title: Blocking microglial reactivity via purinergic receptors prevents long-term cognitive deficits after transient ischemic attacks

city: Munich

first: Arthur

last: Liesz

address: Feodor-Lynen-Straße 17

department: Institute for Stroke and Dementia (ISD)

institute: LMU Hospital

summary: Our research introduces a novel animal model for transient ischemic attack (TIA), mimicking brief episodes without cell loss but resulting in long-term behavioral and neuronal deficits. We identified excessive microglial reactivity, driven by hyperacute ATP release, as a pivotal contributor to post-TIA neurological deficits, which was alleviated by inhibiting the P2Y12 receptor. This finding suggests that targeting microglial reactivity offers a promising strategy to prevent cognitive decline in TIA patients, opening avenues for further research in this under-explored area.

overall_design: Single cell RNA sequencing was performed on live cells sorted from the brain after experimental TIA (ipsilateral hemisphere) and naive mice as control.

first: Gemma

last: Llovera

first: Steffanie

last: Heindl


title: DC-SIGN+ Macrophages alleviates Non-Alcoholic Steatohepatitis by modulating inflammatory cytokine secretion

status: Public on Apr 22 2026

city: Nantong

first: Chunhua

last: Wan

state: Jiangsu

address: No. 9 Seruan Road

country: China

institute: Nantong University

type: Expression profiling by high throughput sequencing

summary: The modulation of immune responses by innate immune receptors plays a pivotal role in the progression of non-alcoholic steatohepatitis (NASH). In this study, we aim to comprehensively dissect the involvement of the C-type lectin receptor DC-specific-ICAM3-grabbing-nonintegrin (DC-SIGN) in NASH progression. RNA sequencing was conducted on liver samples obtained from mice fed either a control diet or a HFHC diet inducing NASH for 16 weeks. At 8 weeks post feeding, animals were transduced via tail vein with Adeno-Associated Virus 9 (AAV9) expressing CD68 promoter-driven human DC-SIGN (hDC-SIGN) or GFP control. Data obtained from the transcriptomic profiles indicated that macrophage-specific delivery of hDC-SIGN strongly attenuated liver metabolic and inflammatory abnormalities, leading to the amelioration of NASH progression.

overall_design: C57BL/6 mice were fed either the HFHC diet or a control diet for 8 weeks. Mice were tail-vein injected with either AAV9-CD68-EGFP (Control) or AAV9-CD68-hDC-SIGN (1×10^11v.g./mouse) and mice were kept additionally 8wks on the diet before livers were harvested for RNA-seq analyses.

first: Jinxia

last: Liu

first: Haifeng

last: Wu


title: The XPO7-NPAT axis represents key vulnerabilities in TP53-mutated acute myeloid leukemia (RNA-Seq)

city: Fukuoka

first: Yuichiro

last: Semba

address: 3-1-1 Maidashi

country: Japan

institute: Kyushu University

summary: Mutation of TP53, a tumor suppressor in cancer, is common and leads to extremely poor prognosis. To identify vulnerabilities in TP53-mutated tumors, we performed genome-wide CRISPR/Cas9 screens using isogenic Trp53 wild-type and knockout mouse acute myeloid leukemia (AML) lines. Here, we show that histone gene regulation governed by the XPO7-NPAT pathway is essential for survival of TP53-mutated AML cells. In TP53 wild-type cells, XPO7 enhances p53 nuclear localization and functions as a tumor suppressor, but in TP53-mutated cells, XPO7 promotes cell proliferation by retaining NPAT, a histone gene activator, in the nucleus. NPAT depletion led to genome-wide histone loss, enhancing vulnerability to genotoxic stress. Human AML cases show predominant expression of XPO7 and NPAT when TP53 is mutated, suggesting a potential therapeutic vulnerability.

overall_design: To assess Xpo7 depletion effects on p53-dependent transcriptional programs, we performed RNA-sequencing (RNA-seq) in the presence of Nutlin-3a using Xpo7-WT and -KO AML cells on a Trp53 WT background. Moreover, to identify mRNAs downregulated by Npat depletion, we performed RNA-seq using Trp53KONpat_FK2AGFP AML cells, with or without dTAGV-1 treatment.


title: Steatosis shifts the histopathological heterogeneity of liver metastases towards poor prognosis replacement growth in colorectal cancer patients

city: Leuven

first: Juan

last: Fernández-García

address: Campus Gasthuisberg, O&N4, Herestraat 49, box 912

department: VIB-KU Leuven Center for Cancer Biology

country: Belgium

institute: VIB/KU Leuven

summary: Liver metastases are a leading cause of cancer-related deaths, particularly in colorectal cancer. Two distinct histological growth patterns characterize liver metastases: the desmoplastic growth pattern, marked by a stromal encapsulating ring around the metastasis, and the replacement growth pattern, where cancer cells integrate into and replace the native hepatocyte architecture. The replacement pattern is associated with poorer therapeutic responses and worse overall prognosis. Concurrently, obesity, which alters the liver microenvironment, is linked to unfavorable outcomes in colorectal cancer patients. This study explores the interplay between a lipid-rich liver microenvironment and histological growth patterns in metastases. Using resected patient specimens and preclinical mouse models of obesity, we observed a correlation between liver steatosis and a shift toward the more aggressive replacement growth pattern. Mechanistically, lipid-rich environments, both in vitro and in vivo, were found to enhance proline synthesis in colorectal cancer cells, promoting extracellular matrix (ECM) production. This phenotypic switch is driven by fatty acid oxidation, which generates acetyl-coenzyme A, leading to the accumulation of the transcription factor MYC. Inhibiting fatty acid oxidation or silencing MYC reversed the aggressive growth advantage in lipid-rich conditions. Interestingly, cancer cells lose the aggressive phenotype once the lipid abundance is withdrawn. Furthermore, publicly available patient datasets revealed upregulated proline and ECM metabolism in inherent replacement growth patterns. Targeting these pathways significantly reduced liver metastasis outgrowth in preclinical models.

overall_design: RNA-seq profiling of CMT93 spheroids treated with vehicle (ethanol + BSA) or 200 µM palmitate (ethanol + BSA-conjugated sodium palmitate).

first: Yiming

last: Peng-Winkler

first: Sarah-Maria

middle: M

last: Fendt


title: Species-specific gene utilization in the regulation of hemochorial placentation [rTS_Diff_PLAC1_KD]

city: Ames

first: Geetu

last: Tuteja

state: IA

address: 2106 Molecular Biology Building

department: Genetics, Development and Cell Biology

country: USA

institute: Iowa State University

summary: Placenta enriched 1 (PLAC1) is a highly conserved X chromosome-linked gene prominently expressed in the mammalian placenta. The functions of PLAC1 in placentation have yet to emerge fully. The rat shares hemochorial placentation and deep intrauterine trophoblast cell invasion with the human. Herein, we investigated the expression and biological activities of PLAC1 in the rat and human placenta.  Plac1 transcripts were prominently expressed in the junctional zone of the rat placenta, a structure analogous to the extravillous trophoblast cell column of the human placentation site, and in invasive trophoblast cells. A PLAC1 mutant rat model was generated using CRISPR/Cas9 genome editing and used to investigate the role of PLAC1 in rat placentation. Plac1 mutant animals exhibited placentomegaly. Enlarged placentas were characterized by an expanded junctional zone, an irregular junctional zone-labyrinth zone boundary, and a prominent depletion of invasive trophoblast cells within the uterine parenchyma. PLAC1 was required for rat trophoblast stem (TS) cell differentiation. In human TS cell development, PLAC1 does not contribute to the regulation of the human invasive/extravillous trophoblast cell lineage, but instead, PLAC1 expression and actions were linked to syncytiotrophoblast differentiation. Thus, PLAC1 is critically involved in hemochorial placentation; however, the responsive trophoblast cell lineages and its contributions to placentation are fundamentally distinct in the rat versus human.

overall_design: Rat Trophoblast stem (TS) cell transduced with control shRNAs (shSCR)  were used as controls. Cells transduced with  shRNAs targeting PLAC1 (shPLAC1) were used as treatment. RNA-seq was performed in control and treatment cells after 15 days of differentiaiton. 3 biological replicates each conditions (shPLAC1 and shSCR)

first: Ayelen

last: Moreno-Irusta

first: Jovana

last: Rajovic

first: Khursheed

last: Iqbal

first: Arun

middle: S

last: Seetharam

first: Jackson

last: Nteeba

first: Regan

middle: L

last: Scott

first: Marija

last: Kuna

first: Masanaga

last: Muto

first: Keisuke

last: Kozai

first: Andjelka

last: Celic

first: Hiroaki

last: Okae

first: Takahiro

last: Arima

first: Michael

middle: J

last: Soares


title: Comprehensive Molecular and Functional Analysis of NUTM1-Rearranged Leukemia

city: Suita

first: Masaki

last: Nomura

state: Osaka

address: 2-2, Yamadaoka

department: Department of Cancer Pathology

institute: Graduate School of Medicine, The University of Osaka

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Slowed R-loop processing due to defective loading of RNAseH1 by the RPA complex characterizes premature oncogene-induced senescence

city: Udine

first: Raffaella

last: Picco

address: P.le Kolbe 4

department: Department of Medicine

country: Italy

institute: University of Udine

summary: Genome stability is important for organisms and its maintenance depends significantly on the successful activation of the DNA damage response (DDR) and the role of non-canonical chromatin structures (NCSs), which regulate genome replication, transcription and DNA repair. In senescent cells, defective DDR often results in the accumulation of unrepaired DNA damage. Among NCSs, R-loops are three-stranded RNA-DNA hybrids, consisting of a nascent RNA strand that attaches to the DNA template, forming a hybrid that displaces the non-template single-strand DNA (ssDNA). R-loops influence crucial cellular processes and many factors, such as RNase H enzymes, regulate their processing. Additionally, the ssDNA-binding protein RPA enhances RNase H activity to repress R-loops and prevent genomic instability. Dysregulation of proper R-loop processing - excessive accumulation or excessive processing - can lead to increased genomic instability and DNA damage. In this study, we aimed to understand the mechanisms that ensure proper control of R-loops, leading to efficient DNA repair of exogenously induced DSBs, in particular in a senescent context. Efficient DSB repair is ensured by proper kinetics of R-loop processing, which enables precise non-homologous end joining (NHEJ) and homologous recombination (HR). Our experiments revealed that late processing or early degradation of R-loops at DSBs induced by endonucleases alters accurate DNA repair. Therefore, the precise timing of R-loop formation and resolution is crucial for the HR and NHEJ pathway selection and for DSB repair. Using three different models (U2OS EJ5-GFP and U2OS TRI-DR-GFP cells, a deadCas9-based delivery system and LacO-TetO system), we found that forced recruitment of both catalytically active and inactive RNase H1 to DSBs delays DNA repair. This suggests that both premature and delayed removal of R-loops affects DNA repair and the recruitment of repair protein at DSBs. By investigating R-loops’ role in genome stability, our findings showed impaired R-loops control and processing at DSBs in BJ fibroblasts engineered to express the HRASG12V oncogene, a model for oncogene-induced senescence (OIS), compared to proliferating cells and BJ fibroblasts escaping OIS via HDAC4 overexpression. Cells undergoing OIS accumulate more R-loops than proliferating fibroblasts and only a small fraction of them supported BRCA1 loading. DRIP-seq and R-ChIP experiments revealed that unsuccessful recruitment of RNase H1 by the RPA complex to R-loops impairs DDR protein loading at DSBs in OIS cells compared to proliferating and OIS-escaped cells. The trimeric RPA complex, consisting of RPA70, RPA32 and RPA14 subunits, binds to ssDNA and regulates RNase H1 recruitment to R-loops. Our research identified RPA32 phosphorylation (pRPA32) as the signal controlling RNase H1 activity at R-loops in correspondence to DSBs. Hyperphosphorylation of the RPA complex observed in pre-senescent cells alters this mechanism, leading to disassembly of the RPA/RNase H1 complex, accumulation of long-lived R-loops and irreparable DNA damage. Mass spectrometry, surface plasmon resonance (SPR) and in vitro experiments confirmed the decreased processing kinetics of RNase H1 in the presence of pRPA32. Since the molecular details of proper R-loop resolution are not yet fully understood in the literature, modulating R-loop processing kinetics could offer a new therapeutic approach to prevent the development of senescence and replication stress, thereby enhancing DSB repair efficiency.

