title: Proper nuclear compartment reorganization in G1 phase is essential for DNA replication control [BrdU-IP]

first: Ichiro

last: Hiratani

summary: Upon G1 entry after mitosis, mammalian chromosomal DNA is spatially segregated into A and B compartments, which correlate well with classic euchromatin and heterochromatin, respectively. The significance of this spatial segregation, however, has never been explored for lack of means to manipulate this level of chromosomal organization. Through a genome-wide CRISPR screen, we identify GINS4, a component of the replicative DNA helicase complex, as an essential factor for A/B compartment segregation in G1. By manipulating the G1 compartment reorganization process through GINS4, we show that it is required for efficient DNA synthesis and proper DNA replication timing (RT) regulation in the subsequent S-phase. Our findings reveal an unexpected role of GINS4 and highlight the significance of nuclear compartmentalization in DNA replication control.

overall_design: BrdU-IP Repli-seq experiment was performed using the male C57BL/6N mouse embrypnic stem cells (mESCs). Genotype and treatment for each cell line is following: Dppa2-EmGFPd2 control, Dppa2-EmGFPd2 ERCE-deletion mutant, Rex1-EmGFPd2 control, Rex1-EmGFPd2 sgRNA transfected, mAID-Mcm6 control, mAID-Mcm6 5-Ph-IAA treated, Gins4-mAID control, Gins4-mAID 5-Ph-IAA treated, Gins4-mAID nocodazole-released time-course samples, Gins4-mAID 5-Ph-IAA released time-course samples. Metadata for each sample can be found in the Supplementary Table 4.

first: Asami

last: Oji

first: Takako

last: Ichinose


title: Ketohexokinase deletion on liver and small intestine transcriptome

status: Public on Jun 11 2026

city: Louisville

first: MING

last: SONG

state: KY

address: 505 S. Hancock St.

country: USA

institute: University of Louisville

type: Expression profiling by high throughput sequencing

summary: Dietary fructose is a major risk factor driving the progression of metabolic dysfunction-associated steatohepatitis (MASH) and hepatocellular carcinoma (HCC). However, the underlying fructose-induced nutrient-sensing pathway has remained unclear. Here, we report that fructose facilitates iron absorption through the (Ketohexokinase) KHK/PKM2/HIF-2α axis, driving MASH/HCC development. Fructose aberrantly stabilizes intestinal HIF-α compared to glucose; this effect is abrogated by a KHK inhibitor and genetic Khk deletion. Interestingly, reduced HIF-α stability in Khk deficient mice is rescued by a small-molecule inhibitor of pyruvate kinase M2 (PKM2). Conversely, Khk deficient mice exhibit spontaneous systemic iron deficiency, characterized by hypochromic anemia, and markedly reduced blood neutrophil numbers. Moreover, Khk deficiency inhibits iron absorption in a HIF-2α-dependent manner. Finally, fructose promotes MASH/HCC progression in an iron-dependent manner. This study reveals a unique nutrient-sensing pathway by dietary fructose that is therapeutically targetable.

overall_design: To understand the mechanisms of fructose/KHK on iron homeostasis, we performed liver, duodenum, jejunum, and leum bulk RNA-seq analysis in male WT and KHK deficient mice [n=4/group].

first: Ming

last: Song


title: RNA-seq profiling of in vivo injury-associated non-neuronal cells and lesion-derived reactive cultures

city: Alcalá de Henares

first: Sergio

last: Gascón

state: Madrid

address: Avenida de León, 1

department: Department of Molecular and Cellular Neuroscience

country: Spain

institute: Cajal Neuroscience Center - CSIC

summary: We performed RNA-seq analysis to compare lesion-derived reactive cultures (RCs) with non-neuronal cell populations isolated from injured and intact adult mouse cortex, providing a dataset to assess transcriptional similarities and differences between RCs and the in vivo cortical injury response.

