title: Advanced paternal age impacts common loci in the sperm and placenta DNA methylomes

city: Montreal

first: Jacquetta

last: Trasler

state: Quebec

address: 1001 Decarie Boul, Block E, ES1.4380

department: Pharmacology & Therapeutics; Human Genetics

institute: McGill University

type: Methylation profiling by genome tiling array

summary:
Background: Epidemiological studies have reported an association between advanced paternal age at conception and an increased risk of neurodevelopmental disorders in offspring, such as autism spectrum disorder. Evidence suggests that DNA methylation alterations in sperm of older men may be transmitted to the feto-placental unit and associated with offspring brain development and behavioral differences later in childhood.
Objective: We aimed to assess the association of advanced paternal age with DNA methylation alterations in the human placenta and compare the results to previous findings in sperm.
Methods: For this study, 64 placenta samples from the 3D (Design, Develop, Discover) prospective birth cohort study were categorized based on paternal age at conception. DNA methylation of the placenta was interrogated using the Illumina 850K array. There were no differentially methylated sites found to be statistically significant after correction for multiple comparisons, therefore sites with significant nominal p-values <0.05 were assessed and used to define differentially methylated regions (DMRs) associated with genes.
Results: Advanced paternal age was associated with DNA methylation alterations in the placenta at up to 688 genes, with a predominance of hypomethylation (65%), including at 8 imprinted loci. About 7% of genes with age-associated DNA methylation changes in placenta overlapped with genes previously reported to show altered DNA methylation in sperm of older men; seven genes common to placenta and sperm had previously been identified in association with susceptibility to autism spectrum disorder. Amongst loci most affected, we found evidence of sex-specific hypermethylation at genes linked to neurodevelopment (GRM7, EBF3, FOXG1).
Conclusion: Our findings suggest that advanced paternal age at conception is associated with altered DNA methylation in the human placenta, including at genes tied to neurodevelopment. This study highlights the use of the placenta DNA methylome as a surrogate marker for the potential impact of advanced paternal age on the child.

overall_design:
For this study, 64 placenta samples from the 3D (Design, Develop, Discover) Study were categorized based on paternal age. DNA methylation of the placenta was interrogated using the Illumina 850K array.
The two samples (P855 and P856) did not pass the QC (poor signal quality) and therefore were omitted in our analysis.

first: Julia

last: Barnwell

first: Sophia

last: Rahimi

first: Sherri

last: L Jones

first: Donovan

last: Chan

first: Josée

last: Martel

first: Sara

last: Abdessamie

first: Catherine

last: Herba

first: Jean

last: Séguin

first: William

middle: D

last: Fraser

first: Celia

last: Greenwood

first: Tuong-Vi

last: Nguyen

first: Tina

last: Montreuil


title: Single cell transcriptomics analysis of the effect of S100a4 knockout on psoriasis

status: Public on Dec 10 2025

city: Xinjiang Uygur Autonomous Region

first: Huiqin

last: Wang

address: No. 91 Tianchi Road, Tianshan District, Urumqi, Xinjiang Uygur Autonomous Region

country: China

institute: People's Hospital of Xinjiang Uygur Autonomous Region

type: Expression profiling by high throughput sequencing

summary: We employed single-cell RNA sequencing to investigate the pathophysiology of psoriasis and the molecular mechanisms of S100a4 by analyzing alterations in cellular heterogeneity and composition in dorsal skin tissue from differentially treated mice.

overall_design: We generated a global S100a4 knockout mouse model and designed three experimental groups to evaluate the effect of S100a4 knockout on psoriasis: 1) sham-control group with Vaseline application (non-lesional); 2) imiquimod (IMQ)-induced psoriasis group (lesional wild-type); and 3) S100a4 knockout group with IMQ application post-knockout (lesional S100a4 knockout). We selected three independent biological replicates from each of three separete groups to isolate the dorsal skins, and then prepared single-cell suspensions for single-cell transcriptomic sequencing.

first: Weidong

last: Wu


title: Engineering ATP Import in Yeast Uncovers a Synthetic Route to Extend Cellular Lifespan

city: Charlottesville

first: Alaattin

last: Kaya

state: Virginia

address: 1340 Jefferson Park Ave

department: Biochemistry and Molecular Genetics

country: USA

institute: University of Virginia

summary: Aging results from the gradual accumulation of molecular damage as a result of cellular processes and is characterized by impaired functions, most notably an age-related decline in ATP production. However, the causal relationship between cellular ATP homeostasis and aging has not been established. In this study, we used a novel approach by harnessing a nucleotide transporter from a eukaryotic intracellular parasite to facilitate the direct import of extracellular ATP into budding yeast cells, enabling us to effectively manipulate their intracellular ATP levels. We found that depletion of ATP significantly reduces lifespan, while the supplementation of ATP in the growth medium fully restores it thereby extending lifespan. Moreover, gene expression analysis revealed that elevated ATP levels inhibit catabolic processes, indicating a suppression of glucose metabolism. Overall, our study revealed the direct impact of cellular ATP homeostasis on lifespan regulation that has never been directly tested before. This work offers new insights into the bioenergetic control of aging and positions energy metabolism as a promising target for longevity interventions.

overall_design: Yeast strains expressing the Encephalitozoon cuniculi nucleotide transporter NTT1 or empty-vector controls were grown in complete synthetic medium to mid-log phase. Cells were either left untreated or treated with 5 mM extracellular ATP for 1 hour, and total RNA was extracted for RNA-seq analysis. Three independent biological replicates were collected per strain and treatment condition.

first: Naci

last: Oz

first: Hetian

last: Su

first: Vedat

last: Sari

first: Praveen

last: Patnaik

first: Rohil

last: Hameed

first: Jong

middle: H

last: Song

first: Derek

middle: C

last: Prosser

first: Vyacheslav

middle: M

last: Labunskyy

first: Vadim

middle: N

last: Gladyshev

last: Hao


title: Sox11 overexpression restores embryonic pro-growth transcription in mature corticospinal tract neurons [snRNA-Seq]

city: Milwaukee

first: Murray

last: Blackmore

state: WI

address: 561 N 16th St

department: Biomedical Sciences

institute: Marquette University

summary: Neurons in the central nervous system (CNS) display a high capacity for axon growth during early development but mostly lose this ability during a key stage of differentiation marked by synaptic maturation, circuit integration, and a profound shift in gene transcription. Once mature, neurons largely fail to reverse this transcriptional switch after axon injury, fundamentally constraining their intrinsic capacity for repair. Here, we show with single-nucleus RNA sequencing that forced expression of the transcription factor Sox11 in adult corticospinal tract neurons produces large-scale and stable changes in gene expression that are highly enriched for growth-relevant processes, and which strongly resemble those of pre-synaptic embryonic stages. Moreover, Sox11 is equally effective when delivered to chronically injured CST neurons. These data reveal Sox11’s ability to reverse a critical step of neuronal maturation even in otherwise unperturbed neurons, clarifying the transcriptional underpinnings and highlighting Sox11’s potential as a pro-regenerative stimulus.

overall_design: In adult mouse samples, corticospinal tract (CST) neurons were transduced with a retrograde, nuclear-localized fluorophore (mGl) and control or Sox11-expressing virus by retrograde transduction from cervical spinal cord. Animals recevied either no injury or a cervical contusion injury six weeks prior to tissue collection. Animals that received Sox11 and no injury were collected at four time points: 1 week, 2 weeks, 4 weeks, or 6 weeks after viral delivery, with each time point uniquely barcoded and pooled in the same sequencing reaction. Embryonic cortex was collected at embryonic day 18. For all samples, single nucleus RNA sequencing was performed. Adult samples were pre-purified using fluorescent activated nuclei sorting prior to library preparation. E18 embryonic libraries were prepared from ixed cortical tissue.

first: Elizabeth

last: Batsel

first: Zimei

last: Otten

first: Rabia

last: Mohammad

first: Paula

last: Pascal

first: Darby

last: O'Shea

first: Jose

last: Rosas

first: Pantelis

last: Tsoulfas


title: Autologous cell therapy with CD133+ bone marrow-derived stem cells for Asherman Syndrome: a phase 1/2 trial [biopsies]

city: Paterna

first: Carlos

last: Simon

state: Valencia

address: Rda Narcis Monturial, parc. 118 Parque Tecnologico

country: Spain

institute: Carlos Simon Foundation

summary: Asherman Syndrome (AS) is an acquired pathological condition affecting women’s reproductive health, triggered by the substitution of a bona fide endometrium with intrauterine adhesions that cause the uterine walls to adhere to each other. Clinically, AS results in menstrual abnormalities (amenorrhea or oligomenorrhea), pelvic pain, infertility, recurrent miscarriage and abnormal placentation.  Autologous CD133+ bone marrow-derived stem cell (BMDSC) therapy has been designated as an Orphan Drug by the EMA and FDA for the treatment of AS. This phase 1/2, non-randomized, open-label, single-arm trial (EudraCT: 2016-003975-23) assessed the safety and efficacy of this novel therapy in 20 infertile women with moderate to severe AS, unresponsive to prior hysteroscopic treatments.  Single-cell RNA sequencing of endometrium and organoids revealed partial reversion of AS-related changes, and mitochondrial variant tracking offered insights of CD133+ BMDSCs engraftment. These findings suggest that autologous CD133+ BMDSC therapy is a safe and effective treatment for AS.

overall_design:
Patients with moderate-to-severe Asherman syndrome were treated with autologous CD133⁺ bone marrow–derived stem cells, and endometrial responses were evaluated using single-cell RNA-seq of endometrium.

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

first: Xavier

last: Santamaria

first: Maria

last: Pardo-Figuerez

first: Javier

last: Gonzalez-Fernandez

first: Sergi

last: Querol

first: Luciano

last: Rodriguez

first: David

last: Varcárcel

first: Carla

last: Gonzalez

first: Estefanía

last: Fernandez

first: Diego

last: Amorós

first: Michael

last: Robles

first: Sofia

last: Granados-Aparici

first: Sheila

last: Zúñiga

first: Francisco

last: Martínez

first: Diana

last: Valbuena

last: Gómez

first: Julio

last: Herrero

first: Ramón

last: Aurell

first: Juan

last: Torrent

first: Felipe

last: Vilella

first: Petr

last: Volkov

last: Raga

first: Rosa

last: Noguera

first: Hugh

middle: S

last: Taylor


title: Global transcriptome analysis of IL-33, IL-25, IL-13, TSLP, IL-4, and IL-9 overexpression in mouse spleen

city: Tarrytown

first: Kaitlyn

last: Gayvert

state: NY

address: 777 Old Saw Mill River Rd

department: Molecular Profiling & Data Science

institute: Regeneron Pharmaceuticals

summary: IL-33 is an inflammatory cytokine contributing to asthma, Chronic Obstructive Pulmonary Disease (COPD), and autoimmune diseases. Although recent studies suggest that IL-33 can induce the generation of autoantibodies, the role of IL-33 on B cell maturation and tolerance is poorly understood. Here, by inducing systemic overexpression of IL-33 in mice, we show that this cytokine induces the IL-5 and CD4 T cell-dependent accumulation of plasmablasts and plasma cells of all isotypes in the spleen, and leads to an increased antibody production. IL-33 also disrupts splenic architecture and elevates autoantibody production, indicating a break in peripheral tolerance. Consistently, elevated levels of IL-33 exacerbate autoantibody production, kidney damage, and decrease survival in a mouse model of lupus. Additionally, intranasal delivery of IL-33 in mice exposed to house dust mite extract (HDM) increases autoantibodies in the lung. Notably, blocking IL-33 reduced the autoantibodies generated during HDM exposure, indicating that HDM-induced autoantibody production is IL-33 dependent.  Thus, our findings implicate IL-33 in the break of peripheral B cell tolerance, opening new therapeutic avenues for the treatment of infection, COPD and autoimmune conditions.

overall_design: To evaluate the overall impact of IL-33 overexpression in spleen, we performed unbiased global transcriptome analysis following IL-33 HDD and analyzed cell type enrichment. These effects were compared to overexpression of other cytokines (L-25, IL-13, TSLP, IL-4, and IL-9).

first: Wei Keat

last: Lim

first: Eva

last: Conde Garcia


title: Autologous cell therapy with CD133+ bone marrow-derived stem cells for Asherman Syndrome: a phase 1/2 trial [organoids]

first: Carlos

last: Simon

overall_design:
Patients with moderate-to-severe Asherman syndrome were treated with autologous CD133⁺ bone marrow–derived stem cells, and endometrial responses were evaluated using single-cell RNA-seq of epithelial cell–derived organoids generated from endometrial biopsies collected before and after treatment, as well as from healthy controls.

