title: Phenotypic effects of disruption of all four rice HK cytokinin receptors

city: Chapel Hill

first: Joseph

last: Kieber

state: NC

address: 120 South Road

institute: University of North Carolina

summary: The phytohormone cytokinin has diverse functions in plants, most of which have been primarily elucidated in dicots. In order to further characterize the role of cytokinin in a monocot, we used CRISPR-Cas9 to generate rice lines with frameshift alleles in the four putative cytokinin receptors (Histidine Kinases 3,4,5,6) in all single and multiple combinations. The transcriptome of the hk3,4,5,6 mutant is completely insensitive to cytokinin, suggesting that all cytokinin signaling regulating transcription acts through these four HKs, despite the presence of a CHASE-containing Serine-Threonine kinase in rice.

overall_design: RNA-seq profiling of wild-type Kitaake callus and hk3,4,5,6 quadruple mutant callus treated with either 5 μM 6-Benzylaminopurine (BA) or vehicle control for 1 hour.

first: Shouse

last: Eva Mei


title: Sustained MYB activity drives emergent enhancer activation and precise enhancer-promoter interactions [Capture-C]

status: Public on May 01 2026

city: Oxford

first: I-Jun

last: Lau

address: Old Rd

department: Botnar Research Centre

country: United Kingdom

institute: University of Oxford

summary: Transcription factors (TFs) are key effectors of enhancer activity. MYB is a critical hematopoietic TF that is frequently dysregulated in cancer. Despite its well-established role, the exact mechanisms by which MYB influences enhancer function—and the specific stages of enhancer activation at which it operates—remain poorly understood. Using high resolution Micro-Capture-C, we show that upon MYB degradation, highly defined enhancer-promoter interactions at specific MYB binding sites are lost. Loss of these interactions, together with other hallmarks of enhancer activity—reduced H3 lysine-27 acetylation and enhancer RNA transcription—correlates with significant downregulation of target gene expression in leukemia, indicating that MYB mediates transcription activation via maintenance of enhancer function. When anchored to DNA within a gene desert region that is devoid of histone marks and active transcription, the MYB transactivation domain is sufficient and necessary for the nucleation of an enhancer-like region. This results in the activation of transcription from distal cryptic elements and the establishment of long-range chromatin interactions up to 400 kb away from the anchor point. Together, these results indicate that MYB activity alone is sufficient to induce long-range interactions and transcription, achieving this through highly precise enhancer-promoter crosstalk.

overall_design: Capture-C in E14 (TOT2N variant) cell lines containing stable integration of rTetR-MYBTA or TetR-MYBTA constuct ±doxcycline treatment.

first: Nicholas

middle: T

last: Crump

first: Thomas

middle: A

last: Milne


title: Sustained MYB activity drives emergent enhancer activation and precise enhancer-promoter interactions [TT-seq]

type: Expression profiling by high throughput sequencing

overall_design: TT-seq in SEM cells with MYB endogenously tagged with FKBP12(F36V) ±dTAG13 treatment


title: Matched single-cell chromatin, transcriptome, and surface marker profiling captures in vivo epigenomic reprogramming during basal-to-luminal transition in the mammary gland [mm468_OneCell_multiome]

status: Public on Jul 03 2026

city: Paris

first: Céline

last: Vallot

address: 26 Rue D'Ulm

country: France

institute: Institut Curie

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Single-cell multi-omics methods enable simultaneous mapping of chromatin states and transcriptomes, offering deep insights into gene regulation. Yet, the full potential of these approaches remains untapped for rare cell populations, as most methods require thousands of cells and are limited in their ability to capture multiple molecular layers comprehensively within the same cell.  Here, we introduce OneCell CUT&Tag a user-friendly method that provides matched high-resolution epigenome, full-transcriptome, and surface marker quantification from every cell, with input as low as one cell. Using this approach, we uncovered epigenomic priming of basal cells in the mammary gland and captured the dynamics of basal-to-luminal transdifferentiation. We identified a transitional cell population with intermediate epigenomic profiles—absent in reference populations—and demonstrated a continuous epigenomic progression from basal to luminal states, while transcriptomes exhibited a binary switch. Adaptable to diverse samples and tissues, this method also revealed the role of H3K27me3 in shaping zygotic expression programs. By matching multiple layers of molecular information at single-cell resolution, OneCell CUT&Tag dissects the complementary roles of each omics layer in shaping cellular identity and function, opening new avenues to study rare and complex biological systems.

overall_design: OneCell multiome (H3K27me3 + transcriptome) on MDA-MB-468 single-cells

first: Anna

last: Schwager

first: Eve

last: Moutaux

first: Adeline

last: Durand

first: Mélanie

last: Miranda

first: Louisa

last: Hadj

first: Simon

last: Dumas

first: Mathias

last: Schwartz

first: Marthe

last: Laisné

first: Justine

last: Marsolier

first: Manuel

last: Guthmann

first: Délia

last: Dupré

first: Grégoire

last: Jouault

first: Mélissa

last: Saichi

first: Déborah

last: Bourc’his

first: Elisabetta

last: Marangoni

first: Nicolas

last: Servant

first: Leïla

last: Perié


title: CircularRNAs (circRNAs) sequencing in hepatocellular carcinoma (HCC) patients with and without microvascular invasion (MVI)

status: Public on Jul 04 2026

city: HANGZHOU

first: Xin

last: Hu

address: YUHANGTANGROAD 866

country: China

institute: Zhejiang university

type: Non-coding RNA profiling by high throughput sequencing

summary: Formed by cis back-splicing and circularization of introns, exons and other transcripts, circRNAs constitute covalently closed single-stranded loops and are considered as the emerging non-coding RNAs. Accumulating evidence indicates that they are double-edged swords in the process of HCC metastasis. However, the specific mechanism and potential clinical therapeutic significance remain vague. We attempted to profile the regulatory networks of circRNA and RNA-binding proteins.

overall_design: To identify potential circRNAs that promote HCC metastasis, we profiled global circRNA transcripts from 5 tissue pairs of HCC patients with and without MVI using RNA sequencing.

first: Ronggao

last: Chen

first: Guanrong

first: Xiao

last: Xu


title: Improved Small Interfering RNA Therapy Targeting the Long, Non-Coding RNA SMILR For Therapeutic Intervention in Coronary Artery Bypass Graft Failure

city: EDINBURGH

first: Andrew

last: Baker

state: Not applicable

address: 47 Little France Crescent

institute: University of Edinburgh

summary: Coronary artery bypass graft (CABG) surgery remains the gold standard of care to prevent myocardial ischaemia in patients with advanced atherosclerosis, however long-term graft patency remains a considerable and long-standing problem. Excessive vascular smooth muscle cell (vSMC) proliferation in the grafted tissue is recognised as central to late CABG failure. We previously showed that siRNA-mediated silencing of SMILR, a human-specific SMC-enriched lncRNA, blocks vSMC proliferation, suggesting that targeting SMILR expression could be a novel way to prevent neointima formation, and thus CABG failure. Here, we describe the design and synthesis of a library of 76 chemically-enhanced SMILR-targeting siRNA. From this library, we identify a lead siRNA, BHF7, which demonstrates potent and reproducible silencing of SMILR expression and which robustly blocks vascular smooth muscle cell proliferation, both in vitro and up to 14 days in the ex vivo human saphenous vein model. We further demonstrate using RNA-sequencing that BHF7 down-regulates the expression of genes associated with proliferation and does not induce the expression of interferon or apoptosis genes, suggesting it has an acceptable safety profile both on and off-target. Finally, we performed TUNEL staining and measured the levels of cleaved caspase-3 after BHF7 treatment which demonstrated that BHF7 does not induce a cytotoxic response either in vitro or ex vivo.  Collectively, this data represents a pre-clinical package into the function and specificity of BHF7 which warrants further investigation into the possibility of utilising BHF7 as a novel, ex vivo RNA therapeutic for the prevention of CABG failure.

overall_design: RNAseq profiling to find the transcriptional effects in saphenous vein smooth muscle cells(SVSMCs) after knockdown of the long non-coding RNA SMILR via an optimised siRNA (BHF7). Transcriptional profiles of quiescent, proliferative and proliferative/transfected SVSMCs were compared.

last: Brown

first: Anna

middle: L

last: Malinowska

first: Matthew

last: Bennett

first: Andrés

last: Correa-Sánchez

first: Laia

last: Valencia

first: Aimee

middle: P

last: Lucignoli

first: Scott

last: Webster

last: Barton

first: Loic

last: Roux

first: Julie

last: Rodor

first: David

middle: E

last: Newby

first: Mark

last: Cunningham

middle: H


title: Matched single-cell chromatin, transcriptome, and surface marker profiling captures in vivo epigenomic reprogramming during basal-to-luminal transition in the mammary gland [mouse_mammary_gland_multiome]

first: Céline

last: Vallot

overall_design: Mice were sacrificed by cervical dislocation. Six mammary glands (numbers 2, 3, and 4 from each side) were collected and pooled. The pooled tissues were roughly chopped using dissecting scissors, followed by finer mincing with two scalpels. Single-cell dissociation was achieved through enzymatic digestion using 3 mg ml–1 collagenase I (Roche, 11088793001) and 100 U m–1 hyaluronidase (Sigma-Aldrich, H3506) in complete media (HBSS 24020117; 5% FBS) for 2 h under agitation (170 rpm) at 37°C. Cells were then treated with pre-warmed (37°C) PBS 0.25% trypsin-versen (Thermo Fisher Scientific, 15040-033) for 1 min 30s, with pipetting for 45s. Twas further processed with 5 mg ml–1 dispase (Sigma-Aldrich, D4693) and DNase 0.1 mg ml–1 (Roche, 11284932001) in complete media for 6 min at 37°C. Red blood cells were lysed using red blood cell lysis buffer (Thermo Fisher Scientific, 00-4333-57), and the suspension was filtered through a 40 µm cell strainer before cell counting and FACS staining. The cells were stained in the dark at 4°C for 20 min. Stained cells were resuspended at 10 million cells ml–1 in cytometry media (PBS with 1% BSA and 2 mM EDTA).  Three control mice were sorted with the following antibodies: anti-CD45-APC (1:50, BioLegend, 103112), anti-CD31-APC (1:50, BioLegend, 102510), anti-CD24-BV421 (1:50, BioLegend, 101826) and anti-CD49f-PE-Cy7 (1:50, BioLegend, 313622) to stain one million cells.  Sorting was performed using a SH800 sorter with a 100 µm chip, and epithelial cells (CD45-, CD31-, CD24 medium/high, CD49f medium/high) were collected in a 384-well plate, with one cell per well, using a custom single-cell sorting mode (60% mask). Two control mice were sorted with an expanded FACS panel comprising the following antibodies: anti-CD45-BV510 (1:500, BioLegend, 103138), CD31-BV510 (1:100, BD Biosciences, 563089); anti-CD29-PE-Dazzle594 (1:500, BioLegend, 102245), EpCAM-PE-Cy7 (1:500, BioLegend, 118215), Tspan8-BUV395 (1:100, BD Biosciences, 748043). Dead cells were excluded using Zombie NIR Fixable Viability Dye (1:5000, BioLegend, 423106); according to the manufacturer’s instructions. When the expanded panel was applied, 10 million cells were stained to enable capture of the rare Tspan8+ cell population. Cell sorting was performed on a BD Aria Fusion cell sorter. Epithelial cells (CD45-, CD31-, EpCAM medium/high, CD29 medium/high) were index-sorted into 384-well plates at one cell per well. Wells were allocated as follows: 50% luminal cells (CD45-, CD31-, EpCAM high, CD29 medium), 25% Tspan8⁺ basal cells (CD45-, CD31, EpCAM low, CD29 high, Tspan8+), and 25% Tspan8- basal cells (CD45-, CD31-, EpCAM low, CD29 high, Tspan8-).

