Utrecht

summary:
Background & Aims
Heterozygous inactivating mutations of Serine Threonine Kinase 11 (STK11)/Liver Kinase B1 (LKB1) are causative to the Peutz-Jeghers syndrome (PJS), a hereditary disease characterized by gastrointestinal hamartomatous polyposis and increased cancer susceptibility. While LKB1 loss-induced polyp formation has been ascribed to non-epithelial tissues, how LKB1 deficiency increases cancer risk of patients by altering the phenotypical landscape and hierarchical organization of epithelial tissues remains poorly understood.
Methods
Using CRISPR/Cas9, we generated heterozygous and homozygous Lkb1-deficient mouse small intestinal and human colon organoids. These organoids were characterized by an integrated approach that combines imaging, bulk and single-cell RNA sequencing and growth factor dependency assays. Our findings were validated in human PJS-derived tissues using immunohistochemistry and linked to colorectal cancer profiles using the TCGA cancer database.
Results
Our results reveal that heterozygous Lkb1 loss is sufficient to push intestinal cells into a premalignant transcriptional program associated with serrated colorectal cancer, which is further amplified by loss-of-heterozygosity. This altered epithelial growth state associates with persistent features of regeneration and enhanced EGFR ligand and receptor expression, conferring niche-independent growth properties to Lkb1-deficient organoids. Moreover, our newly generated LKB1-mutant signature is enriched in sporadic serrated colorectal cancer, and synergistic cooperation of Lkb1-deficiency with mutant Kras was experimentally confirmed by assessing organoid growth properties and transcriptomes.
Conclusions
Heterozygous loss of LKB1 pushes intestinal cells into a chronic regenerative state which is amplified upon loss-of-heterozygosity. Lkb1-deficiency thereby generates fertile ground for serrated colorectal cancer formation in the intestine, potentially explaining the increased cancer risk observed in PJS.

overall_design: bulk mRNAseq profiling of mouse small intestinal organoids that are genetically edited. Samples include Lkb1+/- and Lkb1-/- organoids and similar Lkb1 mutant organoids with additional oncogenic drivers (Apc-/- or KrasG12V)

first: Susanna

last: Plugge

first: Huying

last: Ma

first: Joep

last: Sprangers

first: Folkert

last: Morsink

first: Despina

last: Xanthakis

first: Cara

last: Jamieson

first: Kirsten

last: Stroot

first: Anneloes

last: Keijzer

first: Thanasis

last: Margaritis

first: Tito

last: Candelli

first: Roy

last: Straver

first: Jeroen

last: de Ridder

first: Frank

last: Holstege

first: Wendy

last: de Leng

first: Johan

last: Offerhaus

first: Alessandra

last: Merenda

first: Madelon

middle: M

last: Maurice


title: DNA-PK Mediated CRTC2 Phosphorylation Promotes CRTC2 Relocation from Transcription to Repair Complexes Enhancing NHEJ and Suppressing Abscopal Effect [CUT&Tag]

first: zhanjie

last: xiu

overall_design: CUT&Tag of CRTC2 and H2ax in AiDIvA cells treated with doxycycline and in the absence or presence of 4-OHT were collected

first: Fangdi

last: Zou


title: KCNN4 mediated potassium ion efflux maintains mitochondrial functions leading to platelet biogenesis

city: Kyoto

first: Koji

last: Eto

address: 53 Kawahara-cho, Shogoin Kawahara-cho, Sakyo-ku

department: CiRA

institute: Kyoto University

summary: Background: While potassium ion (K+) is known to be vital to platelet functions, we have limited knowledge about K+ channels involved in thrombopoiesis from imMKCLs, the iPSC-derived megakaryocyte progenitor cell lines that we have established for ex vivo manufacturing of platelet products for clinical use. Objective: We aimed to elucidate how K+ channels contribute to platelet biogenesis and focused on the role of Ca2+-activated K+ channel KCNN4 (also known as KCa3.1). Methods: Using imMKCLs and human cord blood hematopoietic stem cell-derived megakaryocytes (CB-megakaryocytes), we examined the dynamic changes of intracellular cations during platelet biogenesis. Along with RNA-seq profiling of K+ channels, we investigated the role of KCNN4 by using inhibitors or by direct gene knockdown in proplatelet formation or platelet production. We further examined its relationship with tubulin reorganization, mitochondrial functions, and reactive oxygen species (ROS) levels. Results: Continuous reduction of intracellular K+ levels ([K+]i) was observed during the 6-day of maturing imMKCLs. KCNN4 was expressed at the initiation of platelet generation in megakaryocytes and KCNN4 inhibition resulted in impaired proplatelet formation and reduced platelet productivity in imMKCLs and CB-megakaryocytes, accompanied by decreased [K+]i, diminished mitochondrial membrane potential and an elevated level of ROS. Conclusions: Our findings suggest that the decline of [K+]i via KCNN4 is a key mechanism linking tubulin regulation, ROS, and mitochondrial functions to proplatelet formation and intact thrombopoiesis. This study sheds new light on thrombopoiesis mechanism that contributes to improved ex vivo platelet manufacturing.

overall_design: RNA-seq profiling of imMKCLs at maturation stage (absent of doxcycline, Dox-OFF) from day 0 to day 4

first: Qihao

last: Chen

first: Takuya

last: Yamamoto

first: Sou

last: Nakamura


title: Filamin–ETV4/5 acts as mechanosensor–mechanotransducer axis that drives cell competition-mediated elimination of transformed cells

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

summary: Cell competition is a fundamental surveillance mechanism that preserves epithelial integrity by eliminating aberrant “loser” cells through interactions with surrounding “winner” cells. However, how winner cells sense and eliminate transformed neighbours remains poorly understood. Here, using a synNotch-based transcriptomic screen, we identify a mechanosensor–mechanotransducer axis linking the actin crosslinker filamin to the ETV4/5–PRKG2 pathway that mediates extrusion of oncogenically transformed cells through cell competition. Within an epithelial monolayer, transformed cells increase their volume, inducing membrane stretching. In adjacent normal cells, filamin senses the increased membrane tension and triggers activation of ETV4/5. Activated ETV4/5 then upregulate PRKG2, which promotes volume expansion of normal cells, consequently pushing back and driving the extrusion of transformed cells. These findings reveal that dynamic changes in cell volume can trigger mechanotransduction-driven cell competition, uncovering a fundamental pathway by which epithelial tissues maintain homeostasis and defend against oncogenic transformation.

overall_design: Transcriptome analysis of EpH4 cells directly contacting RasV12-transformed cells using the synNotch system

first: Jiaying

last: Wen

first: Kazuhito

last: Sai

first: Suzuka

last: Masutani

first: Yuki

last: Aoshima

first: Kotaro

last: Yumi

first: Tomoki

last: Kyo

first: Junya

last: Hasegawa

first: Toshiki

last: Itoh

first: Ken

last: Mizuta

first: Tomonori

first: Mitinori

last: Saitou

first: Satoshi

last: Toda

first: Yasuyuki

last: Fujita


title: The effects of different lesions on the downstream signaling mechanisms of vascular cells.

first: Xiaozheng

last: Zhou

summary: In order to investigate the influence of clinical pathological conditions on the downstream signaling mechanism, we analyzed the activation status of the vascular tissue signaling pathways under different pathological conditions.