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

first: Xavier

last: Santamaria

first: Maria

last: Pardo-Figuerez

first: Javier

last: Gonzalez-Fernandez

first: Sergi

last: Querol

first: Luciano

last: Rodriguez

first: David

last: Varcárcel

first: Carla

last: Gonzalez

first: Estefanía

last: Fernandez

last: Amorós

last: Robles


title: Inhibition of PAK2 in endothelial cells suppresses tumor angiogenesis and promotes immune sensitization through CXCL10

first: Jean-Philippe

last: Gratton

address: 2900 Bd Edouard-Montpetit

country: Canada

institute: Université de Montréal

summary: Tumor angiogenesis is driven by pro-angiogenic factors and results in a disorganized tumor vasculature that limits effective perfusion and immune infiltration. The p21-activated kinase 2 (PAK2) regulates endothelial cell (EC) migration, an essential step of angiogenesis, yet its role in tumor angiogenesis remains ill-defined. Here, we show that endothelial-specific deletion of PAK2 in orthotopic tumor mouse models markedly reduces tumor size and angiogenesis. Loss of endothelial PAK2 also normalizes the remaining tumor vasculature and promotes infiltration of dendritic and NK cells. Mechanistically, PAK2 regulates chemokine expression, notably CXCL10. PAK2 depletion enhances CXCL10 secretion from ECs, and CXCL10 expression is required for the inhibitory effects of PAK2 silencing on EC spouting. Moreover, CXCL10 neutralization in mice reverses the vascular and immune changes induced by endothelial PAK2 deletion. Together, these findings identify endothelial PAK2 as a potential target to limit tumor angiogenesis and reprogram ECs to promote immune infiltration through CXCL10 signaling.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-seq of CT-PAK2EC and KO-PAK2EC LLC tumors in mice at day 18 of tumor growth. RNA-seq of siCT and siPAK2-transfected HUVEC, and RNA-seq of siCT, siPAK2, siCXCL10 and siPAK2-siCXCL10 transfected HUVEC

first: Jeanne

last: Corriveau

first: Pascale

last: Monot

first: Chantal

last: Delisle

first: Marie-Anne

last: Goyette

first: Camille

last: Gasse

first: Yassine

last: El Bakkouri

first: Trang

last: Hoang

first: Jean-François

last: Côté


title: Control samples for study "hiv-seq reveals global host gene expression differences between hiv-transcribing cells from viremic and suppressed people with hiv"

city: San Francisco

first: Julie

last: Frouard

state: California

address: 1650 Owens street

department: Virology

institute: Gladstone Institutes

summary: In our study, we aimed to improve the identification of active reservoir cells producing HIV in individuals undergoing antiretroviral therapy (ART). We developed a technique called HIV-Seq to enhance the efficiency of capturing HIV transcripts during single-cell RNA sequencing (scRNAseq) analysis. By applying this technique, we compared the transcriptional features of HIV RNA+ cells before and after ART initiation. Our findings highlight distinct transcriptional signatures of active reservoir cells during viremia and suppression, demonstrating the utility of HIV-Seq in elucidating the mechanisms underlying reservoir persistence during ART.

overall_design: CD4⁺ T cells from two HIV-negative donors were subjected to both the standard scRNA-seq protocol and the HIV-seq protocol in parallel. This was done to validate that the addition of HIV-specific primers in the HIV-seq method does not result in false-positive detection of HIV transcripts. Peripheral blood mononuclear cells (PBMCs) were thawed, and CD4⁺ T cells were isolated by negative selection using the EasySep™ Human CD4⁺ T Cell Enrichment Kit (StemCell Technologies). These purified cells were then used to generate gene expression (GEX) libraries following either the standard 10x Genomics 5′ scRNA-seq protocol or the modified HIV-seq protocol.

first: Sushama

last: Telwatte

first: Xiaoyu

last: Luo

first: Natalie

last: Gill

first: Reuben

last: Thomas

first: Douglas

last: Arneson

first: Pavitra

last: Roychoudhury

first: Rebecca

last: Hoh

first: Steven

middle: G

last: Deeks

first: Sulggi

middle: A

last: Lee

first: Nadia

middle: R

last: Roan

last: Yukl


title: Single-cell transcriptomic analysis demonstrates decreased TNF signaling in patients receiving BAF312 during intracerebral hemorrhage

city: New Haven

first: Jonathan

middle: Howard

last: DeLong

state: CT

address: 300 George St Ste 353

department: Neurology

institute: Yale University

summary: Single cell RNA sequencing of PBMC collected at days 1, 3, and 7 after intracerebral hemorrhage from 5 patients treated with the immunomodulatory drug BAF312 (Siponimod) and 2 patients treated with a placebo control.

overall_design: Patient blood was shipped overnight, then PBMC were isolated and frozen. Samples were thawed and live cells were sorted by flow cytometry. Single cell RNA sequencing was performed utilizing the 10X Genomics platform.

first: Sebastian

last: Díaz-Pérez

first: Kevin

last: Sheth

first: Jang-Ho

last: Cha

first: CJ

last: Malanga

first: Patricia

last: Wagner

first: Nicole

last: Pezous

first: Aurelie

last: Hanin

first: Kyle

middle: B

last: Walsh

first: H

middle: E

last: Hinson

first: Lauren

last: Sansing


title: Identification of a Lipid Oxygen Radical Defense pathway and its epigenetic control

city: Lausanne

first: Evarist

last: Planet

state: Vaud

address: Route Cantonale

country: Switzerland

institute: EPFL

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Gene expression profiling of tunicamycin-induced ER stress in HepG2 hepatoma cells

city: Tartu

first: Tiit

last: Örd

address: Riia 23b/2

department: Institute of Genomics

country: Estonia

institute: University of Tartu

summary: Endoplasmic reticulum (ER) stress, a disruption of ER homeostasis, is involved in the pathophysiology of several human diseases, including metabolic dysfunction-associated steatotic liver disease (MASLD). MASLD, formerly known as nonalcoholic fatty liver disease (NAFLD), is characterized by an excessive accumulation of hepatic lipids. To characterize ER stress-induced changes in the expression of genes involved in lipid metabolism, HepG2 human hepatoma cells  were exposed to tunicamycin, followed by transcriptome profiling. Among genes involved in lipid biosynthesis, GPAT3 was strongly activated by tunicamycin while many other genes involved in this process (e.g., DGAT2, AGPAT2, AGPAT3, GPAT1, DGAT1 and GPAT4) were downregulated. Since GPAT proteins catalyze rate-limiting step in the de novo synthesis of glycerophospholipids and triglycerides, the unique expression pattern of GPAT3 potentially links it to ER stress-associated accumulation of lipids in hepatic cells.

overall_design: RNA-Seq of HepG2 cells treated with tunicamycin or mock treated as control. Five replicate experiments done on separate days.

first: Daima

first: Tõnis


title: Tracing the molecular route to progression in miRNA biogenesis-defective thyroid lesions [Spatial_transcriptomics]

city: Hospitalet de Llobregat

first: Barbara

last: Rivera

address: Granvia de l'Hospitalet de Llobregat, 199

institute: IDIBELL

summary: Germline and somatic alterations in DICER1 and DGCR8 microprocessors confer risk of developing benign and malignant thyroid lesions, yet the molecular events driving malignant transformation remain unclear. We trace the molecular trajectories from benignity to malignancy in DICER1/DGCR8-mutated thyroid lesions using multi-omic profiling on 27 DICER1/DGCR8-mutated samples. Our findings reveal a progressive, specific, and linear accumulation of genetic alterations, which when combined with enhanced downregulation of miRNAs distinguished DICER1/DGCR8-malignant lesions from their benign counterparts. Compensatory hypomethylation of miRNA encoding genes characterised DICER1/DGCR8-benign lesions, but as the tumors progressed to malignancy, methylation was partly reimposed, reversing the attempts to activate miRNA-encoded genes and further compromising miRNA production. Transcriptomic analyses revealed mutation-specific effects on the microenvironment, whereby DICER1 mutations activated canonical thyroid cancer progression pathways, whereas altered DGCR8 associated with immune-related alterations. This work unveils specific molecular events underlying malignant progression of miRNA-biogenesis related thyroid tumors and identifies potential biomarkers and disease etiology mechanisms.

overall_design: We explored the spatial transcriptonal profiles of 1 sporadic DICER1-mutated case and 1 germline DGCR8-mutated case, capturing different histological components in each case. For the DICER1-case, this included a tumour core from a DICER1-mutated PDTC, the tumor’s capsule (DICER1-wildtype), a non-neoplastic nodular area (DICER1-wildtype benign thyroid lesion) and a norma lthyroid area (DICER1-wildtype). For the DGCR8-case, this included a tumour core from a DGCR8-mutated micropapillary thyroid carcinoma, a normal thyroid area adjacent to the tumour (DGCR8-mutated, 3 non-neoplastic nodular areas (DGCR8-mutated benign thyroid lesions) and a normal thyroid area (DGCR8-mutated). Each histological component was further segmented into PanCK+ (representing the epithelial population of the histological component) and VIM+ areas (representing the stroma-enriched population of the histological component). Differential expression analyses were performed between the different histological components at the region of interest level (PanCK+/VIM+), the epithelial level (PanCK+/VIM-) and stromal level (PanCK-/VIM+).

first: Anne-Sophie

last: Chong


title: BCL-11 enables adaptive stress responses to environmental challenges

city: Bonn

first: Daniele

last: Bano

state: NRW

address: Venusberg Campus 1/99

country: Germany

institute: DZNE, German Center for Neurodegenerative Diseases

summary: This study investigated the transcriptional impact of hypomorphic bcl-11 mutations.

overall_design: RNAseq profiling of eggs extracted from daf-2(e1370), daf-2(e1370); bcl-11(bon125) and daf-16(mu86); daf-2(e1370);bcl-11(bon125) adults. Worms were fed with OP50-1 at 20℃. Eggs were incubated at 27℃ for two hours after bleaching.