last: Schwager

first: Eve

last: Moutaux

first: Adeline

last: Durand

first: Mélanie

last: Miranda

first: Louisa

last: Hadj

first: Simon

last: Dumas

first: Mathias

last: Schwartz

first: Marthe

last: Laisné

first: Justine

last: Marsolier

first: Manuel

last: Guthmann

first: Délia

last: Dupré

first: Grégoire

last: Jouault

first: Mélissa

last: Saichi

first: Déborah

last: Bourc’his

first: Elisabetta

last: Marangoni

first: Nicolas

last: Servant

last: Perié


title: tRNA m1A modification promotes benign prostatic hyperplasia through translational regulation of the TGF-β pathway [tRNA-seq]

city: Shenzhen

first: Yuhan

last: Liu

state: Guangdong

address: Xueyuan avenue 1066

institute: Shenzhen University

summary: Benign prostatic hyperplasia (BPH) is a common urological disease affecting elderly men. Although global hypermethylation has been implicated in BPH pathogenesis, the specific role of N1-methyladenosine (m1A) tRNA modifications remains unclear. Here, we find that RNA m1A modification and its methyltransferase TRMT61A were significantly upregulated in BPH tissues. Impaired m1A tRNA modification upon TRMT61A depletion resulted in decreased cell proliferation and contraction, as well as induced cell cycle arrest and apoptosis in prostate cells both in vitro and in vivo. Mechanistically, TRMT61A knockdown decreased m1A-modified tRNAs, impairing global translation and altering translational efficiency of specific genes. Moreover, ribosome profiling and RNA sequencing revealed that genes with reduced translational efficiency upon TRMT61A depletion were enriched in the TGF-β signaling pathway, including TGFβR1, INHBA, SMAD2, FST, and ID2. Codon usage bias contributed to differential translational efficiency in TRMT61A-depleted cells. Our study reveals a novel mechanism by which TRMT61A promotes BPH progression through dynamic m1A tRNA modification and modulation of a codon-dependent translational network.

overall_design: To investigate the cooperative function TRMT61A in the regulation tRNA expression, we established WPMY-1 cell lines in which each target gene has been knock down by shRNA

first: Libo

last: Yu

first: Xinhui

last: Liao

first: Ru

last: Huang


title: Sustained MYB activity drives emergent enhancer activation and precise enhancer-promoter interactions [TOPmentation]

first: I-Jun

last: Lau

overall_design: TOPmentation in SEM cells with MYB endogenously tagged with FKBP12(F36V)

first: Nicholas

last: Crump

first: Thomas

last: Milne


title: Histone post-translational modification changes upon Sfp1 depletion

city: Quebec city

first: Jacques

last: Cote

address: 9 McMahon Street

department: CHU de Québec-Université Laval Research Center

country: Canada

institute: Laval University

summary: In this study, we investigate the physical and functional interaction between NuA4 and Sfp1. Sfp1 was rapidly depleted from yeast nuclei, and histone modification changes were detected by ChIP-sequencing.

overall_design: ChIP-sequencing of H4K8ac, Htz1, H3K9ac and H3 upon nuclear depletion of Sfp1.


title: Dysregulated thymus-ovary axis promotes virtual memory T cell polarization to aggravate PCOS pathology [scRNAseq-human]

city: Beijing

first: Chenlei

last: Xu

address: No. 38 Xueyuan Road, Haidian District

institute: Peking University

summary: Polycystic ovary syndrome (PCOS) is characterized by androgen excess, ovarian dysfunction and polycystic ovarian morphology and is classically considered as a disorder of the hypothalamic-pituitary-gonadal (HPG) axis. However, whether organs beyond the reproductive endocrine axis contribute to PCOS pathogenesis remains elusive. Herein, we identified a functional thymus-ovary axis involved in PCOS development.

overall_design: Using complementary mouse models, we demonstrated that thymic remodeling occurs early during disease development, preceding the onset of aberrant ovarian pathology. Disruption of thymic function or genetic ablation of adaptive immunity markedly attenuated PCOS-related lesions, indicating a central role for T cells. Mechanistically, CD8⁺ T cells acted as the dominant effector subset, with selective expansion of virtual memory CD8⁺ T (TVM) cells during PCOS progression. These cells preferentially accumulated in reproductive tissues, exacerbated ovarian inflammation and prolonged disease persistence following endocrine challenge. Functionally, adoptive transfer of TVM cells enhanced disease severity, whereas depletion of CD8⁺ T cells or selective restriction of TVM cell polarization by JAK inhibition alleviated PCOS phenotypes.

first: Yaruo

last: Qiu

first: Weixuan

last: Wang

first: Yao

last: Feng

first: Dan

last: Lv


title: Functional interaction between the transcription factor Sfp1 and the NuA4 complex in response to nutrient availability [CUT&RUN]

summary: In this study, we investigate the physical and functional interaction between the transcription factor Sfp1 and the NuA4 complex in response to nutrient changes or stress. To study the functional interaction, we rapidly deplete Sfp1 or Esa1 (the catalytic subunit of NuA4) from nucleus, and performed CUT&RUN to profile all Sfp1/NuA4-regulated genes.

overall_design: CUT&RUN sequencing of Sfp1 upon Esa1 depletion, Eaf1 upon Sfp1 depletion; CUT&RUN of Sfp1 (wild-type and mutant) and Eaf1 in normal growth condition or TORC1-inhibited condition.


title: Functional interaction between the transcription factor Sfp1 and the NuA4 complex in response to nutrient availability[RNA]

summary: In this study, we investigate gene expression profile upon carbon source shifts in yeast. RNA-sequencing was performed in Sfp1 wild-type strain and K655/657 mutants growing in different carbon sources.

overall_design: RNA-seq of wild-type Sfp1 and K655/657R, K655/657Q mutants growing in 2% glucose, 2% raffinose, and 15min, 30min upon the addition of glucose after raffinose incubation


title: Nanostring nCounter Myeloid Innate Immunity analysis of CD8 T cells cultured with conditioned media

status: Public on Apr 30 2026

city: South San Francisco

first: Ittai

middle: Ethan

last: Eres

state: CA

address: 750 Gateway Boulevard

department: ARIA

country: USA

institute: Amgen

summary:
The immunosuppressive tumor microenvironment (TME) contributes to resistance against checkpoint inhibitors. However, the precise factors that shape the immune contexture of the TME remain elusive. Here, we report that Single-Stranded DNA Binding Protein 4 (SSBP4), a previously uncharacterized protein, suppresses intratumoral T-cell activation by promoting excessive cholesteryl ester production in tumor cells. Overexpression of SSBP4 in tumor cells decreased T-cell infiltration and accelerated tumor growth in murine syngeneic tumor models. Conversely, genetic ablation of SSBP4 in tumor cells enhanced T-cell infiltration and inhibited tumor growth in a CD8+ T cell–-dependent manner. Mechanistically, SSBP4 upregulated cholesterol synthesis genes, leading to increased production of cholesterol and cholesteryl esters in tumor cells, which directly suppressed CD8+ T-cell activation and function. Furthermore, SSBP4 abrogation significantly improved the efficacy of anti-PD-1 treatment. Thus, in this study, we have identified SSBP4 as a cancer cell–intrinsic regulator of cholesterol metabolism that contributes to tumor immune evasion.
Immune-related gene expression was quantified using the Nanostring nCounter Myeloid Innate Immunity Panel. Total RNA was isolated from splenic CD8 T cells of C57BL/6 mice, where were cultured with conditioned media from SSBP4-wildtype or knockout B16F10 tumor cells. RNA was extracted from CD8 T cells, hybridized, scanned on a Nanostring Digital Analyzer, and raw RCC files were generated. Raw count data were processed and normalized in nSolver software for downstream immune transcriptome profiling.

overall_design: Equal numbers of B16F10 SSBP4-knockout and SSBP4-wildtype cancer cells were regularly cultured for 48 hours prior to culture medium collection. Splenic CD8+ T cells were negatively isolated from C57BL/6 mice and cultured with above-mentioned condition media for 48 hours. CD8 T cells were harvested for RNA extraction. RNA samples included the wildtype control group and the knockout experimental group (n= 4 biological samples per group). Transcriptomic profiling of immune and cancer-related genes was performed via Nanostring nCounter high-sensitivity digital counting. All raw RCC files, official probe annotation CSV, and gene count matrices are provided.

first: Ou

last: Peiqi

first: Eres

last: Ittai

first: Zhao

last: Junjie

first: Han

last: Chia-Jung

first: Oh

last: Jaehak

first: Kim

last: Aeryon

first: Dong

last: Jiayi

first: Zhou

last: Hong

first: Yamawaki

last: Tracy

first: Li

last: Chi-Ming

first: Rankin

last: Andrew

first: Noubade

last: Rajkumar

first: Yu

last: Xin


title: Nanostring nCounter Mouse PanCancer Immune Profiling analysis of murine tumor tissues

summary:
The immunosuppressive tumor microenvironment (TME) contributes to resistance against checkpoint inhibitors. However, the precise factors that shape the immune contexture of the TME remain elusive. Here, we report that Single-Stranded DNA Binding Protein 4 (SSBP4), a previously uncharacterized protein, suppresses intratumoral T-cell activation by promoting excessive cholesteryl ester production in tumor cells. Overexpression of SSBP4 in tumor cells decreased T-cell infiltration and accelerated tumor growth in murine syngeneic tumor models. Conversely, genetic ablation of SSBP4 in tumor cells enhanced T-cell infiltration and inhibited tumor growth in a CD8+ T cell–-dependent manner. Mechanistically, SSBP4 upregulated cholesterol synthesis genes, leading to increased production of cholesterol and cholesteryl esters in tumor cells, which directly suppressed CD8+ T-cell activation and function. Furthermore, SSBP4 abrogation significantly improved the efficacy of anti-PD-1 treatment. Thus, in this study, we have identified SSBP4 as a cancer cell–intrinsic regulator of cholesterol metabolism that contributes to tumor immune evasion.
Immune-related gene expression was quantified using the Nanostring Mouse PanCancer Immune Profiling panel. Total RNA was isolated from the C57BL/6 SSBP4-wildtype or knockout B16F10 tumors on Day 15 post tumor inoculation. RNA was hybridized, scanned on a Nanostring Digital Analyzer, and raw RCC files were generated. Raw count data were processed and normalized in nSolver or ROSALIND software for downstream immune transcriptome profiling.

overall_design: 2 × 10e5 B16F10 SSBP4-knockout (experimental) and SSBP4.wildtype (control) cancer cells were injected subcutaneously. Tumors were harvested post 15-day tumor inoculation and snap-frozen by liquid N2 for long-term storage. Frozen tumor samples were thawed and dissociated for single cell suspension, followed by RNA extraction. RNA samples included the wildtype control group and the experimental group (n= 5 mice per group). Transcriptomic profiling of immune and cancer-related genes was performed via Nanostring nCounter high-sensitivity digital counting. All raw RCC files, official probe annotation CSV, and gene count matrices are provided.


