title: Interleukin-2 is a potent latency reversal agent in people with treated HIV-1

city: Cleveland

first: Konstantin

last: Leskov

state: OHIO

address: 2109 Adelbert Rd, Wood W200

department: Molecular Biology and Microbiology

institute: Case Western Reserve University School of Medicine

summary: Eliciting human immunodeficiency virus type 1 (HIV-1) expression from latently-infected CD4+ T cells allows these rare reservoir cells to become targets of the immune system and may also result in death of reservoir cells via virus-induced cytopathy. We asked whether administration of recombinant interleukin-2 (rIL-2) to people with HIV-1 (PWH) on antiretroviral therapy (ART) would induce HIV-1 replication and activate cellular immunity. Nine men with ART-suppressed HIV-1 completed a single 4-day cycle of rIL-2 administration. Plasma HIV-1 RNA levels rose from <20 copies per milliliter at entry to a mean of 301 copies per milliliter at day 7 (an average increase of 0.82 log10; P=0.008). Additionally, we observed robust natural killer (NK) and T cell activation, with a modest increase in Treg-like cells. Thus, rIL-2 appears to be one of the most potent latency-reversing agents tested in PWH on ART.

overall_design: Single-cell RNAseq results (BD AbSeq) from peripheral blood mononuclear cells (PBMCs) acquired at baseline and day 7 from 4 male participants of a clinical trial of recombinant IL-2 administration (aldesleukin; subcutaneous injections of 5 million international units, twice daily, for four consecutive days) (Clinical Trials[dot]gov #NCT03308786).

first: Michael

middle: L

last: Freeman

first: Brian

last: Clagett

first: Daniela

last: Moisi

first: George

last: Yendewa

first: Scott

middle: F

last: Sieg

first: Gregory

last: Laird

first: Jonathan

last: Karn

first: Jeffrey

last: Jacobson

first: Benigno

last: Rodriguez

last: Lederman


title: Regenerating Skeletal Muscle of Ovariectomized Mice

status: Public on Dec 19 2025

city: Arlington

first: Barbra

last: St. Pierre Schneider

state: Texas

address: 701 S. Nedderman Drive

country: USA

institute: The University of Texas at Arlington

summary: In this study, we found more stable Siglec1 expression and stronger CD169+ macrophage staining in the muscle of 17-β-estradiol-treated mice than in that of the placebo-treated mice. However, Siglec1 was correlated with more interferon-related genes in the muscle of the placebo-treated mice. These findings suggest that Siglec1/IFN1 activity may be part of the inflammatory response during muscle regeneration. Future studies are warranted to investigate this role.

overall_design: We studied female mice implanted with placebo or 0.18 mg 17‑β‑estradiol pellets, gave a closed crush injury to the right hindlimb after 7 days of treatment, harvested right lateral gastrocnemius at ~32, 96, and 192 h post‑crush for Affymetrix Mouse Gene 1.0 ST microarray profiling, and compared gene expression between estradiol- and placebo-treated groups at each timepoint.

first: Barbara

first: Juli

last: Petereit


title: Transcriptomic analysis of low-level vagus nerve stimulation      effects on cardiac remodeling in pressure overload-induced      heart failure

city: Wuhan

first: Zhen

last: Guo

address: Donghu Road 169

country: China

institute: 武汉大学

type: Expression profiling by high throughput sequencing

summary: Heart failure (HF) affects approximately 56 million people worldwide with a 5-year mortality rate exceeding 50%. This study investigated the molecular mechanisms underlying the cardioprotective effects of low-level vagus nerve stimulation (LL-VNS) delivered via a biodegradable triboelectric nanogenerator (BTENG) in a murine aortic banding model. Male C57BL/6 mice underwent aortic banding surgery to induce pressure overload-induced heart failure. LL-VNS treatment (4 μA peak-to-peak, 2 Hz) was initiated at different timepoints (1, 2, or 4 weeks post-surgery) to evaluate stage-specific therapeutic effects. Two stimulation durations (10 or 20 minutes daily) were tested for the 1-week intervention group. RNA sequencing was performed on cardiac tissue collected at 8 weeks post-surgery to identify gene expression changes and pathway alterations. Results demonstrate that LL-VNS significantly modulates extracellular matrix remodeling, programmed cell death, and muscle structure development pathways across different intervention timepoints, providing molecular evidence for its therapeutic efficacy in preventing and reversing cardiac remodeling and heart failure progression.

overall_design: Seven experimental groups were analyzed with n=3 biological replicates per group: (1) Sham-operated controls, (2) Aortic banding (AB) without therapy, (3) AB with device implant only (no stimulation), (4) AB with 20-minute daily LL-VNS starting at 1 week post-AB (preventive intervention, 7 weeks treatment), (5) AB with 20-minute daily LL-VNS starting at 2 weeks post-AB (early intervention, 6 weeks treatment), (6) AB with 20-minute daily LL-VNS starting at 4 weeks post-AB (late intervention, 4 weeks treatment), and (7) AB with 10-minute daily LL-VNS starting at 1 week post-AB (preventive intervention, 7 weeks treatment). All groups reached the same endpoint at 8 weeks post-surgery for cardiac tissue collection. Paired-end RNA sequencing was performed on Illumina NovaSeq 6000 platform.

first: Sheng-Yu

last: Chao

first: Chun-Yan

last: Kong

first: Ling-Ling

last: Xu

first: Xi

last: Cui

first: Yuan

last: Xi

first: Yi-Chang

last: Quan

first: Ming-Yu

last: Wang

first: Yu-Lan

last: Ma

first: Xiu-Jun

last: Dai

first: Zhou

last: Li

first: Qi-Zhu

last: Tang


title: Gene expression profiling during osteogenic differentiation of mouse MSCs

city: Obu

first: Kiyoaki

last: Ishii

state: Aichi

address: Morioka-cho 7-430

country: Japan

institute: Natuional center for geriatrics and gerontology

summary: Total RNA was isolated from mouse primary MSCs and osteoblasts cultured for 3 or 21 days to examine gene expression changes during osteogenic differentiation.

overall_design: Three groups were analyzed: MSCs (day 0), osteoblasts (day 3), and osteoblasts (day 21).


title: Elucidating Cooperative Genetic Events in DCIS Progression in Mutant p53-Driven Breast Cancer [WGS]

city: Houston

first: Xiaoping

last: Su

address: 7300 Brompton St, Apt 5633

institute: MD Anderson Cancer Center

type: Genome variation profiling by high throughput sequencing

summary: Ductal carcinoma in situ (DCIS) is a mammary lesion characterized by abnormal epithelial cells occurring in mammary ducts while still being confined to the luminal space. Not all DCIS becomes invasive, and no strategy currently exists in patients to stratify indolent DCIS from DCIS at risk of progression. The standard of care includes surgical resection and radiation therapy, which constitutes overtreatment for most women whose DCIS would not progress forward. Several studies of human DCIS and breast cancer suggest that TP53 mutations occur early in DCIS, suggesting a critical role for mutant TP53 in driving disease progression. Using a somatic mouse model of Trp53R245W induced breast cancer (equivalent to the TP53R248W hotspot mutation in humans), we identified DCIS lesions. Through exome-sequencing and low-pass whole genome sequencing, we identified genomic changes shared between DCIS and invasive tumors. This comparison nominated seven murine candidate genes, with eight human orthologs. We assessed the cooperativity of these genes with mutant TP53 in MCF-10A cells using acinar morphogenesis and migration assays. Overexpression of TMEM267 in cells with mutant TP53 caused a significant increase in the filled duct, DCIS-like phenotype. We nominate TMEM267 as a cooperating event with mutant TP53 in DCIS progression.

overall_design: Paired end Low-Pass Whole Genome Sequencing of MaPR245W/+ murine mammary tumors and DCIS lesions

first: Rhiannon

last: Morrissey

first: Guillermina

last: Lozano


title: Maternal Immune Activation Induces Long-Term, Cell-Specific Transcriptomic Changes in the Amygdala of Rhesus Macaque Offspring

city: Sacramento

first: Bradley

last: Ander

state: CA

address: 2805 50th Street - Room 2434

department: Neurology

institute: University of California, Davis

summary: Prenatal exposure to a heightened maternal immune response, such as that triggered by viral infection in the mother, can alter fetal brain development and increase risk of neurodevelopmental disorders in offspring, including autism (ASD) and schizophrenia. However, the cellular and molecular mechanisms linking early inflammatory signals to long-term changes in brain function remain unclear. While rodent models of maternal immune activation (MIA) display brain and behavioral disruptions, their translational relevance to humans is limited. To address this gap, we utilized a nonhuman primate (NHP) MIA model to examine how transient maternal immune responses in early gestation alter gene expression in the amygdala—a brain region essential for socioemotional behavior and implicated many neurodevelopmental disorders. Pregnant macaques were administered the viral mimic Poly(I:C) during the late first trimester, and amygdala samples were collected from 4-year-old male offspring for single-nucleus RNA sequencing (>71,000 nuclei). We identified 2,768 unique differentially expressed genes (DEGs), concentrated in excitatory and inhibitory neurons of the lateral nucleus and microglia of the central nucleus. These DEGs converge on synaptic structure, neurotransmission, and neuroimmune signaling—core processes in circuit assembly and behavioral regulation. MIA-associated DEGs significantly overlap with high-confidence ASD- and psychosis-risk gene sets, directly linking prenatal immune events to human disease pathways. This study provides the first region- and cell-type-specific evidence in a primate model that transient prenatal maternal immune responses lead to lasting transcriptomic dysregulation. These findings reveal how early immune insults may alter neurodevelopment and offer a translational framework for identifying molecular targets for early intervention.

overall_design: Expression profiling by high throughput sequencing

middle: P

first: Erin

last: Carlson

first: Shawn

last: Kamboj

first: Kari

last: Hanson

first: Karl

middle: D

last: Murray

first: Andrew

middle: S

last: Fox

first: Melissa

last: Bauman

first: Cynthia

middle: M

last: Schumann


title: Harnessing lipid-driven immuno-metabolic pathways in omental metastases to enhance immunotherapy in ovarian cancer

city: Gosselies

first: Meggy

last: Suarez-Carmona

address: Rue des Professeurs Jeener et Brachet, 12

country: Belgium

institute: ULB

summary: Despite the potential of immune checkpoint blockade (ICB) in epithelial ovarian carcinoma (EOC), its clinical efficacy remains limited. Our study investigates the immuno-metabolic landscape of omental metastases to identify therapeutic targets. Using patient-derived explants (PDEs), we demonstrate that lipid-rich omental environments preserve effector T cell function, while lipid processing in tumor-associated macrophages (TAMs) induces oxidative stress and immune suppression. Targeting lipid metabolism via CCR5 inhibition (e.g., maraviroc) or anti-CD36 treatment reprograms TAMs, restores T cell activity, and enhances anti-tumor immunity. These findings reveal a metabolic-inflammatory axis that can be modulated to improve ICB outcomes in EOC.

overall_design: Following MDA-MB-231 tumor growth in MISTRG humanized mice, we perfored scRNA-sequencing analysis on human tumor-infiltrating immune cells to analyse the effects of Maraviroc on the antitumor immune response. In total, cells from 7 treated mice and 7 untreated mice were sequenced after hashing.