overall_design: RNA-seq was performed on three sample groups: non-neuronal cell populations isolated from intact adult mouse cortex, non-neuronal cell populations isolated from cortical tissue collected 3 days after stab-wound injury, and lesion-derived RCs generated from cortical tissue collected 24 h after stab-wound injury and analyzed after 8 days in vitro. For the in vivo samples, dissociated cortical cells were processed by flow cytometry to exclude debris, dead cells and the CD171+/ACSA-2− neuronal fraction before RNA extraction. Each group included three biological replicates.

first: Dulce María

last: Arzate

first: Víctor

last: Álvaro

first: Ana Victoria

last: Prádanos-Senén

first: Lucía

last: Gallego

first: Alba

last: Méndez-Alejandre

first: Diana

last: Manzano

first: Celia

last: Llorente-Sáez

first: Rocío

last: Bartolomé

first: Alessia

last: Ferrarini

first: Juan Antonio

last: López

first: Elisa

last: Murenu

first: Benedikt

last: Berninger

first: Felipe

last: Ortega

first: Gabriel

last: Piedrafita

first: Magdalena

last: Götz

first: Christophe

last: Heinrich


title: Investigation of the Effect and Target of SchA in the Treatment of Triple-Negative Breast Cancer

city: Wuhan

first: Yu

last: Zhou

address: No. 16, West Huangjiahu Road, Hongshan District

country: China

institute: Hubei University of Chinese Medicine

summary: SchA, one of the key bioactive components derived from Schisandra chinensis, was found in our study to exert a significant inhibitory effect on breast cancer cell viability. To elucidate the underlying mechanism, we integrated bioinformatics analysis with network pharmacology approaches to predict potential targets of SchA. The findings suggest that SchA may exert its anti-tumor effects by modulating IDO1 (indoleamine 2,3-dioxygenase 1), providing a foundation for further mechanistic investigation.

overall_design: MDA-MB-231 cells were treated with 30μM Schizandrin A for 24 hours, and then compared with untreated cells, respectively.


title: Loss of endothelial ALK1 signaling induces the emergence of a KIT+ angiogenic endothelial cluster driving brain arteriovenous malformations II

city: Montréal

first: Gael

middle: Louis Max

last: Cagnone

state: QC

address: 3175 Chemin de la Côte-Sainte-Catherine

department: The Montreal single-cell Academy

country: Canada

institute: CHU Sainte Justine

summary: Background Hereditary Hemorrhagic Telangiectasia type 2 (HHT2) is a genetic disorder caused by mutations in the Alk1 (Acvrl1) gene, encoding a receptor for Bone Morphogenetic Proteins 9 and 10 (BMP9/BMP10). HHT2 patients frequently develop brain arteriovenous malformations (bAVMs), abnormal connections between arteries and veins. Currently, surgical resection is the only treatment, associated with significant risks and complications. Despite evidence suggesting endothelial cell (EC) heterogeneity in bAVMs, it remains poorly characterized, limiting our ability to identify new therapeutic avenues. Methods We employed endothelial cell-specific and inducible Alk1 knockout mice (Alk1iECKO) with tamoxifen-induced deletion at postnatal day 6 (P6). We separately analyzed the perineural (PNVP) and intraneural (INVP) vascular plexuses, which differ in vessel composition and flow dynamics, at P8. Single-cell RNA sequencing (scRNAseq) was performed to characterize EC heterogeneity and identify transcriptomic changes in both vascular plexus of mutant mice. Results Loss of endothelial ALK1 signaling triggered bAVM formation predominantly in PNVP vascular network. scRNAseq revealed that Alk1 deletion promoted brain capillaries differentiation into angiogenic-1 ECs, whereas it drove PNVP venules EC proliferation and the emergence of the unique angiogenic-2 cluster. The latter shares transcriptomic features with human AVM ECs, including angiogenic tip cell markers and a strong glycolytic signature. Among its defining markers, Kit emerged as a direct downstream target of BMP9-ALK1 signaling. Pharmacological KIT inhibition using Masitinib, Imatinib, or KIT-blocking antibodies prevented bAVM formation in Alk1iECKO mice. Conclusion Our study uncovers a previously unrecognized EC population, the angiogenic-2 cluster, as a key contributor to bAVM development. We identify Kit as a central regulator of this cluster, establishing it as a promising therapeutic target for preventing bAVMs in HHT2.