title: Cancer cell intrinsic SSBP4 enables tumor immune evasion by promoting cholesterol biosynthesis

summary: The immunosuppressive tumor microenvironment (TME) contributes to resistance against checkpoint inhibitors. However, the precise factors that shape the immune contexture of the TME remain elusive. Here, we report that Single-Stranded DNA Binding Protein 4 (SSBP4), a previously uncharacterized protein, suppresses intratumoral T-cell activation by promoting excessive cholesteryl ester production in tumor cells. Overexpression of SSBP4 in tumor cells decreased T-cell infiltration and accelerated tumor growth in murine syngeneic tumor models. Conversely, genetic ablation of SSBP4 in tumor cells enhanced T-cell infiltration and inhibited tumor growth in a CD8+ T cell–-dependent manner. Mechanistically, SSBP4 upregulated cholesterol synthesis genes, leading to increased production of cholesterol and cholesteryl esters in tumor cells, which directly suppressed CD8+ T-cell activation and function. Furthermore, SSBP4 abrogation significantly improved the efficacy of anti-PD-1 treatment. Thus, in this study, we have identified SSBP4 as a cancer cell–intrinsic regulator of cholesterol metabolism that contributes to tumor immune evasion.

overall_design: RNA-seq data were generated from parental MC38 (5 samples) and huMSLN-transfected MC38.T4 (5 samples) murine melanoma cell lines.


title: Sustained MYB activity drives emergent enhancer activation and precise enhancer-promoter interactions [MCC]

first: I-Jun

last: Lau

overall_design: Micrococal-Capture-C (MCC) in SEM cells with MYB endogenously tagged with FKBP12(F36V) ±dTAG-13 treatment.

first: Nicholas

last: Crump

first: Thomas

last: Milne


title: Cancer cell intrinsic SSBP4 enables tumor immune evasion by promoting cholesterol biosynthesis [RNA-Seq]

first: Ittai

last: Eres

overall_design: RNA-seq data were generated from MC38 (7 samples) and B16-F10 (8 samples) murine melanoma cell lines. In each respective cell line, both wild type and genetically modified replicates were included. For MC38, overexpression of the murine Ssbp4 gene was achieved using retroviral transduction; for B16-F10, knockout of the murine Ssbp4 gene was achieved using CRISPR-cas9.


title: Cancer cell intrinsic SSBP4 enables tumor immune evasion by promoting cholesterol biosynthesis [ATAC-Seq]

overall_design: ATAC-seq data were generated from B16-F10 murine melanoma cells (4 total samples). Two of the samples were wild type, and the other two had their Ssbp4 gene knocked out using CRISPR-cas9 technology.

first: Ou

last: Peiqi


title: Peersim [RNA-Seq]

city: Gif sur Yvette

first: Etienne

last: Delannoy

address: avenue des Sciences

institute: INRAE

summary: Omics analyses are now a ubiquitous first step in the search for condition-specific events such as differentially expressed genes, often relying on Venn diagrams to highlight unique responses. In stress experiments, for instance, the presence of differentially expressed genes exclusive to combined stresses is frequently interpreted as evidence of non-additive effects: the effect of combined stresses is different from the sum of the effect of single stresses. Using a multi-stress dataset with 22 replicates, we here argue that this reasoning is likely to be false because of the inherently low statistical power of most studies, which use only a few (often three) biological replicates. While it is well known that low statistical power reduces sensitivity, its detrimental impact on specificity has been largely overlooked. We emphasize the need for careful interpretation of any claim of specificity, regardless of the number of replicates, and plead for improved experimental design and statistical modelling to avoid misleading biological interpretations.

overall_design: The Peersim project produced 22 replicates of Arabidopsis thaliana adult leaf samples treated with either 1000ppm CO2 (eCO2), 30C for 30h (eTemperature) or a combination of both (eC_eT). Multiple omic analyses (total RNA-seq, smallRNA-seq, proteomics, metabolomics (GC-MS and LC-MS) as well as PAM-fluorescence measurements were generated for each sample

first: Marie-Laure

last: Martin

first: Guillem

last: Rigaill

first: Benoit

last: Castandet

first: Médine

last: Benchouaïa

first: Stéphanie

last: Pateyron

first: Alexandra

last: Launay-Avon

first: José

last: Caïus

first: Christine

last: Paysant Le Roux

first: Véronique

last: Brunaud

first: Jérémy

last: Ferraro

first: Michael

last: Hodges

first: Axel

last: de Julien de Zélicourt


title: Micro-regional bulk RNA sequencing data obtained from human thoracic aorta

city: Tsukuba

first: Erna

last: Raja

address: 1-1-1 Tennodai

department: TARA center

country: Japan

institute: University of Tsukuba

summary: Capturing gene expression changes within the aortic wall is critical for understanding the pathogenesis of aortic diseases. To investigate gene expression alterations associated with disease progression in the human aortic media, we performed micro-regional RNA sequencing analysis.

overall_design: Total RNA was extracted and cDNA libraries were constructed according to the manufacturer’s protocol. The data included four patients with aortic dilatation and three patients with aortic dissection. The punch biopsies (100 μm) were collected from 4 distinct areas on cross sections within the aortic media, which were defined as I (first 100 μm from the aortic lumen, excluding subendothelial ECM), L (adjacent 100 μm), M (medial midline) and A (100 μm adjacent to the adventitia). Each punch was analyzed in duplicate or triplicate (n = 2 or 3).

first: Kenichi

last: Kimura

first: Chiho

last: Tokunaga

first: Kaori

last: Sugiyama

first: Hiroko

last: Matsunaga

first: Haruko

last: Takeyama

first: Yuji

last: Hiramatsu

first: Hiromi

last: Yanagisawa


title: NAD-dependent redox control enables endothelial quiescence and vascular stabilization during angiogenesis

city: Philadelphia

first: Wencao

last: Zhao

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: The process of angiogenesis requires endothelial cells (ECs) to toggle between states of quiescence versus high replication, migration, and tissue invasion. Little is known regarding how ECs return to quiescence during this process. This project aims to understand the role of NAD in endothelial cell proliferation and the transition of from proliferation to quiescence.

overall_design: RNA-seq profiling was performed on human umbilical vein endothelial cells (HUVECs) under the following conditions: control, NAMPT inhibition, and NAMPT inhibition with NMN supplementation. HUVECs were sparsely seeded and harvested either 2 days (day 2) or 5 days (day 5) after seeding. At day 2, cells were analyzed under control and NAMPT-inhibited conditions. At day 5, cells were analyzed under control, NAMPT-inhibited, and NAMPT-inhibited plus NMN-supplemented conditions. Under these culture conditions, cells at day 2 remain sparsely distributed and proliferative, whereas by day 5 they typically reach full confluence.

first: Zoltan

last: Arany

first: Yifan

last: Yang


title: Proteomic screening identifies HNRNPA2B1 as a novel factor that controls Epstein-Barr virus reactivation through chromatin regulation

city: Pittsburgh

first: Febri

last: Sugiokto

state: Pennsylvania

address: 5117 Centre Avenue

institute: University of Pittsburgh

summary: Epstein-Barr virus (EBV) establishes lifelong persistent infection in most human populations. The virus persists as an episome in the host cells during latency and periodically reactivates through transcriptional activation of the immediate-early genes. While epigenetic regulation is central to maintaining viral latency, the host factors that enforce repression at these promoters remain incompletely defined. Here, we employed a novel Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9-based engineered DNA-binding molecule-mediated chromatin immunoprecipitation coupled with mass spectrometry (enChIP-MS) approach to identify proteins associated with the promoter of EBV immediate-early (IE) gene ZTA. This approach revealed an enrichment of multiple heterogeneous nuclear ribonucleoproteins and identified HNRNPA2B1 as a potential regulator of EBV ZTA gene expression. Functional analyses across multiple EBV+ cell models demonstrated that HNRNPA2B1 acts as a restriction factor for EBV lytic reactivation. Depletion of HNRNPA2B1 led to increased expression of IE and downstream lytic genes, enhanced RNA polymerase II recruitment to the ZTA and RTA promoters, and elevated the proportion of cells entering the lytic cycle. Conversely, enforced expression of HNRNPA2B1 suppressed EBV lytic reactivation. Mechanistically, HNRNPA2B1 enhances repressive viral chromatin states by facilitating recruitment of the histone demethylase KDM1A to EBV IE gene promoters, thereby limiting the activating histone H3K4 trimethylation. Together, these findings identify HNRNPA2B1 as a key epigenetic regulator of EBV latency and link RNA-binding proteins to chromatin control of viral reactivation.

overall_design: RNA-seq profiling of wiltype HNRNPA2B1 and depleted HNRNPA2B1 in Akata (EBV+) cell line

first: Sugiokto

last: Febri Gunawan

first: Li

last: Renfeng


title: Mitochondrial OXPHOS restricts SARS-CoV-2 replication

first: Douglas

middle: C

last: Wallace

address: 3501 Civic Center Blvd

department: Center for Mitochondrial and Epigenomic Medicine

institute: Children's Hospital of Philadelphia

summary: SARS-CoV-2 rewires host metabolism to optimize virus production. While glycolysis is necessary for virus production, the importance of mitochondrial oxidative phosphorylation (OXPHOS) is unknown. The mitochondrial DNA (mtDNA) codes for 13 critical OXPHOS polypeptides plus the 22 tRNAs and 2 rRNAs for mitochondrial protein synthesis. We discovered an approximately 5 to 100-fold greater SARS-CoV-2 virus production in infected human ACE2-expressing A549 lung cells when OXPHOS was inhibited by mtDNA depletion (ρ⁰ cells), inhibition of mitochondrial translation with chloramphenicol (CAP), or chemical inhibition of OXPHOS complexes. OXPHOS inhibition led to a marked increase in the size and distribution of viral replication centers and accelerated the production and release of infectious particles, occurring approximately two hours earlier than in parental A549-ACE2 (WT) cells. Subsequently, we found that increased glycolytic capacity was required for enhanced viral replication while differences in innate immune pathway activation were not. Reintroduction of mtDNA from a well-defined maternal lineage into the ρ⁰ cells reinstated OXPHOS, impaired SARS-CoV-2 replication, and reversed associated viral and glycolytic correlates. Thus, metabolic balance regulates SARS-CoV-2 replication, with OXPHOS exerting an antiviral effect.

overall_design: To determine whether OXPHOS capacity is the predominant driver of transcriptional variation and glycolytic reprogramming in host cells, bulk RNA-sequencing was performed on A549-ACE2 cells spanning a gradient of mitochondrial function—ρ0 (mtDNA-depleted) clones, CAP-treated (mitochondrial translation-inhibited) cells, wild-type (WT), and ρ+ Uk cybrid (mtDNA-replenished) clones—alongside mock-infected and UV-inactivated virus controls, infected with SARS-CoV-2 WA1 at MOI=5.0 and collected at 6 and 24 hours post-infection. RNA was extracted using the RNAEasy Plus Mini kit, depleted of rRNA using QIAGEN FastSelect, and sequencing libraries constructed with the NEBNext Ultra II RNA Library Preparation Kit and sequenced on the Illumina NovaSeq 6000 using a 2x150 paired-end configuration. Differential gene expression (DEG) analysis was performed using DESeq2 (padj < 0.05, |log2FC| > 1) with PCA, Venn diagram, and volcano plot analyses applied to curated OXPHOS and glycolysis/HIF1α gene sets to assess the relationship between bioenergetic status and transcriptional programming, complemented by Seahorse glycolysis stress test validation of the metabolic phenotypes. These plots as well as curated gene lists, DEGs, and gene ontology analyses are available in the manuscript main and supplementary material.