first: Mareike

last: Hampel

first: Xin-Wen

last: Zhang

first: Alexandra

last: Pöchmann

first: Silke

middle: A

last: Grauling-Halama

first: Nektarios

last: Valous

first: Pornpimol

last: Charoentong

first: Dyke

last: Ferber

first: Jannis

last: Wissfeld

first: Alicia

last: Höflich

first: Stanislas

last: Goriely

first: Aurélie

last: Detavernier

first: Abdulkader

last: Azouz

first: Anthony

last: Rongvaux

first: Sven

last: Zukunft

first: Ingrid

last: Fleming

first: Jürgen

middle: G

last: Okun

first: Vickie

last: Baracos

first: Mathias

last: Heikenwälder

first: Laurence

last: Zitvogel

first: Xinyi

last: Xu

first: Chenqi

first: Michael

last: Volkmar

first: Daniel

last: Schraivogel

first: Lars

last: Steinmetz

first: Junzo

last: Hamanishi

first: Masaki

last: Mandai

last: Gaida

first: Theresa

last: Mokry

first: Johanna

last: Nattenmüller

first: Oliver

last: Sedlaczek

first: Nanna

last: Monjé

first: Roxanna

last: Schwab

first: Annette

last: Hasenburg

first: Regina

last: Johanna Boger

first: Frederik

last: Marmé

first: Athanasios

last: Mavratzas

first: Sarah

last: Schott

first: Niels

last: Halama


title: FGFR signaling and neddylation facilitate SARS-CoV-2 infection by modulating interferon induction and viral entry respectively

city: Edmonton

first: Alberto

last: Felix-Lopez

state: Alberta

department: Medical Microbiology and Immunology

country: Canada

institute: University of Alberta

summary: SARS-CoV-2 is the causative agent of COVID-19, and although vaccines have reduced disease severity, emerging variants remain a significant public health issue. Broadly effective therapeutics are still needed, particularly those targeting host pathways essential for coronavirus infection. Here, we used a CRISPR knockout screen to identify druggable host factors required for SARS-CoV-2 infection. The screen revealed NAE1 and FGFR1 as key contributors to infection. FDA-approved or in clinical trials inhibitors of these pathways reduced replication of both ancestral and contemporary viral variants. Mechanistic studies showed that FGFR1 promotes viral replication through downstream MEK/ERK signaling, while neddylation appears to support viral entry or infectivity rather than replication itself. In a murine model of severe COVID-19, inhibitors of NAE1 and FGFR1 significantly decreased viral load and lung pathology. These findings support the development of host-targeted antiviral strategies.

overall_design: CRISPR KO screen to identify host factors required for SARS-CoV-2 infection

first: Joaquin

last: Lopez-Orozco

first: Mohamed

last: Elaish

first: Nawell

last: Fayad

first: Zaikun

last: Xu

first: Tekeleselassie

last: Woldemariam

first: Bardes B.

last: Hassan

first: Rashmi

last: Panigrahi

first: Juveriya

last: Qamar Khan

first: Megha

last: Rohamare

first: Irv

last: Mayers

first: Mark

last: Glover

first: Joyce

last: Wilson

first: Darryl

last: Falzarano

first: Anil

last: Kumar

first: Tom C

last: Hobman


title: Uptake of exogenous phospholipids by Borrelia burgdorferi

city: Boston

first: Peter

last: Gwynne

state: MA

address: 136 Harrison Ave

department: Molecular and Microbiology

institute: Tufts University

summary: The Lyme disease pathogen Borrelia burgdorferi can take up environmental phospholipids for membrane biosynthesis. These phospholipids include those also produced de novo by the bacterium (PC and PG) and some that are mammalian-like. We examined the effect of exogenous phospholipids on gene expression.

overall_design: RNAseq analysis of B. burgdorferi cells grown in standard medium or medium supplemented with extra phospholipids.

first: Jeff

last: Bourgeois

first: Linden

last: Hu


title: Single-cell RNA sequencing of human salivary glands and organoids

city: Beijing

first: XINYUAN

last: ZHANG

address: No.22 ,Zhongguancun South  Avenue, Haidian District

institute: Peking University School and Hospital of Stomatology

summary: We performed single-cell RNA sequencing (scRNA-seq) on human salivary gland tissues and derived organoids to investigate their cellular composition, differentiation states, and regenerative potential. Four samples were dissociated into single-cell suspensions and processed using the 10X Genomics Chromium platform.

overall_design: Human salivary gland tissues and organoids at defined culture timepoints were enzymatically dissociated, viability-checked by AO/PI staining, and subjected to scRNA-seq using the 10X Genomics Chromium 3' v3 system.

first: Xinyuan

last: Zhang

first: Zhigang

last: Cai


title: Multi-omics analysis identifies intrinsic Trp53 driven metastatic breast cancer subtypes [WES]

first: Xiaoping

last: Su

summary: Metastatic breast cancer is the leading cause of death amongst patients that develop breast cancer. The molecular drivers of metastatic breast cancer are largely unknown. Treatment of metastatic breast cancer is limited to systemic cytotoxic chemotherapies, which often deteriorate patient quality of life, and tumors often become refractory, resulting in incurable disease. The most frequently mutated gene associated with metastatic breast cancer is TP53. The TP53R248W hotspot missense mutation is associated with poor prognosis in breast cancer. To understand the intrinsic transcriptomic and genomic landscape of metastatic breast cancer driven by mutant p53, we generated a somatic mouse model driven by mammary epithelial specific expression of Trp53R248W. Primary tumors were highly metastatic and reflected the human molecular subtypes of luminal A, luminal B, HER2, and TNBC, with TNBC comprising the majority (79%) of these tumors. Transcriptomic profiling revealed primary tumor heterogeneity characterized by three intrinsic subtypes (1) stem-cell like; (2) well-differentiated metabolic like; and (3) immune suppressed. Stem-cell like tumors activate ribosome biosynthesis and E2F signaling. These tumors harbor amplifications in Met, Birc3, Yap1 and deletions in Nf1, Pik3r1, and Rad17. Well-differentiated metabolic like mammary tumors activate cytochrome P450 enzymes, estrogen signaling and branched chain amino acid degradation and harbor mutations in the Pten pathway. Immune suppressed tumors enrich for processes related to immune suppression. These tumors have high mutation burden, frequently mutate Traf7 and delete Cdkn2a. This is the most comprehensive transcriptomic and genomic profiling of mutant p53 driven breast tumors and sheds light on their heterogenous nature and distinct intrinsic programs that may inform targeted therapy for metastatic breast cancer.

overall_design: Paired end Whole Exome Sequencing of MaPR245W/+ murine mammary tumors collected at end point

first: Joy

last: McDaniel

first: Guillermina

last: Lozano


title: Multi-omics analysis identifies intrinsic Trp53 driven metastatic breast cancer subtypes [RNA-seq]

overall_design: Paired end RNA Seq of MaPR245W/+ murine mammary tumors collected at end point


title: SATB1 Condensates Reinforce Super-Enhancer Architecture to Lower the Threshold of Thymocyte Positive Selection

city: Guangzhou

first: Hao

last: bingtao

address: ShataiNan Road, Baiyun District, Guangzhou, Guangdong Province

institute: Southern Medical University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The generation of mature CD4⁺ helper and CD8⁺ cytotoxic T cells from double-positive (DP) thymocytes is a central step in building an effective adaptive immune system. This process relies on positive selection, whereby αβTCR⁺ thymocytes are tested for recognition of self-peptide–MHC complexes presented by cortical thymic epithelial cells. Thymocytes with insufficient signaling die by neglect, while those receiving appropriately tuned signals survive and differentiate. Positive selection thus plays a dual role: establishing MHC restriction and directing lineage commitment into the CD4 or CD8 fate. After TCR rearrangement is completed, T cells can interact with APCs to transmit TCR signals and produce CD69 protein. SO, CD69+DP cells is undergoing positive selection. Here, we explored the mechanism of SATB1 regulating thymocyte positive selection. Firstly, We analysis the function of SATB1 in the transtion of CD69-DP to CD69+DP by CUT&Tag, ATAC and HiC assays. Then, Single-cell RNA sequencing assay of SATB1-deficient thymocytes showed that the cell identity of CD69+DP thymocytes was changed, and the genes differently expressed in CD69+DP cells. Smart-seq2 showed the similar tendency. CUT&Tag , ATAC-seq and HiC data show the mechanism for SATB1 in T cell positive selection or before this stage. ACC-seq confirms that SATB1 forms phase separation at these sites and regulates gene expression, These data helps us to understand the role of SATB1 in thymocyte positive selection.

overall_design: scRNA-seq analysis of Satb1+/+ and Satb1-/- CD69+DP thymocytes(2 replicates); Bulk Smart-seq2 analysis of Satb1+/+ and Satb1-/- for CD69-DP and CD69+DP thymocytes(4 replicates); SATB1, CTCF, RAD21, H3K4me3 and H3K27ac CUT&Tag analysis of Satb1+/+ and Satb1-/- for CD69-DP and CD69+DP thymocytes(3 replicates); ATAC-seq analysis of Satb1+/+ and Satb1-/- for CD69-DP and CD69+DP thymocytes(4 replicates);Hi-C analysis of Satb1+/+ and Satb1-/- CD69-DP and CD69+DP for thymocytes(4 replicates); ACC-seq analysis of Satb1+/+ and Satb1-/- for thymocytes(2 replicates).

first: Wei

last: Xue

first: Bingtao

last: Hao


title: Transcriptomics DNAJC15 and DNAJC19 knockdown in HeLa cells

city: Cologne

first: Lara

last: Kroczek

address: Joseph-Stelzmann-Straße 9B

country: Germany

institute: Max-Planck Institute for Biology of Ageing

summary: To better understand how OMA1 affects mitochondrial proteostasis and stress responses, we performed a proteomic survey of OMA1-deficient cells for proteolytic substrates. We demonstrate that OMA1 cleaves the mitochondrial chaperone DNAJC15 facilitating its degradation by the mitochondrial m-AAA protease. The loss of DNAJC15 alters protein import by TIM23 protein translocases in the IM and limits the accumulation of OXPHOS-related mitochondrial matrix and IM proteins. Non-imported mitochondrial preproteins accumulate at the endoplasmic reticulum (ER) and trigger an ATF6-related unfolded protein response. These results demonstrate that OMA1 allows to adapt mitochondrial protein biogenesis to stress and reveal an intricate network of cellular stress responses to proteostasis disturbances.

overall_design: RNA-seq profile of scrambled control HeLa cell versus DNAJC15 and DNAJC19 knock down.

first: Kroczek

last: Lara

first: Langer

last: Thomas


title: S1P/S1PR4 Promotes the Differentiation of CD8+TRM Cells Aggravating Bile Duct Injury in Biliary Atresia

first: Dingding

last: Wang

state: None Selected

address: 56 Nanlishi Road

institute: Beijing Children Hospital, Capital Medical University

summary: BACKGROUND AND AIMS: Biliary atresia (BA) is the most common and serious neonatal biliary disease, characterized by progressive biliary inflammation and fibrosis. We aim to comprehensively and systematically investigate the complex pathological process of BA from multiple molecular dimensions, combining transcriptomics, proteomics, metabolomics, and single-cell RNA sequencing. METHODS: Integration of multi-omics data detected and localized aberrant metabolite regulation in immune cells of BA liver tissue. By flow cytometry sorting of specific immune cell subsets and in vitro experiments, we verified the role and mechanism of the aberrant metabolite signaling pathway in the progression of BA. In vivo experiments confirmed the effect of inhibiting the aberrant signaling pathway in alleviating bile duct injury and fibrosis. RESULTS: Based on multi-omics data, the sphingolipid metabolism pathway was abnormally activated in the S1 subtype of BA, a molecular subtype characterized by abnormal immune inflammation and poor prognosis. By integrating single-cell RNA profiling, Sphingosine-1-Phosphate Receptor 4 (S1PR4), a receptor of Sphingosine-1-Phosphate (S1P), was primarily expressed in CX3CR1+CD8+effector T (Teff) cells. In vitro, S1P/S1PR4 signaling promoted the migration of CX3CR1+CD8+Teff cells, and facilitated the differentiation of CX3CR1+CD8+Teff cells into CD8+ tissue-resident memory T (TRM) cells. Co-culture of CD8+TRM cells and cholangiocytes could induce the apoptosis of cholangiocytes. In vivo, S1PR4 inhibitor could alleviate liver inflammation and fibrosis by inhibiting the accumulation of CD8+TRM cells. CONCLUSIONS: Our study revealed that activation of the S1P/S1PR4 signaling pathway promotes the differentiation of CD8+ TRM cells, which subsequently induces cholangiocyte injury. Targeting the activation of the S1P/S1PR4 signaling pathway is a promising therapeutic strategy for BA, especially for patients with the S1 subtype.