overall_design: Conduct comparative gene expression profiling analysis on the RNA-seq data of vascular tissues

first: Zhiyong

last: Du


title: Instant fluorescence lifetime imaging microscopy reveals mechano-metabolic reprogramming of stromal cells in breast cancer peritumor microenvironment

city: Notre Dame

first: Julian

last: Najera

state: IN

address: 2031 McCourtney Hall East

institute: University of Notre Dame

summary: The breast peritumor microenvironment (pTME) is increasingly recognized as a mediator of breast cancer progression and treatment resistance. However, how tumor compressive forces (i.e., solid stresses) influence it remains unclear. Using instant fluorescence lifetime imaging microscopy (FLIM), we show that in vitro compression metabolically reprograms stromal cells found in the breast pTME. Namely, compression shifts fibroblasts and differentiated adipocytes toward a more glycolytic state, but promotes increased oxidative phosphorylation in undifferentiated adipocytes. Through RNA-sequencing, we confirmed that compression downregulates oxidative phosphorylation and upregulates glycolysis in fibroblasts. By elucidating tumor-host mechano-metabolic interactions, these results will inform the development of innovative treatment strategies to improve survival.

overall_design: RNA-seq profiling of NIH3T3 fibroblasts subjected to 0.14 kPa of compression or 0 kPa of compression (uncompressed).


title: Genomic analysis to identify correlates of the inflamed tumor phenotype in patients with advanced malignancies receiving immunotherapy

city: Chicago

first: Thomas

last: Gajewski

state: IL

address: 929 E 57th St

institute: University of Chicago

summary: This biomarker study will analyze tissues from patients with cancer who are receiving immunomodulatory treatment (or therapy that could be hypothesized to modulate the immune response), to correlate molecular/genetic features of the tumor cells, the host, and the intestinal microbiome with the immunologic phenotype of the tumor microenvironment. Recent data have suggested that patients with pre-existing T cell infiltration in the tumor microenvironment and/or an “inflamed” gene expression profile in tumor sites have better clinical outcome following treatment with several immunotherapeutic approaches. However, the mechanism by which this spontaneous anti-tumor immune response develops in only a subset of patients is not understood. Potential correlations between mutational patterns in the tumor, germline genetic polymorphisms, peripheral blood immune response parameters, and the composition of intestinal microbiota and the presence or absence of a T cell-infiltrated tumor microenvironment will be sought. Understanding these mechanisms will have important implications for future patient selection for treatment with immunotherapies and highlight new potential pathways for therapeutic development. Mechanisms of secondary resistance to immunotherapies also will be interrogated using tissues obtained at time of recurrence.

overall_design: Adult patients with advanced cancer, willing to provide at least a subset of tissues can be enrolled in the study. Blood, stool, and tumor specimen are collected prior to and during the course of treatment. Genetic and/or immune histochemical analysis are performed with tumor tissue, germline samples to identify patterns of genetic alterations and germline polymorphisms associated with the presence or absence of a T cell-infiltrated tumor microenvironment. In addition, species composition of the intestinal microbiota and circulating  factors in the peripheral blood are analyzed to determine their association with the presence or absence of a T cell-infiltrated tumor microenvironment. This submission includes 15 samples submitted previously in GSE285619 (see metadata.txt).

first: Daniel

last: Olson


title: Gene expression profiling of tumor organoids of colorectal liver metastases.

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

summary: We have performed gene expression profiling of patient-derived tumor organoids (PDOs) and tissue samples of resected liver metastases from patients with metastatic colorectal cancer.

overall_design: This series consists of PDOs (n=119) cultured from resected liver metastases from patients with colorectal cancer, as well as corresponding tumor tissue samples for a subset (n=50). PDOs were cultured from multiple metastatic lesions from a subset of the patients. All samples were analyzed on Affymetrix Human Transcriptome 2.0 Arrays.

first: Kushtrim

last: Kryeziu

first: Ragnhild

last: Lothe


title: RNA-seq from Drosophila heads differentiating place preference

city: Sai Kung

first: Yukinori

last: Hirano

address: Clear water bay

department: LIFS

country: Hong Kong

institute: The Hong Kong University of Science and Technology

summary: In Drosophila, we tried to determine the stress-induced gene expression change associated with the behavioral mode examined by a place preference test. We conducted RNA-seq analysis from total RNA obtained from individual Drosophila heads, either in naive state or after electric shock. Using an optimized data analysis workflow, we mapped about 6-12 million reads to Drosophila reference genome, dm6. The genes showing significant difference were found in most between naive group and shocked group showing medium avoidance from a confined space.  Our study demonstrated that Toll-signaling related genes are enriched after electric shock.

overall_design: After obtaining total RNA from individual head using standard Trizol-based method, mRNA was purified with oligo dT magnetic beads, and used to prepare library. After deep sequencing using illumine Hiseq X, the adaptors were trimmed via Trimommatic, followed by mapping to the Drosophila reference genome, dm6 from UCSC using STAR. The reads with low mapping quality below 8 and the non-primary mapped reads were eliminated. The filtered reads were analyzed with HTSeq-count to obtain numbers of the reads mapped on exons, which was further analyzed on R using DESeq2

first: Abdalla

middle: G

last: Alia


title: UBA1-CDK16: A Female-Specific Chimeric RNA Emerging Through Evolution and Involved in Immune Regulation

city: Charlottesville

first: Shafaque

last: Zahra

state: VA

address: MR6, 345 Crispell Drive

department: Pathology

institute: University of Virginia

summary: Chimeric RNAs resulting from intergenic splicing represent a novel mechanism for transcriptome expansion. To explore the role of this new layer of the transcriptome in sex-specific immunity, we analyzed RNA-seq data from 425 blood samples and identified the first female-specific chimeric RNA, UBA1-CDK16, which was further validated in over 1,200 blood samples. This chimeric RNA forms via cis-splicing between two adjacent X-linked parental genes, UBA1 and CDK16, despite both being expressed in both sexes. We demonstrated that a female-specific chromatin loop at the UBA1-CDK16 junction sites facilitates the intergenic splicing. Evolutionary analysis revealed that UBA1-CDK16 became female-specific in humans through at least two independent paths. Functional studies suggested UBA1-CDK16 is enriched in the myeloid lineage and may regulate myeloid cell development and inflammatory responses. Notably, its abnormal expression in female COVID-19 patients correlates with altered neutrophil counts, highlighting its potential role in disease pathogenesis.

overall_design: The experiment compares single-cell transcriptomes of CD34+ female cells: non-targeting control (shGFP) and targeted knockdown (shUBA1-CDK16). Both populations are harvested at the same time point, Day 3 of in vitro myeloid differentiation, to identify gene expression changes driven by the knockdown.

first: Xinrui

last: Shi

first: Loryn

last: Facemire

first: Sandeep

last: Singh

first: Shailesh

last: Kumar

first: Robert

last: Cornelison

first: Chen

last: Liang

first: Fujun

last: Qin

first: Aiqun

last: Liu

first: Shitong

last: Lin

first: Yue

last: Tang

first: Justin

last: Elfman

last: Manley

first: Martyna

last: Glowczyk

first: Anam

last: Tajammal

first: Timothy

last: Bullock

first: Doris M

last: Haverstick

first: Peng

last: Wu

first: Hui

last: Li


title: Effects of loss of KAT6A on histone acetylation and methylation levels, as well as MLL1 and POLR2A occupancy

city: Parkville

first: Waruni

last: Abeysekera

state: Victoria

address: 1G Royal Parade

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

summary: Heterozygous variants in the KAT6A gene encoding the histone lysine acetyltransferase KAT6A (MOZ, MYST3) cause Arboleda-Tham syndrome, an intellectual disability syndrome. The profound effects of pathogenic variants in only one allele of KAT6A on cognitive development and functions raises the question what effects heterozygous and homozygous loss of KAT6A may have on gene expression and chromatin modifications, specifically in a neural cell type that is functionally affected by loss of KAT6A. To address this question, we established that murine neural stem and progenitor cells form fewer neurons after loss of one and two alleles of Kat6a and used these cells to conduct automated chromatin profiling. We determined within the same cell preparation acetylation at histone H3 lysines 9, 14 and 23, RNA polymerase II (POLR2A) and MLL1 occupancy, as well as levels of methylation at histone H3 lysine 4 (H3K4), the MLL1 target, and compared these chromatin profiling results to the effects of loss of KAT6A on gene expression.