first: Yentli

last: Soto Albrecht


title: Transcriptomic features of GFP+ RPE cells in Serpine-Gfp heterozygous mice at 2 months III

city: Bethesda

first: David

last: McGaughey

state: MD

address: 10 Center Dr

department: NEI

institute: NIH

summary: Heterogeneous degeneration of retinal pigment epithelium (RPE) leads to irreversible blindness in diseases associated with macular atrophy. However, the underlying mechanisms of regional RPE degeneration remain poorly understood. To address this gap, this study first identifies a novel RPE subpopulation through the spatial, transcriptomic, and functional analyses, thereby contributing to the understanding of the heterogeneity of degenerative RPE cells. Specifically, omics analyses in human and macaque RPE reveal a peripheral RPE cell population with high SERPINE3 expression, while SERPINE3-GFP knock-in mice show comparable expression patterns. In addition, SMART-seq2 analysis further distinguishes transcriptomic profiles between GFP-positive and GFP-negative RPE cells. Under oxidative stress, SERPINE3 expression increases, and GFP-positive cells exhibit improved survival and reentry into the cell cycle. Notably, genetic studies indicate that SERPINE3 is essential for the oxidative stress resistance of GFP-positive cells. Moreover, loss of SERPINE3 results in regional RPE degeneration and increased microglial accumulation in aged mice. Mechanistically, proteinase screening and co-immunoprecipitation indicate that SERPINE3 targets Caspase-1. Importantly, delivery of SERPINE3 via AAV-Serpine3 prevents RPE degeneration in a geographic atrophy disease model. These findings advance the understanding of RPE heterogeneous degeneration and highlight SERPINE3 as a novel protective factor with therapeutic potential for macular atrophy.

overall_design: RNA-seq profiling of peripheral GFP positive cells and central non GFP RPE cells

first: Huirong

last: Li

first: Robert

middle: B

last: Hufnagel

first: Vincent

last: Kunze

first: Wei

first: Bin

last: Guan


title: miRNA expression profiles in extrracellular vesicles released from mouse CD4+  T cells

city: Tokyo

first: Chika

last: Mochizuki

address: 7-3-1 Bunkyo, Hongo

institute: The University of Tokyo

summary: CD4+ T cells release extracellular vesicles during their differentiation process. It is known that miRNAs encapsulated within these extracellular vesicles (EVs) are involved in the regulation of cellular function and the control of disease. It has become increasingly clear that secretory PLA2 (sPLA2), an extracellular metabolic enzyme, metabolizes the membrane lipids of EVs and regulates their function. Therefore, we focused on PLA2G12A, a member of the sPLA2 family, and investigated whether its deficiency alters the miRNA profile. We isolated naive T cells from mouse spleens, differentiated them into Th17 cells using a Th17 differentiation culture system, and analyzed the EVs released during this process. Although no significant overall differences were observed between wild-type and gene-deficient, differences in expression levels were confirmed for specific miRNAs. These miRNAs were factors regulating Th17 cell differentiation. These results suggest that PLA2G12A alters the composition of EVs.

overall_design: We used wild-type  and Pla2g12a-deficient mice on the C57BL/6 background. Six mice from each group were pooled to form a single sample, which was used for analysis. The experiment was conducted once.


title: Transciptional effects of coronary vessel loss on epicaridal cells in juvenile zebrafish

city: New York

first: Michael

last: Harrison

state: NY

institute: Weill Cornell Medicine

summary: During cardiac development, the myocardium expands in response to physiological demands to achieve proper cardiac morphology and functional contractility, while simultaneously integrating with the developing coronary vasculature. However, the mechanisms governing this ordered expansion and the role of coronary vasculature formation in this process remain poorly understood. Here, we found that regional hypoxia drives local tissue thickening, which in turn exacerbates a hypoxic microenvironment. We demonstrate that epicardial hypoxia serves as a central regulatory mechanism, coordinating both coronary angiogenesis and myocardial expansion during juvenile zebrafish heart development. This mechanism activates discrete spatial patterns of epicardial gene expression, including for vegfaa, loxl2a, and col12a1b. Through live and fixed imaging, we find that cardiomyocytes and endothelial cells exhibit coordinated migration patterns through third-party epicardial signals. We further demonstrate that epicardial subpopulations are required for both coronary development and myocardial expansion. Using cxcr4aum20 mutants lacking functional coronary vessels, we show that coronary vessels function as a negative feedback mechanism to epicardial hypoxia, while positively responding to the same hypoxic cues that drive myocardial expansion. Importantly, disruption of this negative feedback on epicardial hypoxia also leads to increased myocardial stiffness through dysregulated extracellular matrix crosslinking. Thus, we provide mechanistic insights into pathological conditions characterized by myocardial stiffness such as cardiomyopathies. These findings establish the role of regional epicardial hypoxia within a fundamental regulatory network that drives appropriate regional tissue growth with integrated vascular supply during cardiac morphogenesis.

overall_design: Ventricles were isolated from Tg(tcf21:nEGFP) zebrafish at 70 days post-fertilization (dpf), with similar body size. Cell dissociation was performed. For isolation of epicardial cells, tcf21:nEGFP-positive cells were sorted using a MA900 cell sorter (Sony). For total RNA extraction, sorted cells were immediately lysed in RLT buffer from the RNeasy® Micro Kit (Qiagen), and RNA was purified according to the manufacturer’s protocol. Purified RNA was submitted to the Genomics Core Facility of Weill Cornell Medicine for bulk RNA-seq library preparation using SMART-Seq v4 Ultra Low Input RNA plus Nextera XT DNA Sample Preparation. Libraries were sequenced on an Illumina NovaSeq X Plus using a paired-end flow cell with 2 × 100 cycles.


title: Multimodal profiling reveals a Notch-responsive regenerative subpopulation of cochlear supporting cells [1]

city: Omaha

first: Litao

last: Tao

state: NE

address: 2500 California Plaza

department: Biomedical Sciences

institute: Creighton University

summary: Regeneration enables organisms to repair damaged tissues, yet this capacity is strikingly limited in the cochlear sensory epithelium, essential for sound detection. A major cause of hearing loss arises from the irreversible loss of sensory hair cells (HCs) in the cochlea. While supporting cells (SCs) have a latent ability to trans-differentiate into HCs, this regenerative potential is rapidly lost after development. Using live imaging and single-cell multiomics of cochlear explants, we uncovered the cellular and molecular heterogeneity underlying the limited regenerative capacity of the neonatal mouse cochlea. Notch repression broadly silenced key SC genes, yet only a rare subpopulation of Deiters cells (DC), termed responsive DCs, initiated the trans-differentiation into HC fate. These cells underwent coordinated transcriptional and enhancer remodeling, linking epigenetic priming with morphological plasticity, while other SCs remained refractory despite robust Notch targets downregulation. Our study provides a molecular definition of a fate-primed SC state, revealing Notch inhibition as a selective trigger that unmasks rare regenerative competence.

overall_design: Ex vivo organotypic cultures were established with dissected cochleae from P0 animals and treated with either CompE to inhibit Notch signaling pathway or DMSO as vehicle control. Twenty-four hours after treatment, organs were collected, enzymatically digested, and mechanically triturated into single cell suspension. Nuclei were then extracted from the single cell suspension and processed for single cell multiome library prep following the protocl by 10X Genomics.

first: Lama

last: Khalaily

first: Shahar

last: Kasirer

first: Katherine

last: Domb

first: Mi

last: Zhou

first: Buwei

last: Shao

last: Taiber

first: Ran

last: Elkon

last: Sprinzak

first: Karen

last: Avraham


title: Unleashing the potential of mRNA-seq to uncover the microbiome structure and their crosstalk with host cells: the vulvar case

city: Torino

first: Emanuele

last: Monteleone

address: Via Nizza, 52

department: Department of Life Sciences and Systems Biology

country: Italy

institute: Universita' di Torino

summary: To comprehensively describe both host gene expression and microbiome composition in a single sample, parallel experimental and computational workflows -mRNA sequencing and either 16S or metagenomics- have been traditionally applied. Here, following in vitro validation of the reliability of Poly(A)-enriched mRNA sequencing in reconstructing the microbiota composition on a defined microbial mock community, we process a cohort of 30 vulvar mRNA-seq samples to fully analyze not only the transcriptome of the vulvar cells, but  also the composition of microbial communities and their parallel changes. This three-level analysis on the very same specimens further enables a gene-level exploration of the reciprocal molecular crosstalk between host and microbes. The vulvar milieu represents an area of emerging research for its role in health and disease.  Being at the anatomical intersection between the vaginal milieu and the perineal area, the vulvar microbiome displays an intermediate signature, with contamination from both ecosystems. Using this unified framework, we reveal marked heterogeneity and high inter-individual variability in the vulvar microbiota of healthy individuals, identifying community state types that mirror those described in the vaginal ecosystem. Importantly, we show that distinct microbial configurations are associated with specific host transcriptional programs: Lactobacillus crispatus dominated communities correlate with epithelial differentiation and barrier integrity, whereas communities enriched in taxa associated with dysbiosis exhibit transcriptional signatures linked to inflammation. Beyond providing new biological insights into an understudied anatomical niche, our study introduces a broadly applicable strategy with substantial impact for the field. With tens of thousands of human RNA-seq datasets already available in public repositories, our approach enables retrospective extraction of microbiome information and host-microbe interaction signals from existing transcriptomic data, without the need for additional sequencing or specialized microbiome protocols. This unlocks a powerful and cost-effective opportunity to revisit archived RNA-seq studies across tissues, diseases, and low-biomass environments, revealing previously inaccessible layers of host-microbiome crosstalk and maximizing the scientific value of data that already exist.

overall_design: mRNA-Seq profiling and DNA-Seq of vulvar swab samples from healthy individuals

first: Marco A.

last: Cianci

first: Federica

last: Loperfido

first: Alessia

last: Albano

first: Gloria

last: Griffante

first: Luna

last: Brasi

first: Fulvio

last: Borella

first: Niccolo'

last: Gallio

first: Alessandra

last: Marchi

first: Giacomo

last: Donati

first: Ivan

last: Molineris

first: Valentina

last: Proserpio


title: Targeted RNA sequencing of resected hepatocellular carcinoma specimens to characterize immune gene expression associated with spatial PD-L1(+) TAM–CD8(+) T cell interactions

city: Yoshida-gun

first: Takuto

last: Nosaka

state: Fukui

address: 23-3 Matsuoka, Eiheiji-cho

department: Second Department of Internal Medicine

institute: University of Fukui

summary: This study investigates immune-related gene expression profiles associated with spatial interactions between PD-L1-positive tumor-associated macrophages (TAMs) and CD8-positive T cells in hepatocellular carcinoma (HCC). RNA was extracted from tumor regions of formalin-fixed paraffin-embedded (FFPE) specimens obtained from eight patients who underwent hepatectomy. Targeted RNA sequencing was performed using custom AmpliSeq panels covering cancer progression– and immunity-related genes. Raw sequencing data and processed gene expression matrices are provided to enable downstream reanalysis.

overall_design: Tumor regions were microdissected from FFPE sections of resected HCC specimens. Targeted RNA sequencing was performed using custom AmpliSeq RNA panels, and gene expression profiles were compared between tumors with high and low spatial interaction between PD-L1(+) TAMs and CD8(+) T cells.

first: Masahiro

last: Ohtani

first: Junki

last: Yamashita

first: Yosuke

last: Murata

first: Yu

last: Akazawa

first: Tomoko

last: Tanaka

first: Kazuto

last: Takahashi

first: Tatsushi

last: Naito

first: Yoshiaki

last: Imamura

first: Kenji

last: Koneri

first: Takanori

last: Goi

first: Yasunari

last: Nakamoto


title: Expression data from rank-deficient Danio rerio intestines

city: Edmonton

first: Edan

last: Foley

email: ef796@bath.ac.uk, efoley@ualberta.ca

state: Alberta

address: 116 st and 85 ave

department: Medical Microbiology and Immunology

institute: University of Alberta

summary: We used RNA-seq to examine the effect of rank deficiency on Danio rerio intestinal function.