overall_design: We collected 25 biliary atresia (BA) liver tissues and 20 control (Ctrl) liver tissues from adjacent hepatoblastoma, employing high-throughput detection techniques to obtain RNA-SEQ data.

first: Dayan

last: Sun

first: Lulu

last: Jia

first: Jiucun

first: Li

first: Shen

last: Yang

first: Jinshi

last: Huang


title: RNA Decay via the Nuclear Exosome is Essential for Piwi-Mediated Transposon Silencing [PRO-seq]

city: Vienna

first: Julius

middle: Fabian

last: Brennecke

address: Dr. Bohr Gasse 3

country: Austria

institute: IMBA-Institute for Molecular Biotechnology

summary: Small RNA pathways in the nucleus safeguard genome integrity by directing transcriptional silencing and heterochromatin formation at transposon loci. Yet, how these pathways achieve effective repression despite requiring transcription for Argonaute targeting has remained unclear. Here, we show that in Drosophila, the Piwi–piRNA pathway enforces transposon silencing through RNA degradation by the nuclear RNA exosome. Using comprehensive proximity proteomics at piRNA target sites combined with genetic analyses, we identify two previously uncharacterized paralogs, TEsup-1 and TEsup-2, which connect Piwi to nuclear exosome adaptor complexes via a distinct binding module for proline-rich peptides. Disruption of this Piwi–TEsup–exosome axis leads to accumulation and nuclear export of transposon RNAs. Strikingly, transposons that evade heterochromatin-based repression, exemplified by the P-element, are repressed primarily through this RNA-decay pathway. These findings reveal a molecular mechanism by which the nuclear piRNA-pathway couples target recognition to RNA degradation, providing a framework that reconciles small RNA-guided heterochromatin formation with ongoing transcription at target loci.

overall_design: Precision Run-On Sequencing (PROseq) analyis of nascent transrption changes in cultured ovarian somatic cells (OSCs) after siRNA mediated depletion of CG31510, CG7065, dZfc3h1, dZcchc7 or dZcchc8, compring to control knockdown.

first: Changwei

last: Yu

first: Toni

last: Manolova

first: Laszlo

last: Tirian

first: Dominik

last: Handler

first: Ulrich

last: Hohmann

first: Filip

last: Nemčko

first: Júlia

last: Portell-Montserrat

first: Guillaume

last: Giraud Collet

first: Jakob

last: Schnabl

first: Ellie

last: Blake

first: Peter

last: Duchek

first: Maria

last: Novatchkova

first: Elisabeth

last: Roitinger

first: Felipe

last: Karam Teixeira

first: Sebastian

last: Falk


title: Prenatal and postnatal effects of gestational immune activation on synaptic and neurodevelopmental pathways via epigenetic mechanisms (ChIP-seq)

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

summary: Previous epidemiological research suggests that maternal immune activation (MIA) during early pregnancy is a significant risk factor for neurodevelopmental and psychiatric disorders in offspring. Epigenetic factors and chromatin-related phenomena remain largely plastic during the course of prenatal and early postnatal development, allowing a dynamic impact of environmental effects on access to genes and regulatory elements. In this study, we tested the effects of maternal infection with the mouse-adapted influenza A/WSN/33 (H1N1) virus as a MIA model. Additionally, to assess the prenatal and postnatal effects of MIA, we cross-fostered half of the neonatal mice immediately after birth.This study includes RNA-seq and ChIP-seq profiling (H3K27ac, H3K4me3) from the prefrontal cortex of MIA-exposed and control mice. RNA-seq and ChIP-seq data are submitted under separate Series and linked via sample annotations.

overall_design: This study examined transcriptomic and epigenomic changes in offspring following maternal immune activation (MIA) via prenatal influenza infection. Timed pregnant CD1 mice were intranasally infected with 5 × 10³ pfu of influenza A/WSN/33 (H1N1) or mock-treated on embryonic day 9.5. At birth, ~50% of pups were cross-fostered to surrogate dams (MIA or control) to separate prenatal and postnatal influences. Offspring were weaned at P21, housed by sex, and assigned to one of seven groups based on birth and rearing conditions: Group A (Mock-Mock): Offspring born to control mother and raised by their birth mother, together with stepsiblings born to MIA-exposed mother. Group B (MIA-Mock): Offspring born to MIA-exposed mother but raised by control surrogate mother, together with stepsiblings born to this control mother. Group C (Mock-MIA): Offspring born to control mother but raised by MIA-exposed surrogate mother, together with stepsiblings born to this MIA mother. Group D (MIA-MIA): Offspring born to MIA-exposed mother and raised by their birth mother, together with stepsiblings born to control mother. Group E (Mock-Mock_1): Offspring born to control mother and raised by their birth mother, together with stepsiblings born to a different control mother. Group F (Mock-Mock_2): Offspring born to control mother but raised by control surrogate mother, together with stepsiblings born to the control surrogate mother. Group G (Mock-Mock_3): Offspring born to control mother and raised by their birth mother with no stepsiblings. Mice were sacrificed in adulthood. Frontal cortex (bregma 1.90–1.40) was collected for MOWChIP-seq profiling of H3K4me3 and H3K27ac. Neuronal nuclei were isolated via FACS (NeuN⁺), with ~10,000 nuclei used per ChIP replicate. Libraries were prepared using Accel-NGS 2S Plus and sequenced on an Illumina HiSeq 4000 (single-end, 50 bp), yielding ~15 million reads per sample.

first: Bohan

last: Zhu

first: Gaoshan

last: Li


title: Prenatal and postnatal effects of gestational immune activation on synaptic and neurodevelopmental pathways via epigenetic mechanisms (RNA-seq)

overall_design: This study examined transcriptomic and epigenomic changes in offspring following maternal immune activation (MIA) via prenatal influenza infection. Timed pregnant CD1 mice were intranasally infected with 5 × 10³ pfu of influenza A/WSN/33 (H1N1) or mock-treated on embryonic day 9.5. At birth, ~50% of pups were cross-fostered to surrogate dams (MIA or control) to separate prenatal and postnatal influences. Offspring were weaned at P21, housed by sex, and assigned to one of seven groups based on birth and rearing conditions: Group A (Mock-Mock): Offspring born to control mother and raised by their birth mother, together with stepsiblings born to MIA-exposed mother. Group B (MIA-Mock): Offspring born to MIA-exposed mother but raised by control surrogate mother, together with stepsiblings born to this control mother. Group C (Mock-MIA): Offspring born to control mother but raised by MIA-exposed surrogate mother, together with stepsiblings born to this MIA mother. Group D (MIA-MIA): Offspring born to MIA-exposed mother and raised by their birth mother, together with stepsiblings born to control mother. Group E (Mock-Mock_1): Offspring born to control mother and raised by their birth mother, together with stepsiblings born to a different control mother. Group F (Mock-Mock_2): Offspring born to control mother but raised by control surrogate mother, together with stepsiblings born to the control surrogate mother. Group G (Mock-Mock_3): Offspring born to control mother and raised by their birth mother with no stepsiblings. Mice were sacrificed in adulthood. Frontal cortex (bregma 1.90–1.40) was collected for RNA-seq. Neuronal nuclei were isolated and sorted via FACS (NeuN⁺);  ~6,000 nuclei per RNA-seq replicate. Libraries were prepared using SMART-seq v4 and Nextera XT (RNA-seq), and sequenced on an Illumina HiSeq 4000 (single-end, 50 bp), yielding ~11M per RNA-seq library.


title: Human bladder cell spatial mapping

first: Angela

middle: H

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

summary: We used Xenium In Situ assay with a custom probe panel to visualize a human bladder cross-section. The custom probe panel contains probe sets against bladder cell type marker genes and RNA isoforms to enable cell identification. We detected 33 distinct cell groups consisted of urothelial cell states, immune cells, and various stromal cell types.

overall_design: A 10 µm, FFPE bladder sample from a 42 year old female deceased organ donor was sectioned onto a Xenium slide. Hybridization follows manufacturer's protocol. Data processing includes QC based on number of genes and transcripts per cell and downstream analysis was performed using the standard Seurat workflow for image-based spatial data. Cell type identification was finalized using both marker gene and polyadenylation isoform data.

first: Alexandra

last: Krylova


title: Hydrogel with cell-cell adhesion cues enhances neural regeneration

city: Nantong

first: Xiaoxuan

last: Tang

address: 19 Qixiu road

institute: Nantong university

summary: Cell-cell adhesion is crucial for maintaining cell functions and the integrity of tissue structure in organisms. However, cell-cell adhesion cue has not been effectively replicated in biomaterials and cell-cell adhesion associated mechanisms that enhance neural regeneration remained largely unexplored. Here, we present a diffusive N-cadherin functionalized hydrogel system, which provided cell-cell adhesion cue to modulate intercellular communications to significantly promote the formation of active neural network. The dynamic assembly of N-cadherin at cell membrane-hydrogel interface driven by adhered cells occurred at a timescale of minutes, facilitating the reshaping of membrane protrusions to initiate intercellular adherens junctions and modulate long-term cell-cell communications. Focusing on the mechanisms, it is associated with Thrombospondin-1 (THBS-1) mediated neural communication and activation of TGF-β/Smad pathway. Further, this hydrogel system promisingly promoted neurological function recovery in rats following traumatic brain injury. Our study provided the principles of replicating diffusive cell adhesion molecules to mediate cell-cell adhesion in hydrogels, which may have broad applications in the development of engineered biomaterials aimed at modulating cell fates in regeneration of various tissues.

overall_design: To reveal the molecular mechanism of cell-cell adhesion cue in hydrogel promoting neural growth, primary cells from cerebral cortex were cultured on hydrogels for 24 hours, respectively. The differentally expressed genes were screened by RNA sequencing. The transcriptome sequencing studies were performed by deep sequencing, using Illumina NovaSeq 6000.

first: Yumin

last: Yang

first: Jue

last: Ling

first: Yifan

last: Ge

first: Shuxuan

last: Zhang

first: Mengke

last: Liu

first: Yuxin

last: Liang

first: Yulan

last: Fan

first: Xinyue

last: Sun

last: He

first: Xuewa

first: Rong

first: Xiaoling

last: Jin

first: Qianxing

last: Zhuang


title: A microreactor system for point-of-care viral genome sequencing

first: Chang

last: Lu

summary: Viral genome sequencing is critical for understanding viral biology, identifying strain mutations, and managing public health during pandemics. Although sequencing technologies have progressed over the years in terms of throughput and cost, a portable platform that integrates sample processing, library preparation, and sequencing remains critical for point-of-care viral sequencing that combats viral outbreaks in the field. In here, we demonstrate a semi-automated, field-deployable microreactor system to produce nanopore sequencing libraries from viral samples. The system integrates isothermal amplification, purification, and enzymatic processing within a closed-channel format, minimizing contamination risk and operational complexity. Using Senecavirus A (SVA) as a surrogate for high-consequence pathogens, we demonstrate the system’s ability to prepare sequencing libraries targeting three dispersed genomic regions comprising ~16% of the viral genome and identify single nucleotide variations with high confidence. Together with a portable nanopore sequencer, this microreactor offers a robust solution for decentralized genomic surveillance and rapid diagnostics in resource-limited or outbreak-prone environments.