first: Patrizia

last: Niedworok

first: Rossella Erminia

last: Ciliberti

first: Beijia

last: Xie

first: Amal John

last: Mathew

first: Elena

last: De-Domenico

first: Stefan

last: Paulusch

first: Marc

last: Beyer


title: Ly6G+Nur77+ macrophages initiate the type-2 immune response to allergens in the lung

city: Bethesda

first: Ana

last: Olivera

state: Maryland

address: Building 10, Room 11N240, 10 Center Drive

department: NIAID

institute: NIH

summary: The mechanisms of allergen sensing and type 2 immune response initiation remain unclear. Using a house dust mite (HDM)-induced allergic airway model, we demonstrated that host detection of protease activity in HDM was crucial for initiating T helper type 2 (Th2) responses. This process was driven by the major allergen Der p 1, a cysteine protease, which was sensed by protease-activated receptor 2 (PAR2) on a novel population of perivascular lung macrophages expressing Ly6G and nuclear receptor Nur77. These macrophages required PAR2 and Nur77 for activation and accumulation and regulated conventional dendritic cell (mDC) migration to draining mediastinal lymph nodes (mLN) via cysteinyl leukotriene (CysLTs) production. CysLTs enhanced CCR7-driven migration of mDCs toward its ligand, CCL21, facilitating arrival to mLNs for T cell priming and expansion. Inhibiting CysLTs biosynthesis reduced mDC migration and dampened Th2 allergic responses, highlighting new therapeutic paths and mechanisms in type 2 immunity.

overall_design: This study aims to compare allergen-activated Ly6G⁺ macrophages (Ly6G⁺ MΦ) and non-classical monocytes in the lung using single-cell RNA sequencing (scRNA-seq). Eight-week-old C57BL/6J mice (Mus musculus) were treated intranasally with 10 µg of the cysteine protease papain in a 100 µL volume. After 24 hours, lungs were processed into a single-cell suspension, and two distinct cell populations were isolated by fluorescence-activated cell sorting (FACS): Ly6G⁺Ly6C⁺CX3CR1⁺CD11b^hi SIGLEC-F⁻ macrophages (Ly6G⁺ MΦ) and Ly6G⁻Ly6C⁻CX3CR1⁺CD11b⁺SIGLEC-F⁻CD16.2^hi non-classical monocytes. The sorted cells were subjected to scRNA-seq to characterize their transcriptional profiles. This dataset provides insights into the relationship and functional differences between these allergen-responsive myeloid subsets in the lung.

first: Audrey

last: Meloun

first: Holly

last: Bachus

first: Crystal

last: Lewis

first: Brittany

last: Dulek

first: Shivangi

last: Dave

first: Dave

last: Durell Hill

first: Gabriela

last: Pessenda

first: Jose

last: Carlos Gonzalez

first: P’ng

last: Loke

first: Alexander

middle: F

last: Rosenberg

first: Beatriz

last: León


title: Tracing the molecular route to progression in miRNA biogenesis-defective thyroid lesions [miRNA_profiling_data]

first: Barbara

last: Rivera

overall_design: In the study presented here, a cohort of 23 DICER1-/DGCR8-mutated thyroid lesions (10 benign and 13 malignant) was used to identify unique and shared miRNA profiles of mutant benign (DICER1, N=4; DGCR8, N=6) and malignant  (DICER1, N=10; DGCR8, N=3) thyroid lesions distinguishing them from  6 benign and 9 malignant non-DICER1/non-DGCR8 follicular-patterned thyroid lesions. This was performed with a total of 540 mature miRNAs.


title: PHLPP1 Cut&Tag profiling of untreatment (UT) and IL-4 treated alveolar macrophage

city: Shanghai

first: Xingguang

last: Liu

address: Xiangyin road 800

department: National Key Laboratory of Immunity & Inflammation

institute: Naval medical university

summary: Purpose: To transcriptome widely reveal genes regulation by PHLPP1, we performed Cleavage Under Targets and Tagmentation (CUT&Tag) analysis of wild-type (WT) AMs. Methods: Mouse AMs were generated from bronchoalveolar lavage fluid (BALF). AMs were stained to confirm the surface expression of CD11C and Siglec-F. Cells with purity >97.5% were used for subsequent experiments. WT AMs were stimulated with IL-4 (20ng/ml) for 4 hours. Results: We carried out a CUT&Tag assay using antibodies against PHLPP1,and found the global influence of PHLPP1 in regulating genes for pro-fibrosis macrophage effector function.

overall_design: Cleavage Under Targets and Tagmentation (CUT&Tag) analysis for PHLPP1-binding DNA  in WT AMs stimulated with IL-4.

first: Yuyu

last: Jiang

first: Yunkai

last: Zhang


title: Ly6G+Nur77+ perivascular macrophages initiate type-2 immune responses to allergens in the lung

city: BETHESDA

state: MD

address: 10 CENTER DR

department: Division of Intramural Research (DIR)

institute: National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH)

overall_design: three groups of samples: 1) lung perivascular macrophages isolated after 24h papain treatment (4 mouse replicates), 2) lung perivascular macrophages isolated from untreated mice (3 mouse replicates), 3) CCR2+ bone marrow monocytes isolated from untreated mice (3 mouse replicates)

last: Hill

last: Gonzales

first: P'ng


title: VGLL1 KO in colon cancer cells primary culture clone E3, clone 22

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

institute: University of Geneva

summary: In order to explore the potential role of VGLL1 in metastasis we knocked it out using CRISPR. Here we performed an RNAseq of the mutated cells and the wt cells to have an overview of the transcriptome regulation of cells without VGLL1 protein.

overall_design: Total RNA from each culture (control wt and KO) were extracted using TRIzol Reagent (Ambion) following the manufacturer's protocol. Each condition was independently processed in triplicates and the libraries were prepared using Illimina TruSeq protocols. The samples were sequenced on a HiSeq Illumina 2500 machine with 50bp reads followed by standard analyses.

first: Ariel

last: Ruiz i Altaba

first: Marianna

last: Silvano

first: Luca

last: Dall' Olio

first: Ana

middle: I

last: Borges Grazina


title: Transcriptomic profiles of liver biopsies in obese patients with metabolic dysfunction-associated steatotic liver disease

city: Singapore

first: Qing

last: Zhao

address: 28 Medical Dr

country: Singapore

institute: NUS

summary: The molecular mechanisms underlying early-stage metabolic dysfunction-associated steatotic liver disease (MASLD) is poorly understood. This study characterized the transcriptomic alterations in obese patients with no pathology or early-stage MASLD.  94 snap-frozen liver biopsies were analyzed through high-throughput RNA sequencing. Distinct features involved in the development of hepatic steatosis and fibrosis were identified. This study also provided novel insights in mechanisms involved in the onset of fibrosis, highlighting potential therapeutic targets.

overall_design: 94 snap-frozen liver biopsies were processe for RNA sequencing on the NoveSeq6000 platform.

first: William

last: De Nardo

first: Hyungwon

last: Choi

first: Matthew

middle: J

last: Watt

first: Philipp

last: Kaldis


last: León

summary: The mechanisms of allergen sensing and type 2 immune response initiation remain unclear. Using a house dust mite (HDM)-induced allergic airway model, we demonstrated that host detection of protease activity in HDM was crucial for initiating T helper type 2 (Th2) responses. This process was driven by the major allergen Der p 1, a cysteine protease, which was sensed by protease-activated receptor 2 (PAR2) on a novel population of perivascular lung macrophages expressing Ly6G and nuclear receptor Nur77. These macrophages required PAR2 and Nur77 for activation and accumulation and regulated conventional migratory dendritic cell (mDC) migration to draining mediastinal lymph nodes (mLN) via cysteinyl leukotriene (CysLTs) production. CysLTs enhanced CCR7-driven migration of mDCs toward its ligand, CCL21, facilitating arrival to mLNs for T cell priming and expansion. Inhibiting CysLTs biosynthesis reduced mDC migration and dampened Th2 allergic responses, highlighting new therapeutic paths and mechanisms in type 2 immunity.

overall_design: This study aims to characterize the early immune cell populations involved in the response to protease allergens in the lung using single-cell RNA sequencing (scRNA-seq). Eight-week-old C57BL/6J mice (species Mus musculus) were treated intranasally with 10 µg of Alexa Fluor 647-labeled cysteine protease papain in a 100 µL volume. Twenty-four hours later, lungs were processed into a single-cell suspension, and papain⁺ cells were isolated using fluorescence-activated cell sorting (FACS). The sorted cells were then subjected to single-cell RNA sequencing (scRNA-seq) to characterize their transcriptional profiles. This dataset provides insights into early immune interactions in the lung following allergen exposure.

first: Audrey

last: Meloun

first: Holly

last: Bachus

first: Crystal

last: Lewis

first: Brittany

last: Dulek

first: Shivangi

last: Dave

first: Dave

last: Durell Hill

first: Gabriela

last: Pessenda

first: Jose

last: Carlos Gonzalez

first: P’ng

last: Loke

first: Alexander

last: Rosenberg


title: Loss of EGFR prevents the synergistic early-phase impact of obesity-associated metabolic and humoral stress on primary VSMC – stressor synergy, sex-dependence

city: Halle (Saale)

first: Virginie

last: Dubourg

address: Magdeburger Str. 6

department: Julius Bernstein Institute for Physiology

institute: Martin Luther University - Halle-Wittenberg

summary: RNAsequencing was performed for murine primary aortic smooth muscle cells (SMC) and endothelial cells (EC) from wildtype animals (WT) and animals with conditional EGFR knockout in VSMC (KOsmc) after exposing the cells to obestity-associated stress factors.

overall_design: Cells were exposed to for 24h  to 20 mM glucose + 100 µM free fatty acids (HG+FFA) or 30 nM angiotensin II + 300 nM epinephrine (AII+NA) or all four stressors together (ALL).

first: Sindy

last: Rabe

first: Narjes

last: Ansari-Nasiri

first: Michael

last: Kopf

first: Sigrid

last: Mildenberger

first: Gerald

last: Schwerdt

first: Barbara

last: Schreier

last: Gekle


title: Epithelial-Mesenchymal Plasticity is Associated with Immunosuppressive Features in Canine Mammary Carcinomas

city: Ithaca

first: Kimaya

middle: Milind

last: Bakhle

address: 930 Campus Road VRT T7012

department: Department of Biomedical Sciences

institute: Cornell University

summary: Epithelial-mesenchymal plasticity (EMP) is a cellular process activated in carcinoma cells to drive invasiveness, metastasis, and chemoresistance. Recently, we have demonstrated that activation of the EMP program also results in the assembly of an immunosuppressive tumor microenvironment and resistance to immunotherapy in an immunocompetent orthotopic murine model. However, it has yet to be shown whether these findings can be translated to canine carcinomas. Here, we show that in spontaneous canine mammary carcinomas (CMCs), which share similar histopathologic, molecular, and clinical features with human breast cancers, EMP activation is linked to the recruitment of immunosuppressive cells including regulatory T-cells and M2-like macrophages. Additionally, through transcriptomic profiling of CMCs, we identify that the glycoprotein CD109 is associated with EMP-mediated immunosuppression across canine, murine, and human breast cancer models. CD109 has been previously associated with tumorigenicity, but not immunosuppression in cancers of any species. Finally, we identified upregulation of several immunosuppressive paracrine factors across multiple canine carcinomas, including oral squamous cell carcinoma, urothelial carcinoma, and pulmonary carcinoma samples. These findings demonstrate for the first time that the EMP program is associated with immunosuppression in canine carcinomas, with direct translational implications for human breast cancers.

overall_design: RNA-seq data from 15 formalin-fixed paraffin-embedded canine mammary carcinoma samples across three states: epithelial, heterogeneous, and quasi-mesenchymal.