overall_design: Rank mutant and wildtype siblings were co-housed for 8 weeks then their intestinal transcriptomes were sequenced.


title: Targeting XPO1/DDX1-mediated nuclear export of R-loops in inflammaging [CUT&Run]

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

summary: R-loops are three-stranded nucleic acids containing DNA-RNA hybrid and a third displaced ssDNA and are widely distributed across the genome. Dysregulation in R-loop dynamics cause DNA damage and genome instability. Although its role has been extensively investigated in various pathological processes, whether R-loops are perturbed during senescence and tissue aging remains unclear. Here we observe a global decline in R-loop stalling across the genome during senescence. While R-loops in nucleus were dramatically decreased, we detected their significant accumulation in the cytoplasm in senescent cells. We identify their source as nuclear R-loops with a specific enrichment in alpha-satellites, a subset of repetitive elements. Notably, these cytoplasmic R-loops localize into cytoplasmic chromatin fragments (CCF) to induce cGAS-STING innate immune response, and this nucleocytoplasmic transport is dependent on exportin 1 (XPO1)/DEAD-Box helicase 1 (DDX1) complex. Targeting R-loop nuclear export by XPO1 inhibitor Selinexor (KPT-330) suppresses the inflammatory response in senescent cells and relieves inflammaging in aged mice. In summary, our findings linked aberrant accumulation of cytoplasmic R-loops to inflammaging, rendering their nucleocytoplasmic transport process an ideal target for suppressing inflammaging.

overall_design: We conducted CUT&RUN method-based MapR-seq in proliferating and senescent IMR90 cells to chracterize R-loop dynamics during senescence.

first: Xue

last: Hao

first: Qingqing

last: Yan

first: Andrew

last: Kossenkov

first: Rugang

last: Zhang


title: Boosting CAR T-cell functionality with oncolytic viruses for the treatment of pediatric diffuse midline gliomas

city: Stockholm

first: Konstantinos

last: Vazaios

address: Alfred Nobels allé 8

country: Sweden

institute: Karolinska institute

summary: Although the potential of CAR (chimeric antigen receptor) T-cells has been demonstrated in hematological malignancies, their efficacy remains limited in the treatment of solid tumors such as pediatric diffuse midline gliomas (DMGs). Contributing factors hampering the success of CAR T-cells include the immunosuppression induced by the DMGs and the surrounding tumor microenvironment (TME). Oncolytic viruses (OVs) have shown to reverse this immunosuppressive effect, suggesting a potential combinatorial benefit of OV and CAR T-cells. Infection with high concentrations of the Goravir adenovirus and R124 reovirus induced DMG (n=6 cultures) lysis without affecting viability of GD2 or B7H3 directed CAR T-cells. In addition, RNA sequencing of tumor cells showed altered gene expression of cell cycle and antiviral response pathways. When used in combination, cytotoxicity of the CAR T-cells was enhanced and complemented with increased release of pro-inflammatory cytokines and chemokines, especially with R124. Furthermore, CAR T-cells co-cultured with OV-infected DMGs demonstrated a more cytotoxic effector phenotype compared to co-cultures with non-infected DMGs. Finally, these data demonstrate the enhanced benefit of DMG pre-infection with OVs for boosted CAR T-cell activity.

overall_design: RNA profiling of six diffuse midline glioma (DMG) patient-derived cell cultures. The collection included untreated DMG cells at timepoint 0, 24 and 72 hours, DMGs infected with 200 multiplicity of infection Goravir for 24 and 72 hours. As weel as DMG cells infected with 100 multiplicity of infection R124 for 24 and 72 hours

first: Antonio

last: Tallon Cobos

first: Louisa

last: van Oosterhout

first: Piotr

last: Waranecki

first: Annelisa

middle: M

last: Cornel

first: Noël

last: Dautzenberg

first: Marliek

last: van Hoesel

first: Caitlyn

last: Forbes

first: Stefan

last: Nierkens

first: Vera

last: Kemp

first: Rob

last: Hoeben

first: Jasper

last: van der Lugt

first: Friso

middle: G

last: Calkoen

first: Esther

last: Hulleman


title: Targeting XPO1/DDX1-mediated nuclear export of R-loops in inflammaging [cytoDRIP-seq]

first: Yuan

last: Qi

overall_design: We performed cytoDRIP-seq (cytoplasmic DNA-RNA-hybrid immunoprecipitation-seq) in proliferating and senescent IMR90 cells to identify the origins of cytoplasmic R-loops, and we combined it with NuclearDRIP to confirm their sources as nuclear R-loops. In CytoDRP-seq, we also treated senescent cells with DDX1 knockdown to determine if DDX1 is required for nucleocytoplasmic transport of R-loops.

first: Xue

last: Hao


title: Targeting XPO1/DDX1-mediated nuclear export of R-loops in inflammaging [RIP-Seq]

overall_design: We performed RIP-seq (RNA-immunoprecipitation-seq) in proliferating and senescet IMR90 cells to confirm that DDX1-bound RNAs overlapped RNA moiety from cytoplasmic R-loops.

first: Rugang

last: Zhang


title: Eosinophils Orchestrate Intestinal Remodeling and Promote Innate Defense During Reproduction [scRNA-seq]

city: Princeton

first: Yuri

last: Pritykin

state: New Jersey

address: 245 Carl Icahn Lab, Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

summary: Mammalian reproduction requires profound maternal immune adaptations to safeguard reproductive success and ultimately shape the evolutionary trajectories of a species. While systemic and placental immunity is known to shift toward tolerance during pregnancy, how maternal immunity adapts in barrier tissues, sites of frequent infection and inflammation, from pregnancy through the postpartum lactation period remains poorly understood. Here, we discovered a previously unrecognized role for eosinophils, a type of granulocyte typically associated with allergies and helminth infections, in remodeling the intestinal barrier during reproduction. Beginning in pregnancy and peaking during lactation, eosinophils originating from bone marrow accumulate in the small intestine in the absence of infection or inflammation. Using genetic and pharmacological perturbations, organoid cultures, and single-cell and spatial transcriptomics, we show that eosinophils promote goblet cell differentiation in a stem-cell-intrinsic manner, leading to increased mucus production. This adaptation culminates during lactation, limits pathogen entry and dissemination, conferring broad innate protection against enteric bacterial infections. Remarkably, both eosinophil accumulation and goblet cell induction persist after lactation, revealing durable remodeling of the intestinal immune and epithelial landscapes with sustained innate defense. Our findings demonstrate that, despite a general trend toward systemic immunosuppression during reproduction, the maternal intestine undergoes remodeling to strengthen innate defense against enteric pathogens, a mechanism that may have evolved to protect mothers and offspring in pathogen-rich environments. More broadly, our work establishes a framework for studying tissue immune adaptation across the reproductive cycle and highlights that tissue can retain memory of physiological states, with lasting implications for host defense and reproductive health.

overall_design: scRNA-seq of EPCAM+ intestinal epithelial cells (IECs) from the duodenum of nulliparous, pregnant, and lactating mice.

first: Chenyan

last: Huang

first: Amanda

last: Sun

first: Jojo

last: Reyes

first: Jessica

last: Ribeiro de Souza

first: Thomas

middle: R

last: Cafiero

first: Krist

last: Antunes Fernandes

first: Fabricio

last: Marcus Silva Oliveira

first: Yujie

last: Qiao

first: Pedro

last: Gazzinelli-Guimaraes

first: Ai Ing

last: Lim


title: Eosinophils Orchestrate Intestinal Remodeling and Promote Innate Defense During Reproduction

overall_design: Xenium spatial transcriptomics of mouse small intestine for nulliparous and lactating mice. The first 10 cm of small intestine were collected, fresh-frozen with isopentane, and embedded in OCT. Tissues cryosectioned at 10 μm were analyzed using the Xenium Prime 5k Mouse Panel. Samples were taken from two nulliparous and two lactating mice, with one nulliparous and one lactating sample placed on the same Xenium slide.


title: Effects of mutation of the SUMO protease Ulp1 on chromatin-associated sumoylation genome-wide in budding yeast

city: Toronto

first: Emanuel

last: Rosonina

state: ON

address: 4700 Keele Street

department: Biology

institute: York University

summary: Steady-state levels of SUMO post-translational modifications are determined by the balance between sumoylation and desumoylation machineries. Eukaryotic cells can modulate cellular levels of SUMO conjugation by regulating the enzymes involved in these processes. In budding yeast, for example, heat shock induces a global increase in SUMO conjugation, at least in part by triggering the degradation of the major SUMO protease, Ulp1. ChIP-seq analyses by our group and others have identified hundreds of sites across the yeast genome that contain sumoylated proteins, including the promoter regions of 265 protein-coding genes, consistent with a role for sumoylation in regulating transcription widely. Paradoxically, despite the overall increase in SUMO conjugation upon heat shock, chromatin-associated sumoylation decreases at most of these loci when temperatures rise. Here, we show that a similar pattern is observed in a strain expressing a partially defective form of Ulp1, which exhibits constitutively elevated SUMO conjugation yet reduced sumoylation at sites across the genome. One possible explanation is that reduced Ulp1 activity, whether through heat shock-mediated degradation or mutation, indeed elevates sumoylation of chromatin-bound proteins, but this then promotes their rapid dissociation from chromatin. This model aligns with our previous findings that sumoylation triggers the release of the Gcn4 and Sko1 transcription factors from their genomic binding sites.

overall_design: SUMO ChIP-seq was performed in wild-type and ulp1-mt SUMO protease-deficient yeast strains.

first: Moallem

last: Marjan


title: Transcriptome profiling of budding yeast expressing a mutant form of the SUMO protease Ulp1

summary: Steady state levels of SUMO post-translational modifications depend on the competing activities of the sumoylation and desumoylation machineries. Eukaryotic cells can modulate cellular levels of  SUMO conjugation by regulating enzymes involved in these processes. For example, budding yeast exhibit an overall elevation of SUMO conjugation in response to heat shock, at least partly by triggering the degradation of the major SUMO protease, Ulp1. The effects of elevated sumoylation during heat shock, and whether they play a protective or adaptive role to the stress, remain unclear. Since a large number of transcription-related proteins are targets of sumoylation, one possibility is that increased sumoylation during heat shock facilitates the expression of heat shock genes by altering the properties of key transcription factors. To explore this, we analyzed the transcriptome of a yeast strain, ulp1-mt (ulp1-I615N), which expresses a mutant form of Ulp1 with reduced SUMO protease activity. The strain displays constitutively elevated levels of SUMO conjugation, mimicking the transient sumoylation surge observed during heat shock. Intriguingly, the ulp1-mt transcriptome largely resembles the transcriptome of heat-shocked yeast, suggesting that elevated sumoylation alone can drive much of the stress-induced gene expression program.

overall_design: RNA-seq profililng of wild-type and ulp1-mutant budding yeast strains.