overall_design: RT-LAMP sequencing of vesicular lession fluid extracted from SVA-positive pigs using an Oxford Nanopore Minion device with Flongle attachment. SVA positive pigs (as determined by RT-PCR) had total RNA extracted from collected vesicular lession samples. RNA  samples underwent reverse transcription loop mediated isothermal amplification (RT-LAMP), performed on a custom designed microfluidic device. This device was then used to purify the generated RT-LAMP amplicons, before performing library preparation for nanopore sequencing. Sequenced samples were analysed to evaluate diagnostic and variant monitoring capabilities of the designed platform.

first: Thomas

last: Hadlock

first: Jacob

last: Neice


title: Single-cell mapping of regulatory DNA:Protein interactions III

city: New York

first: Dan

last: Landau

state: NY

address: 413 East 69th Street

institute: Weill Cornell Medicine

summary: Gene expression is coordinated by a multitude of transcription factors (TFs), whose binding to the genome is directed through multiple interconnected epigenetic signals, including chromatin accessibility and histone modifications. These complex networks have been shown to be disrupted during aging, disease, and cancer. However, profiling these networks across diverse cell types and states has been limited due to the technical constraints of existing methods for mapping DNA:Protein interactions in single cells. As a result, a critical gap remains in understanding where TFs or other chromatin remodelers bind to DNA and how these interactions are perturbed in pathological contexts. To address this challenge, we developed a transformative single-cell immuno- tethering DNA:Protein mapping technology. By coupling a species-specific antibody-binding nanobody to a cytosine base editing enzyme, this approach enables profiling of even weak or transient factor binding to DNA, a task that was previously unachievable in single cells. Thus, our Docking & Deamination followed by sequencing (D&D-seq) technique induces cytosine-to-uracil edits in genomic regions bound by the target protein, offering a novel means to capture DNA:Protein interactions with unprecedented resolution. Importantly, this technique can be seamlessly incorporated into common single-cell multiomics workflows, enabling multimodal analysis of gene regulation in single cells. We tested the ability of D&D-seq to record TF binding both in bulk and at the single-cell level by profiling CTCF and GATA family members, obtaining high specificity and efficiency, with clear identification of TF footprint and signal retention in the targeted cell subpopulations. Furthermore, the deamination reaction showed minimal off-target activity, with high concordance to bulk ChIP-seq reference data. Applied to primary human peripheral blood mononuclear cells (PBMCs), D&D-seq successfully identified CTCF binding sites and enabled integration with advanced machine-learning algorithms for predicting 3D chromatin structure. Furthermore, we integrated D&D-seq with single-cell genotyping to assess the impact of IDH2 mutations on CTCF binding in a human clonal hematopoiesis sample, uncovering altered binding and chromatin co- accessibility patterns in mutant cells. Altogether, D&D-seq represents an important technological advance enabling the direct mapping of TF or chromatin remodeler binding to the DNA in primary human samples, opening new avenues for understanding chromatin and transcriptional regulation in health and disease.

overall_design: Deamination of cytosine to uracil around DNA binding sites of a target protein using nanobody-tethered deaminase DddA9

first: Wei-Yu

last: Chi

first: Sang-Ho

last: Yoon

first: Evrim

last: Goksel

first: Levan

last: Mekerishvili

first: Joe

last: Pelt

first: Yiyun

last: Lin

first: Saravanan

last: Ganesan

first: Catherine

last: Potenski

first: Franco

last: Izzo

first: Dan A.

first: Ivan

last: Raimondi


title: Single-cell mapping of regulatory DNA:Protein interactions II


title: The yeast F-box protein Mfb1 and the human DJ-1 homolog Hsp31 are required for cell survival under mitochondrial protein import clogging conditions

city: Syracuse

first: Dr. Xin Jie

last: Chen

address: 750 East Adams St

department: Biochemistry and Molecular Biology

institute: State University of New York Upstate Medical University

summary: Mitochondrial biogenesis requires the import of many nuclear-encoded proteins across the Translocase of Outer Membrane (TOM), and the Translocase of Inner Membrane (TIM) 22 or 23 complexes. Protein import defects cannot only impair mitochondrial function but also cause mitochondrial Precursor Overaccumulation Stress (mPOS) in the cytosol. Recent studies showed that specific mutations in the nuclear-encoded Adenine Nucleotide Translocase 1 (ANT1) cause musculoskeletal and neurological diseases by clogging TOM and TIM22 and inducing mPOS. Here, we found that overexpression of MFB1, encoding the mitochondrial F-box protein 1, suppresses cell growth defect caused by a clogger allele of AAC2, the yeast homolog of Ant1. Disruption of MFB1 synergizes with a clogger allele of aac2 to inhibit cell growth. This is accompanied by increased retention of mitochondrial proteins in the cytosol, suggesting a severe defect in mitochondrial protein import. Proximity-dependent biotin identification (BioID) suggested that Mfb1 may interact with Tom22, a component of the TOM complex. Loss of MFB1 under clogging conditions activates genes encoding cytosolic chaperones including Hsp31. Interestingly, disruption of HSP31 creates a synthetic lethality with protein import clogging under respiring conditions. We propose that Mfb1 functions to maintain mitochondrial protein import competency under clogging conditions, whereas Hsp31 plays an important role in protecting the cytosol against mPOS. Mutations in human mitochondria-associated F-box proteins (e.g., Fbxo7) and the human Hsp31 homolog, DJ-1, are known to cause early-onset Parkinson’s disease. Our work may improve the understanding of how these mutations cause neurodegeneration.

overall_design: Yeast cells grown at 25 deg Celsius under strictly respiring conditions (Glycerol +Ethanol) to an OD600 value between ~1-2

first: Gargi

last: Mishra

first: Xiaowen

last: Wang

first: Eamon

last: Fitzpatrick

first: Auyon

last: Ghosh

first: Xin Jie


title: Cyclic di-GMP Suppresses Cancer Metastasis by Targeting PSMD3 independently of STING

city: New Orleans

first: HUA

last: LU

state: LA

address: 1430 Tulane Ave

institute: TULANE UNIVERSITY

summary: To elucidate the molecular mechanism(s) underlying c-di-GMP-mediated metastasis inhibition, we performed RNA sequencing (RNA-seq) analysis in MDA-MB-231 cells treated with 5 uM of c-di-GMP for 24 hours.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MDA-MB-231 breast cancer cells from c-di-GMP treated and non-treated groups.

first: Jieqiong

first: Kewen

last: Hu

first: Shelya

middle: X

last: Zeng

first: Hua

last: Lu


title: Single-cell mapping of regulatory DNA:Protein interactions

first: Dan

last: Landau

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

overall_design: Refer to individual Series


title: Elucidating Cooperative Genetic Events in DCIS Progression in Mutant p53-Driven Breast Cancer [WES]

first: Xiaoping

last: Su

summary: Ductal carcinoma in situ (DCIS) is a mammary lesion characterized by abnormal epithelial cells occurring in mammary ducts while still being confined to the luminal space. Not all DCIS becomes invasive, and no strategy currently exists in patients to stratify indolent DCIS from DCIS at risk of progression. The standard of care includes surgical resection and radiation therapy, which constitutes overtreatment for most women whose DCIS would not progress forward. Several studies of human DCIS and breast cancer suggest that TP53 mutations occur early in DCIS, suggesting a critical role for mutant TP53 in driving disease progression. Using a somatic mouse model of Trp53R245W induced breast cancer (equivalent to the TP53R248W hotspot mutation in humans), we identified DCIS lesions. Through exome-sequencing and low-pass whole genome sequencing, we identified genomic changes shared between DCIS and invasive tumors. This comparison nominated seven murine candidate genes, with eight human orthologs. We assessed the cooperativity of these genes with mutant TP53 in MCF-10A cells using acinar morphogenesis and migration assays. Overexpression of TMEM267 in cells with mutant TP53 caused a significant increase in the filled duct, DCIS-like phenotype. We nominate TMEM267 as a cooperating event with mutant TP53 in DCIS progression.

overall_design: Paired end Whole Exome Sequencing of MaPR245W/+ murine mammary tumors and DCIS lesions

first: Rhiannon

last: Morrissey

first: Guillermina

last: Lozano


title: Single-cell mapping of regulatory DNA:Protein interactions I

first: Wei-Yu

last: Chi

first: Sang-Ho

last: Yoon

first: Evrim

last: Goksel

first: Levan

last: Mekerishvili

first: Joe

last: Pelt

first: Yiyun

last: Lin

first: Saravanan

last: Ganesan

first: Catherine

first: Franco

first: Dan A.


title: Spatially distinct cellular and molecular landscapes define prognosis in triple negative breast cancer [2]

city: Pasadena

first: David

middle: Eugene

last: Frankhouser

address: 1500 E Duarte Rd

department: Population Sciences

institute: City of Hope

summary: Triple-negative breast cancer is a prevalent breast cancer subtype with the lowest 5-year survival. Several factors contribute to its treatment response, but the inherent molecular and cellular tumor heterogeneity are increasingly acknowledged as crucial determinants. Here we report on the spatial and molecular heterogeneity underlying a retrospective, treatment-naïve group of women with differential prognoses (17 with >15 years survival- good prognosis (GPx) and 15 with <3 years survival-poor prognosis (PPx)) profiled using GeoMX® DSP. Analyses revealed that the state of epithelia and its microenvironment (TME) are transcriptionally distinct between the two groups. Invasive epithelia in GPx shows a significant increase in immune transcripts, with the TME exhibiting increased immune cell presence (via IF). PPx epithelia, in contrast, are more metabolically and translationally active, with the TME being more mesenchymal/fibrotic. Notably, pre-cancerous epithelia in PPx display a prescience of aggressiveness, as evidenced by increased EMT-signaling. We identify distinct epithelial gene signatures for PPx and GPx, that can, with high accuracy, classify samples at the time of diagnosis and are likely to inform therapy.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: GeoMx human whole transcriptome atlas was performed on ROIs that were selected from 32 FFPE sections from good prognosis (GPx) and poor prognosis (PPx) triple negative breast cancer samples.

first: Kavitha

last: Mukund

first: Darya

last: Veraksa

middle: E

first: Lixin

last: Yang

first: Jerneja

last: Tomsic

first: Raju

last: Pillai

first: Srijan

last: Atti

first: Zahra

last: Mesrizadeh

first: Daniel

last: Schmolze

first: Xio-Cheng

last: Wu

first: Mary-Anne

last: LeBlanc

first: Lucio

last: Miele

first: Augusto

last: Ochoa

first: Victoria

last: Seewaldt

first: Shankar

last: Subramaniam


title: Spatially distinct cellular and molecular landscapes define prognosis in triple negative breast cancer [1]


title: Atherosclerosis licenses for an exceeding immune response in COVID-19 disease by interferon priming in circulating myeloid cells