overall_design: Mutant mice and littermate controls were injected with a KIT-blocking antibody (500 µg, InVivoMAb anti-mouse c-Kit, BioXCell, BE0293-5MG-A) or an isotype control (500 µg, InVivoMAb rat IgG2b isotype control, BioXCell, BE0090-5MG-A) at P6 and P7. CD31 antibody (BD Pharmingen, 550274) was incubated with Dynabeads (Thermo Fisher, 11035) at 4°C overnight. Beads were then washed with PBS containing 0.1% BSA using a magnetic separator (DynaMag™-15, Thermo Fisher, 12301D) and resuspended in PBS containing 0.01% BSA. At P8, mice were euthanized, and brains were collected, finely chopped, and digested for 1 hour at 37°C in Collagenase/Dispase (Sigma, 11097113001) supplemented with DNase I (50 µg/mL, DN25) and TLCK (0.147 µg/mL, T7254). The reaction was stopped with DMEM containing 5% FBS, and the suspension was filtered through a 40 µm cell strainer (Fisher, 087711). Myelin and debris were removed using a 25% BSA gradient in DMEM. After a wash with PBS, cells were incubated in PBS containing 0.1% BSA with 100 µL of CD31-coated beads for 30 minutes at room temperature under agitation. Cells were then washed using a magnetic separator, lysed, and total RNA was extracted using the Monarch® Total RNA Miniprep Kit (NEB, T2010S). Following quality control, RNA libraries were prepared using a poly(A)-enriched RNA library preparation protocol, and sequenced in 2 batches on an Illumina NovaSeq platform (paired-end 100 bp, ~25 million reads per sample ±5M reads; Genome Québec).

first: Elise

last: Drapé

first: Anquetil

last: Typhaine

first: Dubrac

last: Alexandre


title: rRNA 2′Omethylation landscape is shared between cytosolic and ER-associated ribosomes in human cells

city: Copenhagen

first: Anders

last: Lund

address: Ole Maaløes Vej 5, Floor 4, Lund Group

department: Biotechnology Research and Innovation Centre (BRIC)

country: Denmark

institute: Univeristy of Copenhagen

type: Methylation profiling by high throughput sequencing

summary: Ribosome heterogeneity arising from variable rRNA 2′O‑methylation (2′O‑Me) has been proposed as a potential mechanism for translational specialization, but whether such heterogeneity contributes to compartment‑specific translation remains unknown. Here, we systematically compare the 2′O‑Me landscapes of cytosolic and endoplasmic reticulum (ER)–associated ribosomes across three human cell types: HEK293 cells, H9-derived neural progenitor cells (NPCs), and neurons differentiated from these NPCs. Using detergent-based fractionation combined with RiboMeth-seq, we generate site-resolved rRNA methylation profiles for each compartment. Within each cell type, cytosolic and ER-associated ribosomes display highly similar 2′O‑Me patterns, with only modest compartment-specific differences observed at 18S:462 in NPCs and 28S:2043 in neurons. Across all samples, differences in 2′O‑Me patterns are more pronounced between cell types than between compartments. Together, these findings indicate that 2′O‑Me does not establish a broad ER-specific methylation signature and is unlikely to be a major determinant of ribosome localization or function at the ER.

overall_design: RiboMethSeq analysis of ribosomes isolated from the ER and cytoplasmic fraction of HEK293, H9-derived neural progenitor cells (NPCs), and neurons differentiated from these NPCs. Three biological replicates per condition.