first: Marjan

last: Moallem


title: Antigen-presenting cancer-associated fibroblasts in murine pancreatic tumors differentially regulate T-cell phenotype and function

city: Baltimore

first: Saumya

last: Maru

address: 1550 Orleans St, CRB-I, Room 422

institute: Johns Hopkins

summary: Pancreatic ductal adenocarcinoma (PDAC) is characterized by a complex tumor microenvironment (TME) including stromal cells that influence resistance to therapy. Recent studies have revealed that stromal cancer-associated fibroblasts (CAFs) are heterogeneous in origin, gene expression, and function. Antigen-presenting CAFs (apCAFs), are defined by major histocompatibility complex (MHC)-II expression and can activate effector CD4+ T cells that have the potential to contribute to the anti-cancer immune response, but also can induce regulatory T cell (Treg) differentiation. Whether apCAFs promote or restrain the antitumor response remains uncertain. Using tumor clones of the KPC murine PDAC model differing in sensitivity to immune checkpoint blockade (ICB), we found that immunosensitive (sKPC) tumors were characterized by higher immune cell and apCAF infiltration than resistant (rKPC) tumors. IMC analysis showed proximity of apCAFs and CD4+ T cells in both sKPC and rKPC tumors implicating interaction within the TME. apCAF-depleted sKPC tumor-bearing mice had diminished sensitivity to ICB. apCAFs from both sKPC and rKPC tumors activated tumor-infiltrating CD4+ T cells and induced Treg differentiation. However, transcriptomic analysis showed that Tregs induced by apCAFs were overexpressed for immunosuppressive genes in rKPCs relative to sKPCs, and that this is associated with differential chemokine signaling from apCAFs depending on tumor origin. Together these data implicate apCAFs as important mediators of the antitumor immune response, modulation of which could facilitate the development of more effective anti-tumor immune based approaches for PDAC patients.

overall_design: scRNA-seq profiling of naïve OT-II CD4 T cells alone or following overnight coculture with apCAFs isolated from murine PDAC tumors (clones sKPC and rKPC), with or without cognate peptide.


title: Extracellular vesicles from SB431542-conditioned human adipose-derived stem cells enhance in vitro and in vivo osteogenesis via a miR-20a-5p-BAMBI-BMP/canonical Wnt signaling axis

city: Stanford

first: Julika

last: Huber

address: 257 Campus Drive

institute: Stanford University

summary:
Critical-sized bone defects resulting from tumors, trauma, or surgery present a significant clinical challenge due to its poor self-regenerating capabilities and limited therapeutic options. Mesenchymal stem cells (MSCs) have shown promise in bone regeneration, possibly mediated through their secretion of bioactive factors rather than direct engraftment and differentiation. MSC-derived extracellular vesicles (EVs) deliver micro-RNAs (miRs), proteins and lipids that may modulate bone regeneration.
EVs were isolated by differential ultracentrifugation from osteogenically induced human adipose tissue-derived MSCs (hASCs), treated with or without the small molecule SB431542, an inhibitor of TGFß-signaling (EV-hASCs[-/+]SB). EVs were characterized using Western Blot and Nanoparticle Tracking Analysis. hASCs were cultured with EV-hASCs[-/+]SBs to assess bone regeneration in vitro. Bone regeneration was assessed in vivo in calvarial defects treated with (EV-hASCs[-/+]SB). EV content was analyzed via miR-analysis and gain- and loss-of-function transfection assays were performed with identified miR.
Enhanced osteogenesis is shown in vitro and in vivo upon treatment with EV-hASCs[+]SB. EV-hASCs[-/+]SB-enriched miR-20a-5p was identified as a modulating factor in osteogenesis, silencing BAMBI and enhancing early downstream phosphorylation of SMAD1/5 and late activation of ß-Catenin in ASCs undergoing osteogenic differentiation, targets of BMP- and Wnt-signaling pathways.
EVs act as carriers for miR-mediated paracrine signaling, harnessing the therapeutic potential of MSCs, while circumventing the high immunogenicity and risk of neoplastic transformation associated with cell-based therapies.

overall_design: Isolation of miR from extracellular vesicles harvested on day 6 of osteogenic differentiation of human adipose tissue-derived stem cells treated with/without the TGFß-inhibitor SB431542.

first: Michael

last: Longaker

first: Natalina

last: Quarto


title: Mechanism-guided identification of antidepressant  G protein-coupled receptor drug targets

city: New York City

first: Hermany

last: Munguba

state: New York

address: 1300 York Ave

department: Psychiatry

summary: Depression is a psychiatric disorder that is widely thought to be driven by dysregulation at the molecular and synaptic levels that disrupts the function of discrete neural circuits which, ultimately, drive behavioral symptoms. While therapeutic approaches have typically been based on the serendipitous identification of symptom-alleviating compounds, a deeper understanding of the mechanisms underlying the pathophysiology and treatment of depression is needed to guide the development of new therapeutics. Here we decipher mechanisms of action of the fast-acting antidepressant ketamine to enable the identification of new G protein-coupled receptor (GPCR) antidepressant targets. We find that the behavioral effects of ketamine rely on agonism of mu-opioid receptors, which are enriched in somatostatin-expressing interneurons (Sst+ INs) in the medial prefrontal cortex (mPFC). Chronic stress drives presynaptic hypertrophy of mPFC Sst+ INs and excessive inhibition of pyramidal neurons, which is rescued by ketamine. Driven by these findings, we use RNA sequencing to identify a plethora of mPFC Sst+ IN-enriched GPCRs and validate the antidepressant potential of novel GPCR targets. Synergistic targeting of multiple Sst+ IN-enriched GPCRs enables potent antidepressant-like responses with a reduced side effect profile compared to ketamine. Together this study provides new mechanistic insights with promise to improve antidepressant strategies while revealing a general approach to identifying new therapeutic GPCR targets for brain disorders.

overall_design: Bulk RNA sequencing (RNAseq) of sorted Sst:tdT+ and Camk2:tdT+ pyramidal neurons (PNs) from the prefrontal cortex of control and chronically stressed mice.

first: Anisul

last: Arefin

first: Ryota

last: Hasegawa

first: Luca

last: Posa

first: Giovanna

last: Romano

first: Teja

middle: N

last: Peddada

first: Alexander

last: Donatelle

first: Ashna

last: Singh

first: Vanessa

last: Gutzeit

first: Akshara

last: Vijay

first: Prerana

last: Vaddi

first: Melanie

last: Kristt

first: Daniel

last: Shaver

first: Shanjida

last: Hoque

first: Johannes

last: Broichhagen

first: Joseph

last: Stujenske

first: Francis

last: Lee

first: Evan

last: O'Brien

first: Joshua

last: Levitz

first: Conor

last: Liston


title: DUSP1 deletion is synthetic lethal to JAK2V617F induced MPN

city: Cincinnati

first: Mohammad

last: Azam

address: 3333 burnet avenue

institute: CCHMC

summary: Despite significant advances in developing selective JAK2 tyrosine kinase inhibitors (TKI), its clinical efficacy is not durable. Reactivation of compensatory MEK-ERK and PI3K survival  pathways sustained by inflammatory cytokine signaling causes treatment failure. Here, we show that JAK2V617F and cytokine signaling converge to induce MAPK negative-regulator, DUSP1,  which accelerates P53 turnover by blocking P38 mediated phosphorylation and stabilization. Deletion of Dusp1 increases P53 phosphorylation and stabilization that results in selective demise of Jak2V617F clones. However, inhibition of Dusp1 by a small molecule inhibitor (BCI)  failed to impart Jak2V617F clonal selectivity due to pERK1/2 rebound caused by off-target inhibition of DUSP6. Ectopic expression of Dusp6 and BCI treatment restored clonal selectively and eradicated the Jak2V617F cells. Our study shows that inflammatory cytokines and JAK2V617F signaling converge to induce Dusp1, which downregulates P53 that results in a higher apoptotic threshold. These data provide evidence that selectively targeting of DUSP1 will impart a curative response in JAK2V617F-driven MPN

overall_design: Gene expression analysis of cells transduced with oncogene JAK2V617 and MPL 515L. Total RNA from BM-derived Kit+ cells expressing Jak2V617F or MplW515L were used to perform RNA-seq (20 million reads with paired ends) at DNA sequencing core of Cincinnati Children’s

first: Meenu

last: Kesarwani

last: Azhar

first: Jacob

last: Menke

last: Schwieterman

first: Sekhu

last: Ansari

first: Angela

last: Reaves

first: Micheal

last: Deininger

first: Ross

last: Levine

first: Leighton

last: Grimes


title: Human cerebellar organoids to study medulloblastoma pathogenesis and treatment. [methylation]

city: London

first: James

last: Nicholson

address: 4 Newark St

department: Blizard Institute

institute: Queen Mary University of London

summary: Faithful in vivo models of Group 4 medulloblastoma (G4 MB) are currently unavailable and recent studies showed the unique role of human-specific progenitors in the development of G3 and G4 MB. Here, we obtained cerebellar organoid (CbO) from expanded potential stem cells (EPSC) and developed them in vitro as 3D structures. We performed extensive characterisation of the epigenetic and transcriptomic profile of the mature CbO confirming the presence of sub compartment-specific cerebellar lineages linked to MB formation, including populations expressing signature genes reminiscent of the G3 and G4 MB cell-of-origin never described before. In parallel we have established a protocol to co-culture primary MB cells with our CbO to generate CbO-MB models. We confirmed that CbO sustains MB cells proliferation and invasion while preserving their molecular identity, and that CbO-MB recapitulated the efficacy of in vivo anti-tumour therapy, hence representing a suitable model to gain insight into G3/G4 MB pathogenesis and to set up pre-clinical drug screening.

overall_design: DNAme analysis of cerebellar organoids derived from 2 EPSC lines during development, then comparison of DNAme profiles of cerebellar organoids to human foetal cerebellum during development

first: Thomas

last: Willott

first: Yunchen

last: Xiao

first: Sara

last: Badodi

first: Silvia

last: Marino


title: SroA links SigS-dependent stress signaling to repression of nitrate respiration in Staphylococcus aureus

status: Public on Apr 29 2026

city: Washington, DC

first: Karl

last: Thompson

address: 2201 Georgia Ave, NW

institute: Howard University

summary: Analysis of the transcriptome changes in vector control vs. sroA over-expression samples.

overall_design: S. aureus RNA was extracted to determine transcriptome changes upon the over expression of sroA.

first: Shahad

last: Alqahtani

first: Sagar

last: Pasham

first: Jamilah

last: Alsulami

first: Brooke

last: Tomlinson

first: Emily

last: Felton

first: Lindsey

last: Shaw


title: Transcriptomic features of GFP+ RPE cells in Serpine-Gfp heterozygous mice at 2 months I

city: Bethesda

first: David

last: McGaughey

summary: Heterogeneous degeneration of retinal pigment epithelium (RPE) leads to irreversible blindness in diseases associated with macular atrophy. However, the underlying mechanisms of regional RPE degeneration remain poorly understood. To address this gap, this study first identifies a novel RPE subpopulation through the spatial, transcriptomic, and functional analyses, thereby contributing to the understanding of the heterogeneity of degenerative RPE cells. Specifically, omics analyses in human and macaque RPE reveal a peripheral RPE cell population with high SERPINE3 expression, while SERPINE3-GFP knock-in mice show comparable expression patterns. In addition, SMART-seq2 analysis further distinguishes transcriptomic profiles between GFP-positive and GFP-negative RPE cells. Under oxidative stress, SERPINE3 expression increases, and GFP-positive cells exhibit improved survival and reentry into the cell cycle. Notably, genetic studies indicate that SERPINE3 is essential for the oxidative stress resistance of GFP-positive cells. Moreover, loss of SERPINE3 results in regional RPE degeneration and increased microglial accumulation in aged mice. Mechanistically, proteinase screening and co-immunoprecipitation indicate that SERPINE3 targets Caspase-1. Importantly, delivery of SERPINE3 via AAV-Serpine3 prevents RPE degeneration in a geographic atrophy disease model. These findings advance the understanding of RPE heterogeneous degeneration and highlight SERPINE3 as a novel protective factor with therapeutic potential for macular atrophy.