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research

summary: Aims: Patients with cardiovascular disease (CVD) have an increased risk of developing severe respiratory infections, including COVID-19. However, the underlying molecular mechanisms have not been investigated. It has been previously shown that cardiovascular disease predisposes to an altered responsiveness to subsequent inflammatory triggers by an imprinted epigenetic memory in innate immune cells. Therefore, we analysed if patients with preexisting atherosclerotic cardiovascular disease (ASCVD) and COVID-19 display an increased inflammatory response compared to patients without ASCVD due to epigenetically altered immune cells.  Methods and results: Single-cell RNA sequencing revealed a dysregulated myeloid immune response with hyperinflammatory and immunosuppressive features in patients with ASCVD and moderate COVID-19. Assay for Transposase-Accessible Chromatin sequencing and in-vitro experiments with isolated monocytes infected with SARS-CoV-2 showed epigenetic priming of monocytes from patients with ASCVD towards increased inflammation and type I interferon signalling. In a German nationwide cohort (NAPKON), using multiplex cytokine assays, enzyme-linked immunosorbent assays, and bulk-RNA-sequencing, we confirmed that patients with CVD display an increased inflammatory response during moderate COVID-19.  Conclusions: This is the first study to demonstrate that patients with ASCVD show a dysregulated myeloid immune response when infected with SARS-CoV-2. Mechanistically, epigenetic imprinting sensitizes myeloid cells of patients with ASCVD to an exaggerated typ I interferon-associated immune response.

overall_design: ATAC-sequencing of PBMC-derived monocytes from individuals with and without atherosclerotic cardiovascular disease (i.e. coronary artery disease)

first: Julian

last: Leberzammer-Deuster

first: Sebastian

last: Cremer


title: iPSC-derived keratinocytes to study epidermal defects in atopic dermatitis [bulk RNA-seq]

city: Nijmegen

first: Jo Huiqing

last: Zhou

address: Geert Grooteplein 26/28

country: Netherlands

institute: Radboud University

summary: Human induced pluripotent stem cells (iPSC) can be derived from patients or be genome-edited to introduce or correct disease-related genetic variants, and subsequently be differentiated into any skin cell type. Yet, the potential of induced keratinocytes (iKC) derived from iPSC has not been explored to model the chronic inflammatory skin disease atopic dermatitis (AD), partially because iKC are often immature and heterogeneous as compared to primary keratinocytes (pKC). We aimed to optimize iPSC to keratinocyte and subsequent epidermal differentiation protocols, and compared the response of iKC to inflammatory cytokines involved in the AD pathophysiology. We found that CELLnTEC (CnT)-30 medium greatly increased the iKC culture homogeneity based on morphology and transcriptome (e.g., 130-fold higher KRT5) as compared to commonly used keratinocyte serum free medium (KSFM). Single cell RNA sequencing of iKC revealed different cell populations in the iKC culture, and indicated cell surface markers to enrich for keratinocyte-like cells. In addition, iKC passaging enhanced overall keratinocyte marker gene expression like KRT14 to similar levels as primary keratinocytes (pKC) while maintaining the cobblestone keratinocyte morphology. Upon 2D calcium or fetal bovine serum (FBS) stimulation iKC showed flattened morphology and increased KRT1 and IVL expression, typical for epidermal differentiation. Epidermal differentiation markers were reduced again by AD cytokines IL-4, IL-13 and IL-22, mimicking the epidermis defects in AD. Finally, air exposure also induced 3D epidermal differentiation, including presence of all epidermal layers, and KRT10, IVL and FLG expression, while maintaining the proliferative capacity of keratinocytes in the basal layer based on Ki67 expression. Altogether, we show the potential of iPSC-derived keratinocytes to study epidermal defects in AD, which could facilitate patient-derived skin tissue modeling in translational research.

overall_design: Induced pluripotent stem cells (iPSC) were differentiated into keratinocytes in keratinocyte serum free medium (KSFM) and CELLnTEC (CnT)-30 medium with retinoic acid (RA) and bone morphogenetic protein 4 (BMP-4) for the first two weeks, followed by two weeks without RA and BMP-4 and bulk RNA-sequencing was performed on the resulting induced keratinocytes (iKC), primary keratinocytes (pKC) and initial iPSC before differentiation

first: Luca

last: Meesters

first: Camille

last: Laberthonnière

first: Huiqing

first: Ellen

last: van den Bogaard


title: Controlled pyroptosis of engineered macrophages enables in situ biphasic antitumor via the release of oncolytic bacteria and inflammatory signals

city: Nanjing

first: Zichun

last: Hua

state: Jiangsu

address: Xianlin Road No.163

department: School of Life Sciences

institute: Nanjing University

summary: Engineered macrophage-based therapies offer promising potential for cancer treatment but are limited by slow, uncontrolled drug release and the risk of macrophage reprogramming into tumor-promoting phenotypes. Here, we developed a thermally induced macrophage autolysis release system, the macrophage-microbe encapsulation bomb (MME-Bomb), which combines engineered macrophages loaded with indocyanine green (ICG)-encapsulated nanoparticles and antitumor attenuated Salmonella typhimurium strain. This system utilizes photothermally triggered pyroptosis to induce controlled macrophage rupture within the tumor microenvironment, releasing intracellular bacteria to stimulate prolonged antitumor immunity. By integrating light-responsive biomodulation, our approach enables site-specific activation of engineered cells, enhancing the rapid delivery of therapeutic agents and maximizing the synergy between macrophage-based and bacterial therapies. In preclinical cancer models, MME-Bomb significantly reduces the tumor burden and improves survival outcomes, both alone and in combination with checkpoint inhibitors. This innovative strategy offers a versatile and precise framework for advancing cancer immunotherapies.

overall_design: A total of 1×10^6 4T1 cells were orthotopically inoculated into the mammary fat pads of 6-week-old female BALB/c mice to establish primary breast tumor. When tumor volumes reached approximately 60-90 mm^3, mice were randomly allocated into experimental groups. The cohorts received intratumoral injections of either saline or engineered cells (5.0×10^5 cells per mouse). Tumors in the engineered cells+NIR group were locally exposed to 980 nm NIR irradiation (1.5 W/cm^2), while other groups remained untreated. To mitigate spatial heterogeneity, entire tumors were homogenized and thoroughly mixed prior to RNA extraction. The extracted RNA was then subjected to RNA sequencing.

first: Leyang

first: Chenyang

last: Li

first: Lin


title: Precision Tumor Immunotherapy via a Dual-Gated Macrophage-Bacterial Activation Platform

summary: Immunotherapy based on live microorganisms has shown promise in preclinical studies, but its clinical translation has been hampered by limited efficacy and innegligible toxicity. Here, we developed M-BLAST (Macrophage-Bacteria encapsulation Lytic Autoactivated Synergistic Therapeutics), a dual-gated macrophage-mediated bacterial tumor-targeted delivery and in situ activation system. M-BLAST incorporates density-regulated virulence-enhanced attenuated Salmonella strains as the therapeutic core, thermally-controlled GSDMD-N-expressing macrophages as the delivery vector, and copper selenide, a photothermal material, as a heat-shock “primer.” Following systemic administration, localized near-infrared irradiation at the tumor site triggers macrophage pyroptosis, ensuring rapid and complete bacterial release. This disrupts the immunosuppressive tumor microenvironment and elicits a widespread cascading antitumor response just like a “immune bomb”, while dual-gating design of bacterial density and heat-shock ensures safety by preventing off-target activation in non-tumor regions. M-BLAST promises to enhance the therapeutic utility of living engineered bacteria for cancer while ensuring safety.

overall_design: A total of 1×10^6 4T1 cells were orthotopically inoculated into the mammary fat pads of 6-week-old female BALB/c mice to establish primary breast tumor. When tumor volumes reached approximately 70 mm^3, mice were randomly allocated into experimental groups. The cohorts received intraperitoneal injections of either saline or M-BLAST cells (3.0×10^5 cells per mouse). Twelve hours post-administration, tumors in the M-BLAST+NIR group were locally exposed to 980 nm NIR irradiation (1.5 W/cm^2) for 10 minutes, while other groups remained untreated. Tumors were harvested 36 hours post-treatment. To mitigate spatial heterogeneity, entire tumors were homogenized and thoroughly mixed prior to RNA extraction. The extracted RNA was then subjected to RNA sequencing.


title: Vaccine Delivery Platforms Affect Heterologous Protection by Hemagglutinin-Based Influenza Vaccines in Pigs

city: Lincoln

first: Hiep

last: Vu

state: Nebraska

address: 4240 Fair St

department: Animal Science and Nebraska Center for Virology

institute: University of Nebraska-Lincoln

summary: Vaccine-associated enhanced disease (VAED) poses a significant challenge in vaccine development for certain diseases. Vaccine-associated enhanced respiratory disease (VAERD), a form of VAED, has been observed in pigs vaccinated with whole-inactivated vaccine against influenza A virus (IAV) vaccines, followed by an exposure to antigenically mismatched virus strains. Similar outcomes have been reported in pigs vaccinated with a protein-based vaccine containing hemagglutinin (HA), a key viral surface antigen of IAV.  We recently developed a lipid nanoparticle encapsulated DNA vaccine encoding the HA gene of IAV, which induced robust immune responses after a single immunization and protected pigs against homologous IAV challenges. This study compared the immunogenicity and efficacy of HA-protein-based and HA-DNA-based vaccines against an antigenically mismatched IAV strain in pigs. While the HA protein-based vaccine exacerbated lung consolidation compared to non-vaccinated controls, the HA-based DNA vaccine prevented gross lung lesion development. Transcriptome analysis revealed distinct gene expression profiles, highlighting differences in host immune responses. These findings provide direct evidence that the same vaccine antigen, when delivered through different platforms, can result in different outcomes: protection versus disease enhancement. This underscores the importance of selecting appropriate delivery platforms for vaccine development. Furthermore, the IAV vaccine in pigs could be a valuable model for studying the immunological mechanisms underlying vaccine-enhanced diseases.

overall_design: A total of 18 pigs, 3 weeks old and seronegative for swine influenza A virus, were assigned to three treatment groups. After a 1-week acclimation period, Group 1 received a single intramuscular dose of the pdm09-LNP vaccine, which consisted of 500 µg of a DNA plasmid encoding the HA protein of the H1N1 pdm09 influenza virus, encapsulated in lipid nanoparticles. Group 2 received the pdm09-protein vaccine, administered as two intramuscular doses 21 days apart. This vaccine contained 10 µg of purified recombinant HA protein expressed using a baculovirus expression system and emulsified in an oil-in-water adjuvant. The doses were given at 4 and 7 weeks of age. Group 3 did not receive any treatment and served as a negative control. Peripheral blood mononuclear cells (PBMCs) were collected at 10 weeks of age and sent to Azenta Life Sciences for RNA sequencing. Total RNA was extracted, and poly(A) RNA was purified. RNA sequencing was performed on an Illumina platform with 2 × 150 bp reads, generating approximately 20 million paired-end reads per sample.