first: Sophie

last: Nelissen

first: Lynna

last: Li

first: Ioannis

last: Ntekas

first: Iwijn

last: De Vlaminck

first: Santiago

last: Peralta

first: Andrew

last: Miller

first: Anushka

last: Dongre


first: Daniele

last: Bano

overall_design: RNAseq anaylsis of adult wildtype, bcl-11(bon125), bcl-11(bon144), daf-2(e1370), daf-2(e1370);bcl-11(bon125) and daf-2(e1370);bcl-11(bon144) mutant Caenorhabditis elegans.

first: Patrizia

last: Niedworok

first: Rossella Erminia

last: Ciliberti

first: Beijia

last: Xie

first: Amal John

last: Mathew

first: Elena

last: De-Domenico

first: Stefan

last: Paulusch

first: Marc

last: Beyer


title: CSAG1 Knock out in clone E3 from colon cancer CC14 primary culture

first: Celine

last: Delucinge

summary: In order to explore the role of CSAG1 in the metastatic potential of the highly metastatic clone E3 we knocked it out using CRISPR/Cas9 system . Here we aimed to explore the transcriptome of E3 cells on which the expression of CSAG1 has been supressed.

overall_design: CSAG1 KO mutations were induced using CRISPR/Cas9 system in E3 clonal cells from primary colon cancer cells (CC14). These cells were cloned and mutations analysed by sequencing. One out of frame mutation with  ATG deletion was chosen and functionnaly tested. CSAG1 KO cells were thenharvested and total RNA extracted using TRIzol Reagent (Ambion) following the manufacturer's protocol. Each condition was independently processed in triplicates and the libraries were prepared using Illumina TruSeq protocols. The samples were sequenced on a HiSeq Illumina 4000 machine with 50bp reads followed by standard analyses.

first: Ariel

last: Ruiz i Altaba

first: Yann

last: Tapponnier


title: Parkinson’s disease-associated shifts between DNA methylation and DNA hydroxymethylation in human brain

city: Piscataway

first: Alison

last: Bernstein

state: NJ

address: 170 Freylinghuysen Rd

department: Pharmacology and Toxicology

institute: Rutgers University

summary: The large majority of Parkinson’s disease (PD) cases are due to a complex interaction between aging, genetics, and environmental factors and epigenetic mechanisms are thought to act as critical mediators of the complex interactions between aging, genetics, the environment, and disease. Evidence for a role of epigenetic regulation in PD has been building, particularly for DNA modifications, over the past 10-15 years. 5-methylcytosine (5mC) is one of the most well-studied epigenetic marks. However, there is a growing recognition that 5-hydroxymethylcytosine (5hmC) plays an important role in gene regulation as it has tissue-, cell-, and age-specific patterns across the genome distinct from 5mC. 5hmC occurs at its highest levels in the brain and is now thought to be particularly important in the central nervous system, particularly in the response to neurotoxicants. While multiple studies to date have explored the role of DNA modifications in PD, most studies have relied on bisulfite (BS) conversion, which does not distinguish between 5mC and 5hmC. Only a handful of existing studies focus specifically on 5hmC; these initial studies support a role for 5hmC in regulation of expression of genes important for PD pathogenesis and indicate that additional studies are warranted. Here, to identify changes in 5hmC in PD, we profiled 5hmC and 5-methylcytosine (5mC) simultaneously in an enriched neuronal population from PD post-mortem parietal cortex. This study expands on our previously published epigenome-wide association study (EWAS) performed on DNA isolated from neuron-enriched nuclei from human postmortem parietal cortex from the Banner Sun Health Research Institute Brain Bank. Because we previously used BS conversion and the Illumina MethylationEPIC array, we were unable to differentiation between 5mC and 5hmC. Here, we utilized additional DNA isolated from the samples and performed oxidative BS (oxBS) conversion paired with the EPIC array to specifically measure 5mC and estimate 5hmC from paired BS-oxBS data. From this, we analyzed both 5hmC and 5mC as related measures using our recently proposed mixed effects model for reconciling base-pair resolution 5mC and 5hmC data.

overall_design: This data includes paired BS/oxBS data for 56 male subjects used in the final analyses, including 29 control and 27 PD subjects, and 44 subjects where data did not pass QC and filtering steps and/or sex was female (female subjects were excluded due to small sample size and lack of statistical power after QC and filtering steps).

first: Joseph

last: Kochmanski

first: Juliana

last: Choza

first: Mahek

last: Virani

first: Nathan

last: Kuhn

first: Marie

last: Adams


title: A SET domain-containing protein and HCF-1 maintain transgenerational epigenetic memory

city: cambridge

first: Jonathan

middle: Lewis

last: Price

address: The Sanger Building Tennis Court Road

department: Biochemistry

country: United Kingdom

institute: University of Cambridge

type: Non-coding RNA profiling by high throughput sequencing

summary: Epigenetic information can be inherited through a process known as transgenerational epigenetic inheritance (TEI). TEI can be initiated and maintained by small RNAs and histone modifications. The latter includes histone methylation, deposited by proteins with methyltransferase activity, including SET domain-containing proteins. Other SET domain-containing proteins with no catalytic methyltransferase activity, also adopt roles in chromatin and gene expression regulation. Here, we describe SET-24, a SET domain-containing protein in Caenorhabditis elegans that belongs to a family of catalytically inactive SET proteins. SET-24 localises to germline nuclei and is required for germline immortality. Additionally, the inheritance of small RNA-driven epigenetic silencing is compromised in set-24 mutants. Using quantitative proteomics and yeast two-hybrid assays, we found that SET-24 interacts with Host Cell Factor 1 (HCF-1), a protein involved in epigenetic regulation and associated with known chromatin remodelling complexes, like COMPASS, which deposits H3K4me3. In set-24 mutants, hundreds of genes display increased H3K4me3 levels at their transcription start sites. While these changes are not matched at the transcriptional level, small RNA production is disrupted in approximately one fifth of those genes, which are normally targeted by small RNA pathways. We propose that SET-24 is a factor required to maintain epigenetic memory in the germline by maintaining a chromatin environment permissible to small RNA biogenesis over generations.

overall_design: We perfomed RNASequencing, ChIP sequencing and small RNA sequencing to discover the function of set-24

first: Chenming

last: Zeng

first: Giulia

last: Furlan

first: Miguel

last: Vasconcelos Almeida

middle: L

first: Juan

last: C. Rueda-Silva

first: Jonas

last: Mars

first: Pedro

last: Rebelo-Guiomar

first: Meng

last: Huang

first: Shouhong

last: Guang

first: Falk

last: Butter

first: Eric

last: Miska


title: ATP11C Knock down in clone E3 from colon cancer CC14 primary culture

first: Celine

last: Delucinge

summary: In order to explore the role of ATP11C in the metastatic potential of the highly metastatic clone E3 we knocked it down using an shRNA in a lentiviral backbone. Here we aimed to explore the transcriptome of E3 cells on which the expression of ATP11C has been knocked down.

overall_design: E3 clonal cells from primary colon cancer cells (CC14) were infected with pLKO.1 empty backbone as control or with shATP11C, 10 days after infection, cells were harvested and total RNA extracted using TRIzol Reagent (Ambion) following the manufacturer's protocol. Each condition was independently processed in triplicates and the libraries were prepared using Illumina TruSeq protocols. The samples were sequenced on a HiSeq Illumina 4000 machine with 50bp reads followed by standard analyses.

first: Ariel

last: Ruiz i Altaba

first: Yann

last: Tapponnier

first: Céline


title: Autoantibody-induced arthritis pain caused by a sustained type I interferon signaling

city: Solna

first: Patrik

last: Ernfors

address: Biomedicum, Solnavägen 9

department: MBB/Molneuro

country: Sweden

institute: Karolinska Institutet

summary: Pain in rheumatoid arthritis is highly debilitating, impacts quality of life and lacks adequate treatment options. Although the presence of pathogenic autoantibodies and systemic and joint inflammation are distinctive features of the disease, the molecular and neuronal basis of pain remains unclear. Here, we identify the molecular mechanism and causative neurons for autoantibody-induced pain in mice. Single-cell RNA sequencing analysis during arthritis pain revealed interferon-stimulated genes, with a persistent nociceptor neuron sensitization, local inflammation and a causative role of interferons acting on polymodal GFRa3-positive C-fiber-nociceptors, as the origin of pain. Consistently, interferon inhibition blocked gene expression alterations and prevented onset as well as reversed established and residual arthritis pain. The discovered pain-causative mechanism may represent a novel therapeutic approach for treatment of pain in rheumatoid arthritis.

overall_design: Mouse dorsal root ganglion cells isolated at different timepoints after induction of experimental arthritis and analyzed using scRNA-seq

first: Jie

last: Su

first: Ming-Dong

middle: D

last: Zhang

first: Jussi

last: Kupari

first: Dongoh

last: Kwak

first: Laurence

last: Picton

first: Bingze

last: Xu

first: Leandro

last: Flores do Nascimento

first: Yizhou

last: Hu

first: Alejandro

last: Gonzalez

first: Dmitry

last: Usoskin

first: Zhongwei

first: Marcin

last: Szczot

first: Abdeljabbar

last: El Manira

first: Rikard

last: Holmdahl


title: Microvascular smooth muscle cells exhibit divergent phenotypic switching responses to platelet-derived growth factor and insulin-like growth factor 1

status: Public on Dec 09 2025

city: Oklahoma City

first: Shannon

middle: M.

last: Conley

state: Oklahoma

address: 940 Stanton L Young Blvd BMSB 100/105

department: Cell Biology

institute: University of Oklahoma Health Campus

summary: Objective: Vascular smooth muscle cell (VSMC) phenotypic switching is critical for normal vessel formation, vascular stability, and healthy brain aging. Phenotypic switching is regulated by mediators including platelet derived growth factor (PDGF)-BB, insulin-like growth factor (IGF-1), as well as transforming growth factor-β (TGF-β) and endothelin-1 (ET-1), but much about the role of these factors in microvascular VSMCs remains unclear. Methods: We used primary rat microvascular VSMCs to explore PDGF-BB- and IGF-1-induced phenotypic switching. Results: PDGF-BB induced an early proliferative response, followed by formation of polarized leader cells and rapid, directionally coordinated migration. In contrast, IGF-1 induced cell hypertrophy, and only a small degree of migration by unpolarized cells. TGF-β and ET-1 selectively inhibit PDGF-BB-induced VSMC migration primarily by repressing migratory polarization and formation of leader cells. Contractile genes were downregulated by both growth factors, while other genes were differentially regulated by PDGF-BB and IGF-1. Conclusions: These studies indicate that PDGF-BB and IGF-1 stimulate different types of microvascular VSMC phenotypic switching characterized by different modes of cell migration. Our studies are consistent with a chronic vasoprotective role for IGF-1 in VSMCs in the microvasculature while PDGF is more involved in VSMC proliferation and migration in response to acute activities such as neovascularization. Better understanding of the nuances of the phenotypic switching induced by these growth factors is important for our understanding of a variety of microvascular diseases.

overall_design: RNAseq profiling of wildtype S31 rat primary vascular smooth muscle cells serum starved and treated with recombinant rat PDGF-BB (25 ng/ml) or with  recombinant human IGF-1 (25 ng/ml). Control cells received fresh serum-free medium lacking any added growth factors. Total RNA was extracted at 24 hours post treatment for (control & IGF-1) and 48 hours post treatment (PDGF-BB).

