title: Clonal expansion of cytotoxic CD8+ T cells in lecanemab-associated ARIA

city: Lexington

first: Joshua

last: Morganti

state: KY

address: 789 S. Limestone St

department: Sanders-Brown Center on Aging

institute: University of Kentucky

summary: Amyloid-related imaging abnormalities (ARIA) remain the principal safety concern limiting adoption of anti-amyloid therapies such as lecanemab, yet their underlying biology is poorly defined. To address this, we performed deep multi-omic profiling of peripheral blood mononuclear cells from three Alzheimer's disease (AD) patients who developed ARIA and three matched controls. Single-cell RNA sequencing, CITE-seq, V(D)J clonotyping, and metabolomic/lipidomic profiling revealed a coordinated reprogramming of the CD8+ compartment in ARIA+ patients. CD8+ TEM and TEMRA subsets were numerically expanded, transcriptionally enriched for cytotoxic and migratory programs, and exhibited increased clonal expansion. Transcription factor inference and metabolomics converged on a glycolytic bias, supporting short-lived effector activity. Ligand-receptor modeling identified ARIA-associated signaling from CD14+ and CD16+ monocytes that augmented antigen presentation, adhesion, and chemokine axes directed toward effector CD8s. Finally, integration with an external cerebrovascular atlas confirmed that ARIA-associated TEM/TEMRAs are transcriptionally "addressed" for vascular engagement.

overall_design:
Six individuals receiving bi-weekly infusions (10 mg/kg) of lecanemab were recruited. Three subjects with radiographically confirmed ARIA were matched with three controls by age (± 2-5 years), sex, APOE genotype, and lecanemab infusion number (± 1). PBMCs were collected immediately prior to infusion and processed using 10x Genomics Chromium Single Cell 5' chemistry with simultaneous capture of transcriptomic and surface protein expression using TotalSeq-C antibody-derived tags (ADTs) targeting 137 surface proteins. T cell receptor sequences were captured using 10x Genomics V(D)J enrichment. Libraries were sequenced on an Illumina NovaSeq 6000.

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

first: Lance

last: Johnson

first: Kai

last: Saito

first: Akhil

middle: V

last: Pallerla

first: Jessica

last: Funnell

first: Ashley

last: Ezzo

first: Chelsea

last: Song

first: Douglas

last: Harrison

first: Noah

last: Norton

first: Lauren

last: Moore

first: Linda

last: Van Eldik

first: David

middle: W

last: Fardo

first: Greg

last: Cooper

first: Josh


title: Improved lipid production and transcriptomic profiling in Crypthecodinium cohnii with alternative ethanol treatment

status: Public on Jan 20 2026

city: Bangkok

first: Vetaka

last: Tharasiriavat

address: Phaya Thai

department: Biochemistry

country: Thailand

institute: Chulalongkorn University

type: Expression profiling by high throughput sequencing

summary: In the absence of light, the heterotrophic microalga Crypthecodinium cohnii accumulates lipids rich in docosahexaenoic acid (DHA). However, limited genetic data restricts understanding of its metabolism, especially DHA synthesis with ethanol. Next-generation sequencing identified numerous transcripts for fatty acid and carbohydrate production. qRT-PCR confirmed increased expression of genes linked to energy, carbohydrate, lipid, terpenoid, and polyketide metabolism. Upregulation of genes in ethanol metabolism, fatty acid synthesis, glycerophospholipid, and pyruvate pathways raised acetyl-CoA and key metabolite precursors.

overall_design: Comparison of Crypthecodinium cohnii cultured under 5 g/L glucose and 15 g/L ethanol conditions, collected on day 5

first: Saowarath

last: Jantaro

last: Tharasirivat

first: Nattapon

last: Pengbubpha


title: Genome-wide maps of chromatin state changes upon NFATc3 overexpression in mouse bone marrow-derived macrophages

city: Guangzhou

first: Sijia

last: Liang

address: 74 Zhongshan 2 Rd

department: Pharmacology

country: China

institute: Sun Yat-Sen University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To explore the role of macrophage NFATc3 on steatohepatitis, macrophage-specific Nfatc3 knockin mice (Nfatc3-MKI) were generated. Lyz2-Cre mice were used as control. Mouse bone marrow-derived macrophages (BMDMs) were isolated from Lyz2-Cre and Nfatc3-MKI mice and then were subjected to ChIP sequencing analysis.

overall_design: ChIP-seq was performed to analysis the chromatin state changes and NFATc3 enrichment in BMDMs from Lyz2-Cre and Nfatc3-MKI mice.

first: Si-Jia


title: Lactobacillus acidophilus AG01 and Bifidobacterium animalis AG02 reduce Clostridium perfringens pathogenicity through different and complementary modes of action

city: Chapel Hill

first: Adam

last: Rosenthal

state: North Carolina

address: 1521 East Franklin Street, Apartment C213

department: Microbiology and Immunology

country: USA

institute: UNC

summary: Necrotic enteritis is an economically important disease in poultry production caused by the opportunistic pathogen Clostridium perfringens. With the phasing out of antibiotics for prophylaxis and growth promotion, alternative solutions are needed to prevent diseases. We investigated the effect of two potentially beneficial bacteria, Lactobacillus acidophilus AG01 and Bifidobacterium animalis subspecies lactis AG02, on C. perfringens pathogenicity and observed two distinct but complementary modes of action. Live L. acidophilus AG01 cells had a strong deleterious effect on the survival of C. perfringens 25037-CP01 when grown in co-cultures, likely caused by the production of lactate resulting in the acidification of the media. Using our recently developed single cell RNA-seq method for bacteria, ProBac-seq, we observed a strong effect of the cell-free supernatant (CFS) of both bacteria on overall gene expression and the expression of virulence factors in C. perfringens 25037-CP01. Cells exposed to 5% CFS of B. animalis AG02 were enriched in RNA polymerases, and genes involved in oxidative phosphorylation and fatty acid biosynthesis. Cells exposed to 5% B. animalis AG02 or 3% L. acidophilus CFS showed significant expression reduction of netB, the virulence factor associated with necrotic enteritis. Five other virulence factors had significantly reduced expression in cells exposed to 5% B. animalis AG02 CFS. Epithelial HT-29 cells suffered significantly lower cytotoxicity when exposed to C. perfringens 25037-CP01 cells grown during exposure to 5% B. animalis AG02 CFS. These findings show that interactions among bacteria can reduce pathogenicity of an opportunistic pathogen. The two bacteria tested here reduce C. perfringens pathogenicity in different ways and could be used as an alternative to the administration of preventative  antibiotics.

overall_design: Before microfluidic encapsulation, bacteria were fixed in 1% paraformaldehyde to preserve transcripts and permeabilized by mild lysozyme treatment. Permeabilized bacteria were then incubated with the corresponding DNA probe library. Non-hybridized probes were removed with repeated washes . Next, the bacteria were run through a 10X Chromium Controller, where the DNA probes were captured and barcoded in a manner analogous to the barcoding of the transcriptome of eukaryotic cells

first: Jeffrey

middle: P

last: Meisch

first: Melanie

middle: B

last: Evans

first: Katharine

middle: R

last: Minker

first: Qiong

last: Cheng

first: Ryan

last: McNulty

first: Kirsty

last: Gibbs

first: Sasha

last: van der Klein

first: Marion

last: Bernardeau

middle: Z

first: Gerda

last: Saxer


title: GPR39 activation inhibits AQP2 trafficking and alters cytoskeletal organization

city: Baltimore

first: Mackenzie

last: Kui

state: Maryland

address: 725 N Wolfe Street

department: Physiology

institute: Johns Hopkins

summary: G protein-coupled receptor 39 (GPR39) is an orphan receptor that is highly expressed in renal collecting duct principal cells. GPR39 activation in vivo leads to reduced urinary concentration capacity. In this study, we utilized mpkCCD cells, a model of principal cells in the collecting duct, to examine the cell biological effects of GPR39 activation. Pharmacological activation of GPR39 with the synthetic agonist cpd1324 impaired vasopressin-mediated aquaporin-2 (AQP2) apical trafficking and reduced total AQP2 expression following long-term treatment, consistent with its known in vivo role. These effects were absent in GPR39 knockout cells. In addition, GPR39 activation altered apical membrane morphology, disrupted the tight junction network, and reduced cortical F-actin expression, suggesting a shift toward a dedifferentiated phenotype. GPR39 activation also increased glycolytic ATP production while reducing mitochondrial ATP output without affecting proliferation. RNA-seq analysis of acutely treated mpkCCD cells revealed upregulation of inflammatory and dedifferentiation-associated gene programs, including cytokines. These findings indicate that the role of GPR39 in principal cells goes beyond AQP2 regulation and imply that GPR39 functions as a negative regulator of epithelial differentiation, perhaps acting to coordinate metabolic and inflammatory responses to stress.

overall_design: Without transformation (WT) and Gpr39 knockout (KO) mpkCCD cells were seeded onto 12-well transwell inserts and cultured in complete media without dDAVP for 9 days to allow for full polarization. Cells were then switched to simple media for 24 hours prior to treatment. Cells were treated with either 1 µM cpd1324 + 10 µM ZnCl₂ or vehicle control (0.1% DMSO + 10 µM ZnCl₂) for 2 hours. Following treatment, total RNA was extracted using the RNeasy Mini Kit (Qiagen, Cat# 74104) according to the manufacturer’s instructions.

first: Jessica

last: Zhang

first: Ibrahim

last: Ahmed

first: Shishir

middle: K

last: Patel

first: Tarah F

last: Rastegar

first: Hamid

last: Rabb

first: Jennifer

middle: L

last: Pluznick


title: Transcription factor reveals interconnected regulation of carbon source utilization and carbon catabolite repression in an oleaginous yeast

city: Ithaca

first: Josh

last: Kerkaert

state: NY

address: 236 Tower Rd

institute: Cornell University

summary: Cells must sense and respond to available nutrients to survive. Microbes evolved mechanisms to activate genes necessary to utilize a carbon source specifically when it is present. To efficiently grow in mixed carbohydrate environments, microbes repress genes necessary to utilize carbon sources that require substantial resources to catabolize when a simpler carbon source is present, known as carbon catabolite repression. We investigated nutrient utilization in the basidiomycete, oleaginous yeast Rhodotorula (Rhodosporidium) toruloides. R. toruloides is a saprophytic fungus that utilizes the building blocks of complex polysaccharides found in plant cell walls. A transcription factor homologous to the cellulose degradation regulator CLR-2/ClrB in Ascomycete filamentous fungi, which we named Cbr1, is required for cellobiose utilization in R. toruloides. Although the role of CLR-2/ClrB is limited to regulating expression of genes involved in cellulose and hemicellulose utilization, Cbr1 is also involved in fucose and tricarboxylic acid cycle intermediate utilization. Additionally, Cbr1 inhibits carbon catabolite repression specifically during utilization of glucose-glucose disaccharides, which may have evolved to limit the glucose-mediated repression of genes encoding proteins that cleave disaccharides into glucose. In fungi, it is thought carbon source-specific transcription factors activate genes necessary for carbon source utilization, while carbon catabolite repression is regulated by transcription factors that broadly repress all nonpreferred carbon source utilization genes when a preferred carbon source is present. Our data provide evidence for a noncanonical carbon catabolite repression mechanism and suggest transcriptional mechanisms regulating carbon catabolite repression may be less broadly conserved than previously thought.

overall_design: 3'mRNA-seq profiling of Rhodotorula (Rhodosporidium) toruloides wild type and cbr1 deletion strains exposed to fucose as the sole carbon source for 8h, wild type, cbr1 deletion, and bgl1bgl2 double deletion strains exposed to cellobiose as the sole carbon source for 4 hours, and wild type, cbr1 deletion, and tct1 deletion exposed to citrate as a sole carbon source for 24 hours. Reads were counted using a GFF3 file generated by the peaks2utr software v. 1.4.1 in order to improve annotation of 3'UTRs. Wild type BAM files from the above experiments, as well as wild type cells exposed to 1% succinate as the sole carbon source for 24 hours, and wild type cells exposed to Vogel's minimal media with NH4Cl and 2% glucose as the sole nitrogen and carbon sources, respectively, were combined and used as the input for peaks2utr. The GFF3 file generated by peaks2utr is included as a supplementary file. Each experiment was performed in biological triplicate.