overall_design: We performed automated CUT&Tag chromatin profiling on NSPCs isolated from the dorsal telencephalon (the cerebral cortex precursor) of Kat6a+/+ (3 replicates), Kat6a+/– (4 replicates) and Kat6a–/– (3 replicates) E12.5 embryos, to detect in the same biological sample cell preparation multiple chromatin marks. These included the acetylation targets proposed for KAT6A, namely H3K9ac, H3K14ac and H3K23ac. We had previously observed MLL1 occupation of HOX genes to be dependent on the presence of KAT6A. Therefore, we assessed  MLL1. Within its four to five partite protein complex, MLL1 is a H3K4me2/3 methyltransferase. We assessed H3K4me3, which is the target of MLL1 that is most closely associated with mRNA levels. Lastly, we included RNA polymerase II subunit A phosphorylated on Ser2 [POLR2A; also known as Phospho-Rpb1 CTD]. Phosphorylation of POLR2A at Ser2 is required for elongation and allowed us to determine if the absence of KAT6A affected POLR2A progression through a gene locus.

first: Gordon

last: Smyth

first: Anne

last: Voss

first: Tim

last: Thomas

first: Johannes

last: Wichmann


title: Western diet-induced MASH in PWK/PhJ mice identifies disruptions in amino acid and sphingolipid metabolism contributing to cardiac dysfunction

city: LAUSANNE

first: Johan

last: Auwerx

address: Station 15

department: SV-IBI

country: Switzerland

institute: Ecole Polytechnique Fédérale de Lausanne EPFL

summary: Metabolic dysfunction-associated steatotic liver disease (MASLD) and metabolic dysfunction-associated steatohepatitis (MASH) are liver disorders strongly associated with cardiovascular disease (CVD). The PWK/PhJ mouse strain is an emerging model for severe MASH, highly susceptible to Western diet (WD) and closely mimicking the clinical and molecular profile of human MASH. Here, we demonstrate that male and female PWK/PhJ mice exhibit accelerated hepatic fibrosis and cardiac dysfunction following a WD challenge. Elevated cholesterol levels and altered transcript profiles associated with translation and lipid metabolism characterize the early metabolic changes induced by WD. Chronic exposure to WD exacerbates hepatic lipid accumulation, inflammation, and fibrosis, disrupts amino acid metabolism, and increases ceramides and deoxy-ceramides synthesis. We propose that these hepatic changes contribute to the cardiac dysfunction observed in PWK/PhJ mice and may be closely associated with an elevated risk of CVD, thus, positioning the PWK/PhJ strain as a robust model for investigating liver-heart disease connection.

overall_design: BRB-seq profiling of liver and heart tissues from PWK/PhJ male and female mice after a dietary challenge with either chow diet (CD) or Western diet (WD). Samples were collected at days 3, 9, and 27, as well as at weeks 9 and 17 post-challenge under thermoneutral housing (TN). At week 17, an additional group of animals was also housed at room temperature (RT).


title: EPIC-array 850k data from human HCT116 wild-type cells, HCT116 DNMT1 hypomorphs, and HCT116 UHRF1 hypomorphs.

city: Guangzhou

first: Jiongliang

last: Wang

state: Guangdong

address: 190 Kaiyuan Avenue

institute: GUANGZHOU INSTITUTES OF BIOMEDICINE AND HEALTH,CHINESE ACADEMY OF SCIENCES

type: Genome binding/occupancy profiling by genome tiling array

summary: DNA methylation profiling (Illumina’s Infinium Methylation EPIC Bead Chip v1.0 microarray) were performed in human HCT116 wild-type cells, HCT116 DNMT1 hypomorphs, and HCT116 UHRF1 hypomorphs.

overall_design: Overall design Bisulphite converted DNA from all samples were hybridized to the Infinium MethylationEPIC 850k Beadchip


title: RNA-seq data from human HCT116 wild-type cells, HCT116 DNMT1 hypomorphs, and HCT116 UHRF1 hypomorphs.

summary: transcriptome profiling were performed in human HCT116 wild-type cells, HCT116 DNMT1 hypomorphs, and HCT116 UHRF1 hypomorphs. The paired-end RNA-seq on the Illumina platform was employed to obtain comprehensive gene expression profiles.

overall_design: Human HCT116 wild-type cells, HCT116 DNMT1 hypomorphs, and HCT116 UHRF1 hypomorphs


title: Effect of ethylene on potato tuber dormancy during postharvest storage

city: Fargo

first: Tadeu

middle: dos Reis de

last: Oliveira

state: ND

address: 1616 Albrecht Blvd. North

department: Edward T. Schafer Agricultural Research Center

institute: USDA-Agricultural Research Service

summary: To investigate transcriptomic and hormonal responses of Russet Burbank potato tubers under ethylene treatment during dormancy progression and postharvest storage.

overall_design: Comparative gene expression analyses were conducted on potato tubers subjected to continuous ethylene treatment (10 ppm) for 15 weeks. Tissue samples, including primary meristems and flesh tissues, were collected at 3-week intervals (0, 3, 6, 9, 12, 15 weeks) and weekly post-treatment (16, 17, 18 weeks).

first: Munevver

last: Dogramaci

first: Dipayan

last: Sarkar


title: Translational changes upon aging and dietary restriction in progeroid DNA-repair-deficient mice [Ribo-Seq]

first: Wilbert

last: Vermeij

address: Heidelberglaan 25

institute: Princess Máxima Center

summary: Aging is a complex multifactorial phenomenon largely driven by damaged macromolecules. We showed recently that with aging time- and exposure-dependent accumulation of DNA damage derails the basal process of transcription physically stalling RNA polymerase, lowering and skewing the transcriptional landscape in a gene-length-dependent fashion. However, how this influences the translational output and whether translation is similarly affected is largely unknown. Here, we present a parallel analysis of transcriptional and translational liver profiles from the well-characterized Ercc1Δ/− progeroid, DNA repair-deficient mouse model compared to wildtype under ad libitum conditions and upon dietary restriction (DR), which strongly delays aging in this mutant.  Using ribosome profiling, we found that transcriptional changes during accelerated, normal, and delayed aging are largely preserved at the translational level ruling out a major translational impact on gene expression in aging in our models. Moreover, in both Ercc1Δ/− and aged wild-type mice there was a prioritization of inflammation, metabolic redesign, and expression of translation initiation factors, along with a shift in codon occupancy. While translation initiation factors were further increased by DR, codon occupancy was partially normalized showing a discordant response. Additionally, increased ribosomal pausing and a relative reduction of upstream open reading frame expression were both further intensified by DR.  Together these data infer a finetuning of the translational output, e.g. by regulating upstream open reading frames under various cellular stress situations. This study uncovers a complex interplay between DR, DNA damage, aging, and translational regulation, highlighting the potential of DR to modify DNA damage-driven translational dynamics during aging.