first: Ülkü

last: Uzun


title: Dysbiosis-induced expansion of AXL-positive inflammatory type 3 dendritic cells triggers pre-clinical autoimmunity

city: Bethesda

first: Grozdan

last: Cvijetic

state: Maryland

address: 30 Convent Dr, Building 30, Room 332

institute: NIH/NIDCR

summary: Conventional dendritic cells (cDC) are key sentinels at epithelial barriers, regulating immunity to microbial pathogens and commensals while preserving tissue integrity. NOTCH2 deficiency in CD11c-expressing cells (Notch2cKO) disrupts type 2a DC (cDC2a) development, impairs intestinal TH17 immunity, and increases susceptibility to enteropathogenic bacteria. This lead to persistent dysbiosis within our Notch2cKO colony, characterized by low-grade inflammation and systemic autoimmune features, including elevated autoantibody titers and renal immune-complex deposition. Dysbiosis preceded expansion of highly inflammatory AXL-expressing type 3 DC (AXL+inf-DC3), promoting chronic inflammation and tertiary lymphoid structures driving adaptive immune responses. Notably, dysbiosis was defined by three dominant pathobionts and was transferable to WT mice, recapitulating the autoimmune features observed in Notch2cKO mice. Collectively, these findings identify a microbiota–DC axis linking intestinal pathobionts to systemic autoimmunity, establishing inflammatory DC3 as the cellular bridge between dysbiosis, chronic inflammation and autoimmune pathogenesis.

overall_design: We used single-cell RNA sequencing (scRNA-seq) to analyze the heterogeneity of sorted Lin-CD26+CD11c+MHCII+ dendritic cells from the mesenteric lymph nodes (mLN) and colon lamina propria (CoLP) of eubiotic or dysbiotic WT and Notch2-deficient mice: Control WT (Notch2fl/fl), Control Re-derived Notch2cKO (Notch2fl/fl CD11cCre+), dysbiotic WT (Notch2fl/fl CD11cCre-) and dysbiotic Notch2cKO (Notch2fl/fl CD11cCre+).

first: Daniel

last: Martin

first: Siqi

last: Zhao

first: Roxane

last: Tussiwand


title: Prkci-Ect2 gain drives lung adenocarcinoma metastasis and lineage infidelity through enhanced cellular plasticity

city: Rochester

first: Cheng

last: Zhang

state: MN

address: 200 1st street SW

institute: Mayo Clinic

summary: Lung adenocarcinoma (LUAD), the most common subtype of lung cancer, is characterized by extensive tumor heterogeneity, early metastatic spread, and poor response to therapeutic intervention. The oncogenic KrasG12D and Trp53 loss (KP) mouse model recapitulates many aspects of LUAD tumorigenesis, however these mice rarely develop distant metastases and fail to exhibit the progenitor-like tumor cell states associated with human LUAD metastases. Emerging evidence indicates that exhibit a high degree of cellular plasticity, enabling them to effectively adapt to and overcome the diverse barriers of the metastatic cascade. However, the oncogenic events that drive cell plasticity and link tumor cell states to metastatic progression remain poorly defined. We have identified Protein Kinase C iota (PRKCI) and Epithelial Cell Transforming Sequence 2 (ECT2) as cooperative oncogenes in LUAD. PKCι directly phosphorylates and activates ECT2, while copy number gain (CNG) of PRKCI and ECT2 within the recurrent 3q26 amplicon drives their coordinated overexpression in ~30% of human LUADs and is associated with poor survival. To model PRKCI-ECT2 CNG, we generated KP mice harboring conditional knock in alleles of Prkci and Ect2 (KP-Gain). Prkci-Ect2 gain fundamentally alters LUAD biology by promoting cell plasticity through progressive dedifferentiation along the lung developmental pathway in a cell of origin dependent manner. Specifically, KP-Gain tumors initiated from alveolar type II (AT2) cells dedifferentiate into a distal SOX9-high progenitor-like cell state, exhibit increased tumor size and grade, and harbor frequent metastases to the liver. Interestingly, KP-Gain tumors initiated in bronchiolar club cells undergo further reprogramming, giving rise to a more primitive foregut SOX2-high progenitor-like state. Club cell-derived KP-Gain tumors are markedly more aggressive and exhibit extreme lineage infidelity giving rise to adeno-squamous carcinoma, small cell lung cancer and pleomorphic carcinomas, and display both liver and brain metastasis. Taken together, our results indicate that Prkci-Ect2 gain promotes primary LUAD tumor progression, distant metastasis, and histological infidelity by driving tumor cells into more primordial lung developmental cell states.