first: Brandon

last: Reyes-Chavez

first: Joshua

middle: D

first: Lori

last: Huberman


title: Lysine-specific demethylase 6B promotes STAT1-mediated macrophages activation during atherosclerosis development [MeRIP-Seq 2]

status: Public on Jan 21 2026

city: hangzhou

first: huan

last: chen

state: Zhejiang

address: Hangzhou, Zhejiang Province, China

institute: Zhejiang Chinese Medical University

summary: Atherosclerosis (AS) induced coronary heart disease is still the first killer threatening human health due to high morbidity and mortality. How N6-methyladenosine modification (m6A) in macrophage participates in atherosclerosis progression is still completely unclear. In this study, by performing meRIP-seq in macrophages during differentiation and activation processes, we aim to understand the landscape of m6A spectrum in macrophage from different stages. Moreover, we also find a large class of histone methylation modification enzymes were regulated by m6A modification. Western blot, qPCR and ChIP-seq results demonstrate m6A modification regulates Lysine-specific demethylase 6B (Kdm6b)-dependent macrophage activation. In mechanism, Kdm6b interacts and methylates Jak1 inducing its phosphorylation-mediated macrophage activation. Furthermore, RIP-qPCR detection indicates following macrophage differentiation and activation, both m6A writers Mettl3 and Rbm15 participates in m6A modification of Kdm6b mRNA. Finally, by performing atherosclerotic model on macrophage-specific Kdm6b knockout mice on Ldlr-/- background, we demonstrate Kdm6b promotes macrophage activation-mediated atherosclerosis by amplifying inflammation and destabilizing plaque. This study will provide a new understanding of the pathogenesis of AS and is expected to develop a new target for the treatment of AS.

overall_design: m6A sequencing data analysis: Effects of IFNγ on m6A modification sites on RNA molecules in mouse bone marrow-derived macrophages


title: Cell cycle-resolved Hi-C reveals unexpected plasticity of A/B compartments across interphase

city: Kobe

first: Ichiro

last: Hiratani

state: Hyogo prefecture

address: 2-chōme−２−3, Minatojima Minamimachi, Chuo ward

country: Japan

institute: RIKEN BDR

summary: The spatial organization of chromatin into active (A) and inactive (B) nuclear compartments is fundamental to genome regulation, yet their cell-cycle dynamics remain largely unexplored. Most research on chromatin dynamics during the cell cycle has primarily focused on events surrounding mitosis, providing only limited insight into chromatin behavior during S-phase. To address this gap, we developed a simple, drug-free approach that combines the Fucci cell-cycle indicator with in situ Hi-C to comprehensively analyze A/B compartment dynamics throughout interphase in mouse embryonic stem cells (mESCs). Unexpectedly, and contrary to prevailing views, we found that A/B compartment strength increased abruptly upon S-phase entry, stabilized during S-phase, and subsequently declined in late S/G2. This abrupt strengthening, which we termed ‘compartment maturation,’ required passage through the G1/S transition but was independent of active DNA synthesis. This maturation involved substantial architectural remodeling, particularly within the A compartment, which consolidated into a more organized structure as individual A domains rearranged to form long-range interactions. Moreover, compartment maturation was not limited to mESCs but was also observed across different developmental contexts in mice. Based on these observations, we propose a revised, stepwise model of nuclear compartmentalization during cell-cycle progression, consisting of four distinct stages: chromosome unfolding (G1), chromatin maturation (G1/S), stabilization (S phase), and refolding (G2). These findings reveal the unexpected plasticity of A/B compartments and underscore the G1/S transition as a critical period for their reorganization.

overall_design:
In situ Hi-C profiling of Fucci mESCs during the cell cycle (early G1, mid G1, late G1, early S, mid S, late S, G2), at G1/S arrest and at G1/G0 arrest.

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Raw sequencing data are available under BioProject PRJDB37948 at DDBJ
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first: Linda

last: Choubani


title: TEAD-independent mechanisms of YAP function in cardiomyocytes

city: Cincinnati

first: Jeffrey

last: Steimle

email: jeffrey.steimle@cchmc.org, jeffrey.steimle@bcm.edu, jsteimle@uchicago.edu, jsteimle@alumni.nd.edu

state: OH

address: 240 Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Medical Hospital Center

summary: Adult mammalian hearts exhibit limited regenerative capacity due to the restricted renewal of cardiomyocytes. Recent studies reveal that mammalian hearts exhibit transient regenerative potential within a short time frame after birth, suggesting a regulatory mechanism that prevents adult hearts from initiating a regenerative response to cardiac injury. Here, we discovered that an active form of YAP, named YAP6SA, which is not inhibited by the Hippo signaling pathway and does not interact with TEADs, induces cardiomyocyte cell cycle re-entry. In addition, YAP6SA interacts with scaffold protein MPDZ to regulate Rho GTPases and promote cell cycle progression in cardiomyocytes (CMs). Importantly, YAP6SA overexpression is well tolerated in mammalian hearts. These findings provide new insights into YAP function in cardiomyocytes.

overall_design: Wildtype ICR mice were subcutaneously injected with 1*10^11 viral genomes of AAV9 virus containing cTnT-GFP, cTnT-YAP5SA, or cTnT-YAP6SA expression constructs at P6. Two hearts from each virus were collected at P9 and cardiomyocyte nuclei were enriched using anti-PCM1 pulldown. RNA was isolated using the RNeasy Plus Micro kit and poly-A enriched, non-directional libraries were generated by Novogene America and sequenced on the Illumina NovaSeq6000. Reads were mapped to the mouse genome (mm10, Ensembl GRCm38.94) using STAR. Lowly expressed genes were removed within each condition using median log2-transformed counts per gene per million mapped reads of 1, and a union set of genes was generated from each condition. Differential expression analysis was performed using edgeR using a general linear model framework with an additional covariate to mitigrate an apparent batch effect.

first: Bing

last: Xie

first: James

middle: F

last: Martin


title: Comparative Landscape of Small RNAs in Tissue and Liquid Biopsies for Liver Transplant Outcomes [Perfusate small RNAseq]

city: Birmingham

first: Zhangli

last: Su

state: Alabama

address: 720 20th Street South

department: Department of Genetics

institute: University of Alabama

type: Non-coding RNA profiling by high throughput sequencing

summary: Ischemia-reperfusion injury (IRI) is an inevitable consequence of liver transplantation, arising during donor organ procurement and reoxygenation. Severe IRI is a leading contributor to early allograft dysfunction (EAD), a post-transplant complication associated with reduced graft survival. Current postoperative biomarkers provide limited time for intervention, highlighting a need to identify preoperative biomarkers of IRI. Meanwhile, tRNA fragments (tRFs) have emerged as novel biomarkers in various diseases, but remain unexplored in the context of liver transplant. We performed small RNA sequencing on donor liver biopsies to investigate IRI-associated transcript changes. In parallel, donor liver perfusates were analyzed as a non-invasive surrogate for tissue profiling.

overall_design:
Liver tissue and perfusate samples were obtained from adult orthotopic liver transplant (OLT) recipients (?18 years old) at Methodist University Hospital after obtaining informed consent. All procedures were conducted under protocols approved by the University of Tennessee Health Science Center Institutional Review Board (IRB#20-07742-XM and IRB#20-07640-XP). Participants in the LUT cohort were recruited between September 2018 and March 2020, and those in the UTL cohort were recruited between December 2020 and December 2022.
Needle biopsy specimens (L1: pre-implantation; L2: post-reperfusion) were immediately immersed in RNAlater (Thermo Fisher Scientific, Cat. #AM7021) and incubated at 4 °C overnight to ensure complete permeation. RNAlater was then removed, and the samples were stored at ?80 °C until RNA extraction.
Perfusate samples were collected at the end of organ procurement concurrently with pre-implantation liver (L1) biopsies. The solutions were centrifuged at 2,400 rpm for 30 minutes at room temperature to remove debris. The resulting supernatant was aliquoted and stored at ?80 °C until RNA isolation.
Patients were grouped based on transplant outcome, measured by day 1 AST (aspartate aminotransferase) values.  EAD (early allograft dysfunction): day 1 AST more than 2000; NF (normal function): day 1 AST less or equal to 2000.

first: Monima

last: Anam

first: Christine

last: Watkins

first: Grace

last: Rucker

first: Katie

last: Marlow

first: Mattew

last: Khalil

first: Murat

last: Dogan

last: Eason

first: Jason

last: Vanatta

first: Corey

last: Eymard

first: Cem

last: Kuscu

first: Canan


title: HP1α depletion and TGFβ activation exert antagonistic effects on 3D genome organization

city: Oslo

first: Fabiana

last: Patalano

address: Blindernveien 31

country: Norway

institute: University of Oslo

summary: The three-dimensional (3D) organization of the human genome plays a critical role in regulating gene expression and is frequently disrupted in cancer. However, how key factors like Heterochromatin Protein 1 alpha (HP1α) and Transforming Growth Factor beta (TGFβ) remodel this architecture to drive tumorigenesis remains poorly understood. We investigated the effects of HP1α knockdown and TGFβ treatment on higher-order chromatin structure and gene expression in human mammary epithelial cells. Our findings reveal that HP1α depletion and TGFβ stimulation exert distinct and opposing effects on genome compartmentalization and subcompartmentalization. HP1α knockdown drives a genome-wide shift of chromatin from transcriptionally inactive B compartments to active A compartments. This is accompanied by a stepwise redistribution of A subcompartments toward the most transcriptionally active state (A3), and the upregulation of oncogenic genes involved in EMT and proliferation. In contrast, TGFβ treatment promotes chromatin compaction, increases the proportion of B compartments, and drives a stepwise reduction in active A subcompartments. Our results highlight the differential roles of HP1α and TGFβ in shaping the 3D genome and underscore how precise, stepwise architectural changes contribute to malignant transformation. This study provides critical insight into how chromatin architecture acts as a regulatory layer in breast cancer development.

overall_design: We generated Hi-C and RNA-seq datasets for MCF10A, MCF10A HP1a knockdown, and MCF10 treated with TGFB cell lines to investigate changes in 3D genome conformation and the impact on gene expression.

first: Oda

last: Hovet

first: Roberto

last: Rossini

first: Maxim

last: Nekrasov

first: Yasmin

last: Dijkwel

first: Bhumika

last: Azad

first: Tatiana

last: Soboleva

first: Rein

last: Aasland

first: David

last: Tremethick

first: Jonas

last: Paulsen


title: Hypothyroidism Reduces Myogenic Diversity and Impairs Skeletal Muscle Regeneration After Injury by Altering Myogenic and Non-Myogenic Pathways

city: Los Angeles

first: Paola

last: Aguiari

state: California

address: 4650 W Sunset Blvd

institute: Children's Hospital, Los Angeles

summary: Thyroid hormone signaling is an essential regulator of skeletal muscle development, function, and metabolism, yet the specific signaling pathways required for muscle regeneration are not yet defined. We utilized scRNA-seq and a cell cycle reporter mouse model (FUCCI, Fluorescent Ubiquitination-based Cell Cycle Indicator) to examine how hypothyroidism impacts repair processes after cardiotoxin-induced injury in mice. During regeneration, and up to 2 months after injury, hypothyroid muscles displayed smaller myofibers and a shift to slower oxidative fiber types.scRNA-seq of tibialis anterior muscle during regeneration revealed that hypothyroidism reduces myogenic lineage diversity. Cell cycle analysis confirmed delayed cell cycle progression at 5 and14 days after injury, with skeletal muscle stem cells stalled at the G1/S transition, hindering differentiation. Transcriptomic data revealed altered non-myogenic dynamics, including elevatedactivated fibro-adipogenic progenitors (FAPs) early in repair and persistent pro-inflammatory macrophages. Integrative regulon and ligand-receptor analysis further demonstrated that T3 acts through dual modes: a direct transcriptional control of myogenic cell cycle and oxidative programs and an indirect paracrine remodeling mediated by FAP and immune signaling networks. This study identifies novel effects of hypothyroidism on myogenic heterogeneity and reduced tissue repair, offering insights into muscle-wasting mechanisms relevant to hypothyroidism-associated myopathy and sarcopenia.