overall_design: 6 different groups (n=4 per group): Wildtype 16 weeks ad libitum fed, Wildtype 16 weeks 30% dietary restriction, Wildtype 104 weeks ad libitum fed, Ercc1Δ/− progeroid 7 weeks ad libitum fed, Ercc1Δ/− progeroid 16 weeks ad libitum fed, Ercc1Δ/− progeroid 16 weeks 30% dietary restriction

first: Ivar

last: van Galen

first: Rutger

last: Ozinga

first: Jip

last: van Dinter

first: Sebastiaan

last: van Heesch

first: Jan

middle: H

last: Hoeijmakers

middle: P


title: DNA-PK Mediated CRTC2 Phosphorylation Promotes CRTC2 Relocation from Transcription to Repair Complexes Enhancing NHEJ and Suppressing Abscopal Effect [RNA-Seq]

first: zhanjie

last: xiu

address: HUANHU XI ROAD, TIYUAN BEI, HEXI DISTRICT

institute: TIANJIN MEDICAL UNIVERSITY CANCER INSTITUTE & HOSPITAL

summary: DNA damage repair and transcription are antagonistic cellular processes that require precise spatiotemporal coordination to maintain genomic integrity. Transcriptional silencing at DSB sites is essential for efficient repair, mediated through localized histone modifications and direct inhibition of RNA polymerase II (Pol II). However, the role of transcriptional activators in coordinating DSB repair with transcriptional silencing remains elusive. Here, we identify the transcriptional coactivator CRTC2 as a key coordinator of DNA repair and transcriptional regulation. We demonstrate that CRTC2 promotes canonical non-homologous end joining (c-NHEJ) both in vitro and in vivo. Mechanistically, PARP1 activation recruits CRTC2 to DNA breaks, where it facilitates DNA-PKcs recruitment and assembly of the DNA-PK holoenzyme, thereby driving c-NHEJ. DNA-PK–mediated phosphorylation of CRTC2 at Ser433 dissociates it from transcriptional complexes, suppressing target gene transcription, and promoting its incorporation into DNA repair complexes. Thus, establishing a positive feedback loop that enhances NHEJ efficiency. CRTC2 loss radiosensitizes cancer cells, potentiates irradiation-induced cGAS–STING activation, promotes cytotoxic CD8⁺ T cell infiltration, and enhances the abscopal effect. Furthermore, AAV8-mediated targeting of CRTC2 sensitizes tumors to radioimmunotherapy. Our results reveal CRTC2 as bifunctional nodal effector coupling transcriptional silencing to DNA repair and propose its inhibition as a promising strategy for radioimmunotherapy sensitization in resistant malignancies.

overall_design: RNA-seq profiling of  AiDIvA cells treated with doxycycline and in the absence or presence of 4-OHT were collected

first: Fangdi

last: Zou


title: Mapping self-associating chromatin hubs identifies Id proteins as key determinants of exhausted T cell fate

city: washington dc

first: Shaoqi

last: Zhu

state: WASHINGTON

address: 725 21st st nw

institute: the george washington university

summary: This study aims to define how Id2 and Id3 regulate exhausted CD8+ T cell fate. We found that Id2 deletion reduced the Tex-eff population, whereas Id3 ablation in CD4-Cre mice diminished Tpex cells, indicating subset-specific roles for Id2 and Id3. Mechanistically, E2A is a major target of Id2/3, and Runx3 interacts with E2A. Pulldown of Id2/3 recovered both E2A and Runx3, supporting an Id2/3?E2A?Runx3 regulatory complex. To map the genomic occupancy of Id2 and Id3, we expressed 3×T7-tagged Id2 or Id3 in in vitro-primed CD45.2+ P14 cells, adoptively transferred these cells into CD45.1 recipient mice, and infected the recipients with LCMV Clone 13. On day 6 post-infection, Tex-eff and Tpex cells were isolated for T7 CUT&RUN to define Id2 binding in Tex-eff cells and Id3 binding in Tpex cells, with the empty T7 vector backbone used as a negative control.

overall_design:
Sort-purified cells were treated with TN5 transposase to generate tagged DNA fragments. TN5-tagged DNA fragements were purified, PCR amplified to build ATAC-seq libraries. The resulting libraries were seqeunced with Illumina NovaSeq 6000 platform.

Genome-wide mapping of E2A binding profiles in WT (sgThy1) and Id2-KO (sgId2) exhausted effector (Tex-eff) CD8+ T cells.

Genome-wide mapping of Runx3 binding profiles in WT (sgThy1) and Id2-KO (sgId2) exhausted effector (Tex-eff) CD8+ T cells.

Genome-wide mapping of T7-tagged Id2 binding profiles in Tex-eff cells and T7-tagged Id3 binding profiles in Tpex cells.

first: Hai-Hui

last: Xue

first: Weiqun

last: Peng

first: Wei

last: Hu


title: Impact of chronic kidney disease (CKD) on heart remodeling after myocardial infarction (MI)

city: Aachen

first: Julia

last: Wollenhaupt

address: Pauwelsstraße 30

department: Institute for Molecular Cardiovascular Research

country: Germany

institute: Uniklinik RWTH Aachen

summary: Uremic cardiomyopathy is a clinically highly relevant cause of cardiovascular events in patients with chronic kidney disease (CKD). Additionally, after acute myocardial infarction (MI), CKD-patients exhibit an increased risk of death. To investigate the underlying molecular mechanisms causing the adverse effects of CKD on cardicac outcome after MI, male mice were fed with an adenine-supplemented diet combined with western type diet (CKD mice) or with western type diet only (control mice). Invasive heart function evaluation and histological analyses were performed 7 days after MI-induction through left anterior descending artery (LAD) ligation. For a deeper look on molecular level, RNA sequencing of heart tissue was performed.

overall_design: Heart tissue of male mice was studied with RNAseq, comparing adenine-fed mice (CKD mice) vs. control mice 7 days post-MI.

first: Heidi

last: Noels

first: Corinna

last: Schulte

first: Eva

last: Harlacher

first: Han

last: Jin


title: Transcripts identified by microarray analysis that were deregulated in E15.5 Pax2-cre/+;Trp63(dN-flox/dN-flox) (ΔNp63-cKO) ureters

city: Hannover

first: Mark-Oliver

last: Trowe

address: Carl-Neuberg-Str. 1

department: Molekularbiologie

institute: Medizinische Hochschule Hannover

summary: Evaluation of the transcriptional changes in E15.5 ureters upon loss of ΔNp63 in the ureteric epithelium.

overall_design: Total RNA from dissected ureters of E15.5 ΔNp63-cKO and control embryos was analyzed by microarray analysis.

first: Andreas

last: Kispert

first: Fairouz

last: Qasrawi


title: 16s rDNA amplicon sequencing from Drosophila associated with age-dependent sleep fragmentation

first: Yukinori

last: Hirano

summary: In Drosophila, we tried to determine the microbiota associated with age-dependent sleep fragmentation. To this end, the aged male flies showing sleep fragmentation was sampled to compare with those without showing sleep fragmentation. Using an optimized data analysis workflow, we obtained about 0.1 million reads of 16s rDNA from single flies. Data indicated different microbiome between two groups.

overall_design: After obtaining DNA from individual body, 250 bp of 16s rDNA was amplified by PCR. The PCR product was used to prepare a library for sequencing. After deep sequencing using NovaSeq, the adaptors were trimmed via Trimommatic, followed by classified according to Amplicon sequence variant (ASV).

first: Priyanshu

last: Bhagava


title: Rare ADAR1 loss-of-function variants alter RNA editing and drive interferon-dependent inflammation in psoriasis

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

summary: In 4 unrelated pedigrees, we report rare heterozygous loss-of-function ADAR1 mutations cosegregating with autosomal dominant, early onset psoriasis and increased type I interferon (IFN)-stimulated gene (ISG) transcripts in skin lesions and/or blood. We identified 6 additional variants in a psoriasis cohort. Skin single cell transcriptomics identified keratinocytes and melanocytes as key IFN sources. ADAR1 knockdown in keratinocytes and melanocytes, and transduction of ADAR1G1119R and ADAR1P3A alleles in keratinocytes, led to reduced A-to-I RNA editing and upregulation of ISG expression, reversed by JAK1 and TYK2 inhibition, mirroring their clinical benefit in these patients. This set of data defines a new IFN-dependent psoriasis subtype resulting from inborn errors of ADAR1-dependent RNA editing, leading to IFN constitutive dysregulation, and opens new avenues in precision medicine.

overall_design:
Single-cell RNA sequencing (scRNA-seq) was conducted on cell suspensions derived from FFPE skin biopsies collected from healthy controls, as well as from lesional and nonlesional skin of patients with psoriasis and ADAR1-mutant psoriasis.