overall_design: RNA-seq profiling of peripheral GFP positive cells and central non GFP RPE cells

first: Huirong

last: Li

first: Robert

last: Hufnagel

first: Vincent

last: Kunze

first: Wei

first: Bin

last: Guan


title: Involvement of trefoil factor family 2 in the enlargement of intestinal tumors in ApcMin/+ mice

city: Sasebo

first: Kyoko

last: Fujimoto

state: Nagasaki

address: 2825-7 Huis Ten Bosch

department: Pharmacy

institute: Nagasaki International University

summary: It is assumed that tumor size may be associated with malignant tumor conversion. However, the molecules responsible for determination of tumor size are not well understood. We counted the number of intestinal tumors in 8, 12 and 30-week-old ApcMin/+ mice and measured tumor sizes, respectively. Genes involved in determining tumor size were examined using microarray analysis. Cultured cells were then, transfected with a mammalian expression vector containing a candidate gene to examine the functional role of the gene. The effect of forced expression of candidate gene on cell growth was evaluated by measuring the doubling time of the cultured cells and the growth of grafted cells in nude mice. Unexpectedly, microarray analysis identified trefoil factor family 2 (Tff2) rather than growth related genes and/or oncogenes as a most variable gene. Overexpressing Tff2 in cultured cells reduced doubling time in vitro and rapidly increased xenograft tumor size in vivo. We found Tff2 as a novel important factor that to be able to enlarge an intestinal tumor size.

overall_design: We compared intestinal tumors larger than peak size (4–5 mm in diameter; designated as L) with those smaller than peak size (≤2 mm in diameter; designated as S) in 30-week-old ApcMin/+ mice.Tumors were collected from two individual mice (mouse 1 and mouse 2), and three tumors from each mouse were respectively pooled into a single tube prior to RNA extraction.

first: Gen

last: Fujii

first: Kenichi

last: Taguchi

first: Kaori

last: Yasuda

first: Yuta

last: Matsuo

first: Airi

last: Hashiyama

first: Michihiro

last: Mutoh

first: Hiromitsu

last: Tanaka

first: Morimasa

last: Wada


title: U2AF1 mutations rescue deleterious exon skipping induced by KRAS mutations

city: Boston

last: Walter

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: The mechanisms by which mutations of the splicing factor gene U2AF1 contribute to lung adenocarcinoma pathogenesis are not well understood. Here, we used prime editing to modify the endogenous U2AF1 gene in lung adenocarcinoma cells and assessed the resulting impact on alternative splicing. One specific KRAS mutation, G12S, leads to skipping of KRAS exon 2 and generation of a non-functional KRAS transcript. However, expression of the U2AF1 S34F mutant reverts this exon skipping and restores KRAS function, leading to an enrichment of U2AF1 S34F mutations in KRAS G12S-mutant lung adenocarcinomas. A comprehensive analysis of splicing factor/oncogene mutation co-occurrence in cancer genomes also revealed significant co-enrichment of KRAS Q61R and U2AF1 I24T mutations. Experimentally, KRAS Q61R mutation leads to KRAS exon 3 skipping, which in turn can be rescued by the expression of U2AF1 I24T. Our findings provide evidence that splicing factor mutations can rescue splicing defects caused by oncogenic mutations in a dynamic process of cascading selection.

overall_design: To determine the impact of U2AF1 mutations on splicing of KRAS and other targets, we performed long-read RNA-sequencing of engineered lung adenoarcinoma cell lines with mutations in U2AF1

first: Katherine

last: Cho

first: Smruthy

last: Sivakumar

first: Daniel

last: Denney

first: Iris

last: Lee

first: Anders

last: Dohlman

first: Jakob

last: Heinz

first: Ethan

last: Shurberg

first: Kevin

middle: X

last: Jiang

first: Akansha

last: Gupta

first: Garrett

last: Frampton

first: Matthew

last: Meyerson


title: Androgen Excess Uncouples Circulating and Hepatic Lipid Homeostasis in Females on a High-Calorie Diet

city: Philadelphia

first: Sheng

last: Wu

address: 3500 N Broad Street

department: CMDR

institute: Temple University

summary: Androgen excess (AE) is a common feature of polycystic ovary syndrome, congenital adrenal hyperplasia, gender affirming hormone therapy and is a known driver of disrupted glucose homeostasis. However, its impact on hepatic lipid regulation remains poorly understood with conflicting results. In age and weight matched female mice, dihydrotestosterone (DHT) treatment under a regular chow diet did not alter hepatic or circulating lipid levels. In contrast, under a western diet, DHT protected against metabolic dysfunction–associated steatotic liver disease (MASLD) by reducing hepatic triglyceride (TG) accumulation, even as it exacerbated systemic hypertriglyceridemia. These effects occurred without changes in hepatic insulin–Akt signaling and were independent of hepatic androgen receptor (AR) signaling. Multiomics profiling revealed that DHT reprogrammed hepatic transcription toward a male like pattern driven by pulsatile growth hormone (GH)–STAT5 signaling. DHT enhanced hepatic STAT5 activation, suppressed expression of the fatty acid (FA) transporter Cd36, and reduced hepatic FA uptake, even in the presence of elevated circulating FFA. DHT also increased VLDL-TG secretion and altered hepatic FA composition. Continuous GH infusion, which mimics the female GH secretion pattern, reversed these effects by attenuating STAT5 activation and restoring Cd36 expression. Together, these findings identify a GH‑dependent, hepatic AR‑independent pathway through which AE shapes hepatic lipid homeostasis. They further show that DHT elicits divergent systemic effects, with impaired glucose homeostasis and enhanced lipolysis occurring alongside reduced hepatic lipid accumulation but increased TG secretion.

overall_design: RNA seq data of livers from female mice on a Western Diet for 8.5 weeks, and treated with Veh or DHT(10mm)

first: Wu

last: Sheng

first: Joseph

last: Serene


title: Inhibition of PRMT5 sensitizes B-cell non-Hodgkin lymphoma cells to both intrinsic and extrinsic apoptotic cell death

first: Fen

last: Zhu

state: MA

address: 440 Brookline Ave, Mayer 553

summary: Protein arginine methyltransferase 5 (PRMT5), a type II arginine methyltransferase, is overexpressed in several aggressive B cell malignancies and facilitates cancer cell growth. JNJ-64619178, a selective small molecule inhibitor targeting PRMT5, has previously shown promising pre-clinical activity across a range of hematologic malignancies; however, the clinical activity of JNJ-64619178 monotherapy is limited despite strong target engagement. Thus, we sought to identify rational combination partners for JNJ-64619178 to achieve improved activity in B cell malignancies. Using dynamic BH3 profiling, a functional assay to evaluate the net increase in pro-apoptotic signaling in response to drugs, we found that JNJ-64619178 increased mitochondrial apoptotic priming and BCL-2 dependence particularly in diffuse large B cell lymphoma (DLBCL) and mantle cell lymphoma cell lines (MCL).In other B-cell non-Hodgkin lymphoma (NHL) cell lines that are primarily MCL-1 dependent and less BCL-2 dependent, JNJ-64619178 increased mitochondrial apoptotic priming without switching anti-apoptotic dependence from MCL-1 to BCL-2. Co-targeting PRMT5 and BCL-2 synergistically induced apoptosis in DLBCL and MCL cell lines that displayed at least partial BCL-2 dependence at baseline but not in less BCL-2-dependent B-cell NHL cell lines. Interestingly, we found that JNJ-64619178 upregulated DR4 and DR5 expression on the cell membrane of B-cell NHL cells, thereby sensitizing them to recombinant TRAIL-induced extrinsic apoptotic cell death. These findings highlight a role of PRMT5 in regulating both intrinsic and extrinsic apoptosis and suggest potential combination partners with PRMT5 inhibitors to explore for potential clinical application in B-cell NHL.

overall_design: study the transcriptional profile changes of DLBCL cells lines OCI-Ly1 and SUDHL4 upon 72 hours exposure to DMSO or 1µM of JNJ-64619178

middle: S

last: Davids


title: An appendiceal cancer organoid biobank identifies phenotypic evolution and druggable dependencies of peritoneal carcinomatosis

city: New York

first: Jura

last: Pintar

email: pintarj1@mskcc.org, ganeshk@mskcc.org

address: 1275 York Avenue

department: Molecular Pharmacology Program

institute: Memorial Sloan Kettering Cancer Center

summary: Peritoneal carcinomatosis is a common yet deadly manifestation of gastrointestinal cancers, with few effective treatments. To identify targetable determinants of peritoneal metastasis, we focused on appendiceal adenocarcinoma (AC), a gastrointestinal cancer that metastasizes almost exclusively to the peritoneum. Current treatments are extrapolated from colorectal cancer (CRC), yet AC has distinct genomic alterations, mucinous morphology and peritoneum restricted metastatic pattern. Further, no stable preclinical models of AC exist, limiting drug discovery and representing an unmet clinical need. We establish a first-in-class stable biobank of 16 long-term cultured AC patient-derived organoids (PDOs), including 3 matched primary AC-peritoneal carcinomatosis (AC-PC) pairs. By enriching for cancer cells, AC PDOs enable accurate genomic characterization relative to paucicellular AC tissue. We establish an organoid orthotopic intraperitoneal xenograft model that recapitulates diffuse peritoneal carcinomatosis and show that PC-organoids retain increased metastatic capacity, decreased growth factor dependency and sensitivity to standard of care chemotherapy relative to matched primary AC organoids. Single cell profiling of AC-PC pairs reveals dedifferentiation from mucinous differentiated states in primary AC into intestinal stem cell and fetal progenitor states in PC, with upregulation of oncogenic signaling pathways. Through hypothesis-driven drug testing, we identify RAS inhibitor RMC-7977 and Wnt-targeting tyrosine kinase inhibitor WNTinib as novel, clinically actionable strategies to more effectively target AC-PC.

overall_design: scRNA-seq of 3 matched pairs of primary appendiceal adenocarcinoma (AC) and peritoneal carcinomatosis (PC) patient-derived organoids (PDOs).

first: Ahmed

last: Mahmoud

first: Christine

last: Sukhwa

first: Michael

last: Giarrizzo

first: Philip

last: Choi

first: Henry

last: Walch

last: Zhao

first: Jonathan

last: Bermeo

first: Sebastian

last: Chung

first: Manisha

last: Raghavan

first: Samhita

last: Bapat

first: Qingwen

first: Julia

last: Meredith

first: Canan

last: Firat

first: Andrea

last: Cercek

last: Foote

first: Nikolaus

last: Schultz

first: Walid

middle: K

last: Chatila

last: Nash

first: Jinru

last: Shia

first: Francisco

last: Sanchez-Vega

first: Steven

last: Larson

first: Arvin

last: Dar

first: Neal

last: Rosen

first: Georgios

last: Karagkounis

first: Karuna

last: Ganesh


title: NOD2 drives regenerative fetal-like reprogramming in the intestinal epithelium

first: Derek

middle: Ka Long

last: Tsang

state: Ontario

address: 1 King's College Circle

department: Immunology

institute: University of Toronto

summary: Inflammatory injury to the intestine triggers a reprogramming of the intestinal epithelium to a fetal-like state, facilitating rapid restoration of the epithelial barrier. Although the intestinal microbiota is a key modulator of inflammation, its role in driving epithelial fetal-like reversion and promoting restitution remains unclear. Using irradiation (IR) injury as a model for small intestinal epithelium restitution, we found that the intestinal microbiota accelerated epithelial restitution by amplifying a repair-associated inflammatory response that promoted the emergence of fetal-like intestinal epithelial cells (IECs), marked by Ly6a and Clu. NOD2, the strongest genetic link to the development of Crohn’s disease, was expressed in fetal-like IECs following injury. Notably, stimulation of NOD2 by its peptidoglycan ligand in an ileal organoid model potentiated an inflammatory gene signature characterized by interferon (IFN) signaling, coinciding with enterocyte recovery. NOD2 deficiency exacerbated epithelial apoptosis following IR injury, while epithelial-specific NOD2 signaling promoted the emergence of fetal-like IECs and enhanced epithelial proliferation. Together, these results identify a critical role for microbiota and microbial sensing by NOD2 in controlling the fate of fetal-like IECs following injury, thereby contributing to the protective effect of this microbial sensor during intestinal inflammation.