first: The

middle: N

last: Nguyen

first: Danh

middle: C

last: Lai

first: Hung

middle: Q

last: Luong

first: Sushmita

last: Kumari

first: Kassandra

last: Matinez

first: Sarah

last: Sillman


title: Spatially distinct cellular and molecular landscapes define prognosis in triple negative breast cancer

first: David

last: Frankhouser


title: Exploratory Study on the Mechanism of Left Ventricular Function Recovery After Left Ventricular Assist Device Implantation in Pediatric Dilated Cardiomyopathy

city: Suita

first: Yosuke

last: Kugo

state: Osaka

address: 2-2 Yamadaoka

department: Cardiovascular Surgery

institute: Graduate School of Medicine Faculty of Medicine, Osaka University

summary:
This study investigated factors associated with left ventricular (LV) recovery in pediatric dilated cardiomyopathy (DCM) following left ventricular assist device (LVAD) implantation, using single-cell multiomics analysis.
Twenty-five pediatric DCM patients who underwent bridge-to-transplant LVAD (BTT-LVAD) implantation at our institution were categorized as either recovery (R) cases, defined by successful LVAD explantation with sustained stability on medical therapy, or non-recovery (NR) cases, defined by the need for transplantation or death. Single-nucleus RNA (snRNA) sequencing and chromatin accessibility analyses were conducted on six subcases (three from each group). Candidate genes and pathways identified were further validated through histological and serological assessments in all cases.
Pseudobulk analysis revealed higher expression of NPPB, MYL7, and PCDH9 in cardiomyocytes from the R group, with NPPB exhibiting the highest baseline expression and corresponding changes in chromatin accessibility. Gene Ontology analysis highlighted pathways regulating apoptosis. Serum BNP, a protein product of NPPB, was significantly elevated in the R group at the time of LVAD implantation and correlated with a higher proportion of non-apoptotic cells.

overall_design: Single cell RNA/ATAC sequencing of left ventricular myocardium from pediatric dilated cardiomyopathy patients undergoing left ventricular assist device implantation.

first: Takuji

last: Kawamura

first: Akima

last: Harada

first: Yuji

last: Tominaga

first: Kenji

last: Miki

first: Hidekazu

last: Ishida

first: Takayoshi

last: Ueno

first: Shigeru

last: Miyagawa


title: CXCR4/CXCR7-SDF1 Axis-Based Targeting Treatment of Huntington’s Disease with Blood-Brain Barrier Permeable Neural Stem Cell-Derived Nanovesicles Reinforced by Biomimetic Nanozymes

first: Yanteng

last: Xu

state: Guangdong

address: 600# Tianhe Road

department: Centre for Nanomedicine

institute: The Third Affiliated Hospital of Sun Yat-sen University

type: Non-coding RNA profiling by high throughput sequencing

summary: Commencing with the production of toxic mutant huntingtin protein, many pathogenic factors, including mitochondrial dysfunction, overproduced reactive oxygen species (ROS) and neuroinflammation interactively accelerate the progression of Huntington’s disease (HD), causing the dysfunction and death of neurons, especially striatal medium spiny neurons. In light of that, we developed versatile neural stem cells (NSCs)-derived nanovesicles incorporating ultrasmall citrate modified-manganese oxide nanoparticles (CMnNZs) as well as pre-stimulating with IFNγ (MnINNVs). CMnNZs and IFNγ markedly increased the level of therapeutic factors in MnINNVs. Furthermore, MnINNVs are able to bypass the blood-brain barrier and target the inflammatory sites of HD through the SDF1-CXCR4/CXCR7 axis. After being uptake by neurons, microglia, and astrocytes, MnINNVs alleviate HD-like mice phenotype by scavenging ROS, promoting the conversion of microglia and astrocytes phenotypes to reduce neuroinflammation, and further rescuing neurons. Our study not only offers a novel therapy for HD but also presents new strategies to enhance the wholesome effects of NSCs-based therapies.

overall_design: Native NSC-derived nanovesicles (NNNVs) and CMnNZ- and IFNγ-treated NSC-derived nanovesicles (MnINNVs) were separately prepared by sequentially extruding NSCs through polycarbonate membranes with pore sizes ranging from 5 to 0.2 μm. Following purification by density-gradient ultracentrifugation, the resulting precipitates of NNNVs or MnINNVs were resuspended in Trizol and lysed on ice to isolated the total RNA. Subsequently, the RNA purification, reverse transcription, PCR, gel purification, library construction, and sequencing using the HiSeq 2500 system (Illumina, USA) were conducted at LC-Bio Technology (Hangzhou, China).

first: Ling

last: Long

first: Hao

last: Tian

first: Yixin

last: Zhang

first: Yu

last: Tao

first: Mingqiang

last: Li


title: Enhanced non-enzymatic H2S generation extends lifespan and healthspan in male mice

city: Seville

first: Alejandro

last: Martin-Montalvo

address: Av/ Américo Vespucio 24

country: Spain

institute: CABIMER

summary: Hydrogen sulfide is a gasotransmitter with biological functions, including roles in antioxidant defenses, mitochondrial bioenergetics and cellular signaling via cysteine persulfidation. Several longevity-promoting interventions enhance endogenous hydrogen sulfide generation. However, whether enhanced hydrogen sulfide generation extends healthspan and lifespan in mammals remains unknown. Here, we investigated the in vivo effects of the non-enzymatic hydrogen sulfide generation promoted by natural diallyl sulforated compounds. Diallyl sulforated compounds extended lifespan and improved the main aspects of healthspan, including glucoregulation, locomotor function and neurocognition in wild type male mice across their lifespan. At histological and molecular levels, we observed reductions in hepatic lipid-droplet size, attenuation of transcriptional and proteomic signatures associated with mTOR and immune-related pathways, and increased cysteine persulfidation in proteins. In humans, greater protein persulfidation in individuals with polypathological conditions was associated with increased muscle strength and lower triglyceride levels, supporting its physiological relevance. Our findings uncover the potential of enhanced hydrogen sulfide generation to promote healthy aging.

overall_design: Mice were fed with a standard healthy diet, a high fat diet, a high sucrose diet or a high fat high sucrose diet. Mice were treated with DAS, DAD or DAT for 3 hours or 18 weeks. Liver tissue was harvested and processed for RNA-seq.

first: María Ángeles

last: Cáliz-Molina

first: Raúl

last: López-Fernández Sobrino

first: Inmaculada

last: Pino-Pérez

first: Concepción

last: Panadero-Morón

first: Maria del Carmen

last: Vilches-Pérez

first: María

last: Camacho-Cabrera

first: Almudena

last: García-Ruíz

first: Leopoldo

last: Pérez-Rosendo

first: Isabel

last: Espadas

last: Sola-García

first: Mario

last: Soriano-Navarro

first: Franz

last: Martin

first: Mónica

last: Venegas-Calerón

first: Joaquin José

last: Salas

first: Enrique

last: Marínez-Force

first: Luis

last: Romero

first: Ángeles

last: Aroca

first: Román

last: González-Prieto

first: Máximo

last: Bernabeu-Wittel

first: Vivian

last: Capilla-González

first: Christopher

last: Hine

last: Martín-Montalvo


title: THAP1 is a maternal effect factor required for the first cell cycle  via Rrm1 in early mouse embryos

first: xi

last: wu

address: Tsinghua univesity

institute: Tsinghua university

summary: Maternal effect genes (MEGs) produce factors that accumulate in oocytes and play critical roles in embryo development. Mutations of MEGs are frequently linked to reproductive and congenital disorders. The majority of identified mammalian MEGs encode epigenetic factors and RNA regulators. Here, we identify a MEG encoding the transcription factor Thanatos-associated protein 1 (Thap1). Thap1 is highly expressed in mouse oocytes and early embryos. Oocyte-specific deletion of Thap1 results in delayed progression of mouse embryos from the 1-cell to the 2-cell stage and 2-cell arrest, accompanied by defective zygotic genome activation (ZGA) and strongly impaired female fertility. Mechanistically, THAP1 activates a critical subset of genes in oocytes, including Rrm1, which produces ribonucleotide reductase required for generating deoxynucleotide triphosphates (dNTPs). Low-input metabolome profiling across 7 stages during the oocyte-to-embryo transition shows gradual, THAP1-dependent dNTP accumulation that peaks in MII oocytes. Overexpression of Rrm1 in zygotes almost fully restores the 2-cell progression and ZGA in Thap1 maternal-knockout embryos. Our findings identify THAP1 as a key maternal effector critical for the earliest stage of mammalian development.

overall_design: To investigate the function of THAP1 in mouse oocytes and early development, we conducted a Thap1 maternal knockout mouse. RNA-seq was used to examine the transcriptome in control and Thap1 mKO mouse oocytes and embryos.

first: Qiang

last: Fan

first: Xi

last: Wu

first: Yanna

last: Dang

first: Shuyan

last: Ji

first: Wei

last: Xie


title: NFκB1-deficiency associated with Flt3-myeloid leukemia enhances the self-renewal capacity via dysregulated RelA:p52 and SOD2 expression

city: Los Angeles

first: Alexander

last: Hoffmann

state: United States

address: 611 Charles E Young Drive East

institute: University of California, Los Angeles

summary: In acute myeloid leukemia (AML), abnormal expression of NFκB and Flt3 are frequently detected, and dual IKK2/Flt3 inhibitor regimes are used for treatment. However, how NFκB is involved in Flt3-driven myelopoiesis remains unknown. We report that AML is associated with reduced expression of NFKB1, and that Nfkb1 deficiency conveys poor survival in a mouse Flt3-ITD-driven myeloid leukemia model. Interpreting myelopoiesis dynamics with mathematical modeling suggests that Nfkb1-/- hematopoietic stem and progenitor cells possess enhanced self-renewal and are skewed towards plasmacytoid dendritic cells. Single-cell RNA-seq confirmed this interpretation via pseudotime analysis and gene signatures indicating stemness and pDC priming. Biochemical analysis and genetic rescues demonstrate how an imbalanced NFκB signaling system elevates basal nuclear NFκB, where RelA:p52 drives Sod2 expression and enables prolonged progenitor proliferation. Our work reveals how the inflammation response NFκB system controls in stress-responsive myelopoiesis, and how system imbalances can contribute to the pathogenesis of myeloid neoplasms.

overall_design: To investigate the interplay between RelA and p50 during BMDC differentation, bone marrow cells from CD45.1 B6 (Pep Boy), and Nfkb1–/- (CD45.2) mice were mixed at 50:50 ratio and co-cultured with 100ng/ml Flt3L. On day 3 or day 5, three wells of cells were harvested, pooled before staining with surface antibodies for CD3/CD19/CD49b/Ter119-FITC, Gr-1-PECy7, CD45.1-BV711, CD45.2 APCCy7 and DAPI. Live Dump-(CD3/CD19/CD49b/TER119/Gr-1-) CD45.1+CD45.2- (WT) cells and live Dump-CD45.1-CD45.2+ (Nfkb1-/-) cells were sorted by BD FACS Aria II. Sorted cells were stained with unique TotalSeq™-A anti-mouse Hashtag Antibodies (TotalSeq™-A #1,2,3,5 were used) for multiplexing.

first: Yi

last: Liu

first: Yu-sheng

last: Lin


title: β2 ADRENERGIC SIGNALING STIMULATES EARLY IL-1β SECRETION IN MACROPHAGES BY INDUCING MAPK-DEPENDENT Il1b TRANSCRIPTION [ATAC-Seq]

first: Stephen

last: Smale

state: Ca

address: 6-730 MRL 675 Charles E. Young Drive South

department: MIMG

institute: University of California Los Angeles

summary: Activating β2 adrenergic receptor (β2AR) on macrophages inhibits the expression of several proinflammatory cytokines, a phenomenon primarily associated with NF-κB inhibition. IL-1β is a hallmark inflammatory cytokine, and NF-κB plays a role in the transcriptional activation of Il1b in the priming phase of the NLRP3 inflammasome. Here, we report that contrarily to expectations, β2AR signaling stimulated transcription of the Il1b gene, either alone or in combination with TLR ligands. Moreover, in vivo experiments demonstrated that mice with increased sympathetic tonus (Adra2ac-/-) produced higher levels of IL-1β in a β2AR-dependent manner during alum-induced peritonitis. Assay for Transposase-Accessible Chromatin using Sequencing (ATAC-Seq) experiments, genome-wide analyses of clustered genomic regions and the utilization of pharmacological inhibitors revealed that β2AR-induced Il1b expression occurs in PKA-, MAP Kinases- and AP-1-dependent manner. Our findings describe that β2AR signaling can regulate macrophage effector function in a complex way that may involve gene-specific mechanisms increasing the expression of pro-inflammatory cytokines such as IL-1β.