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The table below lists GEO accessions reused/reanalyzed for this study.
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first: Johann

middle: E

last: Gudjonsson

first: Lam

last: Tsoi


title: Intestinal LKB1 loss drives a pre-malignant program along the serrated cancer pathway [scRNA-seq]

first: Jelte

last: van der Vaart

address: Universiteitsweg 100

institute: University Medical Center Utrecht

summary:
Background & Aims
Heterozygous inactivating mutations of Serine Threonine Kinase 11 (STK11)/Liver Kinase B1 (LKB1) are causative to the Peutz-Jeghers syndrome (PJS), a hereditary disease characterized by gastrointestinal hamartomatous polyposis and increased cancer susceptibility. While LKB1 loss-induced polyp formation has been ascribed to non-epithelial tissues, how LKB1 deficiency increases cancer risk of patients by altering the phenotypical landscape and hierarchical organization of epithelial tissues remains poorly understood.
Methods
Using CRISPR/Cas9, we generated heterozygous and homozygous Lkb1-deficient mouse small intestinal and human colon organoids. These organoids were characterized by an integrated approach that combines imaging, bulk and single-cell RNA sequencing and growth factor dependency assays. Our findings were validated in human PJS-derived tissues using immunohistochemistry and linked to colorectal cancer profiles using the TCGA cancer database.
Results
Our results reveal that heterozygous Lkb1 loss is sufficient to push intestinal cells into a premalignant transcriptional program associated with serrated colorectal cancer, which is further amplified by loss-of-heterozygosity. This altered epithelial growth state associates with persistent features of regeneration and enhanced EGFR ligand and receptor expression, conferring niche-independent growth properties to Lkb1-deficient organoids. Moreover, our newly generated LKB1-mutant signature is enriched in sporadic serrated colorectal cancer, and synergistic cooperation of Lkb1-deficiency with mutant Kras was experimentally confirmed by assessing organoid growth properties and transcriptomes.
Conclusions
Heterozygous loss of LKB1 pushes intestinal cells into a chronic regenerative state which is amplified upon loss-of-heterozygosity. Lkb1-deficiency thereby generates fertile ground for serrated colorectal cancer formation in the intestine, potentially explaining the increased cancer risk observed in PJS.

overall_design: single mRNAseq profiling of mouse small intestinal organoids that are genetically edited. Samples include Lkb1+/- and Lkb1-/- organoids

first: Susanna

last: Plugge

first: Huying

last: Ma

first: Joep

last: Sprangers

first: Folkert

last: Morsink

first: Despina

last: Xanthakis

first: Cara

last: Jamieson

first: Kirsten

last: Stroot

first: Anneloes

middle: R

last: Keijzer

first: Thanasis

last: Margaritis

first: Tito

last: Candelli

first: Roy

last: Straver

first: Jeroen

last: de Ridder

first: Frank

last: Holstege

first: Wendy

last: de Leng

first: Johan

last: Offerhaus

first: Alessandra

last: Merenda

first: Madelon

last: Maurice


title: RNA-seq from Drosophila heads and bodies associated with age-dependent sleep fragmentation

first: Yukinori

last: Hirano

summary: In Drosophila, In Drosophila, we tried to determine the genes associated with age-dependent sleep fragmentation. To this end, the aged male flies showing sleep fragmentation was sampled to compare with those without showing sleep fragmentation. Using an optimized data analysis workflow, we mapped about 0.2-0.6 million reads to Drosophila reference genome, dm6. The genes showing significant difference were found in most between naive group and shocked group showing medium avoidance from a confined space. Our study demonstrated differentially expressed genes in aged flies showing sleep fragmentation.

overall_design: After obtaining total RNA from individual head or body using standard Trizol-based method, mRNA was purified with oligo dT magnetic beads, and used to prepare library. After deep sequencing using illumine Hiseq X, the adaptors were trimmed via Trimommatic, followed by mapping to the Drosophila reference genome, dm6 from UCSC using STAR. The reads with low mapping quality below 8 and the non-primary mapped reads were eliminated. The filtered reads were analyzed with HTSeq-count to obtain numbers of the reads mapped on exons, which was further analyzed on R using DESeq2.

first: Priyanshu

last: Bhagava


title: 3D Chromatin organization of signal-induced specific enhancers safeguards early ESC differentiation by promoting cluster gene expression [CUT&Tag]

first: Weipeng

last: Mo

address: 58 Zhongshaner Rd

department: The First Affiliated Hospital

institute: Sun Yat-sen University

summary: Cells undergo fate transformation in response to external signaling stimuli, a process that depends on the precise expression of specific genes, but the intrinsic regulatory mechanisms remain largely unclear. Here, by integrating bulk RNA sequencing, single-cell RNA sequencing, 4D-SmartDIA quantitative proteomics data, and a CRISPR/Cas9-mediated RA receptor deletion model, we find that RA signaling-induced early ESC differentiation is multilineage. During early ESC differentiation, in the context of attenuated and enhanced RA signaling, we identified Cyp26 and HoxB cluster genes as its direct downstream targets. Upon activation of RA signaling, RA receptors induce new specific enhancers in the proximal/distal regions of cluster gene loci, whereas inhibition of RA signaling significantly reduces proximal/distal enhancer activity, chromatin accessibility and cluster gene expression. Mechanistically, we found that proximal/distal enhancers form specific chromatin loops with cluster gene loci under RA induction, and RA receptor deletion significantly reduces these chromatin interactions. Knockout of the proximal/distal enhancers inhibits cluster gene expression, thereby further disrupting RA-induced early ESC differentiation. In summary, our findings reveal an insightful mechanism underlying the signal-induced specific 3D genomic structure and cluster gene expression critical for early ESC fate transitions.

overall_design: To detect enhancer regulation by RA signalling in early ESC differentiation, we examined chromatin immunoprecipitation of H3K27ac as well as RARA/RXRA in WT and DKO cells, respectively.

first: Guangsong

last: Su

first: Wange

last: Lu


title: 3D Chromatin organization of signal-induced specific enhancers safeguards early ESC differentiation by promoting cluster gene expression [ATAC-seq]

overall_design: In order to test whether the RA signal regulates the chromatin accessibility of the proximal and distal enhancers of the cluster genes, we performed ATAC sequencing in WT and DKO cells 24 hours after RA-induced differentiation.


title: Single cell RNA sequencing (scRNA-seq) of embryonic zebrafish and human aortic endothelial cells following flow modulation

city: Boston

first: Aryan

last: Kaveh

address: 60 Fenwood Road

department: Medicine

institute: Brigham and Women's Hospital

summary: The earliest vascular manifestations during atherosclerosis development are incompletely understood. We utilize low density lipoprotein receptor knockout (ldlr-/-) zebrafish and human aortic endothelial cells (HAECs) to discern developmental and flow-dependent features underlying atherosclerosis. ScRNA-seq was used to analyze the transcripitional heterogeneity of endothelial cells from embryonic ldlr-/- zebrafish and HAECs following flow modulation.