first: Marisa

last: Bickel

first: David

last: Sherry

first: Elizabeth

middle: C

last: Bullen

first: Michaela

last: Vance

first: Ken

last: Jones

first: Eric

middle: W

last: Howard


title: The protein phosphatase 2C domain contributes to the pathobiological function of adenylyl cyclase in Cryptococcus neoformans

city: Seoul

first: Yong-Sun

last: Bahn

address: 50, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea

department: Department of Biotechnology

country: South Korea

institute: Yonsei university

summary: Adenylyl cyclase (AC) is the central regulator of cAMP signalling in fungal pathogens, yet fungal ACs uniquely contain a protein phosphatase 2C (PP2C) domain whose function remains unclear. Here, we characterise the PP2C domain of the AC Cac1 in the human pathogen Cryptococcus neoformans. Structural and biochemical analyses show that Cac1-PP2C adopts a non-canonical scaffold but functions as a Ser/Thr-specific metalloenzyme. Deletion of the PP2C or AC catalytic (ACC) domain demonstrated that PP2C is required for full Cac1 activity, influencing melanin and capsule synthesis, sexual differentiation, titan cell formation, and cell wall integrity. Notably, the PP2C-null mutant induced Th2-biased immunity and extensive pulmonary damage yet failed to cause mortality in mice. Integrated transcriptomic and phosphoproteomic analyses further revealed shared and domain-specific signalling outputs mediated by PP2C and ACC. This study provides the first comprehensive characterisation of a fungal AC-linked PP2C domain and defines its pivotal role in C. neoformans pathobiology

overall_design: RNA extraction was performed from cells grown in the same manner as described for phosphoproteome analysis. Briefly, 10 ml cultures for five strains (wild-type H99, cac1Δ, cac1Δ::CAC1, cac1Δ::CAC1PP2CΔ, cac1Δ::CAC1ACCΔ) were grown in triplicates in two media conditions, YNB and YNB + 2% glucose.

first: Soojin

last: Yu

first: Seong-Ryong

first: Myung Kyung

last: Choi

first: Jae-Hyung

last: Jin

first: Vikas

last: Yadav

first: Hee Seong

first: Eui-Seong

last: Kim

first: Hyun-Woo

first: Jae-Seok

last: Jeong

first: Do-Kyun

first: Joseph

last: Heitman

first: Hyun-Soo

last: Cho

first: Kyung-Tae

last: Lee


title: Analysis of gene expression patterns tracking increasing metastatic potential of different clones from  colon cancer CC36 primary culture

first: Celine

last: Delucinge

summary: In order to find genes the expression of which follows the metastatic potential of different clonal cultures from the colon cancer heterogeneous CC36 primary culture. Each of the clonal culture has a different and defined metastatic potential as tested by transfilter assay.

overall_design: Total RNA from each clonal culture extracted using TRIzol Reagent (Ambion) following the manufacturer's protocol. Each condition was independently processed in triplicates and the libraries were prepared using Illimina TruSeq protocols. The samples were sequenced on a HiSeq Illumina 4000 machine with 50bp reads followed by standard analyses.

first: Ariel

last: Ruiz i Altaba

first: Yann

last: Tapponnier

first: Céline


title: NAD⁺ Reduction in Glutamatergic Neurons Induces Lipid Catabolism and Neuroinflammation in the Brain Via SARM1

city: BLOOMINGTON

first: Hui-Chen

last: Lu

state: IN

address: 400 EAST SEVENTH STREET, MULTI-DISCIPLINARY SCIENCE BUILDING 2

department: Gill Institute for Neuroscience

institute: Indiana University Bloomington

summary: NAD⁺ homeostasis is vital for neuronal health, as demonstrated by the opposing roles of nicotinamide mononucleotide adenylyltransferase 2 (NMNAT2), a NAD⁺-synthesizing enzyme, and sterile alpha and TIR motif-containing protein 1 (SARM1), a NAD⁺ hydrolase. Neurodegenerative insults that decrease NMNAT2 activate SARM1, leading to axon loss. To understand how the NMNAT2–SARM1 axis influences brain energy metabolism, we employed multi-omics approaches to investigate the metabolic changes resulting from neuronal NMNAT2 loss. Loss of NMNAT2 in glutamatergic neurons leads to a significant metabolic shift in the cerebral cortex from glucose to lipid catabolism, reduced lipid abundance, and pronounced neurodegenerative phenotypes and motor behavioral deficits. These metabolic disturbances are accompanied by altered glial expression of enzymes regulating glucose and lipid metabolism, enhanced inflammatory signaling, and disrupted astrocytic transcriptomic profiles related to cholesterol synthesis and immune activation. Notably, SARM1 deletion in NMNAT2-deficient mice restored lipid metabolism, astrocyte transcriptomic profiles, and mitigated neurodegeneration and motor behaviors. These findings suggest that neuronal NAD⁺ depletion triggers maladaptive, SARM1-dependent metabolic reprogramming, shifting energy use from glucose to lipids, which in turn promotes inflammation and neurodegeneration.

overall_design: Astrocytes were acutely isolated from the cerebral cortices of postnatal day 16 (P16) mice from three genotypes: Control (Ctrl-2): Nmnat2f/+; NexCre+/-; Sarm1+/-, cKOA: Nmnat2f/f; NexCre+/-; Sarm1+/-, cKOB: Nmnat2f/f; NexCre+/-; Sarm1-/-. Brains were dissected and the cortex region was used for astrocytes isolation using magnetic cell sorting (MACS) with anti-ACSA2 microbeads (Miltenyi Biotec). Total RNA was extracted after the sorting and then sent out for RNAseq analysis.

first: Zhen-Xian

last: Niou

first: Andrea

last: Enriquez

first: Nino

last: Espinas


title: Safety, feasibility and pharmacodynamic activity of intratumoral injections of the agonist anti-CD137 (4-1BB) mAb urelumab in combination with nivolumab

city: Pamplona

first: David

last: Ruiz Guillamón

state: Navarra

address: Av. de Pío XII, 55

department: Programa de Inmunología e Inmunoterapia

institute: Centro de Investigación de Medicina Aplicada (CIMA) - Clínica Universidad de Navarra

summary: Intravenous dosing of the anti-CD137 (4-1BB) agonist monoclonal antibody urelumab is limited to 8 mg flat doses due to liver toxicity, thus reducing bioavailability. Here we explored intratumoral delivery of urelumab to increase bioavailability at the tumor, while reducing systemic exposure, in combination with systemic nivolumab (clinical trial INTRUST, NCT03792724).

overall_design: Bulk RNA-seq of biopsy samples from clinical trial patients at different timepoints.

first: Miguel

last: Sanmamed

last: Ruiz-Guillamón

first: Carlos

last: de Andrea

first: Jose

last: Perez-Gracia

first: Ignacio

last: Melero


title: Molecular and phenotypic blueprint of human hematopoiesis links proliferation stress to stem cell aging

city: Milan

first: Raffaella

last: Di Micco

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

summary: Hematopoietic stem/progenitor cell (HSPC) aging has been associated with myeloid skewing, reduced clonal output, and impaired regenerative capacity, but quantitative immunophenotypic and functional analysis across human aging is lacking. Here, we provide a comprehensive phenotypic, transcriptional, and functional dissection of human hematopoiesis across the lifespan. Although primitive hematopoietic stem cell (HSC) numbers were stable during aging, overall cellularity was reduced, especially for erythroid and lymphoid lineages. Notably, HSPC from aged individuals had similar repopulating frequency of younger counterparts in primary and secondary xenografts; yet aged HSC displayed impaired differentiation capacity, changes in chromatin accessibility, dysregulation of cell cycle, and a reduced capacity to counteract activation-induced proliferative stress with concomitant accumulation of DNA damage and senescence-like features upon xenotransplantation. This age-associated phenotypic and functional decline was recapitulated by enforcing proliferative stress in vivo on human HSPC. Overall, our work sheds light on dysregulated responses to activation-induced proliferation underlying HSPC aging and establishes xenotransplantation-based models as suitable for studying age-associated hematopoietic defects.

overall_design: Human BM HSPC cells were pre-stimultation in cell culture over night and then transplanted in NSG mice, and purified after 20 weeks from mouse BM.

first: Giacomo

last: Farina

first: Edoardo

last: Carsana

first: Raffaellla


title: Effect of BHB on transcriptional changes of antigen-stimulated CART19 cells

city: Philadelphia

first: Marco

last: Ruella

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: This study examines the impact of β-hydroxybutyrate (BHB) on T cell function using RNA-seq, ATAC-seq, and H3K27ac CUT&RUN profiling to characterize BHB-induced transcriptional and epigenetic remodeling.

overall_design: Plates were coated with CD19 protein and incubated overnight at 4 °C. After blocking with 2% BSA the following day, human CAR T19 cells were added and cultured for 48 h in the presence of vehicle or 5 mM β-hydroxybutyrate (BHB).

first: Shan

last: Liu

first: Puneeth

last: Guruprasad

first: Maayan

last: Levy


title: CUT&Tag analysis of the Olig2-targeted genes in adult oligodendrocyte lineage cells

city: Guangzhou

first: Zheng

last: Wu

state: Guangdong

address: 601 West Huangpu Road

institute: Jinan University

summary: In summary, our study identifies and characterizes the direct targets of Olig2 in adult oligodendrocyte lineage cells.

overall_design: Sox10-CreERT2 mice were crossed with Ai14 reporter mice to generate double-transgenic offspring. Tamoxifen induction labeled oligodendrocyte lineage cells with tdTomato. Ten days post-induction, whole brains were dissociated into single-cell suspensions, and tdTomato+ cells were isolated and collected by FACS for CUT&Tag sequencing.

first: Chuying

last: Lai

first: Kaiyu

last: Hou

first: Gong

last: Chen


title: Investigation of the metabolic features of cancer therapy induced senescent cells with TPEF, mass spectrometry and RNA sequencing analysis

first: Italia

last: Bongarzone

state: Milan

address: Via Amedeo, 42

department: Department of Diagnostic Innovation

institute: IRCCS Istituto Nazionale dei Tumori

summary: Background. Despite major advances in cancer therapies, treatment failure remains a significant issue for a subset of patients due to therapy resistance and tumour recurrence. A key contributor to these failures is therapy-induced senescence, wherein damaged cells enter a stable cell cycle arrest while remaining metabolically active, contributing to chronic inflammation and cancer relapse. These senescent cells can promote chronic inflammation and disease relapse. However, the heterogeneous nature of senescence complicates its detection and therapeutic targeting. Methods. We employed a multimodal approach to profile metabolic alterations in senescent cancer cells. Senescent cells were induced either by doxorubicin or γ-irradiation, both widely employed strategies in anti-cancer treatment, across three human cancer cell lines: MCF7, HeLa, and TPC-1. Mitochondrial dysfunction was assessed through MitoTracker and JC-1 staining. Two-photon excitation fluorescence microscopy enabled label-free imaging of mitochondrial coenzymes NAD(P)H and FAD. Lipidomic changes were analyzed using MALDI mass spectrometry imaging following lipid extraction and matrix application. Additionally, transcriptomic profiling via RNA sequencing was performed on control, senescent, and engulfing-senescent MCF7 cells. Bioinformatic analyses included differential gene expression, gene set enrichment analysis, and pathway analysis using GO, KEGG, and Reactome databases Results. Across all models, senescent cells exhibited mitochondrial dysfunction, marked by altered NAD(P)H and FAD distribution and decreased mitochondrial membrane potential. Two-photon excited fluorescence imaging confirmed a broader intracellular redistribution of mitochondrial coenzymes. MALDI analyses revealed consistent lipid remodeling, particularly involving cardiolipin precursors such as PG(18:1/18:1) and PG(18:1/22:6). Transcriptomic profiling of senescent MCF7 cells revealed that a previously observed engulfing subpopulation is marked by enhanced oxidative metabolism and increased lipid catabolism, suggestive of an engulfing phenotype. Conclusion. Our findings delineate both conserved and divergent metabolic features across senescent cell states and highlight specific metabolic vulnerabilities. These insights offer potential avenues for the development of targeted senolytic strategies.