overall_design: Chromatin was purified from each BJ clones at day 2 or day 8, as indicated, after the treatment with 4-OHT (1mM) to induce the expression of HRAS G12V.

first: Cortolezzis

last: Ylenia

first: Picco

last: Raffaella

first: Tolotto

last: Vanessa

first: D'Este

last: Francesca

first: Gualandi

last: Nicolò

first: Xodo

last: Luigi

first: Di Giorgio

last: Eros


title: Species-specific gene utilization in the regulation of hemochorial placentation [BeWo_PLAC1_KD]

first: Geetu

last: Tuteja

overall_design: Choriocarcinoma-derived BeWo cells transduced with control shRNAs (shSCR)  were used as controls. Cells transduced with  shRNAs targeting PLAC1 (shPLAC1) were used as treatment. RNA-seq was performed in control and treatment cells after 6 days of differentiaiton to syncytiotrophoblast (ST-3D). 3 biological replicates each conditions (shPLAC1 and shSCR)BeWo_PLAC1_KD samples with 3 biological replicates each for 2 conditions (control and KD)

first: Ayelen

last: Moreno-Irusta

first: Jovana

last: Rajovic

first: Khursheed

last: Iqbal

first: Arun

last: Seetharam

first: Jackson

last: Nteeba

first: Regan

last: Scott


title: Gut Microbiota Modulation of Regulatory DNA Elements revealed by Massively Parallel Functional Characterization

city: Singapore

first: Benson

last: Chen

address: 60 Biopolis Street, Genome, #04-01

department: Genome Institute of Singapore

country: Singapore

institute: A*STAR

summary: The human genome contains millions of DNA cis-regulatory elements (CREs) that regulate gene expression across different cell types. In liver hepatocytes, CREs enable adaptation to environmental changes by modifying transcriptomes, particularly in response to gut microbiome signals, which are linked to liver diseases. However, our understanding of the functionality of CREs and their responses to gut microbiota signals in vivo remains limited. To address this, we conducted a genome-wide multiplexed reporter assay (MPRA) to map functional CREs in the liver. Using this functional catalog, we discovered a rare functional variant associated with hepatocellular carcinoma in the Asian population that disrupts CRE activity. Additionally, we identify functional CREs regulated by gut microbiota. Overall, this study enhances our understanding of functional CREs and highlights the complex interactions between the gut microbiome and host gene regulation.

overall_design: Functional analysis of ~110,000 sequence regions was conducted utilizing massively parrallel reporter assays in mouse liver and human HepG2 cells.

first: Chadmirah

last: Zaratiana

first: Tiffany

last: Liu

first: Yong-An

last: Lee

first: Agnes

last: Ong

first: Samantha

last: Chang

first: Torsten

last: Wuestefeld

first: Poshen

middle: B


title: Suppression of UCP2 alleviates leukemogenesis by enhancing branched amino acids induced oxidative stress via activating PI3K/AKT/mTOR signaling

city: Shanghai

first: JIAO

last: MA

address: Huangpu District

institute: Shanghai Jiao Tong University School of Medicine

summary: Although the cellular role of uncoupling protein 2 (UCP2) in tumorigenesis have been reported in various solid tumor models, its role in leukemogenesis remain elusive. Here, we demonstrated that UCP2 was highly expressed in AML, and it is significantly associated with chemoresistance and poor prognosis suggesting that UCP2 can be a potential biomarker for AML treatment. Mechanically, in vitro and in vivo silencing of UCP2 significantly impairs AML cell growth, survival and accompanied with the disruption of mitochondria homeostasis. Interestingly, RNA-seq analysis and metabolic mass spectrometry revealed that silencing UCP2 results in accumulation of branched chain amino acids (BCAA), which in turn induced oxidative stress through activating PI3K/AKT and mTOR signaling pathway. Additionally, lack of BCAA restored leukemic cell growth, cell survival and decreased mitochondria ROS production which is induced by inhibiting UCP2. Notably, supplementation of BCAA enhanced anti-tumor activity of Genipin, a selective inhibitor that targets UCP2, results in significant reduction of AML blasts, increased mice survival and magnified oxidative stress. Taken together, our study elucidates the rationale of targeting UCP2-BCAA-PI3K/AKT/mTOR signaling axis in leukemogenesis and provide a novel strategy for leveraging the metabolic dependencies of leukemic cells.

overall_design: RNA-seq profiling of AML cells and their UCP2 knockdown derivatives (shUCP2 Ctrl，shUCP2 #1, shUCP2#2)

first: Ma

last: Jiao

first: Innocent-Okohi

last: Agida

first: Zizhen

last: Xu


title: Neonatal Roselovirus Infection Induces Predisposition to Systemic Autoimmunity

status: Public on Apr 21 2026

city: St. Louis

first: Tarin

last: Bigley

state: MO

address: 1 Children's Pl

department: Pediatrics

institute: Washington University in St. Louis

summary: Autoimmune diseases are characterized by immune dysregulation that begins years prior to the onset of overt disease. Viral infections have been proposed to be a contributing factor to the development of autoimmunity, but in the case of herpesviruses, the onset of autoimmune disease typically occurs years after the initial, acute infection. In this study, we found that adult mice that had been neonatally infected with MRV were predisposed to systemic autoimmunity with features of lupus-like disease after additional immune perturbation with TLR7 stimulation. Single-cell RNA sequencing demonstrated a transcriptional signature and TCR repertoire shift in response to TLR7 stimulation that was unique to prior neonatal infection. .

overall_design: C57BL/6 mice were mock or neonatally infected on day-of-life 0. Starting at 8 weeks, mice were treated 3 times per week topically with vehicle control or R848. At 13 weeks, the spleen was isolated and minced. Single cell suspension was prepared to single cell RNA sequencing with TCR and BCR sequencing using 5'-technology. Each group consist of cells from three mice that were combined.

first: Nillu

last: Ghosh

first: Francisco

last: Victorino

first: Kaarunya

last: Nachimuthu


title: Stable global repertoire architecture masks short- term clonal remodeling in intratumoral TCR repertoires

city: Odense M

first: Sofie

last: Traynor

address: Fioniavej 36

country: Denmark

institute: University of Southern Denmark

summary: Background: Tumor-in ltrating T cell receptor repertoires are increasingly pro led to assess intratumoral T cell dynamics and inform prognosis and treatment response. Most analyzes rely on aggregate diversity metrics, such as Shannon index or clonality, which describe overall repertoire structure but do not resolve changes in clonotype identity over time. Thus, intrinsic temporal dynamics of intratumoral T cell receptor repertoires during tumor progression remain incompletely de ned. Methods: In a bilateral murine cancer model, one tumor was surgically removed, and the paired tumor was collected 11 days later. The T cell receptor repertoires of these tumors, and of synchronously harvested bilateral tumors from separate control animals, were analyzed using diversity metrics, Morisita–Horn similarity, and clonal tracking approaches. Results: Time-matched bilateral tumors exhibited highly similar clonotype composition and abundance. In contrast, time-separated tumors showed reduced clonal overlap, increased fractions of private clonotypes, and redistribution of dominant clones. These changes occurred despite preserved global repertoire metrics, including clonotype number, Shannon diversity, and Gini coef cient. Conclusion: Short-term tumor progression is associated with clear changes in the composition of the intratumoral T cell receptor repertoire, even when overall diversity appears stable. These results suggest that relying solely on global diversity metrics can obscure active clonal remodeling, underscoring the importance of monitoring individual T cell clonotypes to accurately capture intratumoral T cell dynamics over time.

overall_design: TCR sequencing of murine bilateral tumors in a time-matched or time-separated setting with or without treatment with decitabine. Three mice included per group

first: Pernille

middle: G

last: Pedersen

first: Odd

last: Gammelgaard

first: Christina

last: Ruhlmann

first: Aida

last: Hansen

first: Henrik

last: Ditzel

first: Morten

middle: F

last: Gjerstorff

first: Mikkel

last: Terp


title: Single-Cell Spatial Mapping of Human Kidney Development Reveals Cellular Niches and Lineage Dynamics

city: Philadelphia

first: Jonathan

last: Levinsohn

state: PA

address: 3400 Civic Center Blvd, Smilow 12-188

institute: University of Pennsylvania

summary: Organ development is shaped by both cell-autonomous changes and critical environmental cues. While single-cell genomic tools have enabled the characterization of gene expression and regulatory transitions during development, they have not fully captured the influence of neighboring cells. In this study, we combined single-cell spatial transcriptomics with gene expression data to investigate how cellular interactions influence human kidney development. By analyzing a large collection of fetal human kidney samples, we defined cellular differentiation patterns and uncovered two novel differentiation trajectories for parietal epithelial cells, suggesting greater developmental plasticity than previously recognized. Furthermore, using spatial gene expression data we identify novel spatially plausible ligand-receptor interactions that likely mediate differentiation processes. Among these, we highlight the role of WNT, FGF, and RET signaling, which have been classically described in mouse nephrogenesis but are now observed in human kidney development. In examining ligand expression, we estimate and quantify the microenvironment for each cell, enabling us to identify ligands associated with driving differentiation trajectories, and identify microenvironments which predict gene expression within cell types and differentiation status. Using this approach, we identified IGF2-mediated signaling as enriched within the blastema and associated with renewal signals suggesting its role as a niche renewal factor. This finding may explain the alterations in nephrogenesis associated with uncontrolled maternal diabetes, providing new insights how the local cellular environment shapes cellular differentiation in the kidney and potential therapeutic interventions.

overall_design:
We profiled RNA from 5 human fetal kidneys of varying gestational ages. We profiled each kidney once using single cell RNA sequencing.