sample_organism:
Danio rerio
Homo sapiens

platform_organism:
Danio rerio
Homo sapiens

overall_design: For embryonic Tg(flk:GFP) ldlr-/- zebrafish and wild-type (wt) controls, endothelial cells were isolated using fluorescence-activated cell sorting according to the presence of GFP signal. Non-endothelial cells (all other cell types) were also isolated by the absence of GFP signal. Both GFP+ endothelial cells and GFP- embryonic zebrafish cells were analyzed following blood flow inhibition using scRNA-seq. HAECs were harvested following 48 hours of flow modulation and analyzed using scRNA-seq.

first: Antonio

last: Salazar-Martin

first: Wei

last: Dai

first: Aaron

last: Kithcart

first: Emily

last: Pan

first: Ashmita

last: KC

first: Tyler

last: Reinoso

first: Franki

last: Vetrano-Olsen

first: Kusumika

last: Saha

first: Manu

last: Beerens

first: Peter

last: Libby

first: Elazer

last: Edelman

first: Calum

last: MacRae


title: 3D Chromatin organization of signal-induced specific enhancers safeguards early ESC differentiation by promoting cluster gene expression [scRNA-seq]

overall_design: To study the transcriptome of RA signalling regulation, we designed single-cell experiments to discover the intrinsic mechanisms.


title: Translational changes upon aging and dietary restriction in progeroid DNA-repair-deficient mice

first: Wilbert

last: Vermeij

summary: Aging is a complex multifactorial phenomenon largely driven by damaged macromolecules. We showed recently that with aging time- and exposure-dependent accumulation of DNA damage derails the basal process of transcription physically stalling RNA polymerase, lowering and skewing the transcriptional landscape in a gene-length-dependent fashion. However, how this influences the translational output and whether translation is similarly affected is largely unknown. Here, we present a parallel analysis of transcriptional and translational liver profiles from the well-characterized Ercc1Δ/− progeroid, DNA repair-deficient mouse model compared to wildtype under ad libitum conditions and upon dietary restriction (DR), which strongly delays aging in this mutant.  Using ribosome profiling, we found that transcriptional changes during accelerated, normal, and delayed aging are largely preserved at the translational level ruling out a major translational impact on gene expression in aging. Moreover, in both Ercc1Δ/− and aged wild-type mice there was a prioritization of inflammation, metabolic redesign, and expression of translation initiation factors, along with a shift in codon occupancy. While translation initiation factors were further increased by DR, codon occupancy was partially normalized showing a discordant response. Additionally, increased ribosomal pausing and a relative reduction of upstream open reading frame expression were both further intensified by DR.  Together these data infer a finetuning of the translational output, e.g. by regulating upstream open reading frames under various cellular stress situations. This study uncovers a complex interplay between DR, DNA damage, aging, and translational regulation, highlighting the potential of DR to modify DNA damage-driven translational dynamics during aging.

first: Ivar

last: van Galen

first: Rutger

last: Ozinga

first: Sebastiaan

last: van Heesch

first: Jan

last: Hoeijmakers


title: Understanding Isoprenol effect on Pseudomonas putida KT2440 grown on a minimal medium supplemented with glucose

city: Incheon

first: Hyungyu

last: Lim

address: Inha ro 100

country: South Korea

institute: Inha University

summary: Pseudomonas putida KT2440 (KT2440) has been established as an industrially relevant chassis for the production of the jet-fuel precursor isoprenol. However, the wild type KT2440 strain consumed isoprenol as sole carbon source and its growth is inhibited by isoprenol, which is an impediment to high titer, rate, yield production. In this study, we investigated genes responsible for isoprenol catabolism and the stress responses of Pseudomonas putida via RNA-seq.

overall_design: The wildtype Pseudomonas putida KT2440 was grown on either 4 g/L of glucose or isoprenol.

first: Hyun


title: Baseline and Follow-up Methylation Profiling of Whole Blood DNA in Normoglycemia, Prediabetes, and Type 2 Diabetes

city: Thiruvananthapuram

first: Gopika

last: Satheesh

state: Kerala

address: Poojappura

department: Cardiovascular Diseases and Diabetes Biology

country: India

institute: BRIC-Rajiv Gandhi Centre for Biotechnology

type: Methylation profiling by high throughput sequencing

summary: This longitudinal study analyzed whole-blood DNA methylation profiles in adults classified as normoglycemic, prediabetic, or type 2 diabetes mellitus (T2DM). Oxford Nanopore PromethION long-read sequencing (PCR-free ligation preparation) was used to generate genome-wide CpG methylation data at baseline and at six-year follow-up. The dataset includes raw nanopore reads (available in SRA) and processed methylation outputs, including CpG-wise differential methylation, methylation summaries, promoter/CpG island annotation, HOMER functional annotation, and gene–pathway mapping

overall_design: Whole blood DNA was collected from 24 participants (12 baseline, 12 matched follow-up). Samples were grouped by glycemic status at follow-up: normoglycemia (n=4), prediabetes (n=4), and T2DM (n=4). PCR-free ligation libraries were sequenced on the Oxford Nanopore PromethION. Methylation calling was performed via basecalling (Guppy), alignment (Minimap2), and modbam2bed for 5mC extraction. Differential methylation was conducted using MethylKit; functional annotation using HOMER, Bedtools, and pathway mapping pipelines.

first: Abdul

last: Jaleel


title: Evolutionary diversity of cell-type-specific expression and stress response in Brassicaceae roots

city: Stanford

first: Guannan

last: Wang

state: CA

address: 371 Jane Stanford Way

department: Biology

institute: Stanford University

summary: Environmental stresses trigger distinct responses between stress-sensitive and stress-adapted plants. To explore these stress adaptations at the cellular level, we built root single-cell transcriptome atlases for five biodiverse Brassicaceae species, including two stress-sensitive models (Arabidopsis thaliana and Sisymbrium irio), two extremophytes (Eutrema salsugineum and Schrenkiella parvula), and a polyploid oil crop (Camelina sativa), under control, salt, and ABA treatments. Although these species share similar root anatomy, most Arabidopsis cell type markers were not conserved across species. Cortex cell populations with distinct transcriptomes were spatially segregated among species. Lineage-specific gains in stress responses were more common than losses among cell-type responses across species. The homeologs in the allohexaploid C. sativa showed stress response divergence that was often decoupled from the divergence in their coding sequences and control expression levels. Our dataset provides a foundational root atlas across multiple Brassicaceae species enhanced for user accessibility with a cross species searchable browser and provides an analytical framework for comparative single-cell transcriptomics that can be readily transferred to any multi-species system.

sample_organism:
Arabidopsis thaliana
Sisymbrium irio
Eutrema salsugineum
Camelina sativa
Schrenkiella parvula

overall_design: We built root single-cell transcriptome atlases for five biodiverse Brassicaceae species, including two stress-sensitive models (Arabidopsis thaliana and Sisymbrium irio), two extremophytes (Eutrema salsugineum and Schrenkiella parvula), and a polyploid oil crop (Camelina sativa), under control, salt, and ABA treatments.

first: Guanann

first: Kook

last: Ryu

first: Andrea

last: Dinneny

first: Jiyoung

last: Lee

first: Dong-Ha

last: Oh

first: Prashanth

last: Ramachandran

first: Marina

last: Oliva

first: Ryan

last: Lister

first: José

first: John

last: Schiefelbein

first: Maheshi

last: Dassanayake


title: A hPSC-Derived Progressive Pancreatic Ductal Adenocarcinoma Model Reveals Dual Pathways in ERK-Driven Cellular Plasticity

city: New York

first: Wilfred

last: Wong

address: 430 E 67th St

institute: Memorial Sloan Kettering Cancer Center

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

overall_design: Refer to individual Series


title: 3D Chromatin organization of signal-induced specific enhancers safeguards early ESC differentiation by promoting cluster gene expression

first: Weipeng

last: Mo

first: Guangsong

last: Su


title: Assay for Transposase-Accessible Chromatin With High-Throughput Sequencing in Mouse BMDMs Following CD74 Deficiency

status: Public on Apr 19 2026

first: Tao

last: Gui

address: Huangpu Ave

institute: Jinan University

summary: We employed ACAT-Seq technology to perform a genome-wide assessment of chromatin accessibility changes following CD74 knockout in mouse bone marrow-derived macrophages (BMDMs), with a focus on alterations in regulatory elements associated with aerobic glycolysis-related genes. On this basis, we further explored the potential molecular mechanisms by which CD74 regulates the aerobic glycolytic metabolic pathway in macrophages, including its impact on the accessibility of key transcription factor binding sites and the activity of associated signaling pathways.