overall_design: Bone marrow-derived macrophages (BMDM) were treated with 1 µM of a β2 adrenergic receptor (β2AR) agonist at different periods of incubation. The cells were then activated with LPS prior to either RNA extraction for RNA-Seq or crude nuclear extraction for ATAC-Seq library prep.

first: Filipe

last: Menegatti de Melo

first: Philip

middle: O

last: Scumpia

middle: T


title: Identification of mRNAs as potential blood based biomarekrs for diagnosis and therapeutic monitoring of active tuberculosis

city: Busan

first: Jungho

last: Kim

address: 57, Oryundae-ro, Geumjeong-gu, Busan, Republic of Korea

department: Department of Clinical Laboratory Science, College of Health Sciences

country: South Korea

institute: Catholic University of Pusan

summary: To identify potential mRNA candidates for biomarkers for using a transcriptome-based approach, we extracted total RNAs from blood samples of study participants, including a complete set from patients with ATB who underwent a six-month treatment course

overall_design: Through mRNA sequencing, we identified potential differentially expressed mRNAs

first: Eunsol

last: Ahn

first: Young Ae

last: Kang

first: Hyejon

last: Lee


title: Analysis of miRNA profiles associated with anti-tuberculosis treatment responses

summary: To identify potential microRNA candidates for therapeutic response assessment using a transcriptome-based approach, we extracted total RNAs from blood samples of study participants, including a complete set from patients with ATB who underwent a six-month treatment course

overall_design: Through miRNA sequencing, we identified potential differentially expressed miRNAs


title: β2 ADRENERGIC SIGNALING STIMULATES EARLY IL-1β SECRETION IN MACROPHAGES BY INDUCING MAPK-DEPENDENT Il1b TRANSCRIPTION [RNA-Seq]

overall_design: Bone marrow-derived macrophages (BMDMs) were exposed to 1 µM of the β2 adrenergic receptor (β2AR) agonist metaproterenol hemisulfate (MPH) for 2 h before LPS stimulation for 1, 2, or 6 h. Total RNA was isolated, and libraries were prepared using the Illumina Truseq v.2 kit. Libraries were sequenced using 50bp reads with a minimum raw read depth of 20 million reads. Most samples have biological duplicates.

first: Vasileios

last: Ragkousis

first: Kevin

middle: R

last: Doty

first: Giovanni

last: Botten

first: Amber

last: Ruccia


title: Integrin β1 demarks precursors of brain-residing antibody-secreting cells in multiple sclerosis

city: Rotterdam

first: Yifan

last: van Hasselt

state: Zuid holland

address: Dr Molewaterplein 40

department: Immunology

institute: Erasmus MC

summary: Multiple sclerosis (MS) is characterized by B cells that infiltrate the central nervous system (CNS) to mature into antibody-secreting cells (ASCs). To date, it remains to be determined how to benefit from this disease hallmark as a prognostic tool. We aimed to uncover markers that reflect B-cell entry and maturation in the CNS and on that basis explore associations with response to high efficacy therapies in MS. Single-cell RNA sequencing (scRNA-seq) revealed ITGB1 (integrin β1/CD29) as a major discriminator of memory B cells expressing CXCR3, which was validated on protein level by spectral flow cytometry. Functional in vitro assays showed that CD29+CXCR3+ memory B cells preferentially cross a brain microvascular endothelial layer and are more receptive to T-cell help to become ASCs. In MS blood, CD29 and CXCR3 were particularly co-expressed on circulating memory B cells, but not on ASCs. In CNS compartments of MS donors, however, high co-expression of CD29 and CXCR3 was restricted to ex vivo ASCs, which was supported by a stronger upregulation of CD29 on in vitro-differentiated ASCs. In MS, while CD29 was effectively downregulated on CXCR3+ memory B cells that accumulated in the blood of natalizumab-treated patients, CD29 levels were only reduced on CXCR3+ memory B cells that repopulated in cladribine-treated patients without early breakthrough disease activity. Taken together, this study reveals that CD29 defines CXCR3+ B cells with a propensity to infiltrate and develop into ASCs in the CNS, which holds potential to be utilized as a cellular biomarker to predict treatment responses in people with MS.

overall_design: Single-cell RNA-seq profiling of FACS-sorted CD19+ B cells from thawed PBMCs from healthy donors (n=3)

first: Kirsten

last: Kuiper

first: Laurens

last: Bogers

first: Jasper

last: Rip

first: Marie-Jose

last: Melief

first: Annet

last: Wierenga-Wolf

first: Romy

last: Klein-Kranenbarg

first: Eric

last: Bindels

first: Harmen

last: van de Werken

first: Janet

last: de Beukelaar

first: Ide

last: Smets

first: Beatrijs

last: Wokke

first: Joost

last: Smolders

first: Marvin

last: van Luijn


title: The nuclear exosome is required for Piwi-piRNA mediated co-transcriptional gene silencing [smallRNA-seq]

first: Julius

last: Brennecke

address: Dr. Bohr Gasse 3

institute: IMBA-Institute for Molecular Biotechnology

summary: Co-transcriptional gene silencing mediated by small RNA pathways is primarily studied in the context  of heterochromatin formation. These pathways are known to target nascent RNAs, yet their intersection  with cellular processes determining the fate of the nascent transcripts remain unclear. We report that the  nuclear exosome, the central cellular 3’ to 5’ exo-ribonuclease complex, is required for transposon  repression through the Piwi-piRNA pathway in Drosophila. Using somatic ovarian cells, where piRNA  biogenesis and piRNA-guided silencing are separated, we demonstrate that the three adaptor complexes  of the nuclear exosome –PAXT, NEXT, and TRAMP– are redundantly required for degrading piRNA  target transcripts. Furthermore, we identify two paralogous proteins, Creator-1 and Creator-2, as piRNA  pathway factors that physically connect the exosome to the Piwi-silencing complex through a novel  poly-proline binding domain. Our findings uncover an evolutionarily conserved principle whereby the  nuclear RNA exosome is integral to diverse co-transcriptional silencing processes controlled by  small RNAs.

overall_design: Small RNA Sequencing (small-RNA-seq) analyis of small RNA expression changes in cultured ovarian somatic cells (OSCs) after siRNA mediated depletion of CG31510, CG7065, CG31510&CG7065, Dis3, RrP40, Rrp41, dZfc3h1&dZcchc8, or Mtr4, compring to control knockdown.

first: Changwei

last: Yu

first: Toni

last: Manolova

first: Dominik

last: Handler

first: Ulrich

last: Hohmann

first: Laszlo

last: Tirian

first: Filip

last: Nemčko

first: Júlia

last: Portell i de Montserrat

first: Guillaume

last: Giraud Collet

first: Peter

last: Duchek

first: Maria

last: Novatchkova

first: Elisabeth

last: Roitinger

first: Sebastian

last: Falk


title: The nuclear exosome is required for Piwi-piRNA mediated co-transcriptional gene silencing [PRO-seq]

overall_design: Precision Run-On Sequencing (PROseq) analyis of nascent transrption changes in cultured ovarian somatic cells (OSCs) after siRNA mediated depletion of Piwi, CG31510&CG7065, Dis3, Rrp40, Rrp41, dZfc3h1&dZcchc8, or Mtr4, compring to control knockdown.


title: LOXL2 identifies inflammation-associated myofibroblasts predicting kidney allograft dysfunction and fibrosis

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

summary: Chronic allograft nephropathy (CAN) is a major obstacle in kidney transplantation, often leading to long-term graft failure. Early identification of patients at high risk for CAN could be instrumental to improve outcomes. Here, we investigate Lysyl oxidase ligand 2 (LOXL2) as a predictive biomarker for CAN. Using single cell RNA sequencing of transplant biopsies, immunohistochemistry and immunofluorescence microscopy, we find that LOXL2 labels a distinct intertubular myofibroblast subtype with a smooth muscle actin (SMA)-, CXCL12- and PDGFRb-negative and CD68-positive phenotype. These cells are present in non-fibrotic and fibrotic regions utilizing collagen 3 as scaffold, and are associated with a high expression of extracellular matrix (ECM) proteins and related pathways. Native kidneys also harbor LOXL2+ myofibroblasts, albeit at much lower levels, and their presence correlates with the incidence of chronic kidney disease. Following transplant surgery, LOXL2+ cells can rapidly emerge within days, particularly during episodes of rejection, where they associate with leukocyte aggregates. Notably, elevated cell numbers can be normalized as shown in follow up biopsies. A retrospective analysis of 118 biopsies revealed a significant association between LOXL2+ cell abundance and transplant fibrosis, inflammation, and kidney function. However, no correlation was found with transplant age, rejection type and other Banff parameters. Non-rejecting allografts displayed high variability in the number of LOXL2+ cells, with high abundance serving as a long-term predictor of fibrosis and reduced allograft function. Collectively, our findings suggest that LOXL2+ intertubular cells are a subset of inflammation-associated SMA- myofibroblasts and may be useful as a risk biomarker for early fibrogenesis in non-rejecting allografts.

overall_design: Renal graft biopsies of KTx patients were analysed in this study. The indication for graft biopsy was unexplained graft injury as assessed by creatinine or proteinuria. Per patient, 1 biopsy was analysed. In total, 18 patients were included in this study.

first: Konrad

last: Buscher

first: Rebecca

last: Rixen

first: Paula

last: Schütz


title: Generation of a healthy human bladder cell atlas II

city: Houston

first: Angela

last: Ting

address: 1881 East Road

institute: The University of Texas MD Anderson Cancer Center

summary: In this study we present an atllas of gene and isoform expression across major cell types of the healthy human bladder.

overall_design: We leveraged single nuclei RNA sequencing (snRNA-seq) to generate a cell atlas for healthy adult human bladder. We analyzed ten snRNA-seq samples from four anatomic regions (dome, neck, UO, UVJ) from five donors and identified twenty distinct cell types/states.

first: Briana

last: Santo


title: Generation of a healthy human bladder cell atlas I


title: The nuclear exosome is required for Piwi-piRNA mediated co-transcriptional gene silencing [ChIP-seq]

city: Vienna

first: Julius

last: Brennecke

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modification H3K9me3 in OSC reporter cells. And ChIP-seq for histone modification H3K9me3 in OSCs after siRNA mediated depletion of Piwi, CG31510&CG7065, Dis3, Rrp40, Rrp41, dZfc3h1&dZcchc8, or Mtr4, compring to control knockdown.