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We cannot submit the raw reads as that would be potentially identifiable information
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first: Levinsohn

last: Jonathan

first: Susztak

last: Katalin

first: Abedini

last: Amin


title: A novel histone H3K27 reader, CBFA2T2, inhibits H3K27me3 demethylation and tumor growth by regulating metabolic genes and metabolite levels [ChIP-seq II]

first: Rui

last: Guo

address: 131 DongAn Road

institute: Institutes of Biomedical Sciences, Fudan University

summary: Histone H3.1/3.2K27M and H3.3K27M mutation are driver mutations frequently identified in diffuse midline glioma (DMG). However, the precise mechanism by which H3K27M mediates tumorigenesis remains incompletely understood. By carrying out bait Protein-Protein Interaction followed by genome-wide screening (bPPI-seq) in H3.3WT and H3.3K27M mouse NSC models, we identified a novel histone reader CBFA2T2, which recognizes non-mutated or un-modified histone H3K27. Importantly, CBFA2T2 binding to H3K27, mediated by the NHR2 domain, is abrogated by the H3K27M oncogenic mutation. In H3.3 wildtype cells, CBFA2T2 represses transcription of genes involved in carbon metabolism and TCA cycle through its binding to H3K27. This alters the α-KG/Succinate (alpha-ketoglutarate/ Succinate) ratio and indirectly impacts H3K27me3 level, possibly through affecting the H3K27me3 demethylases. CBFA2T2 does not bind the H3.3K27M decorated chromatin in vivo, thus the K to M mutation, partially compromises the CBFA2T2 repressive function. However, over-expressing CBFA2T2 rescues the low H3K27me3 level in H3.3K27M mNSC and H3.3K27M DIPG cells, thus suppressing the H3.3K27M tumor growth. Our findings suggest a new mechanism, which may contribute to the low H3K27me3 level observed in the H3K27M cells, and provide a new strategy for H3K27M therapy through manipulation of CBFA2T2.

overall_design: To generate H3.3WT and H3.3WT Cbfa2t2 knockout (KO) cells, we first knocked out H3f3a in a p53-deficient neuronal stem cell line, NE-4C (referred to as H3f3a KO). Subsequently, we knocked out Cbfa2t2 in the H3f3a KO cells, resulting in H3f3a/Cbfa2t2 double knockoutcells.We then stably expressed HA-tagged wild-type H3.3 in both H3f3a KO and H3f3a/Cbfa2t2 double knockout cells. To generate H3.3K27M cells, we stably expressed HA-tagged H3.3K27M in H3f3a KO cells. Finally, we performed ChIP-seq using various antibodies in these three cell lines.

first: Shengfei

last: He


title: Host-pathogen dual targeting with repurposed drugs identifies a synergistic therapy for intracellular Staphylococcus aureus

city: León

first: Blanca

last: Lorente Torres

address: Cjón. Campus de Vegazana s/n

country: Spain

institute: Universidad de León

summary: Background: Staphylococcus aureus causes persistent infections by surviving intracellularly, where it escapes immune defenses and antibiotics. Repurposing clinically approved drugs provides a rapid strategy to expand therapies against intracellular pathogens. Methods: A high-throughput screen of 5,599 approved compounds was performed in A549 cells infected with S. aureus USA300 LAC. Hits were validated across CA-MRSA, HA-MRSA, and MSSA strains and in non-tumorigenic bronchial epithelial cells. Mechanistic studies combined metabolomics, dual RNA sequencing, and DNA repair mutant panels. Efficacy was assessed in Galleria mellonella and a murine pneumonia model. Results: The nucleoside analog 5-fluoro-2′-deoxycytidine (5-FdC) and rifapentine formed a synergistic combination (5FR) effective across strains and host cell types. 5-FdC induced structural DNA damage beyond thymineless death, confirmed in DNA repair mutants, and triggered host DNA damage responses and metabolic rewiring. Dual RNA-seq revealed bacterial growth arrest alongside host stress pathway activation. The 5FR combination significantly reduced bacterial burdens in larvae and in murine lungs and spleen. Conclusions: This integrative pipeline, from screening to in vivo validation, identifies 5FR as a promising repurposed drug combination against intracellular S. aureus. Targeting both host and pathogen pathways may overcome monotherapy limitations, reduce resistance risk, and expand therapeutic options.

overall_design: RNA-seq profiling of A549 cells treated with 5-Fluoro-2'-deoxycytidine (candidate treatment) to investigate host transcriptional responses associated with the control of intracellular Staphylococcus aureus.

last: Lorente-Torres

first: Helena

last: Á. Ferrero

first: Pablo

last: Castañera

first: Jesús

last: Llano-Verdeja

first: Sergio

last: Fernández-Martínez

first: Amanda

last: Herrero-González

first: Farzaneh

last: Javadimarand

last: F. Aparicio

first: Andrew

last: M. Edwards

first: Volker

last: Behrends

first: Luis

last: M. Mateos

first: Álvaro

last: Mourenza

first: Michal

last: Letek


title: Comprehensive Molecular and Functional Analysis of NUTM1-Rearranged Leukemia [leukemia-RNA-seq]

first: Masaki

last: Nomura

summary: NUTM1-rearrangement (NUTM1-r) represents a significant subset of infant B-ALL, particularly prevalent in cases lacking KMT2A-rearrangements (KMT2A-r). However, the underlying molecular mechanisms for the characteristic leukemia have not been fully elucidated. Our comprehensive analysis reveals that NUTM1-r infant leukemia is characterized by a unique transcriptomic and epigenetic landscape with global hypomethylation, delineating a discrete leukemia entity. Functional interrogation of the BRD9-NUTM1 fusion demonstrates its dual role in promoting B-lineage commitment while conferring leukemic stem cell properties. Strikingly, single transduction of BRD9-NUTM1 is sufficient to induce serially-transplantable pro-B-like leukemia in vivo, recapitulating key features of human NUTM1-r B-ALL, including NUTM1 overexpression, skewed B cell transcriptional programs, and low CD34 expression. Mechanistically, BRD9-NUTM1 expression gives rise to distinctive open chromatin regions with global enhancement of H3K27Ac, particularly at loci associated with Myc, NF-κB, and posterior Hoxa genes. Notably, BRD9-NUTM1 leukemic cells responded robustly to cytarabine, in contrast to the relative resistance observed in KMT2A-r leukemias. Interestingly, our findings highlight a discrepancy observed in the clinical behavior of NUTM1-r leukemias, where the transformed cells display characteristics of stemness, yet tend to lose these properties under chemotherapy due to the dependence on active transcription. Our findings delineate the unique molecular profile of NUTM1-r leukemias, suggesting opportunities for targeted therapies that exploit these specific vulnerabilities.

overall_design: BRD9-NUTM1 (BN1), MLL-AF9 (MA9) and MLL-ENL (ME) murine leukemic cells were sorted by FACS. RNA was extracted, then Poly(A)- selected, and stranded RNA libraries were prepared.

first: Koutarou

last: Nishimura

first: Weijia

last: Zang

first: Daichi

last: Inoue


title: Identification of two genes associated with recurrence in Paget’s disease and construction of a predictive model

city: Fuzhou

first: Pengfei

last: Cha

address: 243xihong road

institute: Fuzhou Dermatology Hospital

summary: In summary, RNA‑seq analysis revealed distinct functional profiles between MPD and EMPD, with recurrence in MPD associated with developmental and differentiation pathways, while EMPD recurrence was linked to immune and inflammatory processes. Using WGCNA, we identified KLF13 and TIA1 as hub genes, which were subsequently validated as independent prognostic biomarkers in internal and external datasets. A risk‑score model based on these genes effectively stratified patients by outcome. Further studies are needed to elucidate the detailed molecular mechanisms underlying their roles in PD progression and recurrence.

overall_design:
A total of 11 patients with EMPD and 28 patients with MPD were enrolled in this study.All participants provided written informed consent voluntarily. Inclusion criteria were: (1) primary tumor resection with R0 margins and no prior treatment; (2) pathological confirmation of Paget cells within the tumor; (3) age between 18 and 80 years; and (4) EMPD tumor originating from the perineal region, specifically the external genitalia, anus, and perineal skin. Patients were excluded if they: (1) had a history of or concurrent other malignancies, or (2) presented with distant metastasis at diagnosis.

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Submitter states that missing raw files are due to file loss.
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title: Spatiotemporal transcriptomics characterizes immune microenvironment during mouse liver aging [Spatial Transcriptomics]

city: Wuhan

first: Jie

last: Cheng

state: Hubei

address: 13 Hangkong Road, Qiaokou District

department: School of Basic Medicine

institute: Huazhong University of Science and Technology

summary: The liver is a major metabolic organ, responsible for synthesizing and breaking down diverse metabolites. Recently, the liver's immunological functions have gradually been unveiled: combating pathogens and maintaining tissue homeostasis. Age-related functional alterations in these immune cells emerge as potential drivers of hepatic dysfunction and age-associated pathologies. However, systematic investigations into spatiotemporal immune cell dynamics during liver aging remain limited. To address this gap, we analyzed young and old mouse livers using single-cell/nuclei and spatial transcriptomics, revealing T cells as the immune cell population with the most pronounced transcriptomic alterations, marked by enrichment of exhausted CD8+ T cells in aged livers. Spatial mapping showed exhausted CD8+ T cells accumulating in portal vein (PV) zone, co-localizing with periportal hepatocytes (PP hepatocytes). Up-regulation of LPIN1 in PP hepatocyte promoted T cell exhaustion. CD8+ T cell exhaustion was tightly associated with disease progression. Therefore, our findings suggest that targeting LPIN1 may alleviate T cell exhaustion, offering potential therapeutic strategies for age-related liver diseases.

overall_design: We collected livers from young and aged mice and performed single-cell transcriptomics (on CD45+ cells only), single-nucleus transcriptomics (on all liver cells), and spatial transcriptomics to investigate changes in the hepatic immune microenvironment during aging.

first: Jiahua

last: Lu

first: Yuqian

last: Wang

first: Wenxue

last: Zhao

first: Zihao

first: Zhaoya

last: Gao

first: Jin

last: Gu

first: Cheng

last: Li


title: ATAC-seq profiling reveals that KLF2 regulates chromatin accessibility programs in HCC

city: Nanchang

first: Xiaohua

last: Yan

address: No. 1299, Xuefu Avenue, Honggutan

institute: Nanchang University

summary: Krüppel-like factor 2 (KLF2) is a tumor-suppressive transcription factor implicated in the regulation of epithelial-mesenchymal plasticity in hepatocellular carcinoma (HCC). In this study, we performed ATAC-seq in HCCLM3 human HCC cells with or without KLF2 overexpression to characterize KLF2-associated changes in chromatin accessibility. Comparative analysis was used to identify differentially accessible chromatin regions and to investigate how KLF2 affects the transcriptional programs associated with Hippo/YAP signaling and EMT/pEMT-related cell plasticity.

overall_design: ATAC-seq of HCCLM3 human HCC cell lines ± KLF2 overexpression

first: Yining

first: Yunjie

last: Liu

first: Hua

last: Yu


title: Single-cell sequencing of carfilzomib-associated HSV-1 encephalitis mouse model

city: Guangzhou

first: Shen

last: Weishan

state: Guangdong

address: 58 Zhongshan 2nd Road

department: cirtical care medicine

institute: The First Affiliated Hospital, Sun Yat-sen University (FAH-SYSU)

summary: A murine model of central nervous HSV-1 infection was established by corneal scarification with HSV-1 to investigate the dynamic cellular composition and transcriptional landscape following administration of carfilzomib(CFZ). Brain tissues were collected 5 days post-HSV-1 inoculation at the onset of encephalitis symptoms. Mice were intraperitoneally administered CFZ or saline every other day from inoculation until euthanasia.

overall_design: The experimental cohorts for single-cell RNA sequencing (scRNA-seq) were organized as follows: HSV1-infection-CFZ_group-1(n=3); HSV1-infection-DMSO_group-1(n=3); Noninfection-control (n=1)；

first: Yaoxing

last: Wu

first: Weishan

last: Shen


title: Reprogramming CAR with cytokine signaling increases the efficacy of CAR-T cell therapy in solid tumour treatment and confers sustained immune memory [Tumor infiltrated CAR-T cells]

city: Nanjing

first: Rongchen

last: Sun

address: Longmian

institute: China Pharmaceutical University

summary: Chimeric antigen receptor (CAR) T-cell therapy has shown remarkable efficacy in hematologic malignancies but remains limited in solid tumors because of the immunosuppressive microenvironment, tumor heterogeneity, poor immune-cell infiltration, and progressive T-cell dysfunction. Because cytokine costimulation is critical for maintaining T-cell fitness, we developed a modular engineering strategy, distinct from previous approaches based on direct insertion of large cytokine receptor fragments, in which the intracellular CAR signaling domain was reconstructed to incorporate compact IL-2/IL-15 receptor–derived activation motifs, thereby enabling antigen-dependent coactivation while preserving the overall architecture of the parental CAR. Through systematic screening, we identified S71 as the optimal construct, with significantly greater antitumor activity than other mutants across multiple solid and hematologic tumor targets. Mechanistically, S71 rewired CAR signaling and reprogrammed tumor-induced metabolic responses through a self-sustaining mechanism, improving mitochondrial function and supporting durable T-cell activity. Functionally, S71 promoted enhanced persistence and robust immune memory responses against solid tumors. These findings demonstrate that modular integration of cytokine signaling motifs into CAR intracellular domains can improve CAR-T-cell fitness and antitumor efficacy, and they establish S71 as a promising strategy for overcoming barriers to CAR-T-cell therapy in solid tumors.