overall_design: Individual tumors were microdissected from moribund KP (KrasG12D; Trp53 fl/fl) and KP-Gain (KrasG12D; Trp53 fl/fl; Rosa26 Prkci/Prkci; Col1a1 Ect2/Ect2) animals infected with either Ad-SPC-Cre or Ad-CCSP-Cre via intratracheal administration (n = 5 tumors/animal; 2-3 animals/genotype). After removal of endothelial cells, red blood cells, and dead cells, scRNA-seq was performed on tumor samples containing both cancer, immune, and fibroblast cells.

first: Duy

middle: T

last: Nguyen

first: Hu

last: Li

first: Alan

middle: P

last: Fields


title: Spatially resolved maternal and fetal cell contributions to severe Preeclampsia

city: London

first: Theodoros

last: Xenakis

address: 20 Guilford Street

country: United Kingdom

institute: UCL

summary: The molecular and cellular pathophysiology of the maternal-fetal interface in preeclamsia remains poorly understood, but it is increasingly clear that both mother and fetus make independent contributions to it. Here, we spatially distinguish these contributions to the severe form of the disease, per tissue and cell type, in its Early and Late presentations in gestation. In addition to concerted hypoxia, angiogenic imbalance, fibrosis and aberrant metabolism in the placenta, new maternal immune signatures, including changes in macrophages, mitochondrial dysfunction and interferon signalling in the placenta, myometrium or choreamniotic membranes, offer an explanation to systemic inflammation and endothelial dysfunction in the mother. These tissue and cell-specific responses are potential targets for therapy, with their prompt consideration in Early gestational disease likely most beneficial.

overall_design: Placenta, myometrium, chorioamniotic membranes and PBMCs were sampled from 20 patients. 10 were preeclamptic and 10 were controls. scRNA seq, snRNA seq and spatial transcriptomics was performed on all samples, with the exception of PBMCs on which spatial transcriptomics was not relevant. The PE patients are:  FCM FAM FGS FEP FVS FFM FRH FSH FD FMM  The control patients are:  FVQ FLR FJJ FVB FLJ FJD FVT FYI FRK FNS

first: Yara

last: Sanchez-Corrales


title: 8-Me-PIQ Expands Cord Blood HSCs via Metabolic Suppression and Inhibition of Ribosome Biogenesis

city: Shanghai

first: Yu

state: Shanghai

address: No.600 Yishan Road

department: Department of Obstetrics and Gynecology

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: 8-methyl-4-((4-isopropylphenyl)amino)-[1,2,4]triazolo[4,3-a]quinoxaline (designated 8-Me-PIQ) is a potent activator of HSC expansion. To gain mechanistic insight into how 8-Me-PIQ promotes ex vivo expansion while preserving HSC stemness, we performed bulk transcriptomic analysis on UCB CD34+ cells cultured for 7 days in the presence of either 8-Me-PIQ or DMSO vehicle control.The convergence of transcriptional changes upon these specific biological processes suggests a coordinated mechanism by which 8-Me-PIQ preserves HSC stemness: attenuation of mitochondrial oxidative metabolism and reduction of global protein synthesis demand, thereby maintaining a quiescence-like state conducive to long-term function.

overall_design: Comparative gene expression profiling was performed using RNA-seq data from umbilical cord blood hematopoietic stem cells (CD34+) ex vivo cultured for 7 days treated with DMSO and 8-Me-PIQ.