overall_design: scRNA profiling of Tibialis Anterior (TA) muscle cells from euthyroid (Control) and hypothyroid mice, at day 0 (NI, non-injured), day 5, and day 14 after cardiotoxin-induced injury.

first: Laura

last: Perin

first: Anna

last: Milanesi


title: A multi-step immune-competent genetic mouse model reveals phenotypic plasticity in uveal melanoma

city: Tampa

first: Xiaoxian

last: Liu

state: FL

address: 13131 USF Magnolia Drive

institute: Moffitt Cancer Center

summary: Uveal melanoma (UM) is a highly aggressive intraocular malignancy with limited therapeutic options for metastatic disease. Existing transgenic UM mouse models inadequately recapitulate human disease progression, while transplant models lack immune competence for studying the tumor immune microenvironment and therapeutic interventions. To address these limitations, we developed a genetically engineered mouse model incorporating stepwise genetic alterations implicated in human UM progression. Spatiotemporally controlled expression of mutant GNAQQ209L from the endogenous locus induced choroidal nevi with limited penetrance. Concomitant BAP1 deletion enhanced nevus formation, while further MYC activation led to fully penetrant intraocular tumors with the potential to disseminate. Single-cell RNA sequencing revealed malignant cells segregated into Melanocytic and Neural Crest-like subpopulations characterized by distinct transcriptional and biosynthetic programs. Trajectory analyses inferred dedifferentiation from the Melanocytic toward the Neural Crest-like state during tumor progression. Comparison to human UM revealed commonalities with highly aggressive Class 2 UM, including gene expression signatures and copy number gains affecting genes that map to human chromosome 8q beyond the activated MYC allele, suggesting cooperative effects of multiple drivers in this chromosomal region. The tumor microenvironment featured immunosuppressive macrophage populations and exhausted T cells, closely resembling human UM. This physiologically relevant, immune-competent model provides a platform for investigating UM biology, functionally characterizing candidate driver genes, and developing immune-based therapeutic strategies.

overall_design: Uveal melanomas were collected from GnaqCA; Bap1CKO; MycCKI mice once ocular enlargement was evident, and tumor tissue was dissected from the choroid and adjacent structures under a stereomicroscope before transfer into enzyme solution. Tumors were enzymatically dissociated using the Miltenyi Tumor Dissociation Kit at 37°C for 30–45 minutes, washed, centrifuged, and resuspended in PBS with 2% FBS to obtain a single-cell suspension. Cell viability and counts were assessed by AO/PI staining on a Nexcelom Cellometer K2, and only samples with >80% viability were included for sequencing.

first: Florian

last: Karreth

first: Xiaonan

last: Xu

first: Xiaoqing

last: Yu


title: RNA-seq analysis of macrophage NFATc3 or ASK1 effects on metabolic dysfunction-associated steatohepatitis

first: Sijia

last: Liang

summary: To explore the roles of macrophage NFATc3 and ASK1 in metabolic dysfunction-associated steatohepatitis, we generated macrophage-specific Nfatc3 knockout mice (Nfatc3-MKO),  macrophage-specific Ask1 knockout mice (Ask1-MKO),macrophage-specific double knockout (MDKO) mice, macrophage-specific Nfatc3 knockin mice (Nfatc3-MKI), and macrophage-specific Ask1 knockin mice (Ask1-MKI). Lyz2-Cre mice were used as control. Eight-week-old male Lyz2-Cre, Nfatc3-MKO, Ask1-MKO, and MDKO mice were treated with methionine- and choline-deficient (MCD) diet for 4 weeks. Subsequently, mouse liver tissues were isolated and subjected to RNA sequencing analysis. In addition, mouse bone marrow-derived macrophages (BMDMs) were isolated from Lyz2-Cre, Nfatc3-MKI, and Ask1-MKI mice and were also subjected to RNA sequencing analysis.

overall_design: RNA-seq was performed to compare the mRNA expression level in mouse livers of Lyz2-Cre, NFATc3-MKO, ASK1-MKO, and MDKO mice, and in BMDMs of Lyz2-Cre, Nfatc3-MKI, and Ask1-MKI mice.

first: Si-Jia


title: Bariatric surgery reverses ORG and exhibits a distinct transcriptomic profiel compared to weight loss through a low-fat diet

city: Sant Joan Despí

first: Maruja

last: Navarro-Díaz

state: Barcelona

address: Oriol Martorell, 12

department: Nephrology

country: Spain

institute: Hospital Sant Joan Despí Moisès Broggi

summary: Weight loss is central to treating obesity-related kidney disease, yet the renal effects of low-fat diet (LFD) versus bariatric surgery (BS) remain incompletely understood. This study compared their impact on obesity-related glomerulopathy (ORG). Twenty-eight male Wistar rats were fed a high-fat diet (HFD) for 10 weeks to induce obesity. Eight rats were sacrificed (HFD group), eight switched to LFD for 10 weeks, and twelve underwent sleeve gastrectomy. Body weight, albuminuria, renal histology, and transcriptomic profiles were analyzed. Weight loss was modest in the LFD group (−1.6%) but substantial after BS (−13.2%), occurring 2.1 times faster. Albuminuria decreased in both interventions compared to HFD (LFD: 7228 ± 514 ng/mL, BS: 6242 ± 418 ng/mL; HFD: 10384 ± 1168 ng/mL; p < 0.01) and correlated strongly with weight loss (R² = 0.78). Glomerular area was reduced in both groups, but only BS achieved complete histological resolution of ORG. Tubular cells in BS-treated rats showed megamitochondria and cristae disruption, while LFD induced milder alterations. Transcriptomics revealed suppression of mitochondrial maintenance genes and upregulation of oxidative stress and immunometabolism pathways. Immune-related genes upregulated in BS clustered into pro-inflammatory/chemotactic and regulatory modules. To the best of our knowledge, this is the first evidence that BS fully reverses ORG, highlighting renal effects beyond weight loss alone.

overall_design: Twenty-eight Wistar rats were first fed a high-fat diet for 10 weeks to induce obesity. They were then divided into three groups: an obese control (HFD group), a low-fat diet (LFD) group, and a bariatric surgery (BS) group, all evaluated for weight, albuminuria, kidney histology, and transcriptomics. Raw data for the the HFD samples are available under PRJNA1092068 (GSE262503).

middle: M

last: Navarro

first: Mariapilar

last: Armengol

first: Mireia

last: Ferrer


title: CD9 regulates macrophage-mediated remodeling of adipose tissue in obesity

city: Philadelphia

last: Hill

state: PA

address: Abramson Research Building, 1208B, 3615 Civic Center Blvd.

department: Division of Allergy and Immunology

institute: Children's Hospital of Philadelphia

summary: Dysfunctional white adipose tissue contributes to the development of obesity-related morbidities, including insulin resistance, dyslipidemia, and other metabolic disorders. Adipose tissue macrophages (ATMs) accumulate in obesity and play both beneficial and harmful roles in the maintenance of adipose tissue homeostasis and function. Despite their importance, the molecules and mechanisms that regulate these diverse functions are not well understood. Lipid-associated macrophages (LAMs), the dominant subset of obesity-associated ATMs, accumulate in crown-like structures and are characterized by a metabolically activated and proinflammatory phenotype. We previously identified CD9 as a surface marker of LAMs. However, the contribution of CD9 to the activation and function of LAMs during obesity is unknown. Using a myeloid-specific CD9 knockout model, we show that CD9 supports ATM-adipocyte adhesion and crown-like structure formation. Furthermore, CD9 promotes the expression of pro-fibrotic and extracellular matrix remodeling genes. Loss of myeloid CD9 reduces adipose tissue fibrosis, increases visceral adipose tissue accumulation, and improves global metabolic outcomes during diet-induced obesity. These results identify CD9 as a causal regulator of pathogenic LAM functions, highlighting CD9 as a potential therapeutic target for treating obesity-associated metabolic disease.

overall_design:
Bulk RNA-seq of CD9+ and CD9- Adipose tissue macrophages isolated from male mice fed a high fat diet for 12 weeks. Samples from CD9+ adipose tissue macrophage samples from GSE113594 were reanalyzed for this study. Bulk RNA-seq of whole epididymal white adipose tissue isolated from male Control and CD9 myeloid-specific (LysMCre+/-) knockout mice fed a high fat diet for 12 weeks.

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

first: Julia

last: Chini

first: Nicole

last: DeMarco

first: Dana

last: Mitchell

first: Sam

middle: J

last: McCright

first: Divyansi

last: Pandey

first: Kaitlyn

last: Shen

first: Rachel

last: Clement

first: Jessica

last: Miller

first: Rajan

last: Jain

first: Deanne

last: Taylor

first: Mitchell

middle: A

last: Lazar


title: Targeting Fused in Sarcoma (FUS): A Novel Antisense Strategy for Treating Idiopathic Pulmonary Fibrosis

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

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

overall_design: Refer to individual Series


title: Comparative Landscape of Small RNAs in Tissue and Liquid Biopsies for Liver Transplant Outcomes [Tissue small RNAseq]

first: Zhangli

last: Su

first: Monima

last: Anam

first: Christine

last: Watkins

first: Grace

last: Rucker

first: Katie

last: Marlow

first: Mattew

last: Khalil

first: Murat

last: Dogan

first: James

last: Eason

first: Jason

last: Vanatta

first: Corey

last: Eymard

first: Cem

last: Kuscu

first: Canan


title: Single-cell RNA sequencing revealed cell heterogeneity in sagittal suture mesenchyme

city: Wuhan

first: Kai

last: Sun

address: No. 237, Luoyu Road, Hongshan District, Wuhan City, Hubei Province

institute: Wuhan university

summary: The formation and homeostatic maintenance of cranial sutures rely on cellular activities within the suture mesenchyme. Mesenchymal stem cells in this niche are characterized by self-renewal capacity and low proliferative activity. However, how they rapidly and extensively contribute to suture formation during early development remains insufficiently explored. In this study, we combined 10x Genomics and Smart-seq3 single-cell transcriptomic sequencing to analyze cellular subpopulations within the sagittal suture mesenchyme.

overall_design: RNA-seq profiling of  sagittal suture  dissected from PN7 wildtype C57BL/6J mice or Gli1-CreERT2; tdTomato mice with tamoxifen induction.

first: Chengyan

last: Ren

first: Ran

last: Wu

first: Chenxin

last: Geng

first: Hu

last: Zhao

first: Weihui

last: Chen


title: Embryonic stem cell factors DPPA2/4 amplify active H3K4me3-H2AK119ub chromatin domains in non-small cell lung cancer (RNA-seq)

city: Melbourne

first: Janith

last: Seneviratne

state: VIC

address: Peter MacCallum Cancer Centre, 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

summary: Embryonic regulators are often re-expressed in cancers, however the functional and molecular significance of this is not always understood. The epigenetic priming factors Developmental Pluripotency Associated 2 and 4 (DPPA2/4) have crucial roles in early development and are implicated in cancer pathogenesis. We reveal in non-small cell lung cancer (NSCLC), DPPA2/4 co-expression is associated with poorly differentiated tumours and impaired patient outcomes. Biochemically, human DPPA2/4 multimerise for their protein stability and enhanced nucleosome binding activity. In NSCLC cells, DPPA2/4 bind CG-rich sequences including promoters of developmental, Wnt signaling and catabolic genes. Chromatin state modelling revealed DPPA2/4 preferentially bind active H3K4me3 and H3K27ac domains that were intriguingly also enriched for PRC1 and its product H2AK119ub, validated by H3K4me3-H2AK119ub sequential ChIP. Knockdown experiments revealed DPPA2/4 were required to maintain RING1B and H2AK119ub at these domains. Surprisingly, despite the presence of PRC2.1, these regions lacked any detectable H3K27me3, suggesting an uncoupling between the recruitment of PRC2 to chromatin and its catalytic product. When exogenously over-expressed in NSCLC cells where they are not normally present, DPPA2/4 bind to and promote active chromatin states, resulting in an increase in vivo xenograft tumour growth. Our results demonstrate how in NSCLC cells, DPPA2/4 act as molecular amplifiers of active and poised chromatin. Together, this highlights how aberrant re-activation of embryonic factors in cancers may take on new functions, promoting tumourigenesis.