overall_design: To obtain the senescent phenotype, adherent cells were treated with 250 nM doxorubicin (Doxo, Sigma), or irradiated at 10 Gy released by γ-rays from 137Cs sources of IBL147 biological irradiator (0.65 Gy=min). Cells were observed and/or analyzed from 6 to 8 days after treatment. Control (untreated) cells, the proliferation of which was not arrested by treatment, were split when necessary to avoid apoptosis due to overgrowth until observation (typically once after seeding and before the end point), or alternatively collected prior to full confluence, typically 72 or 96 hours after seeding. To obtain a MCF7 population enriched in engulfing cells, MCF7 cells were treated with doxorubicin as described above and, after 6 days of treatment, they were collected through trypsinization and re-seeded. Adherent cells were collected 24 hours after being re-seeded.

first: Silvia

last: Ghislanzoni

first: Federica

last: Padelli

first: Alessia

last: Bertolotti

first: Antonino

last: Belfiore

first: Matteo

last: Niero

first: Arianna

last: Bresci

last: Betti

first: Andrea

last: Masella

first: Dario

last: Polli

first: Luca

last: Agnelli


title: Abatacept Restores Dysregulated Transcriptomic and Proteomic Profiling in LRBA Deficiency and CTLA-4 Insufficiency

city: Doha

first: Bernice

last: Lo

address: Al Luqta

department: Research

country: Qatar

institute: Sidra Medicine

summary: This study investigates the effectiveness of abatacept via flow cytometric and multi-omics approaches in treating lipopolysaccharide-responsive beige-like anchor (LRBA) deficiency, an immune disorder characterized by infections, autoimmunity, and lymphoproliferation. Integrative analyses revealed that long-term abatacept use boosted the naive T-cell pool through increased thymic output while simultaneously reducing memory T cells and cytokine productions of CD4+ T cells and decreasing autoreactive B cells. Abatacept also normalized the imbalanced T helper (TH) 1 and TH17 responses. By using targeted and single-cell transcriptomics together with plasma proteomic analyses, we observed a complex interaction involving upregulated CD28 and T-cell receptor signaling pathways, accompanied by increased expression of inhibitory checkpoint proteins to maintain immune homeostasis in the absence of the cytotoxic T-lymphocyte-associated antigen-4 (CTLA-4). The immune dysregulation involved multiple pathway repercussions, including upregulation of inflammatory pathways, cytokine and chemokine-mediated responses, antimicrobial peptides, interferon-related genes, complement system, and toll-like receptor signaling, which normalized under abatacept. Thus, targeted treatment can re-establish the broadly disturbed immune regulation in LRBA deficiency.

overall_design: Patient blood samples were collected before and after abatacept treatment and PBMCs were separated using ficoll density gradient, cryopreserved, then put through single cell RNA sequencing.


title: Analysis of gene expression patterns tracking increasing metastatic potential of different clones from  colon cancer CC14 primary culture

first: Celine

last: Delucinge

summary: In order to find genes the expression of which follows the metastatic potential of different clonal cultures from the colon cancer heterogeneous CC14 primary culture. Each of the clonal culture has a different and defined metastatic potential as tested by transfilter assay.

first: Ariel

last: Ruiz i Altaba

first: Yann

last: Tapponnier

first: Céline


title: 2’-O-Methyl-guanosine 3-base RNA fragments mediate essential natural TLR7/8 antagonism

city: Clayton

first: Michael

middle: P

last: Gantier

state: Victoria

address: 27-31 Wright St

department: Centre for Innate Immunity and Infectious Disease

country: Australia

institute: Hudson Institute of Medical Research

summary: Daily phagocytic clearance of billions of apoptotic cells is fundamental to the maintenance of homeostasis and is normally immune silent. Toll-like receptors (TLR) 7 and 8 are phagosomal innate immune sensors known to instigate inflammation in response to guanosine, uridine, and ~2-3 base long degradation products from endosomal RNAs. Exactly how TLR7 and TLR8 evade activation by degradation products from host-RNAs is currently unknown. The activity of the mouse TLR7 inhibitory sequence GGC-v1 was tested on primary bone marrow-derived macrophages (BMDMs) derived from Tlr7Y264H gain-of-function mutant mice. This Tlr7Y264H gain of function mutation results in constitutive engagement of TLR7 through an increased affinity for guanosine. Overnight treatment of Tlr7Y264H mutant BMDMs with GGC-v1 or the small molecule TLR7/8 inhibitor Enpatoran led to significant down regulation of 20 out of the 22 genes regulated by GGC-v1 that were also down-regulated by Enpatoran, indicating that TLR7 sensing was effectively dampened.

overall_design: Primary bone marrow derived macrophages (BMDMs) from 9-11 week-old Tlr7Y264H heterozygous gain-of-function female mice were extracted and differentiated for 5 days in complete DMEM supplemented with L929 conditioned medium, prior to 24 h incubation with 5 µM GGC-v1 or 100 nM Enpatoran and total RNA purification for RNA sequencing.

first: Sunil

last: Sapkota

first: Alexandra

last: McAllan


title: Colon cancer low metastatic clone after escape of late apoptosis

address: 1 rue Michel Servet

institute: University of Geneva

summary: In order to explore the potential role of escape of late apoptosis in metastasis, we induced apoptosis and subsequently inhibited the death process in a poorly metastatic clone from a primary culture of colon cancer cells. Here we wanted to explore the transcriptome of such "undead" cells  7 days after apoptosis induction.

overall_design: Primary culture CC14 low metastatic clone C11 was treated with STS and 6h after with DIDS and Q-VD_Oph. 7 days after these treatments , cells were harvested and total RNA extracted using TRIzol Reagent (Ambion) following the manufacturer's protocol. Each condition was independently processed in triplicates and the libraries were prepared using Illimina TruSeq protocols. The samples were sequenced on a HiSeq Illumina 2500 machine with 50bp reads followed by standard analyses.

first: Arwen

last: Conod


title: Escape from X inactivation is directly modulated by Xist non-coding RNA [ESC]

first: Jasper

last: Panten

address: Tomtebodavägen 23

institute: SciLifeLab

summary: X-chromosome inactivation silences one copy of the X-chromosome in female cells, but a number of genes escapes this inactivation. We asked whether increased levels of Xist RNA, the molecular actor driving X-inactivation, impacts expression levels of escapees. To this end, we performed transcriptomic profiling of X-linked gene expression in clonal neural progenitor cell lines with transgenes that allow for the overexpression of Xist on the inactive X chromosome. Here, we use the F1 hybrid mouse ESC line from which the NPCs were derived as a control to assess the silencing effect of Xist in ESCs.

overall_design: First generation hybrid embryonic stem cells (from a C57BL6/J x CAST/EiJ cross), that carry  a doxycycline-inducible transgene on the B6 allele were used. Doxycyclin treatment for 24 hours was performed in the ESCs and allele-specific expression was measured using RNA-Sequencing.

first: Edith

last: Heard

first: Agnese

last: Loda

first: Antonia

last: Hauth


title: Escape from X inactivation is directly modulated by Xist non-coding RNA [CUT&Run]

summary: X-chromosome inactivation silences one copy of the X-chromosome in female cells, but a number of genes escapes this inactivation. We asked whether increased levels of Xist RNA, the molecular actor driving X-inactivation, impacts expression levels of escapees. To this end, we performed CUT&RUN profiling for two Xi-enriched histone marks, H2AK119Ub and H3K27me3 in a clonal neural progenitor cell line with transgenes that allow for the overexpression of Xist on the inactive X chromosome. We perform Xist overexpression experiments for up to three weeks and also test the reversibility of Xist overexpression using washout experiments.

overall_design: Clonal neural progenitor cell lines were generated by differentiating first generation hybrid embryonic stem cells (from a C57BL6/J x CAST/EiJ cross). All cell lines carry an inactive B6 X chromosome and a doxycycline-inducible transgene on the Xi. Doxycyclin treatment for 7 and 21 days was performed in the E6 cell line and allele-specific histone mark occupancy was measured using CUT&RUN. Furthermore, samples after washing out of doxycycline were analyzed to assess reversibility.


title: Escape from X inactivation is directly modulated by Xist non-coding RNA [Astrocytes]

summary: X-chromosome inactivation (XCI) silences one copy of the X-chromosome in female cells, but a number of genes escapes XCI. We asked whether increased levels of Xist RNA, the molecular actor driving X-inactivation, impacts expression levels of escapees in Astrocytes. To this end, we performed RNA-seq analysis profiling of X-linked genes upon doxycycline-induced Xist upregulation and following doxycycline washout.

overall_design: Astrocytes were generated by differentiating NPC clone E6 (C57BL6/J x CAST/EiJ). Doxycyclin treatment for 3 and 7 days (and following wash-out) was performed and allele-specific RNA expression was measured.


title: Single cell RNA-sequencing analysis of the inhibitory effects of Olig2 on astrocyte-to-neuron conversion

first: Zheng

last: Wu

summary: Collectively, our study reveals the role of Olig2 in hindering the in vivo AtN conversion and idendifies an inducible barrier to neuronal reprogramming.

overall_design: WT mouse cortex was injected with AAV9 hGFAP-Ngn2-tdTomato in the presence of scramble shRNA or Olig2 shRNA.  Virus-infected brain tissue was collected 18, 20, 22 days post injection (n = 2 mice for each time point), and dissociated into single-cell suspension, which was loaded to microfluidic chip, followed by scRNA-seq processing.

first: Chuying

last: Lai

first: Kaiyu

last: Hou

first: Gong

last: Chen


title: Escape from X inactivation is directly modulated by Xist non-coding RNA [E8.5]

summary: X-chromosome inactivation silences one copy of the X-chromosome in female cells, but a number of genes escapes XCI. We asked whether increased levels of Xist RNA, the molecular actor driving X-inactivation, impacts expression levels of escapees. We tested whether dox-mediated Xist-overexpression affected the expression levels of escapees in extra-embryonic tissues.

overall_design: To investigate the effect of Xist overexpression on imprinted X-inactivation in extra-embryonic tissues, we crossed TX/Y males carrying the rtTA transactivator (Xptet/Y; R26rtTA/rtTA or Xptet/Y; R26rtTA/WT) with wild-type JF1 females. Xist RNA overexpression was induced by adding doxycycline to the drinking water of pregnant females for 5 days, from E3.5 to E8.5. RNA was extracted from the collected extra-embryonic tissues of each embryo. Libraries were prepared using the Smart-Seq2 protocol, and allele-specific expression was determined for X-linked genes.

first: Emma

last: Kneuss


title: CUT&Tag analysis of the inhibitory effects of Olig2 on astrocyte-to-neuron conversion

overall_design: WT mouse cortex was injected with AAV9 hGFAP-Ngn2-tdTomato. Virus-infected brain tissue was collected 7 days post injection (n = 12 mice), and dissociated into single-cell suspension, followed by tdTomato+ cells collecting by fluorescent-assisted cell sorting. The tdTomato+ cells were then subjected to CUT&Tag sequencing.