overall_design: This study employed the Assay for Transposase-Accessible Chromatin using high-throughput sequencing (ATAC-seq) in mouse bone marrow-derived macrophages (BMDMs) to investigate chromatin accessibility changes following CD74 deficiency. BMDMs were harvested from CD74⁺/⁺ and CD74⁻/⁻ mice.

first: Rui

last: Peng

first: Bo

last: Yu

first: Lutian

last: Yao

first: Lei

last: Zhang


title: Effects of D4-MASLD and D5-MASLD Diets on Rats: Pathway Alterations Similar to Human MASLD

city: Barcelona

first: Maria

last: Martell

state: Barcelona

address: Pg Vall Hebron 119

department: Liver Diseases

country: Spain

institute: Institut de Recerca Hospital Vall d'Hebron

summary: Animal models are essential to understand the mechanisms underlying the onset and progression of metabolic associated steatotic liver disease (MASLD), a rapidly growing form of chronic liver disease driven largely by the global rise in metabolic syndrome. However, existing animal models for MASLD often fail to accurately reproduce advanced human liver disease, and have varying degrees of clinical relevance. To address this, we have undertaken efforts to create a dietary translational model of MASLD in rats that closely replicates the full MASLD phenotype observed in humans, including advanced fibrosis, portal hypertension, and metabolic syndrome. Three MASLD rat models were developed by sequentially combining a high-fat glucose-fructose diet (HFGFD) with additional factors: lipopolysaccharide, increased cholesterol (Chol), and cholic acid (CA) at different concentrations. Of these, two diets—D4-MASLD (HFGFD + 2% Chol) and D5-MASLD (HFGFD + 2% Chol + 0.1% CA)—effectively replicated MASLD characteristics.  Transcriptomic analysis revealed that while both diets significantly altered gene expression compared to controls, D5-MASLD had a greater impact on the activation of inflammation and immune response pathways. The inclusion of CA in D5-MASLD exacerbated pathways related to microbiota changes, intestinal barrier dysfunction, and bacterial translocation. Additionally, comparison of the transcriptomic profiles of these diet-induced rat models with data from MASLD/MASH patients further validated the relevance of these models, establishing a robust platform for studying MASLD pathogenesis and evaluating potential therapeutic interventions.

overall_design:
To develop a dietary rat model replicating the full MASLD phenotype observed in human disease we performed three subsequent studies in rats with variations in diet and additional factors, like lipopolysacharides, cholesterol and cholic acid.
Variables analysed were, body weight changes, biochemical parameters (Glucose, ALT, AST, cholesterol, albumin, triglycerides), hemodynamic parameters (MAP, PP, SMABF and SMAR), histological fibrosis, gene expression markers of hepatic insulin resistance and protein markers of endothelial dysfunction and ductular reaction.
We then performed transcriptomic profiling analysis using data obtained from RNAseq of 15 different liver samples from rats feed with 3 diets (Controls, n=5; D4-MASLD, n=5; D5-MASLD, n=5).

first: María

last: Martínez-Gómez


title: Hypoxia-Induced Neural-BBB Coupling via Extracellular Vesicles Delivering CircOGDH

city: Guangzhou,

first: Wei

last: Chen

address: Huangpu Avenue West

institute: Jinan University First Affiliated Hospital

summary: Many nervous system diseases involve changes in neurovascular coupling, the connection between neurons and the blood-brain barrier(BBB). CircOGDH is a circular RNA linked to hypoxic neurons. In this study, we investigated how neuron-derived CircOGDH affects BBB-associated endothelial cells under hypoxic conditions. We reduced neuronal CircOGDH expression in MCAO/R(middle cerebral artery occlusion/reperfusion) mice using a neuron-specific AAV, which led to compromised BBB structure and maintenance in ischemic stroke mice. We found that giving CircOGDH-rich sEVs(small extracellular vesicles) to brain tumors helped blood vessels stay integrity in a glioblastoma model. In addition, we revealed that hypoxic neurons transfer CircOGDH from sEVs to ECs in vitro co-culture system, leading to increased COL4A4 expression and improved ECs functionality. Additionally, analyzing CircOGDH levels in AIS patients' plasma(with and without hemorrhagic transformation) showed a strong link between CircOGDH expression and BBB damage. These findings indicate that neurons under hypoxic stress release sEVs containing CircOGDH into the microenvironment, which interact with ECs and regulate COL4A4 expression, strengthening vascular integrity.

overall_design: To investigate the role of CircOGDH on transcriptome regulation in HBMECs, we established CircOGDH overexpression HBMECs cell lines.

first: Dan

last: Lu

first: Anding

last: Xu

first: Hongcheng

last: Mai


title: Effects of LXR intervention on transcriptome expression in the injury area of mice with spinal cord injury

city: Beijing

first: JianJun

last: Li

address: FengtaiXiluoyuan Road Xiluoyuan 4 Unit No.34 (Xiluoyuan Police Station East), Be

institute: Capital Medical University, School of Rehabilitation

summary: Spinal cord injury (SCI) induces extensive myelin breakdown and releases large amounts of lipids into the lesion microenvironment, driving macrophage-to-foam cell transformation and sustaining chronic inflammation. Reverse cholesterol transport (RCT) is the major pathway responsible for lipid efflux, yet its functional dynamics and regulatory imbalance after SCI remain poorly understood. This study aims to characterize the temporal expression patterns and cellular localization of key RCT components (ABCA1, ABCG1, and APOE) after SCI, and to evaluate whether activation of the LXR/RXR pathway by the agonist AZ876 can modulate RCT function, reduce foam cell accumulation, and improve neurological recovery.

overall_design: A mouse T10 contusion spinal cord injury model was used to investigate lipid efflux dysfunction and RCT imbalance after SCI. Spinal cord tissues were collected at defined time points following injury for molecular and histological analyses. Expression levels of ABCA1, ABCG1, and APOE were assessed using qRT-PCR, Western blot, and immunofluorescence. To evaluate therapeutic modulation of RCT, mice received early post-injury treatment with the LXR agonist AZ876. Transcriptomic profiling was performed to examine AZ876-induced long-term remodeling of lipid metabolism pathways. The dataset includes raw and processed sequencing data generated from spinal cord samples across experimental groups.


title: 3D Chromatin organization of signal-induced specific enhancers safeguards early ESC differentiation by promoting cluster gene expression [RNA-seq]

overall_design:
To detect specific transcriptomes induced by RA signalling, we induced differentiation for 12h and 24h in WT cells that were depleted of LIF/2i or added 2 μM RA (Sigma).
To detect the specific transcriptome regulated by Cyp26a1, we added 2 μM RA (Sigma) after removing LIF/2i in WT cells and Cyp26a1-KO cells and induced differentiation for 24 hours.

first: Wange


title: Transcripts identified by microarray analysis that were deregulated in E18.5 Pax2-cre/+;Trp63(dN-flox/dN-flox) (ΔNp63-cKO) ureters

first: Mark-Oliver

last: Trowe

summary: Evaluation of the transcriptional changes in E18.5 ureters upon loss of ΔNp63 in the ureteric epithelium.