overall_design: The NCI-H661 cell line is derived from lung large cell carcinoma (subtype of non-small cell lung cancer) metastases and expresses both DPPA2 and DPPA4 highly at the mRNA and protein level. In order to investigate the functional consequence of peturbing DPPA2/4 we performed CRISPR-Cas9 mediated knockout, shRNA-mediated knockdown or siRNA-mediated knockdown of DPPA2 or/and DPPA4 in NCI-H661 cells followed by RNA-seq analyses. For CRISPR-Cas9, analyses of the parental (PAR) cell line as well as wild type (WT) and knockout clones (KO) were conducted. We included two clones per genotype for analyses to determine functional phenotypes while accounting for those attributed to clonal heterogeneity. Analyses were conducted for shRNA models as well following 7 days of induction with either H20 vehicle control or 2ug/mL doxycyline, for control shRNA (shREN), shDPPA2, shDPPA4 or both shDPPA2+4. Analyses were conducted for siRNA models following 96h of knockdown with either control siRNA, siDPPA2, siDPPA4 or both siDPPA2+4. All conditions were done in biological triplicates. For siRNA models we additionally assessed DPPA2 or DPPA4 knockdown in  A427, COV318, DMS114 and HUTU80 cancer cell lines. We also performed analyses on NCI-H661 cells treated with either a vehicle control (DMSO) or the p300/CBP inhibitor A-485 (10uM).

first: Melanie

last: Eckersley-Maslin


title: Embryonic stem cell factors DPPA2/4 amplify active H3K4me3-H2AK119ub chromatin domains in non-small cell lung cancer

type: Methylation profiling by high throughput sequencing


title: Embryonic stem cell factors DPPA2/4 amplify active H3K4me3-H2AK119ub chromatin domains in non-small cell lung cancer (ATAC-seq)

overall_design: The NCI-H661 cell line is derived from lung large cell carcinoma (subtype of non-small cell lung cancer) metastases and expresses both DPPA2 and DPPA4 highly at the mRNA and protein level. In order to investigate the functional consequence of peturbing DPPA2/4 we performed shRNA-mediated knockdown of DPPA2 or/and DPPA4 in NCI-H661 cells followed by ATAC-seq analyses. Analyses were conducted for shRNA models following 7 days of induction with either H20 vehicle control or 2ug/mL doxycyline, for control shRNA (shREN), shDPPA2, shDPPA4 or both shDPPA2+4. All conditions were done in biological duplicates.


title: Identification of IDO1 depedent genes upon IFN-γ stimulation

city: Martinsried

first: Assa

last: Yeroslaviz

state: Bavaria

address: Am Klopferspitz 18

department: computational Biology

institute: Max-Planck-Institute for biochemistry

summary: A key mechanism of malignant cell evasion from anti-tumor immunity centers on tryptophan metabolism by indole-2,3-dioxygenase (IDO1). By degrading tryptophan, IDO1 impairs anti-tumor T cell responses, which should be restored by IDO1 inhibitors (IDO1i). All IDO1i have, however, failed their clinical trials. Therefore, we sought to further investigate the cell intrisic biological function of IDO1 in the context of ovarian cancer by combining spatial proteomics and bulk RNA sequencing. We discovered that IFN-γ killed ovarian cancer cells via a linear pathway that required IFN-γ signaling, IDO1, tryptophan depletion followed by a duality of effects of the integrated stress response that initially protect against tryptophan depletion and later initiate cell death, potentially accounting for the heterogenous expression on IDO1 in situ. By contrast, IDO1i rescued these effects and promoted cancer cell survival. In summary, our results uncover a new facet of IDO1 biology in cancer and suggest that further investigation is required to justify IDO1i use in clinics.

overall_design: Bulk RNA-seq profiling of SKOV3 cells wild-type or their IDO1 knock-down counterparts, stimulated or not with 10ng/ml of IFN-γ for 24 hours

first: Teng Teng

last: Xu

first: Rin Ho

last: Kim


title: Serum Amyloid A (SAA) Transcriptomics Sequencing on enteroid

first: George

middle: Henry

last: Sack

address: 725 N. Wolfe Street

department: Department of Physiology, Pharmacology and Therapeutics

institute: Johns Hopkins University School of Medicine

summary: The 104 aa protein Serum Amyloid A (SAA) is a prominent member of the acute phase response (APR) a remarkably conserved and stereotyped set of serum protein changes associated with inflammation and other stimuli. N-terminal fragments of SAA can form fibrils that can accumulate in organs (“amyloidosis”). No specific biologic function has been identified for SAA; it has been considered an inert “biomarker.” In contrast to this perception of passivity, we report that exposure to both N-terminal decapeptides and intact SAA monomers can induce multiple transcripts in both enteroids and HEK293 cells. The spectrum of transcripts prominently includes proteins related to inflammation and NF-κB control, specifically NFKB1A, TNFA1P3 and IER3. SAA thus can act directly through specific transcription to alter cellular physiology with direct effects on inflammation, likely helping explain its remarkable evolutionary conservation as part of primordial defense.

overall_design: RNA-seq profiling of HEK293 cells treated with full-length SAA protein, with corresponding vehicle controls (HOH + 0.05% BSA). Samples were harvested at specific time points to capture transcriptional changes.

middle: H

last: Sack Jr

first: Joseph

last: Yun

first: Conover

last: Talbot Jr


title: Embryonic stem cell factors DPPA2/4 amplify active H3K4me3-H2AK119ub chromatin domains in non-small cell lung cancer (reChIP-seq)

overall_design: The NCI-H661 cell line is derived from lung large cell carcinoma (subtype of non-small cell lung cancer) metastases and expresses both DPPA2 and DPPA4 highly at the mRNA and protein level. In order to investigate H2AK119ub and H3K4me3 co-occupancy relative to DPPA2/4 in NCI-H661 cells we performed sequential ChIP (reChIP) analyses of these histone modifications. Analyses were conducted in parental H661 cells. All conditions were done in biological duplicates.


title: Embryonic stem cell factors DPPA2/4 amplify active H3K4me3-H2AK119ub chromatin domains in non-small cell lung cancer (ChIP-seq)

overall_design: The NCI-H661 cell line is derived from lung large cell carcinoma (subtype of non-small cell lung cancer) metastases and expresses both DPPA2 and DPPA4 highly at the mRNA and protein level. In order to investigate DPPA2/4 binding, transcription factor binding (KDM2A, SUZ12) and histone modifications (H3K4me3, H3K4me1, H3K36me3, H3K36me2, H3K9me3, H3K27me3, H2AK119ub and H3K27ac) in NCI-H661 cells we performed ChIP-seq analyses of these modifications at baseline. We also assessed histone modifications (H3K4me3, H3K4me1, H3K36me3, H3K9me3, H3K27me3, H2AK119ub and H3K27ac) in the NCI-H1299 cell line model following induced expression of DPPA2/4 after 7 days. All assays were controlled with genomic input controls with all conditions having duplicate replicates.


title: Embryonic stem cell factors DPPA2/4 amplify active H3K4me3-H2AK119ub chromatin domains in non-small cell lung cancer (CUT&Run)

overall_design: The NCI-H661 cell line is derived from lung large cell carcinoma (subtype of non-small cell lung cancer) metastases and expresses both DPPA2 and DPPA4 highly at the mRNA and protein level. In order to investigate DPPA2 and DPPA4 co-occupancy as well as other associated transcription factors/histone modifications (RING1B, MTF2, EP300, PCGF1, SOX2, H3K4me3) in NCI-H661 cells we performed cleaveage under targets and release using nuclease (CUT&RUN) analyses of these proteins/modifications. Analyses were conducted in parental H661 cells and also following shRNA mediated knockdown of DPPA2/4. We additionally profiling exogenously expressed DPPA2 (with Flag-tag) and DPPA4 (with V5-tag) in the NCI-H1299 non-small cell lung cancer cell line. All assays were controlled with isotype controls (Rabbit or Mouse IgG's) having either a singular or duplicate replicates.


title: Embryonic stem cell factors DPPA2/4 amplify active H3K4me3-H2AK119ub chromatin domains in non-small cell lung cancer (ChIPRx-seq)

overall_design: The NCI-H661 cell line is derived from lung large cell carcinoma (subtype of non-small cell lung cancer) metastases and expresses both DPPA2 and DPPA4 highly at the mRNA and protein level. In order to investigate histone modifications (H3K4me3, H3K27me3, H2AK119ub and H3K27ac) in NCI-H661 cells we performed ChIP-seq analyses of these modifications with exogenous mouse spike-ins to account for potential global changes (E14 mouse embryonic stem cells) following either shRNA mediated knockdown of DPPA2/4 for 7 days or H3K27ac ablation with the catalytic p300/CBP inhibitor A-485 for 1 day. All assays were controlled with genomic input controls with all conditions having either duplicate or triplicate replicates.


title: Smoking promotes the progression of colorectal cancer via CKAP2L/STAT3/AREG/EGFR axis

city: Chongqing

first: Shasha

address: No.1 Youyi Road, Yuzhong District

department: Gastroenterology

institute: The First Affiliated Hospital of Chongqing Medical University

summary: Smoking is a major risk factor for colorectal cancer (CRC). But the underlying molecular mechanisms by which smoking promotes CRC remain unclear. The positive association between smoking and CRC was confirmed by both cross-sectional study and mendelian randomization analyses. RNA-seq sequencing and bioinformatics analysis were conducted to identify the key genes involved in smoking-induced CRC progression. After treatment with cigarette smoke extract (CSE) in CRC cells, cell proliferation and metastasis were enhanced. Subsequently, we isolated the total RNA of HCT116 cells treated with CSE and subjected it to the RNA-seq to explore the differentially expressed genes.

overall_design: RNA sequencing was performed on the wild type HCT116 cells and HCT116 cells treated with CSE.


title: Embryonic stem cell factors DPPA2/4 amplify active H3K4me3-H2AK119ub chromatin domains in non-small cell lung cancer (BS-seq)

overall_design: The NCI-H661 cell line is derived from lung large cell carcinoma (subtype of non-small cell lung cancer) metastases and expresses both DPPA2 and DPPA4 highly at the mRNA and protein level. In order to investigate the functional consequence of peturbing DPPA2/4 we performed siRNA-mediated knockdown of DPPA2 or/and DPPA4 in NCI-H661 cells followed by whole genome bisulfite sequencing (WGBS) analyses. Analyses were conducted for siRNA models following 96h of knockdown with either control siRNA, siDPPA2, siDPPA4 or both siDPPA2+4. All conditions were done in biological triplicates. We additionally assessed DPPA4 knockdown in the COV318 ovarian cancer cell line.