overall_design: scRNA-seq of crypt-enriched small intestinal epithelium of WT germ-free (GF), WT specific pathogen-free (SPF), and Nod2KO SPF mice 3 days following full-body IR-induced enteritis (12 Gy). RNA-seq of mouse ileal organoids following IFNg and TNF priming (4Hrs), followed by L18-MDP stimulation (days), along with respective time-matched unstimulated controls.

first: Dana

middle: J

last: Philpott


title: The circadian clock component BMAL1 enhances macrophage inflammation by nuclear translocation of peroxisomal β-oxidation enzyme MFP2

city: Fukuoka

first: Akito

last: Tsuruta

department: Pharmaceutics

institute: Kyushu university

summary: This study investigated how the circadian regulators BMAL1 and MFP2 control macrophage inflammatory responses through epigenetic mechanisms. Using H3K27ac ChIP‑seq, we analyzed genome‑wide histone H3 lysine 27 acetylation (H3K27ac) in wild‑type, Bmal1‑deficient, and Mfp2‑deficient RAW264.7 cells, a mouse macrophage‑like cell line. Comparative analyses revealed substantial overlap in H3K27ac regions reduced upon loss of BMAL1 or MFP2, suggesting a coordinated BMAL1–MFP2 axis in the regulation of inflammation‑associated chromatin states.

overall_design: ChIP-seq of th histone modification H3K27ac Naive, Bmal1 knockout, and Mfp2 knockout RAW264.7 cells

first: Nodoka

last: Hirao

first: Megumi

last: Shibata

first: Yuya

last: Yoshida

first: Yoshihiro

last: Izumi

first: Naoya

last: Shindo

first: Yuki

last: Shiiba

first: Kazuhiro

last: Higashi

first: Takuto

last: Inoki

first: Yuichiro

last: Kai

first: Yasuha

last: Hiraoka

first: Tomoaki

last: Yamauchi

first: Akio

last: Ojida

first: Bamba

last: Takeshi

last: Matsunaga

first: Satoru

last: Koyanagi

first: Shigehiro

last: Ohdo


title: RNA-Seq Profiling of Kidney Responses in Wild-Type and Angpt2 Knockout Mice Following a 3-Week Adenine Diet

city: Taipei

first: An Jie

last: Luo

department: Graduate Institute of Physiology

country: Taiwan

institute: National Taiwan University College of Medicine

summary:
Chronic kidney disease (CKD) is characterized by progressive
tubulointerstitial injury, which plays a critical role in renal dysfunction.
Angiopoietin-2 (Angpt2) is implicated in vascular and inflammatory
processes, but its role in CKD remains unclear. In this study,
we performed RNA-seq to analyze gene expression differences
in the kidneys of wild-type  and Angpt2 knockout mice after a 3-week
adenine diet, a well-established model of tubulointerstitial injury.

overall_design:
RNA-seq profiling of the kidney in wild-type and Angpt2 knockout mice
after a 3-week adenine diet.

first: Fan-chi

last: Chang

first: Shuei-Liong

last: Lin


title: A four-dimensional spatial transcriptome atlas of barley caryopsis development and germination

city: Bundoora

first: Marta

last: Peirats Llobet

state: Victoria

address: 5 Ring road

country: Australia

institute: La Trobe University

summary: Spatial transcriptome for barley development and germination

overall_design: Barley (cv La Trobe) caryopsis from development (3, 6, 12 and 20 days after pollination) and germination (0, 1, 3, 6 and 24 hours after imbibition) were collected, snap-frozen and cryosectioned. The sections were processed using Visium (10x Genomics) and sequenced using Illumina.


title: Effect of myeloid specific Trem2 knockout in hepatocellular carcinoma after anti-PD-1 therapy [RNA-seq]

city: Hong Kong

first: Alfred Sze-Lok

last: Cheng

address: Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, CUHK

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: Immune-checkpoint blockade (ICB) therapies have transformed the treatment landscapes of solid malignancies, including hepatocellular carcinoma (HCC), which is currently the sixth most common cancer and the third leading cause of cancer death worldwide. Despite unprecedented success in clinical trials, the immunosuppressive tumor microenvironment constructed by tumor cells restricts the responsiveness of ICB therapies to a minority of patients. Triggering receptor expressed on myeloid cells-2 (TREM2) counteracts inflammation and maintains metabolic fitness in myeloid cells. Emerging single-cell RNA sequencing data in different types of tumors have identified the significance of TREM2+ myeloid cells in tumor development and ICB resistance. In this study, we aimed to investigate the potential role of TREM2 in HCC ICB resistance.

overall_design: RNA-seq of liver tumor from LysM-Cre (n = 3) and Trem2-MKO (n = 3) mice after anti-PD-1 treatment

first: Zhixian

last: Liang

first: Yiling

last: Zhang

first: Siyun

last: Chen

first: Zhewen

last: Xiong

first: Yalin

last: Tu


title: Effect of myeloid specific Trem2 knockout in hepatocellular carcinoma after anti-PD-1 therapy

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

overall_design: Refer to individual Series


title: Fronto-insular circuit mechanisms of accelerated intermittent theta burst stimulation

first: Conor

last: Liston

address: 413 E 69th St Belfer Research Building

institute: Weill Cornell Medical Center

summary: Transcranial magnetic stimulation (TMS) is a widely used neuromodulation treatment for depression, but its underlying mechanisms are not well understood. Indirect evidence from clinical studies suggests that TMS may act by enhancing plasticity locally within the prefrontal cortical (PFC) target or through network-level effects on downstream areas, but establishing causal mechanisms and optimizing a large stimulation parameter space has been challenging. In an optogenetic model of accelerated intermittent theta burst stimulation targeting the prelimbic PFC (PL-aiTBS), we show that PL-aiTBS drives rapid, antidepressant-like effects on multiple measures of motivated approach and avoidance behavior and reverses stress effects on reward devaluation, with repeated stimulation potentiating local aiTBS-evoked neuronal responses. Spatial transcriptomic profiling revealed a host of cell type-specific effects implicating prefrontal intratelencephalic (IT) projection neurons, including altered expression of genes associated synapse assembly, which in turn was associated with increased postsynaptic dendritic spine density and excitatory currents in prelimbic IT neurons. Using SHIELD tissue clearing, c-Fos immunolabeling, and light sheet imaging to map whole-brain responses to aiTBS, we delineate a network of downstream structures activated by PL-aiTBS, including pronounced effects in insular cortex, which were confirmed by fiber photometry. Chemogenetic and projection-specific optogenetic studies established the necessity and sufficiency of a fronto-insular circuit in mediating aiTBS effects on motivated approach and avoidance behavior. Finally, we validate a key role for TMS-evoked responses in the human insula, showing in intracortical stereo-EEG recordings that prefrontal TMS modulates neuronal activity in insular cortex acutely and that resting state fMRI measures of fronto-insular connectivity predict individual differences in antidepressant responses to aiTBS. Together, these results identify a critical role for aiTBS-induced activation of a fronto-insular circuit in supporting specific antidepressant-like behavioral effects and establish a model for studying aiTBS mechanisms and optimizing stimulation parameters.

overall_design: Spatial transcriptomics was performed on single-nuclei isolated from the left prelimbic cortex. Left prelimbic cortical tissue was microdissected from male and female mice that underwent 30 sessions of iTBS optogenetic stimulation, or sham controls.

first: Shane

last: Johnson

first: Devin

last: Rocks

first: Laura

last: Chalencon

first: Kenneth

first: Umair

last: Hassan

first: Anisul

last: Arefin

first: Gülcan

last: Akgül

first: Alexander

last: Donatelle

first: Henry

last: Asher

first: Immanuel

last: Elbau

first: David

last: Estrin

first: Rebecca

first: Alexandra

last: Lenz

first: Rachel

last: Mikofsky

first: Cory

last: Knox

first: Rachael

last: Han

first: Pooja

last: Suganthan

first: Tahrima

last: Chowdhury

first: Christine

last: Kuang

first: Daniel

last: Shaver

first: Parsa

last: Nilchian

first: Puja

last: Parekh

first: Jacob

last: Roshgadol

first: Natalia

last: DeMarco Garcia

first: Matthew

last: Wright

first: Lindsay

last: Victoria

first: Benjamin

last: Zebley

first: Joshua

last: Levitz

first: Corey

last: Keller

first: Aaron

middle: D

last: Boes


title: Insights into intestinal neuroendocrine tumors in relation to normal human EEC differentiation

city: Brookline

first: Ramesh

middle: A

last: Shivdasani

state: Massachusetts

address: SM1052, Smith10, 450 Brookline Ave

department: Medical Oncology

institute: DFCI


title: Insights into intestinal neuroendocrine tumors in relation to normal human EEC differentiation [RNAseq]

summary: Mutationally silent small intestinal neuroendocrine tumors (SI-NETs) characterized by few recurrent alterations, such as those that inactivate the cyclin-dependent kinase (CDK) inhibitor CDKN1B in <10% of cases are not well defined at the molecular level. Since the native enteroendocrine cells (EECs), which these tumors resemble, are scarce; the lack of reference data from normal EECs limits identification of gene and cis-element dysregulation in SI-NETs. We established transcriptional landscapes (RNA-seq) in bulk cultures and at single-cell (sc) resolution during the trajectory of normal human EEC differentiation from ileal stem cells in vitro (PMID 38733993). We compared the findings in SI-NETs against the novel reference profiles of normal human EEC differentiation and maturation. SI-NETs correspond principally to mature EC cells, with discernible features of non-EC and progenitor cells; persistent expression of the latter genes likely contributes to malignant properties. Underlying this aberrant expression pattern we found diverse SI-NET enhancers. EECs normally differentiate through an intermediate HES6hi/ASCL1+ oscillatory state before NEUROD1+ pre-terminal cells emerge; ASCL1 expression then persists only in mature EC cells. In contrast, although SI-NETs express NEUROD1, they strictly lack ASCL1 and other genes normally co-expressed with ASCL1. Notably, ASCL1 and loci encoding transcription factors that define non-EC cell types (ISL1, ARX, PAX6, PDX1) are marked with H3K27me3, signifying epigenetic silencing. SI-NETs express CDKN1B but other CDK inhibitors, e.g., CDKN2A and CDKN1C, are epigenetically silenced, suggesting that tumor cells may especially depend on wild-type CDKN1B function. Chromatin and transcriptional features of SI-NETs, revealed for the first time with respect to normal EEC differentiation, will help identify tumorigenic pathways and candidate therapeutic targets.

overall_design: RNA isolated from 50-100µ frozen sections using the Qiagen RNeasy Micro Kit (74004) and sequeced using Novogene services

first: Pratik

last: Singh


title: Insights into intestinal neuroendocrine tumors in relation to normal human EEC differentiation [ATACseq]

overall_design: ATAC-seq was performed using 100mM frozen sections after isolating nuclei and following Corces and Granja protocol (PMID: 30361341)