overall_design: 15 days after reinfusion of 28Z CAR-T or S71 CAR-T cells into tumor-bearing mice, tumor tissues from five mice per group were dissociated into single-cell suspensions. CD3+ CART cells were enriched using magnetic-activated cell sorting (MACS), and bulk RNA sequencing was performed on the isolated CD3+ tumor-infiltrating CART cells from each mouse.

first: Xue

last: Yang

first: Changshuai

last: Che


title: SIRT1 involvement in the metabolism and differentiation of human stem cells.

city: Mexico City

first: Alejandro

middle: Alarcón

last: Del Carmen

state: Mexico City

address: Circuito Mario de la Cueva

department: Cell Biology

country: Mexico

institute: Instituto de Investigaciones Biomédicas

summary: SIRT1, a histone deacetylase enzyme, is implicated in cellular differentiation and metabolic regulation. However, its dynamic transcriptomic role remains elusive. Here, we investigate SIRT1's involvement using H9 human embryonic stem cells (hESCs) with complete SIRT1 deletion (H9 SIRT1 -/-) undergoing dopaminergic neuron differentiation, followed by scRNAseq analysis

overall_design: H9 human embryonic stem cells (hESCs) from the H9 line (WA09, WiCell Research Institute Inc.) were subjected to a differentiation protocol towards dopaminergic neurons. Two conditions were utilized: H9 wild-type (WT) and H9 SIRT1 knockout (KO), along with two time points during the differentiation process, day 0 and day 6. Each sample was performed as a single replicate.

first: A

last: Alarcón del Carmen

first: E

last: Sánchez-Ramírez

first: L

last: Aguilar-Arnal

first: V

last: Valdes

first: N

last: Cano-Domínguez


title: The XPO7-NPAT axis represents key vulnerabilities in TP53-mutated acute myeloid leukemia (ATAC-Seq)

city: Fukuoka

first: Yuichiro

last: Semba

address: 3-1-1 Maidashi

institute: Kyushu University

summary: Mutation of TP53, a tumor suppressor in cancer, is common and leads to extremely poor prognosis. To identify vulnerabilities in TP53-mutated tumors, we performed genome-wide CRISPR/Cas9 screens using isogenic Trp53 wild-type and knockout mouse acute myeloid leukemia (AML) lines. Here, we show that histone gene regulation governed by the XPO7-NPAT pathway is essential for survival of TP53-mutated AML cells. In TP53 wild-type cells, XPO7 enhances p53 nuclear localization and functions as a tumor suppressor, but in TP53-mutated cells, XPO7 promotes cell proliferation by retaining NPAT, a histone gene activator, in the nucleus. NPAT depletion led to genome-wide histone loss, enhancing vulnerability to genotoxic stress. Human AML cases show predominant expression of XPO7 and NPAT when TP53 is mutated, suggesting a potential therapeutic vulnerability.

overall_design: To assess both local and global chromatin accessibility in the presence or absence of Npat, we next performed ATAC-Seq (for assay for transposase-accessible chromatin with high-throughput sequencing) over a 0, 3 and 12h time course using Trp53KONpat_FK2AGFP AML cells, with or without dTAGV-1 treatment.


title: Dynamic NFκB control during B-lymphopoiesis ensures proteostasis to enable phased proliferation and differentiation decisions

city: Los Angeles

first: Apeksha

last: Singh

state: CA

address: 570 Boyer Hall

institute: University of California, Los Angeles

summary: Aging and inflammation reduce the bone marrow B cell output. While myeloid bias among multipotent progenitors is one cause, how the developmental cascade of B-committed progenitors is affected remains less well characterized. Here, we identify dynamic modulation of NFκB as a hallmark of healthy lymphopoiesis, which is diminished in aged, B-lymphopenic mice. Indeed, dysregulated NFκB dynamics result in severe B-lymphopenia. Model-aided analysis of in vivo progenitor populations and ex vivo experimental time courses reveal that accelerated differentiation of pro-B cells results in skipping critical proliferative phases. Single-cell transcriptomics confirmed premature cell-state transitions, characterized by inappropriate activation of NFκB target genes that cause wholesale increases in protein synthesis rates. This imbalanced proteostasis leaves little spare energetic capacity to support population expansion and impairs the functionality of the few B cells that do emerge. Our findings indicate that developmental NFκB dynamics pace and safeguard B-lymphopoiesis, thereby identifying additional mechanistic causes of age-associated humoral immune deficiency.

overall_design: Bone marrow from a C57BL/6J and an IκB – mouse was isolated and lymphoid progenitors were magnetically enriched as previously described using the biotinylated antibodies at a concentration of 1:50 in staining panel 12. Following enrichment of the lymphoid progenitors, the cells were surface marker-stained using staining panel 9 as previously described. The cells were then sorted with the BD FACSAriaIII sorter in UCLA Janis V. Flow Cytometry Core Laboratory with adequate compensation setup by using UltraComp eBeads™ Compensation Beads and live cells with staining antibodies prior to actual sample sorting. We sorted approximately 204,000 WT and IκB – fraction A-B cells and added 10ng of yeast RNA (strain BY7473, generous gift from T.L. Johnson lab) per 100,000 cells as an internal control. The RNA samples were then submitted to UCLA Technology Center for Genomics & Bioinformatics for library preparation and were sequenced using Novaseq X Plus 10B (1250M/lane). Raw data were filtered for adaptor sequences with cutadapt 4.1 69 with Python 3.10.8. Reads were processed by first concatenating the murine GRCm39 and yeast R64 genomes and annotations, and then aligning with STAR 2.7.1a. Default parameters were used except outFilterType BySJout, outFilterMultimapNmax 20, alignSJoverhangMin 8, alignSJDBoverhangMin 1, and seedSearchStartLmax 30. Aligned reads were filtered based on mapping score (MAPQ≥30) by Samtools 1.9 and transcript counts were quantified using featureCounts v1.6.5. Data were then normalized by dividing counts for each mouse gene by the total number of yeast transcripts and scaling by 1e6.

first: Valentina

last: Alonso

first: Yu-sheng

last: Lin

first: Alexander

last: Hoffmann


title: Species-specific gene utilization in the regulation of hemochorial placentation [hTS_CT27_ST3D_PLAC1_KD]

city: Ames

first: Geetu

last: Tuteja

address: 2106 Molecular Biology Building

institute: Iowa State University

summary: Placenta enriched 1 (PLAC1) is a highly conserved X chromosome-linked gene prominently expressed in the mammalian placenta. The functions of PLAC1 in placentation have yet to emerge fully. The rat shares hemochorial placentation and deep intrauterine trophoblast cell invasion with the human. Herein, we investigated the expression and biological activities of PLAC1 in the rat and human placenta.  Plac1 transcripts were prominently expressed in the junctional zone of the rat placenta, a structure analogous to the extravillous trophoblast cell column of the human placentation site, and in invasive trophoblast cells. A PLAC1 mutant rat model was generated using CRISPR/Cas9 genome editing and used to investigate the role of PLAC1 in rat placentation. Plac1 mutant animals exhibited placentomegaly. Enlarged placentas were characterized by an expanded junctional zone, an irregular junctional zone-labyrinth zone boundary, and a prominent depletion of invasive trophoblast cells within the uterine parenchyma. PLAC1 was required for rat trophoblast stem (TS) cell differentiation. In human TS cell development, PLAC1 does not contribute to the regulation of the human invasive/extravillous trophoblast cell lineage, but instead, PLAC1 expression and actions were linked to syncytiotrophoblast differentiation. Thus, PLAC1 is critically involved in hemochorial placentation; however, the responsive trophoblast cell lineages and its contributions to placentation are fundamentally distinct in the rat versus human.

overall_design: CT27 Trophoblast stem (TS- Okae et.al.) cell transduced with control shRNAs (shSCR)  were used as controls. Cells transduced with  shRNAs targeting PLAC1 (shPLAC1) were used as treatment. RNA-seq was performed in control and treatment cells after 6 days of differentiaiton to syncytiotrophoblast (ST-3D). 3 biological replicates each conditions (shPLAC1 and shSCR)

first: Ayelen

last: Moreno-Irusta

first: Jovana

last: Rajovic

first: Khursheed

last: Iqbal

first: Arun

last: Seetharam

first: Jackson

last: Nteeba

first: Regan

last: Scott

first: Marija

last: Kuna

first: Masanaga

last: Muto

first: Keisuke

last: Kozai

first: Andjelka

last: Celic

first: Hiroaki

last: Okae

first: Takahiro

last: Arima

first: Michael

last: Soares


title: Species-specific gene utilization in the regulation of hemochorial placentation [PLAC1_placenta_13.5]

overall_design: gd 13.5 placental tissue from Plac1 mutant rats and wild type rats (5 biological replicates each)


title: Species-specific gene utilization in the regulation of hemochorial placentation [PLAC1_JZ_18.5]

overall_design: RNA-seq was performed in the junctional zone of the Wild Type or PLAC1 mutant placentation at gd 18.5.gd  (5 biological replicates for mutants and 4 for wildtype)


title: Species-specific gene utilization in the regulation of hemochorial placentation [CT29_ST3D_PLAC1_KD]

overall_design: CT29 Trophoblast stem (TS- Okae et.al.) cell transduced with control shRNAs (shSCR)  were used as controls. Cells transduced with  shRNAs targeting PLAC1 (shPLAC1) were used as treatment. RNA-seq was performed in control and treatment cells after 6 days of differentiaiton to syncytiotrophoblast (ST-3D). 3 biological replicates each conditions (shPLAC1 and shSCR)


title: Identification of PLXNC1 as a novel biomarker for Consensus Molecular Subtype 4 in colorectal cancer

city: Beijing

first: Mingxuan

last: Zhou

state: China

address: No. 2 Nanwei Road, Tianqiao Street

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences

summary: Colorectal cancer (CRC) is the third most diagnosed cancer worldwide. Tumor heterogeneity often causes inconsistent outcomes and drug responses among patients with CRC. Although a recent unified transcriptomic classification categorizes most CRC into four consensus molecular subtypes (CMSs) with clear clinical interpretability, it has not been translated to a routine clinical examination due to the lack of biomarkers. Therefore, it is urgent to find new biomarkers for CMS subtypes. We compared the expression of PLXNC1 in CRC and adjacent tissues using public databases and immunohistochemistry. We then analyzed the impact of PLXNC1 on survival probability by the Kaplan-Meier plot, Cox proportional risk model, and Nomogram diagram. Then we evaluated the accuracy of PLXNC1 in distinguishing CMS4 colorectal cancer. The microenvironment of tumor was investigated by deconvolution algorithms and single cell RNA-seq. We subsequently used siRNA interference and plasmid transfection techniques to detect the effects of PLXNC1 knockdown or overexpression on the proliferation, migration, and invasion of colorectal cells. We further established subcutaneously transplanted tumor models and liver metastasis models to investigate the key role of PLXNC1 in the growth and metastasis of colon cancer. We also verified the essential role of PLXNC1 in maintaining the CMS4-related phenotypes of CRC. PLXNC1 was distinctly upregulated in CRC compared to adjacent tissues. Patients with high PLXNC1 expression tend to have poor prognoses. The expression of PLXNC1 was capable to distinguish the CMS4 subtype from other subtypes. CRC with high expression of PLXNC1 exhibit a distinct mesenchymal phenotype, usually accompanied by high infiltration of stromal components, angiogenesis, complement activation, and immunosuppressive microenvironment. PLXNC1 promotes CRC growth and metastasis by regulating epithelial-mesenchymal transformation and immune escape. Knockdown of PLXNC1 reduced CMS4-related phenotypes in CRC. For the first time, we demonstrated that PLXNC1 can predict the poor prognosis of patients with CRC and accurately distinguish patients with CMS4 CRC. PLXNC1 contributes to the growth and metastasis of CRC by promoting the biological features associated with CMS4 CRC such as epithelial-mesenchymal transformation and immune escape.