title: Radiofrequency regulates the BET-mediated pathways in radial glia differentiation in human cortical development

city: NEW HAVEN

first: Museog

last: Choe

state: CT

address: 10 Amistad Street, Ste 214J

department: Genetics

institute: Yale University

summary: The human brain represents one of the most complex organs in our body, with development regulated by an intricate genetic program. Recently, non-genetic factors, such as prenatal stress, infection, and diet, have been shown to influence brain development. Radiofrequency radiation (RF; 800-2,400 MHz), emitted by natural and artificial sources such as microwaves and cell phones, represents a non-invasive environmental factor. Using human cortical organoids (hCOs) derived from human embryonic stem cells (hESCs), we investigate RF's effects on corticogenesis. We find that RF exposure regulates the differentiation of human and non-human primate radial glia progenitors, maintaining stem cell identity and delaying differentiation. Neurons differentiated under RF treatment show induction of expression of human endogenous retroviruses. Importantly, inhibitors for the BET (bromodomain and extraterminal) protein rescue RF-induced developmental defects in hCOs. Our findings reveal a mechanism by which RF modulates early brain development, offering a non-biological approach to regulate neural stem cell self-renewal.

overall_design: The scRNA-seq analysis was performed on Cortical organoids at Day 70  with/without RF, Aluminum foil, or Sheild. The scATAC-seq analysis was performed on Cortical organoids at Day 70  with/without RF or iBET treatment

first: Bilal

last: Cakir

first: Yoshiaki

last: Tanaka

first: Mu Seog

first: In-Hyun

last: Park


title: Methylation variability and LINE-1 activation in multiple myeloma [RNA-seq]

city: DUARTE

first: Dustin

last: Schones

state: CALIFORNIA

address: 1500 E Duarte Road

institute: City of Hope National Medical Centre

summary: Multiple myeloma (MM) is a type of hematological cancer that arises from uncontrolled proliferation of plasma cells. In addition to frequent genetic mutations, malignant plasma cells are characterized by alterations to the epigenome. Myeloma cells display a genome-wide loss of DNA methylation and a corresponding increase in ‘active’ chromatin modifications. The dramatic epigenetic remodeling that occurs in cancer genomes is associated with loss of silencing at transposable elements, which can impact genome regulation. Through paired epigenome and transcriptome profiling of patient derived MM samples, we have found that loss of DNA methylation in MM genomes results in the formation of partially methylated domains that are variable across patients. This loss of DNA methylation coincides with the expression of hundreds of transcripts driven by LINE-1 (L1) retrotransposons that are epigenetically silenced in normal cells. MM samples can be stratified based on L1 activity with distinct gene expression signatures. The high L1 samples are characterized by a more proliferative, less differentiated state as well as inhibition of interferon and genome defense pathways. Several L1 promoters generate chimeric transcripts with adjacent oncogenes. We further find the KRAB-zinc finger proteins (KZFPs) that are responsible for the epigenetic silencing of L1s have abnormally low abundance in MM samples with high L1 activity. These results indicate that cell proliferation in MM is associated with a loss of KZFP expression and activation of L1 elements.

overall_design: RNA-seq profiling of formalin-fixed, paraffin-embedded (FFPE) tissue samples from plasmablastic multiple myeloma (PMM) patients (N = 8).


title: Inhibition of the Gerozyme 15-Prostaglandin Dehydrogenase Promotes Articular Cartilage Regeneration in Osteoarthritis due to Injury or Aging [scRNA-Seq]

city: Stanford

first: Nidhi

last: Bhutani

address: 240 Pasteur Drive

department: Orthopaedic Surgery

institute: Stanford University

summary: Aging or injury to the joints can lead to cartilage degeneration osteoarthritis (OA), for which there are limited effective treatments. We found that expression of the gerozyme 15-Prostaglandin Dehydrogenase (15-PGDH) was increased in the articular cartilage of aged or injured mice. Both systemic and local inhibition of 15-PGDH with a small molecule inhibitor (PGDHi) led to regeneration of articular cartilage and reduction in OA-associated pain. We used single cell RNA-sequencing and multiplexed immunofluorescence imaging of cartilage), to identify the major chondrocyte subpopulationsInhibition of 15-PGDH decreased hypertrophic-like chondrocytes expressing 15-PGDH and fibro-chondrocytes towards hyaline matrix-synthesizing articular chondrocytes. Regeneration of joint cartilage appears to occur through changes in pre-existing chondrocytes, not stem or progenitor cell proliferation.Gerozyme inhibition could be a potential  identifying a disease-modifying and regenerative approach with potential utility for the treatment of osteoarthritis.

overall_design: Young (3 mo.) and Aged (24-28 mo.) male mice were administered one month of once a day i.p. injection of vehicle (Control group) or the PGDH inhibitor SW033291 (SW group). Following treatment, knee joints from hindlimbs were harvested and the tissue was digested for scRNA sequencing based analysis.

first: Mamta

last: Singla

first: Yu

middle: X

last: Wang

first: Elena

last: Monti

first: Yudhishtar

middle: S

last: Bedi

first: Pranay

last: Agarwal

first: Shiqi

last: Su

first: Sara

last: Ancel

first: Maiko

last: Hermsmeier

first: Nitya

last: Devisetti

first: Akshay

last: Pandey

first: Mohsen

last: Bakooshli

first: Adelaida

last: Palla

first: Stuart

last: Goodman

first: Helen

last: Blau


title: MeCP2 gene dosage-dependent neurodevelopmentally restricted defects arise by SWI/SNF-mediated aberrant activation of cell fate-determining bivalent genes [SAMMY-seq]

city: Milan

first: Michal

last: Kubacki

address: Via Olgettina 58

country: Italy

institute: San Raffaele Scientific Institute

summary: Increased dosage of genes encoding for chromatin factors is thought to inevitably alter gene transcriptional output, leading to cellular dysfunctions. However, a mechanistic understanding of the molecular processes in action and their consistency across different cell types is still lacking. A prototypical gene in this context is MECP2, as its overexpression determines severe neurological deficits in MECP2 duplication syndrome (MDS) and its dosage is considered a crucial safety risk factor in gene therapy for Rett syndrome (RTT). However, in MDS patients, MECP2 dysregulation arises at the embryonic stage while in RTT gene therapy, MECP2 is delivered into the mature brain. Despite these important implications, the molecular consequences of increased MECP2 gene dosage have yet to be fully elucidated. Surprisingly, we found that MeCP2 overexpression induced profound transcriptional alterations in neural progenitor cells (NPCs) while it had minimal or no effects in both mouse and human neurons. Consequently, MeCP2 overexpression in NPCs, but not mature neurons, led to profound functional alterations. Mechanistically, we observed that both endogenous and overexpressed Mecp2 bind to the same CpG island repertoire. In NPCs, lower endogenous Mecp2 levels facilitated stronger deposition of the ectopic protein into CpG islands, driving the transcriptional activation of many developmental bivalent genes, deranging neuronal differentiation. We uncovered that this activation is mediated by the interaction with the SWI/SNF chromatin remodeling complex. Conversely, in neurons, where endogenous Mecp2 is highly expressed, ectopic protein expression leads to minimal CpG island binding and accelerate protein degradation. Our findings reveal that increased gene dosage-dependent effects are highly influenced by cell type, levels of proteins and their mechanisms of action. These results provide a framework to interpret the relationship between Mecp2 chromatin binding and transcriptional output and suggest that Mecp2 overexpression is expected to be well tolerated in gene therapy applications for RTT.

overall_design: This study was designed to investigate the cell-type and developmental-stage-specific consequences of Mecp2 overexpression. We used primary mouse Neuronal Progenitor Cells (NPCs) derived from E13.5 embryos and primary mouse Neurons (Ns) from E18.5 embryos, as well as human iPSC-derived neurons, to compare the effects of Mecp2/MECP2 overexpression versus an EGFP control. To assess the functional outcomes, we performed in vivo experiments using in utero electroporation in E13.5 mouse embryos and systemic AAV-PHP.eB vector delivery in adult mice. The molecular consequences of Mecp2 dosage were analyzed using a combination of high-throughput sequencing techniques: RNA-sequencing was used to profile transcriptional changes, CUT&Tag was employed to map the genomic binding of endogenous and exogenous Mecp2 and the chromatin remodeler Smarcb1, and 4f-SAMMY-seq was used to analyze global chromatin accessibility and organization.

first: Mirko

last: Luoni

first: Serena Gea

last: Giannelli

first: Francesca

last: Morosi

first: Claudia

last: Di Berardino

first: Angelo

last: Iannielli

first: Alessandro

last: Sessa

first: Gaia

last: Colasante

first: Emanuele Di Patrizio

last: Soldateschi

first: Chiara

last: Lanzuolo

first: Vania

last: Broccoli


title: Single-cell transcriptomics of the Drosophila ring gland identifies SoxN–Vvl complex as key regulator of juvenile hormone biosynthesis

city: Guangzhou

first: Suning

last: Liu

state: Guangdong

address: No.55, West of Zhongshan Avenue, Tianhe District

institute: South China Normal University

summary: We have employed a single cell sequencing approach using 10x Genomics scRNA-seq to elucidate the transcriptional landscape of the Drosophila larval corpus allatum (CA). As a a sub-organ within the ring gland, the CA expresses a set of enzymes that mediate steps in the conversion of acetyl-CoA into JH. This study provide single-cell sequencing data of the larval ring gland at early wandering stage, and found that CA-specific expressing SoxN is required for juvenile hormone biosynthesis and metamorphosis.

overall_design: In short, we dissected the ring glands of w1118 larvae at early wandering (EW) stage。

first: Jie

last: Zhang


title: Single‑cell RNA sequencing  of orthotopic GBM tumors following oncolytic adenovirus treatment

city: Chengdu

first: Zhang

last: Zongliang

address: People's South Road 17, Chengdu, P.R. China

department: State Key Laboratory of Biotherapy

institute: Sichuan University

summary: Mice bearing intracranial GL261‑CAR tumors were treated intratumorally with PBS (control), oAd, or oAd‑mCD47/PD‑L1‑mIL‑12 (1 × 109 pfu). Tumors were harvested three days after the second viral injection and dissociated into single‑cell suspensions using the SeekMate Tissue Dissociation Reagent Kit A Pro (SeekGene, K01801‑30).Single‑cell RNA‑seq libraries were constructed using the SeekOne Digital Droplet Single‑Cell 3′ Library Preparation Kit (SeekGene, #K00202).Single‑cell transcriptomic data demonstrate that oAd‑mCD47/PDL1‑mIL‑12 orchestrates a multi‑faceted immune response: expanding cytotoxic and memory T‑cell subsets, polarizing macrophages toward an antigen‑presenting and chemokine‑secreting phenotype, and enhancing reciprocal signaling between immune and cancer cells to promote tumor clearance.

overall_design: To dissect the immune landscape and tumor‑immune interactions following treatment, we performed single‑cell RNA sequencing (scRNA‑seq) on tumors harvested three days after intratumoral injection of PBS, oAd, or oAd‑mCD47/PDL1‑mIL‑12.

first: Zongliang


first: Shasha

last: Wu

summary: Smoking is a major risk factor for colorectal cancer (CRC). But the underlying molecular mechanisms by which smoking promotes CRC remain unclear. The positive association between smoking and CRC was confirmed by both cross-sectional study and mendelian randomization analyses. RNA-seq sequencing and bioinformatics analysis were conducted to identify the key genes involved in smoking-induced CRC progression. After treatment with cigarette smoke extract in CRC cells, cell proliferation and metastasis were enhanced. Subsequently, cytoskeleton associated protein 2 like (CKAP2L) was identified as a key gene involved in smoking-induced CRC and its downregulation inhibited cell proliferation and metastasis. CKAP2L is an important part of the cell centrosome and serves a critical role in spindle formation. Previous studies have demonstrated that CKAP2L mediates the cell cycle in a variety of cancer types, promoting the progression and spread of tumors.A recent study reported that regulatory factor X5-regulated CKAP2L can promote the proliferation and metastasis of CRC cells. In this study, we upregulated CKAP2L in HCT116 cells and downregulated CKAP2L in RKO cells. Then, these cells were subjected to the RNA-seq to explore the expression of relative genes.