first: Mengmeng

first: Bin

last: Guo

first: Rongzhen

last: Jiang


title: Critical role of keratinocytes and PAR2 in secondary lymphedema development

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

summary: Activated keratinocytes play a key role in the pathophysiology of secondary lymphedema through PAR2 by producing Th2-inducing cytokines that modulate skin inflammatory responses.

overall_design: Cells from the skin of patients with lymphedema, from both the affected limb and the unaffected contralateral limb, were sorted using fluorescence-activated cell sorting (FACS) and analyzed by single-cell RNA sequencing (scRNA-seq).

first: Hyeung Ju

last: Park

first: Kataru

last: Raghu

first: Mehrara

last: Babak


title: Effect of free cholesterol on the inflammatory response induced by POPC liposomes

city: La Jolla

first: Antonio

last: De Maio

state: CA

address: 9500 Gilman dr

institute: UC San Diego

summary: Lipid nanoparticles (LNP) have gained increased interest for their use as carriers of therapeutic drugs and vaccines. The main phospholipid within LNP is phosphatidylcholine, which has been considered an inert component. However, we have shown that liposomes made of palmitoyl oleoyl phosphatidylcholine (POPC) induced a massive alteration of gene expression within macrophages (M), particularly genes involved in the inflammatory response. Since cholesterol plays a crucial role in cellular functions and is a regular component of LNP, we investigated the effect of the sterol on the inflammatory response induced by POPC liposomes. We attempt to investigate whether the presence of free cholesterol within liposomes affects the inflammatory response induced by the phospholipid.

overall_design: Total RNA isolated from RAW26.7 macrophages in culture conditions. Cells were incubated with POPC liposomes for 1 hour containing or not free cholesterol (n=3). Control cells were treated with vehicle (PBS) in the same conditions (n-3).

first: David

middle: M

last: Cauvi


title: From encounter to memory: molecular dynamics of heterospecifc recognition in cleaner wrasse

city: Hong Kong

first: Daniele

last: Romeo

address: Pok Fu Lam Rd, Lung Fu Shan

country: Hong Kong

institute: The University of Hong Kong

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Heterospecific individual recognition, the capacity to identify and remember specific members of another species, guides partner choice in mutualisms, reduces costly misclassification, and supports community stability. Yet the molecular machinery enabling such recognition is poorly understood. The cleaner wrasse Labroides dimidiatus makes heterospecific individual recognition a central feature of its behavioural ecology, through ~2,300 daily interspecific interactions it has developed the ability to assess and recall partners rapidly and accurately. To probe the molecular basis of this capacity, we coupled a familiar–unfamiliar two-choice social preference test with forebrain RNA-sequencing and H3K27ac profiling at 0, 30, and 120 min, linking behaviour, transcription, and chromatin state. Behaviourally, familiarisation reduced time spent near the familiar client. At the molecular level, transcriptomes traced a phased trajectory: an immediate dampening of synaptic release and chemosensory drive, a 30-min GABAergic/homeostatic adjustment, and a 120-min consolidation marked by adhesion and dendritic spine remodelling. Chromatin profiling revealed broad baseline accessibility with only modest between-condition differences and stronger within-condition temporal shifts, indicating that chromatin supports, rather than drives, transcriptional change. Overall, this work offers a molecular framework for heterospecific recognition, linking fast circuit tuning to the subsequent stabilisation of social information.