overall_design: All the female 8-week-old C57BL/6 mice were purchased from Vital River Laboratory Animal Technology. PLXNC1-shRNA and NC-shRNA were designed and synthesized by Cyagen Biosciences to silence PLXNC1 in SL4 cells (mouse colon adenocarcinoma cell line). SL4 cells were cultured in DMEM medium (Gibco, Carlsbad, CA, USA) supplemented with 10% FBS and 1% P/S. Lentiviral vectors were transducted to SL4 cells at a multiplicity of infection of 10 to achieve ideal knockdown efficiency, target cells were harvested after 48 h and resuspended to 107 cells/ml in saline. shRNA target sequence was listed in Supplementary Table 4. For implanted subcutaneous tumor model, 100μl SL4 cells (106 cells) were injected into the left hind leg of C57 mice (n = 9 per group). Tumor growth in vivo was detected with PharmaScan 70/16 US (7.0 T, Bruker, Switzerland) MRI scanner on day 14, tumor volume was calculated as the sum of tumor area in each slice multiplied by slice thickness using Radiant software. Mice were sacrificed on day 14 after injection, tumors were dissected and weighed.

first: Min

last: Yang

first: Weiqi

last: Wang


title: Development of novel Hepatocellular Carcinoma drugs, JNK-IN-5A derivatives simultaneously induce Apoptosis and Necrosis

city: Maastricht

first: Han

last: Jin

address: P. Debyelaan 25

country: Netherlands

institute: Maastricht University

summary: In our previous study, we repurposed JNK-IN-5A to targeting PKLR gene which most co-related to hepatocellular carcinoma (HCC). Here, We showed anti HCC effect of JNK-IN-5A and its six derivative compounds SET135, SET156, SET158, SET159, SET171, and SET172 in HepG2 human HCC cell line. Compare to multi-target kinase inhibitor sorafenib and regorafenib, JNK-IN-5A and its 6 derivatives showed p53 induced cell cycle arrest, autophagy, apoptosis and reduced invasiveness. We found two derivatives which also has its own necrotic cell death pathway. SET135 showed p62/SQSTM1 induced autophgic necrotic cell death, and SET171 increased cellular ROS and lipid peroxidation induced necrotic cell death. Bioinformatics analysis also confirmed new derivatives has distinctive different cellular effect with stronger cell cycle arrest and apoptosis compare to sorafenib and regorfenib. Our new derivatives of JNK-IN-5A which has apoptotic and necrotic cell death inducer can be suggested as a new HCC drug candidate.

overall_design: 400,000 HepG2 WT cells were prepared in 6well plate and compounds were treated for 2days at 10μM.RNA samples for RNA sequencing were extracted with RNeasy Plus Mini Kit (74134, QIAGEN). RIN score of total RNA samples were measured using RNA 6000 Nano kit (5067-1511, Agilent). 2100 Bioanalyzer Instrument (G2939BA, Agilent) was used for RIN score test using electrophoresis. Samples with Rof IN score more than 8 were submitted to SZA Omics, Istanbul for RNA sequencing analysis.

first: Woonghee

last: Kim

first: Cheng

last: Zhang

first: Adil

last: Mardinoglu


title: scRNA-seq of cerebral organoids derived from CBP mutant iPSCs

city: Grand Rapids

first: Xiaobing

last: Shi

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

summary: CREB-binding protein (CBP/CREBBP) is a histone acetyltransferase essential for human development. Mutations in CBP are associated with Menke–Hennekam syndrome (MKHK), a neurodevelopmental disorder. To examine the impact of a disease-associated mutation, we performed single-cell RNA sequencing (scRNA-seq) on day 32 cerebral organoids derived from isogenic wild-type and CBP R1868 mutant human induced pluripotent stem cells (iPSCs). This scRNA-seq data captures cellular heterogeneity and gene expression programs during early neurodevelopment and reveals how the CBP R1868W mutation influences lineage specification and transcriptional states in human cerebral organoids.

overall_design: In vitro–cultured day 32 (D32) CBP WT and mutant cortical organoids were collected for scRNA-seq.

first: Longxia

last: Xu

first: Hongwen

last: Xuan


title: RNA-seq for NK-92, and NK-IL-7R-IM cells

city: Daejeon

first: In-Hwan

last: Jang

address: 125, Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea

department: Immunotherapy Research Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: Transcriptional profiling of IL-2 activated NK-92 cells compared to no cytokines activated NK-92 cells overexpressing IL-7R insertional mutation (NK-IL-7R-IM)

overall_design: Four-condition experiment, IL-2 activated NK-92 cells cultured for 2 days (IL-2-D2) or 4 days (IL-2-D4), and no cytokines activated NK-IL-7R-IM cells cultured for 4 days (IL-7R-IM). Biological replicates, 3 samples of IL-2 activated NK-92 cells cultured for 2 days, 3 samples of IL-2 activated NK-92 cells cultured for 4 days, and 3 samples of no cytokines activated NK-IL-7R-IM cells independently grown and harvested

first: Chunli

first: Tae-Don


title: Epigenetic lockdown of type I interferon sensing and signalling in human pluripotent cells.

city: London

first: James

middle: H.

last: Holt

state: London

address: Blizard Institute

department: Blizard Institute

country: United Kingdom

institute: Queen Mary University of London

summary: The Human Silencing Hub (HUSH) complex safeguards genome integrity in human somatic cells by repressing transposable elements and regulating type I interferon (IFN-I) induction. In early development, the IFN-I pathway is inactive, yet its underlying regulation is poorly understood. Here, we use depletion of the HUSH complex in human induced pluripotent stem cells (iPSCs) as a tool to investigate epigenetic control of the IFN-I system in early development. We confirmed that human iPSCs display an attenuated IFN-I pathway, whereas iPSC-derived neural progenitor cells (NPCs) respond robustly to IFN-I pathway agonists. We found that, in iPSCs, depletion of MPP8, a core component of all HUSH complexes, was sufficient to induce both expression of young LINE-1 elements and genes linked to the IFN system including double-stranded RNA sensors and interferon-stimulated genes (ISGs). ISG upregulation had little effect on pluripotency markers and occurred without IFN signalling, suggesting that, in contrast to differentiated cells, these ISGs are direct transcriptional targets of the HUSH complex in early development. Chromatin profiling by CUT&Tag confirmed MPP8 enrichment at HUSH-regulated ISGs and revealed a bimodal binding profile of MPP8 to both ISGs and non-ISGs, the latter largely driven by young LINE-1 elements. We propose that shutdown of the IFN-I system in pluripotent stem cells is essential to prevent lethality from unwarranted self-nucleic acid sensing. This shutdown is achieved through a triple-layer of epigenetic lockdown acting on ligands, sensors, and effectors across the IFN-I pathway.

overall_design: Total RNA seq of Healthy iPSCs from the HIPSCI consortium (cell line wibj2) treated with lentiviral vectors containing shRNAs targeting MPP8 (MPHOSP8) compared to a non-targeting control.

middle: H

first: Rocio

last: Enriquez-Gasca

first: Rachel

middle: P

last: Wilson

first: Elena

last: Bochukova

first: Pierre

middle: V

last: Maillard

first: Helen

last: Rowe


title: Osteocytes produce erythroferrone to regulate liver hepcidin during stress erythropoiesis

city: Bethesda

first: Eva

last: Mezey

state: MD

address: 30 Convent Dr.

department: NIDCR

institute: NIH

summary: The bone marrow microenvironment has a variety of cell types. Osteocytes regulate bone remodeling and were described to participate in bone marrow functions. However, their role in regulating red blood cell production is not known. To understand their role in red blood cell regulation we isolated osteocytes from mice after acute hemorrhagic anemia and performed bulk RNAseq in comparison to controls.  We identified the top upregulated gene in osteocytes as Fam132b or erythroferrone (Erfe). ERFE is known to be produced by erythroblasts in response to erythropoietin (EPO) and mediates hepcidin suppression in the liver during stress erythropoiesis. In our model ERFE expression was 16-fold higher in osteocytes isolated from mice after phlebotomy compared to control mice. The expression level of ERFE in osteocytes was similar to that described in erythroid precursors. Expression in osteocytes was also induced by hypoxia in vitro. In vivo experiments confirmed these findings. When Erfe-/- mice were transplanted with WT BM (thus only the BM can produce Erfe), the hepcidin suppression in the liver was significantly less then in WT mice, when both the osteocytes and the BMcan produce Erfe.  Osteocyte Erfe is produced through their Epo receptors sensing the hypoxia.  So, we tested if eliminating the Epo receptors from bone cells only would have an effect on liver hepcidin and found that these mice could not suppress liver hepcidin as much as control animals did. These two experiments confirmed our hypothesis, that osteocytes produce Erfe in response to EPO and that the Erfe they release has a significant contribution to suppressing liver hepcidin production.  The lowered hepcidin levels make iron available to increase red cell production.  Thus osteocytes actively participate in regaining the balance of the bone marrow by increasing red cell production after bleeding.

overall_design: Changes in the transcriptome of primary osteocytes following hemorrhage in mice.

first: Vamsee

middle: D

last: Myneni

first: Ildikó

last: Szalayova


title: Gene expression profile at single cell level of testicular cells from the adult zebrafish testis

city: suzhou

first: Taole

last: LIU

state: JIANGSU

address: Renai Road 199

department: center for circadian clock

institute: Soochow University

summary: Testicular cells include somatic cells and germ population in zebrafish. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of testicular cells in zebrafish.

overall_design: Whole testes of adult zebrafish males were sampled and analyzed using scRNAseq.

last: Liu

first: Han

last: Wang


title: Wounding activates HSFA1 to promote cellular reprogramming in Arabidopsis

city: Yokohama

first: Duncan

middle: Peter

last: Coleman

state: Kanagawa

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

department: CSRS

institute: Riken

summary: Mechanical injury is a primary trigger for cellular reprogramming during organ regeneration, yet the transcriptional mechanisms that link wounding to reprogramming remain poorly understood. In this study we identify the HEAT SHOCK FACTOR A1 (HSFA1) class of transcription factors, key regulators of the heat stress response, as a central player in wound-induced callus formation and shoot regeneration in Arabidopsis. Loss of HSFA1 function in the hsfa1abd triple mutants severely impairs cellular reprogramming, reducing callus formation from wounded hypocotyls and shoot regeneration from explants. Conversely, overexpression of a gain-of-function HSFA1d variant markedly enhances regeneration. Time-series RNA-seq and ChIP-seq analyses revealed that HSFA1 directly activates key reprogramming regulators, WOUND-INDUCED DEDIFFERENTIATION 1 (WIND1), PLETHORA 3 (PLT3) and ZINC FINGER OF ARABIDOPSIS THALIANA 6 (ZAT6). Furthermore, we demonstrate that the HSFA1d activity is attenuated by SIZ1-mediated SUMOylation, linking post-translational modification to the regulation of wound responses. Our findings establish HSFA1 as an early transcriptional hub that integrates wound signals to activate a broad gene network that drives cellular reprogramming, thereby providing a mechanistic framework for understanding how stress-responsive transcription factors control regeneration.