overall_design: Total RNA from dissected ureters of E18.5 ΔNp63-cKO and control embryos was analyzed by microarray analysis.

first: Andreas

last: Kispert

first: Fairouz

last: Qasrawi


title: Vitamin C facilitates epidermal keratinization through TET-dependent DNA demethylation in basal keratinocytes

city: Tokyo

first: Akihito

last: Ishigami

address: 35-2 Sakae-cho, Itabashi-ku

institute: Tokyo Metropolitan Institute for Geriatrics and Gerontology

summary:
Epidermal keratinization is tightly regulated and associated with epigenetic processes, such as DNA methylation, however, the specific role and mechanisms of TET-mediated DNA demethylation in basal keratinocytes remain unclear.
We analyzed Tet2/3 knockdown-induced transcriptional alterations in newborn rat epidermal keratinocytes, assessed global gene expression profiles. (Microarray)

overall_design: Newborn rat epidermal keratinocytes were treated with or without Tet2/3-targeting small interfering RNA. After 24 h, the cells were treated with vitamin C for 12 h.


title: Transcriptome analysis of wheat seedlings in response to abscisic acid

city: Yokohama

first: June-Sik

last: Kim

state: Kanagawa

address: 1-7-22, Suehiro-cho, Tsurumi-ku

institute: RIKEN CSRS

summary: Screening of an EMS-derived TILLING population based on carbon isotope discrimination and ABA sensitivity during seedling growth identified WS1, a water-saving, drought-tolerant candidate line. We performed transcriptomic analysis to elucidate the regulatory modules underlying the enhanced water-use efficiency and drought tolerance of WS1.

overall_design: Ten-day-old wheat seedlings of WS1 and its progenitor Cadenza (control) were sprayed with either mock solution or ABA solution, and RNA-seq-based transcriptome analysis was conducted 24 h after treatment.

first: Ryosuke

last: Mega

first: Shun-ichiro

last: Hirata

first: Yasuko

last: Watanabe


title: Comparative Study of Phycoerythrobilin Synthases for Fine-Tuning Photosynthetic Light-Harvesting Complexes, Phycobilisomes

city: Setagaya-ku

first: Satoru

state: Tokyo

address: 1-1-1 Sakuragaoka

institute: Tokyo University of Agriculture

summary: Phycobilisomes serve as the major light-harvesting antenna complexes in cyanobacteria; they capture light and transfer excitation energy to the photosystems, and their spectral and functional properties are primarily determined by the types of bilin chromophores attached to phycobiliproteins. We previously revealed that the properties of phycobilisomes can be modulated by altering the biosynthesis of these bilin chromophores. In this study, we introduced two distinct phycoerythrobilin (PEB) biosynthetic enzymes, pcyX and pebS, into the cyanobacterium Synechococcus elongatus PCC 7942 and successfully enabled PEB incorporation into native phycobilisomes. PebS exhibited high PEB synthesis activity comparable to the canonical PebA-PebB pathway, whereas PcyX showed lower activity, enabling fine-tuning of PEB accumulation. Consistent with previous findings, moderate PEB supply enhanced growth under green light; notably, PcyX expression further promoted growth by providing a more balanced pigment supply. Transcriptome analysis confirmed comparable expression of pebA-pebB, pcyX, and pebS, and revealed that increased PEB accumulation triggered broad metabolic remodeling: genes for glucose metabolism, hydrogenase complexes, potassium transporters, and regulatory factors including sigma factors were upregulated, suggesting a shift toward dissipation of excess reducing power. Together, these findings demonstrate that engineering bilin biosynthesis modifies light-harvesting properties and influences cellular metabolic balance, illustrating the potential of pigment pathway manipulation for redesigning photosynthetic function.

sample_organism: Synechococcus elongatus PCC 7942 = FACHB-805

overall_design: Synechococcus elongatus PCC 7942 wild type and its derivative strains were grown in BG-11 medium under continuous illumination (60 µmol photons m⁻² s⁻¹) with CO₂ bubbling and harvested after 4 days of cultivation. Three biological replicates were analyzed by RNA-seq.

first: Kaori

last: Nimura-Matsune


title: Cell-type specific translated mRNA expression in the denervated cervical cord after stroke.

city: Niigata-shi

first: Tokiharu

last: Sato

state: Niigata

address: 1-757 Asahimachidori, Chuo-ku

department: Department of System Pathology for Neurological Disorders

institute: Niigata University, Brain Research Institute

summary: mRNA expressions during the process of reorganization of the corticospinal tract after stroke were examined by RiboTag-RNA-seq in V2a spinal interneurons, astrocytes, and microglia in the denervated cervical cord.

overall_design: RiboTag-RNA-seq was performed with samples of the cervical cord on the denervated side, collected for controls and day 3, 7, 14, and 28 after stroke in Chx10-Cre;RiboTag, Aldh1l1-CreER;RiboTag and Cx3cr1-CreER;RiboTag mice, and 2, 4, and 8 h after rotarod training on day 14 after stroke in Chx10-Cre;RiboTag and Aldh1l1-CreER;RiboTag mice (n = 3 per group).

first: Masaki

last: Ueno

first: Masato

last: Yano


title: Hypoxic injury triggers maladaptive repair in human kidney organoids

city: Clayton

first: Nitika

last: Kandhari

state: VIC

address: Wellington Road

institute: Monash University

summary: Acute kidney injury (AKI) is a common clinical disorder linked to high rates of illness and death. Ischemia is a leading cause of AKI, which can result in chronic kidney disease (CKD) through a maladaptive repair process characterised by failed epithelial regeneration, inflammation, and metabolic dysregulation. No targeted therapies exist to prevent AKI from progressing to CKD, and insight into ischemic AKI and maladaptive repair in humans remains limited. In this study, we report that human kidney organoids recapitulate select molecular and metabolic signatures of AKI and maladaptive repair in response to hypoxic injury. Transcriptional, proteomic, and metabolomic profiling revealed signatures of tubular injury, cell death, cell cycle arrest and altered metabolism in kidney organoids cultured in hypoxic conditions. After a recovery period in normoxic conditions, hypoxic injured organoids had increased signatures associated with maladaptive repair like the TNF signalling pathways and S100A8/9. Single cell RNA sequencing localised AKI and maladaptive repair markers such as GDF15, MMP7, ICAM1, TGFB1, SPP1, C3 and CCN1 to injured proximal and distal tubules. Metabolic phenotypes linked to CKD were also evident including dysregulated glycolysis and gluconeogenesis, amino acid, bicarbonate and lipid metabolism, and elevated ceramide levels. In addition, by developing a kidney organoid-macrophage co-culture model, we showed a significant activation of macrophages in response to hypoxia, marked by a shift towards an inflammatory state. In summary, our multi-omic analysis provides compelling evidence for the use of kidney organoids as a model of human ischemic AKI and maladaptive repair, highlighting new and conserved biomarkers and mechanisms, and opportunities for drug screening.

overall_design:
Eighteen-day-old kidney organoids are exposed to hypoxic conditions (1% O2) for 48h. To assess the development of maladaptive repair following acute injury, kidney organoids are afterwards placed back into normoxic conditions (21% O2) for an extra 5 days. Comparative gene expression profiling analysis of bulk RNA-seq data of kidney organoids on day 20 and day 25 of development for both injury and control groups.

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The table below lists GEO accessions reused/reanalyzed for this study.
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first: Ana B.

last: Nunez-Nescolarde

first: M

last: Piran

first: Laura

last: Perlaza-Jimenez

first: David J.

last: Nikolic-Paterson

first: Alexander N.

last: Combes