overall_design: RNA sequencing was performed on the negative control RKO cells (RKO-NC), knockdown CKAP2L RKO cells (RKO-shCKAP2L), control HCT116 cells (HCT116-Vector), and overexpression CKAP2L HCT116 cells (HCT116-CKAP2L).


title: Molecular improvement of IL-23 inhibition revealed by single-cell RNA sequencing in concurrent psoriasis and systemic lupus erythematosus

city: Seoul

first: So-Jung

last: Choi

state: --- Select One ---

address: 103, Daehak-ro, Jongno-gu, Seoul, Republic of Korea

country: South Korea

institute: Seoul National university

summary: Psoriasis and systemic lupus erythematosus (SLE) are chronic inflammatory diseases with rare coexistence, sharing the IL-23/IL-17 axis as a pathogenic pathway. A 42-year-old male with both conditions was successfully treated with the IL-23 inhibitor guselkumab, improving psoriasis without worsening SLE over 2.5 years. Single-cell RNA sequencing of skin biopsies revealed a decrease in T17 cells and IL-17-related transcripts post-treatment. Gene Set Enrichment Analysis showed reduced IFN-γ and IFN-α responses, indicating broader inflammatory modulation. This study suggests IL-23 inhibitors may be a promising treatment for concurrent psoriasis and SLE, pending larger cohort validation.

overall_design: Skin biopsy samples were collected from a patient with concurrent psoriasis and SLE, including non-lesional, pre-treatment lesional, and post-treatment lesional skin after 12 weeks of IL-23 inhibitor therapy. Single-cell RNA sequencing was performed to analyze gene expression, focusing on T-cell subsets and inflammatory pathways. Gene Set Enrichment Analysis was used to identify differentially regulated pathways, particularly IFN responses, pre- and post-treatment.

first: Jongeun

last: Lee

first: Hyun Seung

first: Seo-Young

first: Hyo Jeong

last: Nam

first: Yun Jung

last: Huh

first: Hyun Je

last: Kim

first: Jeong Eun


title: TL1A-activated Tcells as upstream regulators of perianal fistulizing disease-associated changes in the rectum of Crohn's Disease patients.

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

institute: IDIBAPS

summary: Perianal fistulizing disease (PFD) is a complication that affects about 20% of Crohn’s disease (CD) patients and whose etiology remains unknown. To identify predisposing events driving fistula formation, we investigated cell-specific alterations in the rectal mucosa of CD patients with PFD. Rectal biopsies from CD patients with or without PFD (CD+PFD and CD, respectively; n=31) were subjected to single-cell RNA sequencing. Functional analyses were conducted using peripheral CD3+ T cells, intestinal tissue explants, primary fibroblasts and 2D-epithelial monolayer cell cultures. The rectal mucosa of CD+PFD patients is imprinted with cellular and transcriptomic alterations specific to PFD and independent of luminal inflammation, potentially driven by TL1A activation in CD4+ T cells. We identified lymphotoxin beta (LTB or its functional heterotrimer LTα1β2) as a novel mediator downstream of TL1A that, along with IL-22, induces a PFD-associated signature in rectal fibroblast and epithelial cells, respectively. This signature includes an increased abundance of fibroblasts, an induction of matrix-degrading enzymes and transcriptomic rewiring of the lamina propria S1 fibroblasts, as well as an anti-bacterial and immune responses in epithelial cells. Notably, the induction of LTα1β2 and IL-22 occurs independently of TNF signaling, revealing a new TL1A-LTα1β2/IL-22 axis that remains active under anti-TNF therapy. Our findings revealed unique cellular alterations in the rectum of CD patients with PFD, highlighting the previously unrecognized involvement of TL1A in mediating this signature and supporting the need for exploring the role of TL1A inhibition as a therapeutic approach for PFD.

overall_design: 3D organoid cultures from intestinal tissue were generated and stimulated with 20ng/ml of IL-22 for 24 hours. Isolated RNA was reverse-transcribed to cDNA and sequenced with the Affymetrix GeneChip Human Genome U219 Array (Affimetrix, USA).

first: Victoria

last: Gudiño

first: Jae-won

last: Cho

first: Berta

last: Caballol

first: Angela

last: Sanzo-Machuca

first: Marisol

last: Veny

first: Ana

last: Corraliza

first: Isabella

last: Dotti

first: Livia

last: Genaro

first: Elisa

last: Melón-Ardanaz

first: Carme

last: Casademunt

first: Miriam

last: Esteller

first: Iris

last: Teubel

first: Lisseth

last: Robbins

first: Angel

last: Giner

first: Cristina

last: Prieto

first: Elena

last: Ferrer

first: Raquel

last: Franco-Leal

first: Albert

last: Martin-Cardona

last: Loras

first: Maria

last: Esteve

first: Jordi

last: Rimola

first: Agnes

last: Fernandez-Clotet

first: Ingrid

last: Ordas

last: Ricart

first: Julia

last: Panes

first: Martin

last: Hemberg


title: Disruption of ARID1B recruitment to the nuclear pore complex as a new anticancer therapeutic strategy [RNA-Seq 2]

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

summary: Triple-negative breast cancer (TNBC), a highly aggressive subtype, currently lacks potent targeted therapies. ARID1B, a key SWI/SNF chromatin remodeling complex subunit, is linked to high-grade malignancies and poorer prognosis, making it a potential biomarker and therapeutic target. However, its function and regulation remain unclear. Here, we found that uncontrolled accumulation of ARID1B and its nuclear import promoted oncogenesis and drug resistance. ARID1B negatively regulates ARID1A, impairing SWI/SNF-mediated tumor suppression and enhancing tumor survival. Using protein complex purification and mass spectrometry, we identified KPNA2-KPNB1-RANBP2 as a critical protein cascade that facilitates ARID1B nuclear import. Replacing R1518, H1519, and D1522 residues on ARID1B with T1518, G1519, and G1522 attenuated the ARID1B-KPNA2 interaction, preventing recruitment of ARID1B to the nuclear pore complex. Pharmacological inhibition of KPNB1 suppressed ARID1B translocation, thereby limiting its nuclear levels. Our RNA-seq and ATAC-seq analyses indicated that KPNB1 inhibition also mimicked the effects of the SWI/SNF inhibitor on chromatin accessibility and gene expression, likely due to the reduced nuclear levels of ARID1B. In TNBC mouse models, ARID1B knockout significantly reduced tumor growth and enhanced PARP inhibitor efficacy. Collectively, our findings reveal that disrupting ARID1B nuclear translocation could be a new therapeutic strategy for TNBC.

overall_design: To investigate the interplay between ARID1B and ARID1A and to investigate the mechanisms by which ARID1B promote tumorigenesis in TNBC, we performed RNA-seq analysis in ARID1B OE, ARID1B KO, ARID1A KO and Control MDA-MB-468 cells.

first: Olena

last: Odnokoz

first: Xiaodong

last: Lu

first: Jonathan

last: C. Zhao

first: Yong

last: Wan


title: Innate immune epigenomic landscape following controlled human influenza virus infection

city: New York

first: Stuart

last: Sealfon

address: One Gustave L. Levy Place

department: Department of Neurology

institute: Icahn School of Medicine at Mount Sinai

summary: Viral infections can induce changes in innate immunity that persist after virus clearance. Here, we used blood samples from a human influenza H3N2 challenge study to perform comprehensive multi-omic analyses. We detected remodeling of immune programs in innate immune cells after resolution of the infection that was proportional in magnitude to the level of prior viral load. We found changes associated with suppressed inflammation including decreased cytokine and AP-1 gene expression as well as decreased accessibility at AP-1 targets and interleukin-related gene promoter regions. We also found decreased histone deacetylase gene expression, increased MAP kinase gene expression, and increased accessibility at interferon-related gene promoter regions. Genes involved in inflammation and epigenetic-remodeling showed modulation of gene-chromatin site regulatory circuit activity. These results reveal a coordinated rewiring of the epigenetic landscape in innate immune cells induced by mild influenza virus infection.

overall_design: This study included 45 placebo and 69 vaccinated subjects. Whole blood samples from all subjects were profiled with bulk transcriptomics (RNA-seq) at all time points

last: Zaslavsky

first: William

last: Thistlethwaite


title: Methylation variability and LINE-1 activation in multiple myeloma

first: Dustin

last: Schones

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

overall_design: Refer to individual Series


title: Methylation variability and LINE-1 activation in multiple myeloma [WGBS]

overall_design: Whole-genome bisulfite sequencing (WGBS) was performed on formalin-fixed, paraffin-embedded (FFPE) tissue samples from patients with plasmablastic multiple myeloma (PMM) (N = 15).


title: MeCP2 gene dosage-dependent neurodevelopmentally restricted defects arise by SWI/SNF-mediated aberrant activation of cell fate-determining bivalent genes [Cut & Tag]

first: Michal

last: Kubacki

first: Mirko

last: Luoni

first: Serena Gea

last: Giannelli

first: Francesca

last: Morosi

first: Claudia

last: Di Berardino

first: Angelo

last: Iannielli

first: Alessandro

last: Sessa

first: Gaia

last: Colasante

first: Emanuele Di Patrizio

last: Soldateschi

first: Chiara

last: Lanzuolo

first: Vania

last: Broccoli


title: Methionine metabolism and NOP2 methyltransferase are essential for MYC-Driven liver tumorigenesis

city: San Francisco

first: Sensen

last: Lin

state: CA California

address: HSW 760, UCSF Parnassus, 513 Parnassus Ave, San Francisco

institute: UCSF

summary: Hepatocellular carcinoma (HCC) represents the third leading cause of cancer-related death worldwide and has been increasing in recent years in developed nations.1,2 The MYC oncogene or its paralogs are frequently amplified or overexpressed in particularly aggressive subtypes of cancer associated with stem cell-like features and worse clinical outcomes,3,4 including in liver cancer.5 Unfortunately, selective inhibitors that target MYC or its transcriptional program are not yet clinically available for therapy of HCC. Here, we identified methionine metabolism as a selective vulnerability for MYC but not RAS-driven liver cancers. MYC-driven liver cancer cells are methionine dependent and S-adenosylmethionine (SAM), the predominant methyl donor, partially rescues methionine depletion. A low methionine diet, or the methylation inhibitor 5-azacytidine limited MYC-driven tumor formation, but RAS-driven liver cancer was resistant to a low methionine diet. Metabolic tracing of methionine catabolism in MYC high cells identified increased m5C methylation of genomic DNA or ribosomal RNA. We found NOP2, an rRNA m5C-methyltransferase, was regulated by both MYC and methionine. RNA bisulfite seq demonstrated that methionine depletion reduced methylation levels at 28S rRNA C4099, C3438 and C3683. NOP2 knockdown decreased the methylation at C4099, and slightly affected C3438 methylation, suggesting the involvement of NOP2 in methionine dependence. Depletion of NOP2 selectively inhibited MYC liver cancer cell proliferation, tumorigenesis and in vivo tumor growth. Thus, methionine catabolism is critical for MYC-driven liver tumorigenesis and NOP2 may serve as a new therapeutic target in liver cancer.

overall_design: RNA bisulfite seq in EC4 cells. MYC high and MYC low EC4 cells were cultured with either 10 µM or 200 µM methionine medium for 48 h, and RNA was isolated for bisulfite sequencing. Four groups (in triplicate), MYC high methionine high, MYC low methionine high, MYC high methionine low, MYC low methionine low. For NOP2 knockdown assay, EC4 cells were treated with a pool of siRNAs (20nM) for 72h, and total RNA were isolated for bisulfite sequencing. Two groups (in triplicate), siNOP2 and siNon-Target.