overall_design: ChIP-seq analysis of pHSFA1d-HSFA1d-GFP plants following heat stress or wounding

first: Takamasa

last: Suzuki

first: Keiko

last: Sugimoto

first: Ayako

last: Kawamura


title: SFTSV exploits PPM1K to inhibit apoptosis through the Bcl-2/BAX/Caspase-3 axis for efficient replication

city: changchun

first: baoyan

last: wang

state: jilin

address: No. 5333, Xi'an Road, Lvyuan District, Changchun City, Jilin Province

department: College of Veterinary Medicine, Jilin University

institute: Jilin University

summary: In this study, transcriptomic profiling identified PPM1K as a prominently induced host factor in SFTSV-infected THP-1 cells. We further demonstrate that SFTSV infection promotes endoplasmic reticulum–mitochondria coupling, enabling the viral glycoprotein GC to interact with mitochondrial PPM1K and enhance its expression at both transcriptional and protein levels. Mechanistically, PPM1K dephosphorylates Bcl-2 at Ser248, decreases Bcl-2 ubiquitination, and stabilizes its anti-apoptotic activity, thereby suppressing the BAX–Caspase-3 signaling cascade. This anti-apoptotic remodeling markedly limits apoptosis in infected cells and facilitates efficient SFTSV replication. These findings uncover a previously unrecognized viral strategy in which SFTSV hijacks host PPM1K-dependent mitochondrial signaling to evade apoptosis and promote replication

overall_design: Comparative gene expression profiling analysis of RNA-seq data for THP-1 cell samples and its treatment groups (SFTSV infection for 24 h, SFTSV infection for 48 h, and control group), with three biological replicates in each experimental group and the control group.


title: Chromatin insulators homie and nhomie can interact with distant copies either together or separately, with distinct outcomes for enhancer-promoter interactions

city: Princeton

first: Wenfan

last: Ke

state: New Jersey

address: 119 Lewis Thomas Laboratory

department: Department of Molecular Biology

institute: Princeton University

summary: Chromatin insulators, a.k.a. boundary elements, separate regions of the chromosome with distinct chromatin characteristics, including distinct histone modifications.  This activity affects gene expression by allowing chromatin domains to be stably regulated and maintained.  Insulators also block enhancer-promoter interactions and, somewhat paradoxically, facilitate other interactions, particularly when they stitch together distant regions of the chromosome by pairing with specific partners.  Here we explore how long-range interactions facilitated by insulator pairing are affected by the presence of two potentially competing partners.  Our results show that when two partners are present, they can reduce each other's effects on distant gene expression, suggesting that enhancer-promoter interactions are best facilitated by pairwise insulator interactions.  When a distant copy of an eve insulator (homie or nhomie) is present, it can interact with either or both endogenous insulators.  But when one endogenous insulator is removed, the remaining one interacts more strongly with the transgenic copy, biasing the induced enhancer-promoter interactions toward those nearest the remaining endogenous insulator.  On the other hand, physical interaction data suggest that strictly pairwise interactions are not the rule, suggesting a more complex model involving tripartite interactions.  We further show that removing one or both endogenous eve insulators significantly reduces endogenous eve function at a critical early stage of development, and that the eve Polycomb domain expands in both directions when its insulator boundaries are removed, showing that insulators in their native context are required for each of the main functions that have been ascribed to them based on transgene assays.

overall_design: microC for Drosophila st14 whole embryo samples, 2-3 independent replicates for each genotype

first: Fujioka

last: Miki

first: Ke

last: Wenfan

first: Schedl

last: Paul

first: Jaynes

last: James


title: Forming a Precise and Reproducible Hypoxic Tumor Microenvironment in Glioblastoma by High Cell Density Bioprinting

city: San Diego

first: Emmie

last: Yao

state: California

address: 9500 Gilman Drive, SME 218

institute: UC San Diego

summary: Glioblastoma (GBM) is the most common and malignant brain tumor, characterized by its highly aggressive and rapidly proliferative behavior. In this study, we created a high throughput GBM model with a cell density modulated hypoxic niche to investigate the important role of hypoxia in an in vitro model in shaping GBM progression and therapeutic response.

overall_design: Bulk RNA-sequencing to explore the differential gene expressions between a low cell density glioma stem cell bioprint (named 'Base') and the high cell density (named 'HCD').


title: CD8 T-cells, CD86+ macrophages, and TNF-α signaling pathways are correlated with fetlock osteoarthritis in racehorses

city: Ithaca

first: Erica

last: Secor

state: NY

address: 960 Campus Rd

institute: Cornell University

summary:
Background: There is emerging evidence for the role of the immune system in osteoarthritis (OA) pathophysiology; however, little is known about how immune cells and the synovial transcriptome are altered in naturally occurring equine OA.

Objectives: To evaluate synovial fluid (SF) and synovial membrane (SM) immune cell populations and the SM transcriptome in racehorses with fetlock osteoarthritis.

Methods: Fetlock joints from racehorses euthanized on NY racetracks were considered for inclusion. SF and SM were analyzed by flow cytometry using T-cell (CD3, CD4, CD8) and macrophage (CD14, CD86, CD206) surface markers. OA severity was characterized by gross joint evaluation and SM histology. Bulk RNA-sequencing of SM was performed to identify differentially expressed genes. Flow cytometry data was analyzed with mixed linear modeling, including OA severity as a fixed effect and horse as a random effect. RNA-sequencing was evaluated with mixed linear and quadratic modeling using DREAMSeq method to capture differential gene expression over the range of OA severity.

Results: Twenty-four fetlocks from 12 horses met inclusion criteria. CD8+ T-cells (R2 = 0.25 for SM, 0.35 for SF) and CD86+ macrophages (R2 = 0.14 for SM) were positively correlated with OA severity, while CD4+ T-cells (R2 = 0.17 for SM, 0.31 for SF) were negatively correlated. Macrophages co-expressing CD86 and CD206 correlated with OA severity in SM (R2 = 0.31). Pathways including those associated with TNF-α signaling, connective tissue development, and cell and neuron projection organization/development were differentially regulated in SM with greater OA scores.

Main Limitations: Limited sample size, particularly of horses with severe OA.

Conclusions: CD8+ T-cells, CD86+ macrophages, and macrophages co-expressing CD206 and CD86 are enriched in horses with more advanced OA. Gene set analysis suggests the importance of TNF-α signaling and disinhibition of neuron and cell projection development in OA pathogenesis.

overall_design: Cross-sectional cadaver study

first: Erik

last: Chow

first: Matthew

last: Thomas

first: Lynn

last: Johnson

first: Andrew

last: Siefert

first: Bettina

last: Wagner

first: Julie

last: Engiles

first: Heidi

last: Reesink


title: Transcriptomic profiling of Carfilzomib (CFZ) treatment in HSV-1 infected BV2 microglial cells

city: Guangzhou

first: Shen

last: Weishan

address: 58 Zhongshan 2nd Road

institute: The First Affiliated Hospital, Sun Yat-sen University (FAH-SYSU)

summary: This study investigates the molecular mechanisms underlying the interaction between Carfilzomib (CFZ) and Herpes Simplex Virus type 1 (HSV-1) infection in microglial cells. Using the BV2 microglial cell line, we performed RNA sequencing to dissect the transcriptional responses under different conditions. Cells were either infected with HSV-1 (MOI=1)  for 24 hours or left uninfected, and subsequently treated with 30 nM Carfilzomib (CFZ) or the vehicle control (DMSO) 6 hours post infection.

overall_design: The experimental cohorts for RNA sequencing (RNA-seq) were organized as follows: HSV1-infection-CFZ_group-1(n=3); HSV1-infection-DMSO_group-1(n=3); Noninfection-CFZ_group (n=3);Noninfection-DMSO_group (n=3).

first: Yaoxing

last: Wu

first: Weishan

last: Shen


title: A critical role of necroptosis in the oil cyst formation associated with autologous fat transplantation

city: Guangzhou, Guangdong Provice

first: ruoxi

last: chen

address: 613 West Huangpu Avenue, Tianhe District

institute: Department of Plastic Surgery of the First Affiliated Hospital of Jinan University

summary: Autologous fat grafting is limited by unpredictable long-term outcomes, with oil cyst formation being a major complication whose molecular mechanisms remain elusive. We established a novel surgically-induced mouse model demonstrating that ischemia duration time as the primary driver of oil cyst pathogenesis. Through RNA-sequencing of viable grafts (n=5) versus oil cysts (n=5), we identified the activation of RIPK3-MLKL signaling axis, revealing necroptosis-related pathways as critical molecular divergences.

overall_design: We assumed that a particular ischemia period of fat grafts prepared for （Autologous fat grafting）AFG will cause the oil cyst formation in mice. Therefore, we determined the effect of ischemia durations prior to AFT on the oil cyst formation in the grafted fats in mice. In order to examined the impact of ischemia durations (2 h, 4 h, and 8 h) of fat grafts stored on ice and room temperature (RT) for AFG on oil cyst formation in grafted fats at 2 wks after surgery, We carried out RNA-seq analysis of the transcripts of grafted fats without or with ischemia for 2 h, 4 h, and 8 h prior to transplantation.

first: Canxiang

last: Lin

first: Ruoxi

last: Chen

first: Hongwei

last: Liu


title: Transcriptomic Profiling of the Left Ventricle Using Single-Nucleus RNA Sequencing in Control and Post-MI Mice

city: Columbus

first: Mahmood

last: Khan

state: Ohio

address: 2255 Kenny Rd

department: Emergency Medicine

institute: The Ohio State  University

summary: This dataset features the single-nuclei RNA sequencing (snRNASeq) data from the left ventricle of mice hearts that were isolated post-myocardial infarction (MI) at different time points and were used for nuclei isolation, followed by RNA isolation and sequencing. The data provides insights into the gene expression changes that occur at the early (Week 1) and late (Week 4) phases of myocardial infarction in the mouse heart.

overall_design: Male C57BL/6J wild-type mice (8-9 weeks of age, The Jackson Laboratory, USA) were used to induce the MI using the Left Anterior Descending coronary artery (LAD) ligation method. The hearts were harvested from MI-induced mice at week 1 and week 4 post-MI and from control mice without the induction of MI. Only the left ventricular tissue was isolated from the hearts and immediately flash-frozen in liquid nitrogen. The samples were processed for high-throughput single-nuclei gene expression profiling using the 10x Genomics Chromium Platform.

first: Pankaj

last: Dholaniya

first: Helena

last: Islam

first: Syed

last: Baseeruddin Alvi

first: Muhamad

last: Mergaye


title: Expression data of neonatal brain from male intra-cytoplasmic sperm injection(ICSI)-F2 offspring

city: Kyoto

first: mito

last: shinohara

state: Kyoto

address: Sakyo-ku, Yoshida Konoe

department: Medicine

institute: Kyoto University

summary: Various behavioural abnormalities were observed in the F2 offspring of ICSI (Kanatsu-Shinohara et al., 2023, J. Clin. Invest. 133(22):e170140). The data presented here aim to clarify the cause of these abnormalities, and gene expression in the neonatal brain was investigated using RNA sequencing (RNAseq). ICSI was performed using C57BL/6 epididymal sperm and oocytes. Males from the F1 generation were naturally mated with C57BL/6 females to produce the F2 generation. Gene expression in the neonatal brains of male ICSI-F2 offspring was examined. Each group contains four biological replicates.