first: Changwei

last: Yu

first: Toni

last: Manolova


title: Direct Conversion of Human Umbilical Cord Mesenchymal Stem Cells into Dopaminergic Neurons for Parkinson's Disease Treatment

city: Suzhou

first: Jinming

last: Liu

address: 199 Ren-ai Road

institute: Soochow University

summary: Parkinson's disease (PD) is a neurodegenerative disorder characterized by motor deficits resulting from the depletion of nigrostriatal dopamine. Stem cell differentiation therapy is a promising treatment option for achieving sustained relief from symptoms. In this study, we successfully established a one-step differentiation system using the YFBP cocktail (Y27632, Forskolin, SB431542, and SP600125) to efficiently convert human umbilical cord mesenchymal stem cells (hUCMSCs) into dopaminergic neurons, avoiding the need for genetic modification. This approach addresses the challenge of generating functional neurons rapidly and safely on a large scale. Following a 7-day induction period, the proportion of TUBB3 and NEUN double-positive cells exceeded 80%. Transcriptome analysis revealed the dual roles of the cocktail in inducing fate erasure in MSCs and activating the neuronal program. Notably, the differentiated derivatives did not express HLA class II genes, preserving their immune-privileged status. Additionally, YFBP significantly downregulated p53 signaling, accelerating the differentiation process upon signaling inhibition with pifithrin-α. Wnt/β-catenin signaling was transiently activated within 1 day, with prolonged activation hindering the cascade. After being transplanted into the striatum of mice, YFBP-induced dopaminergic neurons survived well and exhibited neuronal electrophysiological activity, effectively reversing movement disorders in PD animals. In conclusion, our research offers a secure and reliable framework for cell replacement therapy and regenerative medicine.

overall_design: To explore the mechanism underlying the differentiation of human umbilical cord mesenchymal stem cells into neurons induced by YFBP, an intergroup correlation analysis was conducted on the differentially expressed gene sets at multiple time points (0, 3, and 7 days).


title: Transient ER stress cell-autonomously promotes beta cell cycling

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

institute: Vrije Universiteit Brussel - VIB

summary: Regenerating endogenous pancreatic ß-cells is a potentially curative yet currently elusive strategy for diabetes therapy. Mimicking the microenvironment of the developing pancreas and leveraging vascular signals that support pancreatic endocrinogenesis may promote ß-cell regeneration. We aimed to investigate whether recovery from experimental hypovascularization of the endocrine pancreas, achieved by modulating the transgenic production of a VEGF-A blocker in ß-cells, could trigger mouse ß-cell proliferation. Serendipitously, we found that transgene overexpression in ß-cells induces endoplasmic reticulum (ER) stress and that subsequent relief from this stress stimulates ß-cell proliferation independent of vessel recovery. Transient GFP overexpression in vivo and transient chemical induction of ER stress in vitro replicated this ß-cell cycling response. Our findings highlight the potential side effects of ER stress due to transgene overexpression in ß-cells and assert that ER stress relief serves as a potent regenerative stimulus.

overall_design: Pancreatic islets were isolated from RIP-rtTA;TetO-sFLT1 mice and subsequently dissociated. For each condition (No DOX, +DOX, and WD4D), two biological replicates were included, resulting in a total of six samples that were analyzed using scRNAseq.

first: Stephanie

last: Bourgeois

first: Annelore

last: Van Mulders

first: Yves

last: Heremans

first: Gunter

last: Leuckx

first: Lien

last: Willems

first: Sophie

last: Coenen

first: Laure

last: Degroote

first: Julie

last: Pierreux

first: Isabelle

last: Scheyltjens

first: Kiavash

last: Movahedi

first: Miriam

last: Cnop

first: Xiaoyan

last: Yi

first: Chiara

last: Vinci

first: Yue

last: Tong

first: Eelco

last: de Koning

first: Françoise

last: Carlotti

first: Heimberg

last: Harry

first: Nico

last: De Leu

first: Staels

last: Willem


title: The nuclear exosome is required for Piwi-piRNA mediated co-transcriptional gene silencing [RNA-seq]

first: Julius

last: Brennecke

overall_design: RNA-seq analysis of gene and transpable element expression changes in cultured ovarian somatic cells (OSCs) after siRNA mediated depletion of Piwi, CG31510, CG7065, CG31510&CG7065, Rrp6, Dis3, Rrp40, Rrp41, dZfc3h1, dZcchc7, dZcchc8, dZcchc7&dZcchc8, dZfc3h1&dZcchc7, dZfc3h1&dZcchc8, dZfc3h1&dZcchc7&dZcchc8 or Mtr4, compring to control knockdown.

first: Changwei

last: Yu

first: Toni

last: Manolova

first: Dominik

last: Handler

first: Ulrich

last: Hohmann

first: Laszlo

last: Tirian

first: Filip

last: Nemčko

first: Júlia

last: Portell i de Montserrat

first: Guillaume

last: Giraud Collet

first: Peter

last: Duchek

first: Maria

last: Novatchkova

first: Elisabeth

last: Roitinger

first: Sebastian

last: Falk


title: Co-transcriptomic analysis of group A Streptococcus (GAS; Streptococcus pyogenes) invasions of human endothelial cells

city: Taipei City

first: Shu-Wei

middle: Marcia

last: Su

address: No. 155, Sec. 2, Linong St, Beitou District

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary: Group A Streptococcus (GAS, aka Streptococcus pyogenes) causes an array of human diseases from mild pharyngitis to life-threatening necrotizing fasciitis. Invading host cells is a strategy for GAS to avoid antibiotic killing and immune system clearance. Our previous study showed that GAS is able to multiply in human microvascular endothelial cell line-1 (HMEC-1), and has higher survival in HMEC-1 cells due to insufficient acidification in lysosomes. GAS peroxide response regulator (PerR) modulates not only peroxide stress, but also metal homeostasis and bacterial virulence. Therefore, we aimed to investigate the role of PerR during GAS invading endothelial cells. First, we found that ΔperR mutant was more tolerant to H2O2 in vitro using hydrogen peroxide sensitivity assay. We further used cDNA-qPCR analysis to clarify the resistance mechanism of ΔperR mutant. The gene expressions of dpr, ahpC, and ahpF were up-regulated, explaining the enhanced resistance of the ΔperR mutant against peroxide stress. However, the proliferation of the ΔperR mutant in HMEC-1 cells was significantly lower than wild type strain after 5 h post-infection. To explore the underlying mechanisms of ΔperR mutant during infection, we performed dual RNAseq analysis to identify differentially expressed genes, and validated them using cDNA-qPCR analysis. The resulting up-regulated genes of iron efflux pump pmtA, iron/zinc chelating protein dpr, and zinc acquisition system (adcA, lmb/adcAII, phtD), and down-regulated zinc efflux pump czcD gave rise to impaired metal homeostasis in the ΔperR mutant. Furthermore, in vitro growth curve assays showed that the ΔperR mutant was sensitive to zinc deficiency and resistant to zinc toxicity. Taken together, this study has demonstrated the critical roles that GAS PerR plays in protecting from peroxide stress of host innate immune responses and zinc sequestration of nutritional immunity. Our novel findings open a new avenue of strategies in the development of antimicrobial agents. Our study demonstrates the importance of PerR. It aids GAS virulence in immune evasion during the LC3-associated phagocytosis in endothelial cells.

sample_organism:
Streptococcus pyogenes
Homo sapiens

platform_organism:
Streptococcus pyogenes
Homo sapiens

overall_design: For dual RNA-seq analysis, human microvascular endothelial cell line-1 (HMEC-1) cells containing intracellular GAS were collected after 1 hour of infection. We isolated the total RNA samples from HMEC-1 cells only, GAS strain NZ131 wild-type-infected HMEC-1 cells, and GAS strain NZ131 ∆perR-infected HMEC-1 cells from four independent infection experiments.

first: Marcia

last: Shu-Wei Su

first: Jiunn-Jong

last: Wu


title: Functionally redundant roles of ID family proteins in spermatogonial stem cells

city: CLAYTON

first: Robin

middle: Mark

last: Hobbs

state: VIC

address: 27-31 Wright Street

department: Centre for Reproductive Health

country: Australia

institute: Hudson Institute of Medical Research

summary: Spermatogonial stem cells (SSCs) are essential for sustained sperm production and male fertility, but SSC regulatory mechanisms and molecular markers remain poorly defined. Previous studies have suggested that the Id family transcriptional regulator Id4 is expressed at high levels in SSCs and involved in SSC maintenance. Here we have used knock-in reporter and inducible knockout models to define expression pattern and function of Id4 in the adult male germline. Within the spermatogonial pool, Id4 reporter expression and ID4 protein are found throughout the GFRa1+ fraction, comprising the self-renewing population. However, acute deletion of Id4 is tolerated by adult SSCs while revealing unexpected roles in maintenance of meiotic spermatocytes. Cultures of undifferentiated spermatogonia were also successfully established and expanded following Id4 deletion. Importantly, ID4 loss in undifferentiated spermatogonia triggers ID3 upregulation, and both ID proteins associate with transcription factor partner TCF3 in wildtype cells. Moreover, combined inhibition of ID proteins in cultured spermatogonia disrupts the stem cell state and blocks proliferation. Our data therefore demonstrate critical but functionally redundant roles of ID family proteins in the maintenance of SSC function.

overall_design: To assess the role of ID family proteins in SSCs we treated cultured undifferentiated spermatogonia derived from wildtype mice with the pan-ID inhibitor AGX51 (80uM) for 20 hours. Cells were treated with vehicle (DMSO) as control. We treated 4 independent spermatogonial cultures derived from individual mice. We then harvested RNA and performed RNA-seq analysis.

first: Hue

last: La

first: Ai-Leen

last: Chan

first: Ashlee

last: Hutchinson

first: Fernando

middle: J

last: Rossello

first: Ralf

middle: B

last: Schittenhelm


title: Continuous low-intensity ultrasound influences the transcriptomic profile in M1 macrophages by downregulating inflammation and promoting M2-like markers

status: Public on Dec 18 2025

city: HUNTSVILLE

first: Anuradha

last: Subramanian

state: AL

address: 301 Sparkman Drive NW

institute: University of Alabama in Huntsville

summary: Macrophages are key regulators of inflammation, capable of adopting pro-inflammatory (M1) or anti-inflammatory (M2) phenotypes in response to environmental cues. In chronic conditions such as post-traumatic osteoarthritis (PTOA), persistent M1 activation contributes to tissue damage and impaired healing. Traditional models using lipopolysaccharide (LPS) to induce inflammation may not fully capture the complex microenvironment of joint injury. Here, we use fibronectin fragments (Fnfs), which are associated with matrix degradation, to establish a physiologically relevant inflammatory model and to apply transcriptomic analysis to investigate how continuous low-intensity ultrasound (cLIUS), a non-pharmacological biophysical stimulus, modulates macrophage responses under Fnfs-induced conditions. Beyond identifying differentially expressed genes (DEGs), we introduced network-level differential clustering (DC) to capture transcriptional remodeling, revealing context-specific regulators and co-expression shifts overlooked by gene-level analyses. cLIUS reprogrammed Fnfs-induced macrophages toward an M2-like reparative phenotype, marked by downregulation of pro-inflammatory and upregulation of tissue repair and immune-regulatory genes. DC further identified significant genes not detected by DEG analysis, with only partial overlap between ranked gene lists, as quantified by concordance indices of 0.52 for SD genes and 0.42 for DS genes (scale 0–1). These findings highlight the value of integrating clustering-based metrics with expression data to elucidate how biophysical treatments like cLIUS modulate immune cell behavior.

overall_design: Macrophages were polarized to a pro-inflammatory M1 phenotype by stimulation with fibronectin fragments (Fnfs) to model matrix degradation–associated inflammation. Fnfs-induced M1 macrophages were cultured for three days either in the presence or absence of continuous low-intensity ultrasound (cLIUS) treatment. Total RNA was isolated from each condition and subjected to paired-end RNA sequencing. Transcriptomic profiles were compared to assess the effects of cLIUS on Fnfs-induced macrophage gene expression.

first: Shahid

last: Khan

first: Owen

last: Trippany

first: Satyaki

last: Roy