title: Olfr2 drives abdominal aortic aneurysm by promoting monocyte recrutiment

city: Cologne

first: Patrik

last: Schelemei

address: Kerpener Str. 62

department: Internal Med III

institute: University Hospital Cologne

summary: Olfactory receptor 2 is a G-protein coupled receptor expressed on vascular macrophages. Activation by its ligand octanal in conjuction with a toll like receptor 4 stimulus induces the NLRP3 inflammasome with subsequent IL-1alpha and IL-1beta release. In this study we aim to investigate the effects of genetic Olfr2 deficiency on the development of abdominal aortic aneurysm (AAA).

overall_design: RNA seq profiling of sorted Ly6Chigh monocytes from the spleen of Olfr2 WT and KO mice at day 7 after aneurysm induction

first: Holger

last: Winkels


title: Olfr2 deficiency protects from abdominal aortic aneurysm

overall_design: RNA-seq profiling of AAA of Olfr2 WT and Olfr2 KO mice at day 7 after aneurysm induction.

first: Schelemei

last: Patrik

first: Winkels

last: Holger


title: Investigation of gene stability in equine luteal tissue during mid-luteal phase and early pregnancy

first: Jennifer

middle: K

last: Grenier

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

summary: Real- time reverse transcription quantitative polymerase chain reaction (RT-qPCR) is a technique that allows for the quantification of mRNA transcripts present within a tissue of interest. To ensure that quantified amounts of mRNA determined by RT qPCR is due to biological differences rather than a product of variation in testing protocol, results need to be normalized. Normalization has historically relied on the use of reference genes, or genes whose transcript expression does not differ in the tissue of interest independent of the experimental condition. In the field of equine reproductive studies, ACTB and GAPDH have been the most widely used reference genes for normalization of RT-qPCR results. However, recent studies have demonstrated that these genes may have drastically varied expression levels in different tissues and in different physiological states. Our study was aimed at examining different putative reference genes (historic reference genes as well as genes identified by RNA-seq to be stable across different sample types) in equine corpus luteum samples at day 11 and day 13 in pregnant and non-pregnant animals. Stability of genetic expression was evaluated via three stability software analyses (GeNorm, NormFinder and BestKeeper). We hypothesized that the most commonly used historic reference genes (ACTB, GAPDH and B2M) would be the most stably expressed genes in equine corpus luteum samples. COX4I1 and SRP14 were both found to be within the top three most stable genes of all samples for all methods. When assessing the least stably expressed genes, the historic reference genes were frequently identified across the three softwares. Exploration of putative reference genes should be considered when investigating dynamic endocrine organs such as those used in reproductive studies. RT-qPCR studies evaluated with historic genes should be interpreted cautiously.

overall_design: Healthy normal cycling light breed mares (n=8) were enrolled in the study. A transvaginal luteal biopsy was performed in pregnant and non-pregnant mares at day 11 and day 13 post-ovulation. RNA isolation was performed using TRIzol reagent (ThermoFisher) according to the manufacturer's instructions. RNA libraries were prepared using the NEBNext Ultra II Directional Library prep kit (New England Biolabs). RNA sequencing results were used to identify putative stable reference genes across pregnancy status and timepoint.

first: Leah

middle: N

last: Ramsaran

first: Michael

last: Byron

first: Stephen

last: Parry

first: Jennine

last: Lection

first: Bradley

last: Back

first: Soon Hon

last: Cheong

first: Mariana

last: Diel de Amorim


title: CUT&Tag analysis of the inhibitory effects of Olig2 on astrocyte-to-neuron conversion (2)

first: Zheng

last: Wu


title: Stress resilience is associated with transcriptional remodeling in the VTA

city: Princeton

first: Adelaide

last: Minerva

state: New Jersey

address: Washington Road

department: Princeton Neuroscience Institute

institute: Princeton University

summary: Individual responses to chronic stress vary, with some individuals remaining resilient while others exhibit susceptibility. The ventral tegmental area (VTA), a region involved in reward learning, and the lateral habenula (LHb), a region involved in aversive learning, have been implicated in the pathophysiology of stress-related mood disorders. Here, we seek to understand the molecular adaptations in these regions at the level of single cells that mediate susceptibility versus resilience. In particular, it remains unclear whether, at the level of gene expression, different cell-types within different brain regions mediate stress susceptibility versus resilience, or if these phenotypes are mediated by distinct trajectories within the same cell-types. To address this gap, we performed single-nucleus RNA-sequencing of LHb and VTA of mice subjected to chronic social defeat stress. While we found minimal gene expression changes in the LHb after stress, the VTA exhibited widespread, cell-type-specific transcriptional remodeling in resilient individuals and few gene expression changes in susceptible individuals. Across VTA cell-types, resilience was associated with the coordinated upregulation of genes involved in intercellular signaling and neural communication, with maintenance of receptor-ligand interaction strength in resilience that was not present in susceptibility. Within VTA neurons, gene expression changes were most prominent in glutamatergic and dopaminergic clusters. Multivariate analyses of dopamine and glutamate subclusters showed that resilient neurons diverged more from control than susceptible neurons, but along a similar trajectory, supporting a model in which resilience reflects greater stress-related adaptations in these cell-types. Together, these findings highlight the VTA as a key site of molecular plasticity in stress resilience and therefore a potential therapeutic target.

overall_design: VTA and habenula nuclei from C57BL/6 mice were isolated following chronic social defeat stress (CSDS) and analyzed using snRNA-seq. For VTA, we analyzed nuclei from control (3 male, 3 female), susceptible (2 male, 2 female), and resilient (3 male, 3 female) samples. Each VTA sample contained pooled nuclei from two animals of the same sex and experimental condition. For habenula, we analyzed nuclei from control (3 male, 3 female), susceptible (3 male, 3 female), and resilient (3 male, 3 female) samples. Each habenula sample contained nuclei from one animal.

middle: R

first: Brenna

last: McMannon

first: Rixing

last: Lin

first: Anna

last: Zhukovskaya

first: Ilana

last: Witten

first: Catherine

last: Peña


title: Resident CD49a⁺CD103⁺NKG2C⁺ NK Cells Restrict HIV Infection in Human Lymphoid Tissue Explants

city: Barcelona

first: María José

last: Buzón Gómez

state: Barcelona

address: Passeig Vall d'Hebron, 119-129

department: Infectious Diseases

institute: Vall d'Hebron Research Institute

summary: Natural killer (NK) cells are pivotal effectors in antiviral immunity, yet their tissue-specific roles during acute HIV infection remain poorly defined. Using an ex vivo human tonsillar tissue model, we profile NK cell responses to early HIV infection and uncover distinct subsets with specialized functions. We identify a previously uncharacterized memory-like NK population (CD16⁺/⁻CD69⁺CD49a⁺CD103⁺NKG2C⁺) associated with reduced viral burden and enriched in cytotoxic mediators (GNLY, PRF1, GZMB), apoptotic ligands (FASLG, TRAIL), cytokine receptors (IL2RA, ILR2B, IL2RG, IL12RB2, IL18R1) and trafficking molecules (CCL3–5, CCR7, SELL). These cells coexpress NKG2A, suggesting a regulatory balance between activation and inhibition. Although functionally capable of clearing HIV-infected CD4⁺ T cells in a tissue-mimetic environment, they show impaired cytotoxicity and transcriptional signs of exhaustion after infection. Conversely, HIV drives the reprogramming of immature CD16⁻CD69⁺ NK cells toward a more cytotoxic and migratory effector phenotype. These findings reveal dynamic NK cell adaptations in lymphoid tissue during early HIV infection and highlight tissue-resident NK cells as promising targets for immunotherapeutic intervention.

sample_organism:
Homo sapiens
HIV-1 group M

platform_organism:
Homo sapiens
HIV-1 group M

overall_design: Tonsils from a 9-year-old and a 10-year-old child were left overnight in dissection medium to inactivate contaminating microorganisms. Dissection medium included RPMI-1640 medium (Gibco) supplemented with 500 U/ml penicillin (Fisher Scientific), 500 µg/ml streptomycin (Fisher Scientific), 1 µg/ml gentamicin (Gibco), and 5 µg/ml amphotericin B (Gibco). Tonsillar tissue explants (8 mm³ blocks) were cultured on the air-liquid interface on absorbable gelatin sponges (Goodwill). The hemostatic sponges were soaked in RPMI-1640 medium supplemented with 20% Fetal Bovine Serum (FBS) (Gibco), 10 mM HEPES (Biowest), 100 U/ml penicillin, 100 µg/ml streptomycin, and 66 µg/ml amikacin (Vall d’Hebron Hospital pharmacy) (R20 medium). The first day of culture, R20 medium also included 310 µg/ml of timentin (Caisson Labs). Half of the tissue blocks were infected with HIV Bal viral stock (TCID50: 625 units) via dropwise application directly onto the tissue. Medium and sponges were refreshed every 2 days. After 5 days of culture, the tissue blocks were mechanically dissociated and filtered sequentially through 70 µm and 30 µm cell strainers to obtain a single-cell suspension. The CD56+ cell population was enriched from both HIV-infected and uninfected tissue suspensions using the MagniSort™ Human CD56 Positive Selection Kit. Subsequently, CD3- CD56+ cells were further purified by Fluorescence-Activated Cell Sorting (FACS) and analyzed using scRNA-seq.

last: Buzón

first: David

last: Perea

first: Alba

last: González

first: Irene

last: Mota


title: Epigenetic profiling of hematopoietic stem cells identifies KDR and PU.1 as regulators of aging transcriptome and caloric restriction response

city: Baltimore

first: Bongsoo

last: Park

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

summary: The ability to cope with fluctuations in energy supply is essential for an organism's survival and health. While caloric restriction (CR) provides benefits towards many aspects of aging, it is associated with loss of immune function. The mechanisms by which the hematopoietic stem cells (HSCs) respond to this stress and potentially contribute to this loss of immunity remain unclear. In this study, using both lifelong and short-term CR mice models, we found that reduced energy supply leads to a decrease in total peripheral blood white blood cell production that is myeloid- and thrombo-erythroid-biased. This strategy prioritizes the production of cell types essential for survival, such as red blood cells, platelets, and innate immune cells, at the expense of adaptive immune cell differentiation. Consistent with change in blood composition, HSCs under CR are driven into cell cycle to support the myeloid differentiation rather than self-renewal. Interestingly, despite the altered hematopoietic output, lifelong CR mitigates age-associated transcriptome changes of the HSCs, but these modifications are swiftly lost after ad libitum feeding. Epigenetic profiling identified KDR as a key regulator of the CR response and experimental knockdown of Kdr in aged HSCs reproduced the more youthful aging transcriptome observed in lifelong CR HSCs. Additionally, we show that PU.1 acts as an intracellular regulator of the CR response, regulating HSC self-renewal and differentiation under CR conditions by increased binding to its target genes.

overall_design: RNA-seq, ATAC-seq, ChIP-seq sequencig were performed to compare the epigenome between young and old wild type and calorie restriction HSCs.

first: Le

last: Zong

first: Ferda

last: Tekin-Turhan

first: Wakako

last: Kuribayashi

first: Mayuri

last: Tanaka-yano

first: Keefer

last: Li

first: Isabel

last: Beerman


title: Inducible deletion of DGAT1 and 2 from microglia exacerbates neurodegeneration and endolysosomal lipid accumulation in male PS19 mice.