overall_design: Neonatal brain tissue was prepared from male F2 offspring of the C57BL/6 strain, produced by natural mating from male ICSI-F1 offspring. Control brain samples were prepared from a neonate born via natural mating to wild-type C57BL/6 parents. Total RNA samples were extracted using a miRNeasy Mini Kit (Qiagen, Cat. No. 217084), followed by treatment with RNase-free DNase (Qiagen, Cat. No. 79254). cDNA libraries were generated using a TruSeq Stranded mRNA Library Preparation Kit (Illumina, San Diego, CA, USA). Sequencing was performed using a NextSeq 550 (Illumina) with a single-read sequencing length of 76 bp. A total of eight samples were analysed.

first: Mito

last: Kanatsu-Shinohara

first: Takashi

last: Shinohara

first: Takuya

last: Yamamoto

first: Narumi

last: Ogoniki

first: Kimiko

last: Inoue

first: Atsuo

last: Ogura


title: Reprogramming CAR with cytokine signaling increases the efficacy of CAR-T cell therapy in solid tumour treatment and confers sustained immune memory

city: Nanjing

first: Rongchen

last: Sun

address: Longmian

institute: China Pharmaceutical University

summary: Chimeric antigen receptor (CAR) T-cell therapy has shown remarkable efficacy in hematologic malignancies but remains limited in solid tumors because of the immunosuppressive microenvironment, tumor heterogeneity, poor immune-cell infiltration, and progressive T-cell dysfunction. Because cytokine costimulation is critical for maintaining T-cell fitness, we developed a modular engineering strategy, distinct from previous approaches based on direct insertion of large cytokine receptor fragments, in which the intracellular CAR signaling domain was reconstructed to incorporate compact IL-2/IL-15 receptor–derived activation motifs, thereby enabling antigen-dependent coactivation while preserving the overall architecture of the parental CAR. Through systematic screening, we identified S71 as the optimal construct, with significantly greater antitumor activity than other mutants across multiple solid and hematologic tumor targets. Mechanistically, S71 rewired CAR signaling and reprogrammed tumor-induced metabolic responses through a self-sustaining mechanism, improving mitochondrial function and supporting durable T-cell activity. Functionally, S71 promoted enhanced persistence and robust immune memory responses against solid tumors. These findings demonstrate that modular integration of cytokine signaling motifs into CAR intracellular domains can improve CAR-T-cell fitness and antitumor efficacy, and they establish S71 as a promising strategy for overcoming barriers to CAR-T-cell therapy in solid tumors.

overall_design: Bulk RNA-seq with starved CD8+ EDB CAR-T cells manufactured from 3 different donors (Donor1: tumor-bearing patient; Donor2 and Donor3: healthy adult). Each group had different co-cultured treatment with U87MG-WT for 24h at E:T=1:1, EDB-S71 + PBS (Donor1, 2, 3); EDB-28Z + PBS (Donor1, 2, 3); EDB-28Z + hIL2 (5ng/ml, Donor2, 3); EDB-28Z + hIL15 (5ng/ml, Donor1, 2, 3).

first: Xue

last: Yang

first: Changshuai

last: Che


title: Effect of MSCs or tpMSCs on gene expression in hypoxia/LPS-induced dilated acute lung injury

city: Chongqing

first: Yuantong

last: Qi

address: 30 Gaotanyan Main Street

institute: Third Military Medical University

summary: To investigate the intrinsic mechanism of of MSCs or tpMSCs on gene expression in hypoxia/LPS-induced acute lung injury (ALI), we established hypoxia/LPS-induced ALI model mice and MSCs or tpMSCs treated mice, using healthy mice as the normal control. We then performed gene expression profiling analysis of the RNA-seq data obtained from the heart tissues of these three groups of mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data in normal group, ALI model group, MSC treated group. and tpMSC treated group.

first: Jianxiang

last: Zhang


title: RANKL inhibits macrophage pro-inflammatory Toll-like receptor 2 and 4 signaling and impairs killing of intracellular bacteria

city: Nashville

first: James

last: Cassat

state: TN

address: 1161 21st Ave S

institute: Vanderbilt University Medical Center

summary: Monocyte-macrophage lineage cells, crucial components of the innate immune system, can uniquely form bone-resorbing osteoclasts upon exposure to the cytokine receptor activator of NF-κB ligand (RANKL) in the bone microenvironment. Recent studies have also begun to uncover extensive extraskeletal roles of RANKL. However, how monocyte-macrophage lineage cells respond to RANKL outside of the bone, and the impact that this signaling pathway exerts on the host immune response, is not fully understood. In this study, we sought to define how RANKL exposure shapes the macrophage inflammatory response to pathogens by using the model intracellular bacterium Salmonella enterica serovar Typhimurium (STm), which co-opts macrophages to cause life-threatening infections. We found that exposing both mouse and human macrophages to sub-osteoclastogenic levels of RANKL increased intracellular STm burdens and decreased pro-inflammatory cytokine production. RNA sequencing revealed downregulation of pattern recognition receptor (PRR) signaling pathways in RANKL-treated macrophages during the early stages of infection. Therefore, we hypothesized that RANKL impairs PRR-dependent signaling pathways that are important for pro-inflammatory cytokine production. We discovered that RANKL-treated macrophages exhibit reduced NF-κB and IRF3 activation, specifically in response to Toll-like receptor (TLR) 2 and TLR4 stimulation. We determined that prior RANKL exposure decreases abundance of the TLR2 and TLR4 adaptor proteins TRAM and TIRAP. Together, these data suggest that RANKL exposure negatively impacts the macrophage TLR-mediated inflammatory response to bacteria.

overall_design: RNAseq profiling of bone marrow-derived macrophages after 4h or 24h of infection with Salmonella enterica serovar Typhimurium following treatment with or without 100ng/mL of RANKL.

first: Clara

last: Si

first: Christopher

middle: T

last: Peek

first: Sana

middle: R

last: Fatah

first: Andrew

last: Beaudoin

first: Anton

last: Zhelonkin

first: Kara

last: Eichelberger

first: Stacy

last: Hahn

first: Robert

middle: O

last: Watson

first: Denis

middle: A

last: Mogilenko

middle: E


title: NanoString nCounter Mouse PanCancer Immune Profiling of CT26 tumors following chronic in vitro PMS2 inhibition and in vivo anti-PD-1 treatment

city: Altrincham

first: Maria T.

last: Rodriguez Plata

state: Cheshire

address: 3rd Floor, 1 Ashley Road

institute: NeoPhore Ltd.

summary: NanoString nCounter immune profiling revealed that PMS2 inhibitor NP1867-pretreated tumours mounted an enhanced immune response to anti-PD-1 therapy, characterized by increased infiltration of lymphocytes, including T cells and cytotoxic populations, together with enrichment of multiple immune-related pathways. These included adaptive immune responses, antigen processing and presentation, MHC signaling, and interferon pathways, indicating that NP1867 pretreatment primes tumors for improved immunological responsiveness to PD-1 blockade.

overall_design:
CT26 cells were treated in vitro with PMS2 inhibitor NP1867 or vehicle control (DMSO) for 40 weeks. Cells were implanted subcutaneously into immunocompetent (BALB/c) syngeneic mice. Animals were randomized on day 7 post-implantation, when the mean tumor volume was approximately 50 mm³, into two groups per condition and treated with anti-PD-1 (rat IgG2a, κ, clone RMP1-14) or isotype control (rat IgG2a, κ, clone 2A3) administered intraperitoneally (i.p.) twice weekly, for a total of four doses. On day 19, 24 h after the fourth and final dose of anti–PD-1 or isotype control, animals with tumors representative of the group mean tumor volume were assigned to a satellite group (n = 6 per group) for tumor sampling. Tumors were formalin-fixed and paraffin-embedded (FFPE) prior to NanoString nCounter Mouse PanCancer Immune Profiling analysis.
(contributor) NeoPhore Ltd.

first: Maria


title: RNA-seq profiling of cerebral organoids derived from CBP mutant iPSCs

city: Grand Rapids

first: Xiaobing

last: Shi

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

summary: CREB-binding protein (CBP/CREBBP) is a histone acetyltransferase essential for human development. Mutations in CBP are associated with Menke–Hennekam syndrome (MKHK), a neurodevelopmental disorder. To examine the impact of a disease-associated mutation, we performed RNA sequencing on cerebral organoids derived from isogenic wild-type and CBP R1868 mutant human induced pluripotent stem cells (iPSCs) at Day6, Day12, Day18 and Day30 of differentiation. This time-course RNA-seq data captures gene expression programs during early neurodevelopment and reveals how the CBP R1868W mutation influences transcriptional states in human cerebral organoids.

overall_design: In vitro–cultured Day6, Day12, Day18 and Day30 CBP WT and mutant cortical organoids were collected for RNA-seq.

first: Longxia

last: Xu

first: Hongwen

last: Xuan


title: Dual Activation of CD8+ and CD4+ T cells by a PD-1 targeted IL-15 Mutein in Viral Infection

city: Salt Lake City

first: Jaroslav

last: Zak

state: UT

address: 1950 Circle of Hope Dr

department: Department of Radiation Oncology, Huntsman Cancer Institute

institute: University of Utah

summary: Immune checkpoint inhibitors have transformed cancer therapy, yet many patients fail to achieve durable responses, in part due to insufficient T cell reinvigoration. Cytokines remain promising additions to immunotherapy to improve response rates; however, the low therapeutic index and associated side effects have hindered progress. In response to these challenges, immunocytokines, engineered fusion proteins that combine the specificity of antibodies with the immune-stimulatory properties of cytokines, have been employed to enable targeted delivery of cytokine signals to immune cells or the tumor microenvironment to minimize pathological consequences. Here, we describe SAR445877 (SAR’877), a novel PD-1-targeted immunocytokine that fuses a high-affinity anti-PD-1 antibody with a detuned IL-15/IL-15Rα sushi domain complex. SAR’877 simultaneously blocks PD-1/PD-L1 and PD-1/PD-L2 interactions and delivers IL-15 signals selectively to PD-1+ T cells. This design enhances the proliferation and activation of antigen-experienced CD8⁺ and CD4⁺ T cells, as well as NK cells, while limiting systemic inflammatory cytokine release. Mechanistically, SAR’877 preferentially activates STAT5 signaling in PD-1⁺ lymphocytes and restores effector function in exhausted T cells in vitro. A murine surrogate of SAR’877 accelerated viral clearance and reinvigorated exhausted T cells in the chronic LCMV Clone-13 infection model. In multiple syngeneic tumor models, the surrogate induced robust anti-tumor immunity by expanding cytotoxic CD8⁺ T cells and promoting Th1 polarization. Notably, SAR’877 outperformed combination therapy with anti-PD-1 and untargeted IL-15, underscoring the therapeutic potential of targeted IL-15 delivery to PD-1+ cells. These findings position SAR’877 as a promising next-generation checkpoint immunotherapy that augments efficacy while reducing cytokine-associated toxicities.

overall_design: In this single-cell transcriptomic experiment, mice infected with LCMV Clone 13 were treated with mouse SAR'877 (1 mg/kg), anti-PD1 (1 mg/kg), mouse IL-15 mutein (1 mg/kg), anti-PD1+mouse IL-15 mutein (1 mg/kg each) or isotype control (1 mg/kg). At day 30 post infection, splenic T cells were subjected to flow sorting, labeling with DNA-barcoded antibodies and single-cell transcriptome library preparation following the hashtag-multiplexed 10X Genomics 3' sequencing protocol.