first: Andrei

last: Goga


title: Study on the Effects of Retinoids on UVR-Induced Skin Photoaging [Spatial Transcriptomics]

city: Hangzhou

first: Yicheng

last: Xie

address: 3333 Binsheng Rd

institute: Children’s Hospital Zhejiang University School of Medicine

summary: Photoaging contributes to up to 80% of visible facial aging signs, making it a major dermatological concern. While retinoids such as retinol and all-trans retinoic acid (ATRA) promote extracellular matrix (ECM) regeneration, their side effects limit widespread use. We propose that hydroxypinacolone 9-cis retinoate (9-cis HPR), a derivative of 9-cis retinoic acid, activates both retinoic acid receptor (RAR) and retinoid X receptor (RXR), enhancing efficacy while minimizing irritation. However, its in vivo anti-photoaging effects remain underexplored. This study evaluates 9-cis HPR in the UVR-damaged SKH-1 mouse model, investigating its role in inflammation control, ECM regeneration, and melanogenesis suppression.

overall_design: Spatial Transcriptomics profiling of the skin of SKH-1 mice, and the Model-Blank sample contains UVR group (upper), Control group (lower), the Administration sample contains UVR and treated with 0.1% Retinol group (upper), UVR and treated with 0.03% 9-cis HPR group (lower).

first: Fan

last: Hu

first: Qijiang

last: Zhao

first: Chengzhi

last: Zheng

first: Ye

last: Zhong

first: Jian

last: Shen

first: Ruian

last: Qiu

first: Hao

last: Zhu

first: Tongquan

last: Wu

first: Rui

last: Ye

first: Le

last: Du

first: Daqing

last: Ma


title: STL1267 Inhibits Myofibroblast Differentiation in a TGFβ1-Driven Human Lung Fibroblast Model

city: Kansas City

first: Isaac Kirubakaran

last: Sundar

state: KS

address: University of Kansas Medical Center, Dept. of Internal Medicine/Pulmonary Critical Care and Sleep Medicine

department: Internal Medicine

institute: University of Kansas Medical Center

summary: Pulmonary fibrosis is a progressive interstitial lung disease characterized by excessive fibroblast-to-myofibroblast transition (FMT) and extracellular matrix (ECM) deposition, largely driven by transforming growth factor-beta 1 (TGFβ1). Existing therapies offer limited efficacy, particularly in advanced disease. Circadian rhythms have recently emerged as key modulators of lung inflammation and fibrosis. In this study, we developed an in vitro model of chronic fibrotic signaling using adenovirus-mediated TGFβ1 overexpression (Ad-TGFβ1) or human recombinant protein TGFβ1 in primary human lung fibroblasts. Using this model, we investigated the antifibrotic potential of STL1267, a next-generation Rev-erbα agonist with improved potency, specificity, and pharmacokinetic properties. RNA sequencing and pathway analysis revealed that STL1267 significantly reversed Ad-TGFβ1-induced expression of genes associated with ECM remodeling, collagen biosynthesis, and immune suppression. STL1267 also upregulated pathways related to IL-10, IL-4, and IL-13 signaling, which are known to counteract fibrotic responses. Quantitative PCR and immunoblotting confirmed STL1267's ability to downregulate key pro-fibrotic markers, including COL1A1, αSMA, FN1, and FAP, at both gene and protein levels. Comparative studies with other Rev-erbα agonists (GSK4112, SR9009), Saracatinib, and FDA-approved antifibrotic drugs (Pirfenidone, Nintedanib) demonstrated superior efficacy of STL1267 in inhibiting both preventive and post-fibrotic induction models. Moreover, lentiviral overexpression of Rev-erbα suppressed TGFβ1-induced αSMA expression, supporting a direct antifibrotic role. These findings highlight Rev-erbα as a key regulator of myofibroblast differentiation and support both STL1267 and GSK4112 as promising candidates for circadian-based antifibrotic therapy. Future in vivo studies are warranted to evaluate its translational potential in idiopathic pulmonary fibrosis.

overall_design: Stranded mRNA sequencing was performed using the Illumina NovaSeq 6000 Sequencing System. Total RNA quality was assessed using the Agilent TapeStation 4200 with the RNA ScreenTape Assay kit (Agilent Technologies, 5067-5576). Library preparation was conducted using the Universal Plus mRNA-Seq with NuQuant stranded mRNA library preparation protocol (Tecan Genomics, 0520-A01), starting with 500 ng of total RNA. The mRNA fraction was enriched via oligo dT bead capture, followed by fragmentation, reverse transcription into cDNA, end repair, ligation of Unique Dual Index (UDI) adaptors, strand selection, and library amplification (12 cycles) using a Bio-Rad S1000 thermal cycler. Library validation was performed using the Agilent TapeStation 4200 with the D1000 ScreenTape Assay kit (Agilent Technologies, 5067-5582). Library concentrations were determined using the NuQuant module of the library prep kit and measured with a Qubit 4 Fluorometer (ThermoFisher/Invitrogen). Libraries were normalized to a final concentration of 1.9 nM, pooled, and quantified in triplicate using the LightCycler 96 (Roche) with FastStart Essential DNA Green Master (Roche, 06402712001) and KAPA Library Quantification DNA Standards 1-6 (KAPA Biosystems, KK4903). The pooled libraries were then denatured with 0.2N NaOH (final concentration: 0.04N), neutralized with 400 mM Tris-HCl (pH 8.0), and diluted to 380 pM for onboard clonal clustering on a patterned flow cell using the NovaSeq 6000 S1 Reagent Kit v1.5 – 200 cycle (Illumina, 20028318). Sequencing was performed using a 2 × 101 cycle format with dual index reads as follows: Read 1 – 101 cycles, Index Read 1 – 8 cycles, Index Read 2 – 8 cycles, and Read 2 – 101 cycles. Following sequencing, raw data was converted from .bcl to fastq format using the bcl2fastq software and demultiplexed into individual sample sequences. Data were distributed via a secure FTP site or Illumina BaseSpace for downstream analysis.

first: Sundar

last: Isaac Kirubakaran

first: Griffard

last: Rachel

first: Prasad

last: Chandrashekar


title: Study on the Effects of Retinoids on UVR-Induced Skin Photoaging [scRNA-seq]

overall_design: scRNA-seq profiling of the skin of SKH-1 mice, and the groups were divided into control group (repeated 1), model group (repeated 1), low dose group  (repeated 2), middle dose group  (repeated 2), positive control 1 group  (repeated 2), positive control 2 group  (repeated 2).


title: Generation of human pineal gland organoids with melatonin production for disease modeling

first: Museog

last: Choe

summary: The pineal gland regulates circadian rhythms through melatonin production, yet human studies are limited by poor tissue access. To overcome this, we developed human pineal gland organoids (hPGOs) from pluripotent stem cells, modeling pineal development and function. Single-cell RNA sequencing revealed distinct mature and developing pinealocyte populations with transcriptomic profiles closely resembling the in vivo pineal gland. hPGOs produce melatonin, express adrenergic receptors, and respond to noradrenaline, mimicking physiological regulation. To model disease-related impairments, we generated hPGOs from Angelman syndrome (AS) patient-derived iPSCs, which exhibit disrupted pinealocyte differentiation and markedly reduced melatonin synthesis, reflecting AS-related developmental pathology. Additionally, transplanted hPGOs restored circulating melatonin in pinealectomized mice, demonstrating their potential for cell-therapy approaches. These findings establish hPGOs as a robust platform for probing pineal development, circadian regulation, and their disruption in neurodevelopmental and sleep-related disorders.

overall_design: The scRNA-seq analysis was performed on pineal gland organoids at 6 week and 18 week, while the RNA-seq analysis was conducted on 12 week pineal gland organoids derived from Angelman syndrome patients or healty control iPSCs.

first: Ferdi Ridvan

last: Kiral

first: Woo Sub

last: Yang

first: In-Hyun

last: Park


title: Disruption of ARID1B recruitment to the nuclear pore complex as a new anticancer therapeutic strategy [ChIP-Seq]

first: Jindan

last: Yu

summary: Triple-negative breast cancer (TNBC), a highly aggressive subtype, currently lacks potent targeted therapies. ARID1B, a key SWI/SNF chromatin remodeling complex subunit, is linked to high-grade malignancies and poorer prognosis, making it a potential biomarker and therapeutic target. However, its function and regulation remain unclear. Here, we found that uncontrolled accumulation of ARID1B and its nuclear import promoted oncogenesis and drug resistance. ARID1B negatively regulates ARID1A, impairing SWI/SNF-mediated tumor suppression and enhancing tumor survival. Using protein complex purification and mass spectrometry, we identified KPNA2-KPNB1-RANBP2 as a critical protein cascade that facilitates ARID1B nuclear import. Replacing R1518, H1519, and D1522 residues on ARID1B with T1518, G1519, and G1522 attenuated the ARID1B-KPNA2 interaction, preventing recruitment of ARID1B to the nuclear pore complex. Pharmacological inhibition of KPNB1 suppressed ARID1B translocation, thereby limiting its nuclear levels. Our RNA-seq and ChIP-seq analyses indicated that KPNB1 inhibition also mimicked the effects of the SWI/SNF inhibitor on chromatin accessibility and gene expression, likely due to the reduced nuclear levels of ARID1B. In TNBC mouse models, ARID1B knockout significantly reduced tumor growth and enhanced PARP inhibitor efficacy. Collectively, our findings reveal that disrupting ARID1B nuclear translocation could be a new therapeutic strategy for TNBC.

overall_design: To investigate the interplay between ARID1B and ARID1A and to investigate the mechanisms by which ARID1B promote tumorigenesis in TNBC, we performed ARID1A ChIP analysis in ARID1B OE, ARID1B KO, ARID1A KO and Control MDA-MB-468 cells.

first: Olena

last: Odnokoz

first: Xiaodong

last: Lu

first: Jonathan

last: C. Zhao

first: Yong

last: Wan


title: Commensal myeloid crosstalk in neonatal skin regulates cutaneous type 17 inflammation

first: Henry

last: Rodriguez

address: 1322 3rd avenue

institute: University of California San Francisco

summary: Early life microbe-immune interactions at barrier surfaces have lasting impacts on the trajectory towards health versus disease. Monocytes, macrophages and dendritic cells are primary sentinels in barrier tissues, yet the salient contributions of commensal-myeloid crosstalk during tissue development remain poorly understood. Here, we identify that commensal microbes facilitate accumulation of a population of monocytes in neonatal skin. Transient postnatal depletion of these monocytes resulted in heightened IL-17A production by skin T cells, which was particularly sustained among CD4+ T cells into adulthood and sufficient to exacerbate inflammatory skin pathologies. Neonatal skin monocytes were enriched in expression of negative regulators of the IL-1 pathway. Functional in vivo experiments confirmed a key role for excessive IL-1R1 signaling in T cells as contributing to the dysregulated type 17 response in neonatal monocyte-depleted mice. Thus, a commensal-driven wave of monocytes into neonatal skin critically facilitates immune homeostasis in this prominent barrier tissue.

overall_design:
CD45+ cells were isolated from four healthy human donor (one fetal, one pediatric, two adults donors) by FACS and analyzed using scRNA-seq
Please note that this is human data associated to already deposited mouse data under GSE244177.