city: St Louis

first: George

middle: Travis

last: Tabor

state: MO

address: 660 S Euclid Ave

department: Neurology

institute: Washington University in St Louis

summary: Brain myeloid cells accumulate neutral lipids in multiple human neurodegenerative disorders and relevant mouse models. These lipid structures are often assumed to be lipid droplets (LDs), and ‘LD-high microglia’ have generally been characterized as maladaptive. While a number of studies have been performed in cell culture and Drosophila models to characterize glial LD dynamics, it is still unclear what roles microglial LD biogenesis play in mammalian tauopathy. To address this question, we induced the deletion of diacylglycerol acyltransferases 1 and 2 (DGATs), enzymes critical for LD formation, from microglia in the PS19 mouse model of tauopathy. We observed that microglial DGAT KO exacerbated neurodegeneration, induced behavioral deficits, and increased the accumulation of brain cholesterol esters in male PS19 mice. Myeloid cell lipids appeared to largely localize to endosomes/lysosomes not LDs, even in control PS19 mice. Our results suggest that microglial DGAT-dependent LD biogenesis is adaptive in advanced tauopathy. Furthermore, the bulk of the lipidic accumulations in brain myeloid cells do not correspond to true LDs, which has important implications for the development of lipid-modulating therapies for neurodegenerative diseases.

overall_design: snRNA-seq profiling of PU.1+ nuclei from 9.5-month-old WT (CfD) and PS19 (PCfD) mice heterozygous for Cx3cr1-CreERT2 and homozygous for floxed DGAT1 and DGAT2 alleles that were treated with tamoxifen or oil at 3 months of age.  CfD-OIL, CfD-TAM, PCfD-OIL, and PCfD-TAM

middle: T

middle: M

last: Holtzman

first: Elizabeth

last: West

first: Johannes

last: Schlachetzki

first: Christopher

last: Glass

first: Carisa

last: Zeng

first: Maxim

last: Artyomov


title: hiv-seq reveals global host gene expression differences between hiv-transcribing cells from viremic and suppressed people with hiv

city: San Francisco

first: Julie

last: Frouard

state: California

address: 1650 Owens street

department: Virology

institute: Gladstone Institutes

summary: In our study, we aimed to improve the identification of active reservoir cells producing HIV in individuals undergoing antiretroviral therapy (ART). We developed a technique called HIV-Seq to enhance the efficiency of capturing HIV transcripts during single-cell RNA sequencing (scRNAseq) analysis. By applying this technique and surface phenotyping using CITE-seq, we compared the transcriptional features of HIV RNA+ cells before and after ART initiation. Our findings highlight distinct transcriptional signatures of active reservoir cells during viremia and suppression, demonstrating the utility of HIV-Seq in elucidating the mechanisms underlying reservoir persistence during ART.

overall_design:
Paired and longitudinal, archived PBMC samples were obtained from different cohort. Samples were collected prior to ART initiation (Week 0) and following ART suppression (week 24 or week 45). PBMCs were thawed, CD4+ T cells were purified by negative selection using the EasySep Human CD4 T cell enrichment kit (StemCell) and then stained with TotalSeq-C antibodiesfollowed by 10X libraries (ADT and GEX) preparation.
-----------------------------------------
ADT     Barcode sequence
TotalSeq™-C0390 anti-human CD127 (IL-7Rα) Antibody     GTGTGTTGTCCTATG
TotalSeq™-C0081 anti-human CD14 Antibody     TCTCAGACCTCCGTA
TotalSeq™-C0050 anti-human CD19 Antibody     CTGGGCAATTACTCG
TotalSeq™-C0148 anti-human CD197 (CCR7) Antibody     AGTTCAGTCAACCGA
TotalSeq™-C0100 anti-human CD20 Antibody     TTCTGGGTCCCTAGA
TotalSeq™-C0088 anti-human CD279 (PD-1) Antibody     ACAGCGCCGTATTTA
TotalSeq™-C0034 anti-human CD3 Antibody     CTCATTGTAACTCCT
TotalSeq™-C0045 anti-human CD4 Antibody     GAGGTTAGTGATGGA
TotalSeq™-C0048 anti-human CD45 Antibody     TCCCTTGCGATTTAC
TotalSeq™-C0063 anti-human CD45RA Antibody     TCAATCCTTCCGCTT
TotalSeq™-C0087 anti-human CD45RO Antibody     CTCCGAATCATGTTG
TotalSeq™-C0046 anti-human CD8 Antibody     GCGCAACTTGATGAT
TotalSeq™-C0154 anti-human CD27 Antibody     GCACTCCTGCATGTA
TotalSeq™-C0576 anti-human CD49d Antibody     CCATTCAACTTCCGG
TotalSeq™-C0147 anti-human CD62L Antibody     GTCCCTGCAACTTGA

first: Sushama

last: Telwatte

first: Xiaoyu

last: Luo

first: Natalie

last: Elphick

first: Reuben

last: Thomas

first: Douglas

last: Arneson

first: Pavitra

last: Roychoudhury

first: Rebecca

last: Hoh

first: Steven

middle: G

last: Deeks

first: Sulggi

middle: A

last: Lee

first: Nadia

last: Roan

last: Yukl


title: Escape from X inactivation is directly modulated by Xist non-coding RNA [cell line RNA-seq]

first: Jasper

last: Panten

summary: X-chromosome inactivation silences one copy of the X-chromosome in female cells, but a number of genes escapes this inactivation. We asked whether increased levels of Xist RNA, the molecular actor driving X-inactivation, impacts expression levels of escapees. To this end, we performed transcriptomic profiling of X-linked gene expression in clonal neural progenitor cell lines with transgenes that allow for the overexpression of Xist on the inactive X chromosome. We perform Xist overexpression experiments for up to three weeks and also test the reversibility of Xist overexpression using washout experiments. Finally, we demonstrate the role of SPEN in Xist-mediated silencing of escape using an inducible degron.

sample_organism:
Mus
Mus musculus

platform_organism:
Mus
Mus musculus

overall_design: Clonal neural progenitor cell lines were generated by differentiating first generation hybrid embryonic stem cells (from a C57BL6/J x CAST/EiJ cross). All cell lines carry an inactive B6 X chromosome and a doxycycline-inducible transgene on the Xi. Doxycyclin treatment for 3, 7, 14 and 21 days was performed in the E6 cell line and allele-specific expression was measured using RNA-Sequencing. Furthermore, multiple timepoints after washing out doxycycline were analyzed to assess reversibility. To test the effect of SPEN in Xist-induced silencing, the CL30/CL31 cell lines were used in which SPEN is fused to an auxin-inducible degradation domain. Combined treatment with auxin and doxycycline was used to assess silencing in the absence of SPEN.

first: Edith

last: Heard

first: Agnese

last: Loda

first: Antonia

last: Hauth


title: Escape from X inactivation is directly modulated by Xist non-coding RNA [methylation]

type: Methylation profiling by high throughput sequencing

summary: X-chromosome inactivation silences one copy of the X-chromosome in female cells, but a number of genes escapes this inactivation. We asked whether increased levels of Xist RNA, the molecular actor driving X-inactivation, impacts expression levels of escapees. To this end, we performed DNA methylation profiling of X-linked genes in clonal neural progenitor cell lines with transgenes that allow for the overexpression of Xist on the inactive X chromosome. We perform Xist overexpression experiments for up to three weeks and also test the reversibility of Xist overexpression using washout experiments.

overall_design: Clonal neural progenitor cell lines were generated by differentiating first generation hybrid embryonic stem cells (from a C57BL6/J x CAST/EiJ cross). All cell lines carry an inactive B6 X chromosome and a doxycycline-inducible transgene on the Xi. Doxycyclin treatment for 7 and 21 days was performed in the E6 cell line and allele-specific DNA methylation was measured. Furthermore, washing out doxycycline was analyzed to assess reversibility.


title: Molecular and phenotypic blueprint of human hematopoiesis links proliferation stress to stem cell aging

first: Raffaella

last: Di Micco

summary: Hematopoietic stem/progenitor cell (HSPC) aging has been associated with myeloid skewing, reduced clonal output, and impaired regenerative capacity, but quantitative immunophenotypic and functional analysis across human aging is lacking. Here, we provide a comprehensive phenotypic, transcriptional, and functional dissection of human hematopoiesis across the lifespan. Although primitive hematopoietic stem cell (HSC) numbers were stable during aging, overall cellularity was reduced, especially for erythroid and lymphoid lineages. Notably, HSPC from aged individuals had similar repopulating frequency of younger counterparts in primary and secondary xenografts; yet aged HSC displayed impaired differentiation capacity, changes in chromatin accessibility, dysregulation of cell cycle, and a reduced capacity to counteract activation-induced proliferative stress with concomitant accumulation of DNA damage and senescence-like features upon xenotransplantation. This age-associated phenotypic and functional decline was recapitulated by enforcing proliferative stress in vivo on human HSPC. Overall, our work sheds light on dysregulated responses to activation-induced proliferation underlying HSPC aging and establishes xenotransplantation-based models as suitable for studying age-associated hematopoietic defects.

overall_design: RNA-seq analysis of primary HSPCs from bone marrow, cell culture over night

first: Emanuele

last: Lettera

first: Serena

last: Scala

first: Giacomo

last: Farina


title: Escape from X inactivation is directly modulated by Xist non-coding RNA [ATAC-seq]

summary: X-chromosome inactivation silences one copy of the X-chromosome in female cells, but a number of genes escapes this inactivation. We asked whether increased levels of Xist RNA, the molecular actor driving X-inactivation, impacts epigenetic marks around escapees. To this end, we performed chromatin accessibility profiling of X-linked genes in clonal neural progenitor cell lines to identify cis-regulatory elements active in these cell lines.

overall_design: Clonal neural progenitor cell lines were generated by differentiating first generation hybrid embryonic stem cells (from a C57BL6/J x CAST/EiJ cross). All cell lines carry an inactive B6 X chromosome. Chromatin accessibility was measured in two replicates using ATAC-Seq.


title: BACH2 regulates T cell lineage states to enhance CAR T cell function [ATAC-seq]

status: Public on Dec 08 2025

city: St. Louis

first: Nathan

last: Singh

institute: Washington University School of Medicine in St Louis

summary: Nearly all chimeric antigen receptors (CARs) signal in the absence of antigen, referred to as “tonic signaling”. Tonic signaling of CARs containing the CD28 costimulatory domain has been shown to driveT cell exhaustion; in contrast, we found that tonic signaling of 41BB-containing CARs enhances T cell function. Using a panel of CARs targeting CD22, we identified that tonic 41BB signaling activatesBACH2, a transcriptional regulator that directs stem and memory programs. Overexpression of BACH2 prevented tonic CD28-driven exhaustion but locked CAR T cells in quiescent states. To overcome this, we linked BACH2 to a degradation domain and found that tuning BACH2 expression enhanced long-term efficacy of exhaustion-prone CAR T cells targeting liquid and solid tumors. Through interrogation of CAR products, we also found an association between BACH2 activity and clinical outcomes in patients with leukemia. These data identify a central role for BACH2 in regulating CAR T cell efficacy.

overall_design: ATAC-seq of primary human CAR T cells. Four different CARs targeting CD22 were sequenced (CD28 or 4-1BB-costimulatory domain with CD3z stimulatory domain. scFvs contain a Long (L) or Short (S) linker). BBs(BACH2 KO) denotes 4-1BB costimulatory domain, short linker, and CRISPR knockout of BACH2. All samples in technical triplicate.

first: Tien-Ching

last: Chang

first: John

last: Warrington