first: Isaraphorn

last: Pratumchai

first: John

last: Teijaro

first: Kristi

middle: L

last: Marquardt


title: Conservation and divergence of UVR8 photoreceptor-mediated UV-B signaling in Marchantia polymorpha

city: Geneva

first: Roman

last: Ulm

address: 30 Quai E. Ansermet

country: Switzerland

institute: University of Geneva

summary: Ultraviolet-B radiation (UV-B) poses a major challenge to all forms of plant life. The liverwort Marchantia (Marchantia polymorpha) serves as a key model organism for studying signaling pathways and inferring their evolution throughout the green lineage. Marchantia expresses key components of UV-B signaling, including the photoreceptor UV RESISTANCE LOCUS 8 (MpUVR8), the WD40-repeat protein REPRESSOR OF UV-B PHOTOMORPHOGENESIS (MpRUP), the E3 ubiquitin ligase complex CONSTITUTIVELY PHOTOMORPHOGENIC 1 / SUPPRESSOR OF phyA-105 (MpCOP1/MpSPA), and the transcriptional regulator ELONGATED HYPOCOTYL 5 (MpHY5). Here, we show that whereas the core UVR8 photocycle is well conserved, regulatory roles of SPA and HY5 diverged during plant evolution. Unlike the case in Arabidopsis (Arabidopsis thaliana) and in contrast to the strong Mpcop1 mutant phenotype, Mpspa mutants developed only a very weak constitutive photomorphogenesis phenotype, indicating that COP1 function is much more independent of SPA in Marchantia than in Arabidopsis. Moreover, in contrast to Arabidopsis SPAs, Mpspa showed enhanced UV-B acclimation and UV stress tolerance, indicating that MpSPA is a negative regulator of MpUVR8 signaling. Similar to Arabidopsis HY5/HYH, MpHY5 functioned antagonistically to MpCOP1, but its role in UV-B-mediated gene expression changes was more limited. Our findings demonstrate that although core components of UV-B signaling existed in the last common ancestor of extant land plants, regulatory interactions have diversified in different lineages since their divergence more than 400 million years ago.

overall_design: Wild type Tak-1 and Mphy5 mutants gemmalings were grown for 7 days in 50 μmol m-2 s-1 white light and exposed or not to supplemental UV-B (1.5 μmol m-2 s-1) for 3h.

first: Yuanke

last: Liang

last: Podolec


title: Transcriptome analysis of breast tumour tissue and adjacent normal

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

institute: Queen Mary University of London

summary: Patients with cancer that respond to immunotherapy benefit from prolonged and possibly indefinite progression free survival. Response rates vary across cancer types, with solid carcinomas generally being the poorest responders at between 10-20 %. Understanding the differences between responders (the 10- 20%) and non-responders (the 80-90%) could identify ways to improve response rates. In this project we investigate transcriptome changes in breast cancer tissue which may help understanding the differences in treatment responses.

overall_design: Tumour (n = 34)  and non-tumour (n = 6)  tissues (≥2cm away from the tumour) were collected from patients with localised or locally advanced TNBC (T1-3, N0-2, M0) eligible for mastectomy +/- neoadjuvant treatment and analysed by RNASeq.

first: Eleanor

middle: J

last: Tyler

first: Oliver

middle: M

last: Pearce


title: Epigenetic lockdown of type I interferon sensing and signalling in human pluripotent cells [CUT&Tag]

first: James

last: Holt

address: Blizard Institute

summary: The Human Silencing Hub (HUSH) complex safeguards genome integrity in human somatic cells by repressing transposable elements and regulating type I interferon (IFN-I) induction. In early development, the IFN-I pathway is inactive, yet its underlying regulation is poorly understood. Here, we use depletion of the HUSH complex in human induced pluripotent stem cells (iPSCs) as a tool to investigate epigenetic control of the IFN-I system in early development. We confirmed that human iPSCs display an attenuated IFN-I pathway, whereas iPSC-derived neural progenitor cells (NPCs) respond robustly to IFN-I pathway agonists. We found that, in iPSCs, depletion of MPP8, a core component of all HUSH complexes, was sufficient to induce both expression of young LINE-1 elements and genes linked to the IFN system including double-stranded RNA sensors and interferon-stimulated genes (ISGs). ISG upregulation had little effect on pluripotency markers and occurred without IFN signalling, suggesting that, in contrast to differentiated cells, these ISGs are direct transcriptional targets of the HUSH complex in early development. Chromatin profiling by CUT&Tag confirmed MPP8 enrichment at HUSH-regulated ISGs and revealed a bimodal binding profile of MPP8 to both ISGs and non-ISGs, the latter largely driven by young LINE-1 elements. We propose that shutdown of the IFN-I system in pluripotent stem cells is essential to prevent lethality from unwarranted self-nucleic acid sensing. This shutdown is achieved through a triple-layer of epigenetic lockdown acting on ligands, sensors, and effectors across the IFN-I pathway.

overall_design: CUT & Tag of healthy iPSCs from the HIPSCI consortium (cell line wibj2). Antibodies were used against MPP8, H3K9me3, H3K27ac, and IgG.

first: Rocio

last: Enriquez-Gasca

first: Rachel

last: Wilson

first: Elena

middle: G

last: Bochukova

first: Pierre

last: Maillard

first: Helen

last: Rowe


overall_design: Wild type Tak-1, Mpuvr8, Mprup, Mpcop1 and Mpspa mutants gemmalings were grown for 7 days in 50 μmol m-2 s-1 white light and exposed or not to supplemental UV-B (1.5 μmol m-2 s-1) for 3h.


title: A spatial code governs olfactory receptor choice and aligns sensory maps in the nose and brain

city: Boston

first: David

last: Brann

state: MA

address: 220 Longwood Ave

department: Neurobiology

institute: Harvard Medical School

summary: Although topographical maps organize many peripheral sensory systems, mouse olfactory sensory neurons (OSNs) are thought to randomly choose which one of ~1,100 possible olfactory receptors (ORs) to express, with spatial organization in the olfactory epithelium limited to a handful of broad anatomical zones that modestly restrict OR choice. Here we reveal that each OR is instead expressed at a unique mean dorsoventral position, thereby instantiating a stereotyped receptor map in the olfactory epithelium. OSN dorsoventral identities are encoded by a coherent gene expression program, which includes key transcription factors and axon guidance molecules; use of this program reflects a dorsoventral gradient in retinoic acid signaling, translates each physical location into a spatially appropriate distribution of potential OR choices, and aligns receptor maps in the nose and brain. Spatial order in the olfactory system, therefore, arises from a continuously varying transcriptional code that precisely organizes the many discrete channels responsible for smell.

platform_organism:
Mus musculus
synthetic construct

overall_design:
281 replicates of single cell RNA-seq libraries using 10X genomics chromium single cell 3' v3.1 library reagents, 4 replicates with the GEM-X 3' v4 kits. The strain/genotype is given for each sample. Note, analyses and processed data also include data publicly available in GEO accession GSE173947 and bioproject PRJNA727597
Multiplexed error-robust fluorescence in situ hybridization (MERFISH) was performed using the Vizgen MERSCOPE platform. Four replicates of coronal samples from the main olfactoy epithelium (MOE) from young (4-5 week) mice were processed according to the manufacturer's user guides (Vizgen 91600002 Rev E and 91600112 Rev C) with a 300-plex gene panel containing olfactory receptors, marker genes, and dorsoventral genes.
Two replicates of stereo-seq spatial transcriptomics data, from 10 µm coronal sections of the mouse main olfactory epithelium (MOE).

first: Tatsuya

last: Tsukahara

first: Sandeep

last: Datta


title: Biomimetic graphitic carbon nitride nanoparticles enable multiscale biomodulation

city: Aarhus

first: Lin

last: Lin

address: Høegh-Guldbergs Gade 10

department: Department of Biomedicine

institute: Aarhus University

summary: Virtually all organic material on Earth has been produced converting solar energy through photosynthesis in chloroplasts, a sack-like, double membrane organelle in plants and algae, where transmembrane electron transfer occurs from lumen to stroma. Although animals hardly harness the power of photosynthesis, their bioelectrical signals extensively regulate complex electrophysiological behaviors, rendering it a superior target for biomedical innovation. Here, a crude structural mimicry of chloroplast has led us to discover that hollow sphere graphitic carbon nitride nanoparticles (hg-C3N4 NPs) endowed non-genetic, subcellular and intercellular photo-modulation of various excitable and non-excitable cells, accumulatively achieving modulation at tissue/organ function level. The homogeneous hg-C3N4 NPs showed responsiveness to light via both photoelectrochemical and photothermal mechanisms. The hg-C3N4 NPs can be spontaneously internalized with excellent cytocompatibility. Using a focusing laser, the hg-C3N4 NPs enable intracellular optical stimulation with subcellular resolution, inducing calcium transient release in multiple cells and propagation in primary cardiomyocytes and cardiac fibroblasts. At multicellular scale, optical pacing and synchronization of cardiomyocyte beating is readily achieved by LED. Further, we demonstrate that hg-C3N4 NPs can be safely injected into mouse eyes, restoring light sensitivity in blind mice. Finally, application of hg-C3N4 NPs to porcine retinal tissue ex vivo confirmed their modulation capability to reactivate RGCs activity under LED photostimulation. Taken together, these nanostructured biomimetic photocatalytic NPs offer high resolution, leadless optical probing, non-invasive delivery and great biocompatibility, serving as a versatile tool for addressing a range of complex biomedical challenges through subcellular, intercellular and tissue-level photo-modulation across a broad spectrum of scales.

overall_design: Bulk RNA sequencing profile of retinal cells isolated from 5 mice injected intravitreally with carbon nitride naparticles (CNP) compared to retinal cells isolated from 5 PBS-injected eyes at day 14 after injection.

first: Anne Louise

last: Askou


title: Gallic acid chemoprevention of oral carcinogenesis

first: Steve

last: Oghumu

address: 1841 Neil Ave

institute: Ohio State University

summary: Naturally derived phytochemicals such as gallic acid (GA) exhibit multitargeted anticancer properties and favorable safety profiles, yet the molecular mechanisms underlying their chemopreventive effects in head and neck squamous cell carcinoma (HNSCC) remain incompletely defined. Using a 4 nitroquinoline 1 oxide (4NQO) induced oral carcinogenesis mouse model, we evaluated GA’s effects on tumor progression, and related molecular pathways. Phenotypic outcomes were assessed by histopathology, and proliferation markers. Transcriptomic changes were profiled by RNA sequencing, pathway enrichment and validation using RT qPCR. We report GA as a key modulator of transcriptional programs associated with oral carcinogenesis in a 4-nitroquinoline-1-oxide–induced mouse model. Comparative RNA sequencing of wild-type vehicle-treated (WtVeh) and GA-treated (WtGal) oral tissues revealed GA-dependent reprogramming of immune and stress-response pathways. Our data identifies unique molecular pathways associated with GA mediated oral cancer chemoprevention.

overall_design: Mice were administered with 4-nitroquinoline 1-oxide (4NQO) in their drinking water at a concentration of 100 µg/mL. 4NQO exposure continued for 16 weeks, after which mice were provided regular drinking water until the time of terminal sacrifice. Four weeks after the initiation of 4NQO exposure, mice were randomly assigned to receive either GA or vehicle control. Mice in the treatment group received GA at 100 mg/kg body weight via oral gavage five times per week, while control animals received an equal volume of vehicle using the same schedule. Treatment continued until the day of terminal sacrifice. At terminal sacrifice, tongue samples from GA treated and vehicle treated 4NQO mice were processed for bulk RNA seq

first: Puja

last: Upadhaya

first: Felipe

middle: F

last: Lamenza

first: Ravi

last: Ramalingam

first: Kishan

last: Nyati