first: Miqdad

last: Dhariwala

first: Ricardo

last: Carale

first: Andrea

last: DeRogatis

last: Rodriguez-Valbuena

first: Joy

last: Okoro

first: Christina

last: Ekstrand

first: Antonin

last: Weckel

first: Victoria

last: Tran

first: Irek

last: Habrylo

first: Rio

last: Barrere-Cain

first: Oluwasunmisola

last: Ojewumi

first: Allison

last: Tammen

first: Jessica

last: Tsui

first: Saba

last: Shaikh

first: Shivaram

last: Yellamilli

first: Ahmed

last: Aladhami

first: Robin

last: Schwartz

first: John

last: Leech

first: Geil

last: Merana

first: Kamir

last: Hiam-Galvez

first: Matthias

last: Mack

first: Joanna

last: Halkias

first: James

last: Gardner

first: Rachel

last: Rutishauser

first: Gabriela

last: Fragiadakis

first: Matthew

last: Spitzer

first: Alexis

last: Combes

first: Tiffany

last: Scharschmidt


first: Azucena

last: Salas

summary: Single-cell RNA sequencing revealed the increased abundance of some cell types, such as intestinal fibroblasts, in the CD-PFD rectal mucosa relative to CD. Within the stromal subset, the lamina propria S1 fibroblasts showed the highest number of differentially expressed genes (DEGs) between CD and CD-PFD patients, including an upregulation of TFPI2 and a downregulation of the TGFβ-responding gene CTGF. These changes were validated by bulk RNA analysis, where we also observed overexpression of the previously described PFD target genes MMP1 and MMP3. In vitro studies with intestinal fibroblasts confirmed the negative regulation by TGFβ of the PFD-signature, thus ruling out TGFβ as a driver of the PFD-associated fibroblast signature. Next, we investigated DEGs in the lymphoid compartment and identified lymphotoxin beta (LTB) as being upregulated in CD-PFD intestinal CD4+ T cells. LTB interacts with its receptor LTBR, which is expressed in stromal, epithelial and myeloid cells. Interestingly, LTB-LTBR interactions were increased in the CD-PFD group. In vitro studies in primary fibroblasts showed that LTB upregulates TFPI2, while it downregulates CTGF, thus reproducing the PFD-associated signature. Finally, we submitted the top 50 genes overexpressed by CD-PFD CD4+ T cells to the immune dictionary1, which identified TL1A as its most likely driver. In line with this, the TL1A receptor TNFRSF25 was overexpressed in CD-PFD CD4+ T cells. As a link between TL1A and LTB is not described in the literature, we stimulated anti-CD3-activated peripheral T cells with TL1A and observed the significant upregulation of LTa1b2, the functional form of LTB. Intriguingly, we also observed that while TNF can drive the PFD-associated signature in fibroblasts, it cannot induce LTa1b2 in T cells, suggesting that TNF and TL1A/LTB signalling are two independent but potentially complementary pathways in PFD. In summary, we propose a previously unrecognized TL1A-LTB axis as being responsible for inducing PFD-associated alterations in the rectal mucosa, and we hypothesise that inhibition of TL1A might be worth exploring in the context of perianal disease.

overall_design: Rectum biopsies from patients with Crohn's Disease (CD) with and without perianal fistulizing disease (PFD) were digested and processed for scRNA-seq analysis (10x Genomics). A total of 31 patients were included, with distinct clinical characteristics (active inflammation, remission, or uninvolved tissue).

first: Victoria

last: Gudiño

first: Jae-won

last: Cho

first: Berta

last: Caballol

first: Angela

last: Sanzo-Machuca

first: Ana

last: Corraliza

first: Marisol

last: Veny

first: Livia

last: Genaro

first: Elisa

last: Melón-Ardanaz

first: Carme

last: Casademunt

first: Miriam

last: Esteller

first: Agnes

last: Fernández-Clotet

first: Ingrid

last: Ordàs

first: Raquel

last: Franco-Leal

first: Elena

last: Ricart

first: Julia

last: Panes

first: Martin

last: Hemberg


title: Study on the Effects of Retinoids on UVR-Induced Skin Photoaging [RNA-seq]

first: Yicheng

last: Xie

overall_design: RNA-seq profiling of Normal human dermal fibroblasts (NHDF), and the groups were divided into untreated group, treated with 0.1 μ g/mL 9-cis HPR group, and treated with 0.251 μ M retinic acid group, and repeated 3 times.

first: Fan

last: Hu

first: Qijiang

last: Zhao

first: Chengzhi

last: Zheng

first: Ye

last: Zhong

first: Jian

last: Shen

first: Ruian

last: Qiu

first: Hao

last: Zhu

first: Tongquan

last: Wu

first: Rui

last: Ye

first: Le

last: Du

first: Daqing

last: Ma


title: TL1A-activated Tcells as upstream regulators of perianal fistulizing disease-associated changes in the rectum of Crohn's Disease patients [RNA-seq]

first: Azucena

last: Salas

summary: Perianal fistulizing disease (PFD)  is one of the complications observed in Crohn's Disease patients, which consist of the formation of new tracks connecting the anal canal or the rectum with the perianal region. Applying scRNA-seq analysis in the rectum of patients with and without PFD revealed alterations in the stromal compartment as a response to cytokines such as TNF, TGFb and LTB. To investigate the downstream signature of these cytokines especifically in intestinal fibroblasts, we sequenced human intestinal primary fibroblasts upon stimulation to TNF, TGFb and LTB.

overall_design: Human primary intestinal fibroblasts were estimulated with TNF, TGFb and LTB for 24h. RNA was isolated and sequenced by bulk RNA-seq (n=5 per each condition)

first: Victoria

last: Gudiño

first: Jae-Won

last: Cho

first: Berta

last: Caballol

first: Angela

last: Sanzo-Machuca

first: Ana

last: Corraliza

first: Marisol

last: Veny

first: Livia

last: Genaro

first: Elisa

last: Melón-Ardanaz

first: M Carme

last: Masamunt

first: Miriam

last: Esteller

first: Agnès

last: Fernández-Clotet

first: Ingrid

last: Ordàs

first: Julià

last: Panés


title: T cell-intrinsic VISTA deficiency dampens the efficacy of CTLA4 blockade by limiting TCR repertoire diversity and effector function of tumor specific CD8+ cytotoxic T cells

city: Cleveland

first: Lily

last: Wang

address: 9500 Euclid Ave

institute: Cleveland Clinic

summary: This study examines the effects of T cell-intrinsic VISTA deficency on the responses and repertoire of tumor-infiltrating CD8+ T cells in preclinical melanoma models.

overall_design: WildType (WT) and VISTA knockout (KO) Tcells from tumor tissue were analyzed using 10X genomics 5' kit including single cell gene expression with paired VDJ analysis.


title: Mechanism and treatment strategy of N2 lymph node metastasis in T1 NSCLC

city: Xi’an

first: Run-Ze

last: Zhang

address: 569 Xinsi Road

department: Department of thoracic surgery

institute: Tangdu Hospital, Air Force Medical University

summary: Lung cancer has the highest morbidity and mortality rates. Approximately 20% of patients with stage T1 non-small cell lung cancer (NSCLC) have mediastinal (N2) lymph node metastasis. The mechanism underlying N2 lymph node metastasis in stage T1 NSCLC remains unclear. To explore this mechanism, T1N0M0 and T1N2M0 NSCLC samples were subjected to single-cell sequencing.

overall_design: Ten NSCLC samples, including T1N0M0 (n = 4), T1N2M0 (n = 3), and three metastatic N2 lymph node samples from T1N2M0 patients were collected for single-cell sequencing. Through cell composition comparison and differential analysis between T1N2M0 and T1N0M0 samples, we explained the mechanisms of N2 lymph node metastasis in T1-stage NSCLC and proposed corresponding therapeutic strategies.

first: Jinbo

last: Zhao

first: Xiyang

last: Tang

first: Runze

first: Zhibo

last: Feng


title: Commonalities in gene expression and methylation changes across two rat models of acquired epilepsy

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

department: Biomedical Sciences

institute: University of North Dakota


title: ECD co-operates with ERBB2 to promote tumorigenesis through upregulation of unfolded protein response and glycolysis

city: Omaha

first: Vimla

last: Band

state: Nebraska

address: 601 Saddle Creek road

department: Department of Genetics, Cell Biology & Anatomy,

institute: University of Nebraska Medical Center

summary: The mammalian orthologue of the Drosophila ecdysoneless (ECD) mRNA and protein are overexpressed in breast cancer, and its overexpression correlates with poor prognosis and short patient survival, particularly in ERBB2/HER2-positive breast cancer (BC). This work investigates the co-operative oncogenic mechanism of ECD and ERBB2 by deriving transgenic mice overexpressing ECD and/or ERBB2 (huHER2) in mammary epithelium under MMTV promoter (ECD+HER2Tg), as well as human mammary immortal epithelial cell lines (hMECs) overexpressing ECD and/or ERBB2. While huHER2Tg mice developed more homogenous solid nodular carcinomas, double transgenic mice (ECD; huHER2Tg) developed heterogenous and histologically aggressive mammary tumors with basal-like phenotype and epithelial mesenchymal transition (EMT) features, similar to ECDTg tumors.  Importantly, transcriptomic profile of ECD; huHER2Tg tumors revealed upregulation of two major oncogenic pathways, unfolded protein response (UPR) and glycolysis. Consistently, ECD; huHER2Tg tumors exhibited increased mRNA levels of cancer stem cell markers and EMT related genes.  Further, hMECs expressing both ECD and ERBB2 as compared to ECD or ERBB2 expressing cells showed significant increase in oncogenic traits, such as enhanced migration, anchorage independence, mammosphere, and organoid formation. RNA sequencing analysis of single and double transfectants showed significant upregulation of glycolysis and UPR pathways in ECD+ERBB2 expressing cells as compared to ECD or ERBB2 overexpressing hMECs.  Given our recent finding that ECD directly binds to RNA, we demonstrate mRNAs of three key glycolytic enzymes (LDHA, PKM2 and HK2) and mRNA of a major UPR regulated gene GRP78 directly associated with ECD protein using RNA immunoprecipitation assay. Higher expression of glycolytic mRNAs and GRP78 in ECD+ERBB2-expressing cells was due to increased mRNA stability. Lastly, we show an increase in glucose uptake and enhanced glycolytic rate in ECD+ERBB2-overexpressing cells as compared to ECD- or ERBB2-overexpressing hMECs.  Taken together, our findings support a co-operative role of ECD and ERBB2 in oncogenesis by enhancing two major oncogenic pathways, UPR and glycolysis. These results provide experimental proof and mechanistic insights to our previous findings that ECD is overexpressed in ERBB2-positive BC patients, and its’ overexpression correlates with poor prognosis and short survival in patients.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-seq profiling of Vector expressing, ECD overexpressing, ERBB2 overexpressing and ECD+ERBB2 overexpressing 76NTERT human mammary epithelial cells. In adition, RNAseq profiling of ECDTg mouse mammary tumors, huHER2Tg mouse mammary tumors and ECD; huHER2Tg mouse mammary tumors

first: Band

last: Vimla

last: Hamid

first: Mohapatra

last: Bhopal


title: Integrative CSF profiling identifies disease-specific immune responses in leptomeningeal disease

first: Paula

last: Nieto

state: Spain

address: Barcelona Science Park, Carrer de Baldiri Reixac, 4, tower I, 08028 Barcelona

department: CNAG

institute: CNAG

summary: Assessing anti-tumor immune responses and immune microenvironment alterations in central nervous system (CNS) neoplasms like brain tumors and leptomeningeal disease (LMD) provides prognostic insights and predictive biomarkers. Cerebrospinal fluid (CSF) liquid biopsy (LB) is a promising minimally-invasive approach, but its ability to reflect these processes remains unclear. We used single-cell RNA and T cell receptor (TCR) sequencing of CSF cells and spatial transcriptomics of CNS lesions in LMD patients with CNS lymphoma (CNSL), glioblastoma (GB), and brain metastases (BrM), compared to neuroinflammatory CNS disorders to unveil the immune complexity during the disease course. We identified disease-specific CSF environments reflecting parenchymal tumor microenvironment features. CNSL showed robust T cell responses, while BrM and GB were dominated by myeloid cells. Unique mechanisms of disease progression and resistance linked to CSF cell dynamics highlight the potential of scRNAseq-based CSF LB for uncovering disease biology, predicting biomarkers, and developing personalized therapies for CNS neoplasms.

overall_design: Single-cell RNA and TCR sequencing of cerebrospinal fluid (CSF) cells from 17 patients, including serial samples to a total of 21 samples.

first: Svenja

last: Klinsing

first: Ginevra

last: Caratú

first: Joachim

last: Steinbach

first: Pia

last: Zeiner

first: Holger

last: Heyn

first: Juan

middle: C