overall_design:
Cleaner wrasses were tested in a social preference assay after either being familiarised with one client (Familiar treatment) or receiving no prior exposure (Control; both clients novel).
CUT&RUN


title: Antiretroviral therapy during development impairs cardiac reverse remodeling in a rodent model

city: Durham

first: Integrative

last: Bioinformatics

state: NC

address: 111 TW Alexander Drive

department: BCBB

institute: NIEHS

summary: Maternal antiretroviral therapy (ART) during pregnancy and lactation prevents HIV transmission but also represents a key developmental exposure. Many regimens include nucleoside reverse transcriptase inhibitors (NRTIs), which are linked to mitochondrial and cardiac toxicity, raising concerns about effects on offspring heart development. Using a rat model, we show that in utero and lactational exposure to combination ART (cART) alters cardiac mitochondrial metabolism and impairs diastolic function later in life, with stronger effects in males. These changes were accompanied by significant shifts in cardiac gene expression, suggesting that early-life ART exposure can disrupt metabolic programming in the developing heart with lasting consequences.Data herein include heart gene expression that was evaluated by RNA sequencing in rat pups treated with cART at weaning and 4 and 12 months later.

overall_design: Rats were indirectly dosed daily through their mothers from gestational day 6 to weaning (postnatal day, PND21). Cardiac  samples were collected for RNA isolation and sequencing at PND21 (interim), 4 months (terminal) and 12 months.

first: Santos

last: Janine

first: Taube

last: Nicole

first: Delker

last: Don


title: Ketogenic diet exerted anti-seizure function related with alteration of lipid metabolism via pparγ signaling pathway

city: HEFEI

first: Zhiyu

last: Xi

address: 1 Tianehu Road

department: Neurosurgery

institute: The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China

summary: The ketogenic diet (KD) is an established therapy for drug-resistant epilepsy, yet its precise anticonvulsant mechanisms, particularly those linked to its fundamental alteration of lipid metabolism, remain incompletely understood. This study investigated the role of lipid metabolism modulation in the antiseizure effects of KD using a kainic acid (KA)-induced chronic epilepsy mouse model. Mice maintained on KD exhibited significantly reduced seizure frequency, duration, and severity, alongside decreased electrographic spike discharges and neuronal c-Fos expression compared to those on a chow diet (CD). Transcriptomic analysis of temporal lobe tissue revealed several differentially expressed genes (DEGs) in KD-fed mice, with parts identified as lipid metabolism-related. Further analysis and experiments demonstrated key genes and pathways releated to the regulation of KD in lipid metabolism subsquently exerted anti-seizure effects.

overall_design: RNA-seq profiling of temporal lobe brain tissues from KA-induced epileptic mice fed either a Chow diet or a Ketogenic diet for 3 weeks.

first: Xi

last: Zhiyu


title: PerR is a positive regulator of staphyloferrin B-mediated iron acquisition in Staphylococcus aureus

first: Alexander

last: Sheikh

state: Ontario

address: 1400 Western Road

department: Microbiology and Immunology

institute: Western University

summary: Staphylococcus aureus is a globally prevalent Gram-positive pathogen with the remarkable ability to cause infection in numerous tissues. Due to the concerted action of host iron (Fe) sequestration mechanisms, the ability of bacterial pathogens to overcome this nutritional immunity is required for infection. S. aureus expresses an arsenal of Fe acquisition systems the expression of which are coordinated primarily through a well-characterized Fe-sensing transcriptional regulator, Fur. Here, from a screen to identify S. aureus mutants defective for iron-restricted growth, we identified several where genome sequencing identified mutations in the perR gene, encoding a transcriptional regulator involved in resistance to oxidative stress. RNA-seq identified that perR mutants express significantly less transcript from the staphyloferrin B biosynthetic operon, sbn, during growth under Fe starvation. These results were consistent with our finding that perR mutants grew poorly in iron-deficient media in a staphyloferrin B-dependent manner. In a subcutaneous model of S. aureus infection, a perR mutant demonstrated significantly smaller lesion sizes, and this was consistent with our finding that perR mutant had decreased expression of alpha-hemolysin when grown under iron-restriction. All of these findings are consistent with the hypothesis that perR acts to fine tune access to iron as a means to avoid Fe-dependent toxicity. The importance of PerR function to S. aureus was further highlighted by examination of over 8000 bloodstream isolates of S. aureus from humans, showing that PerR sequence was highly conserved among this large cohort of isolates. Together, these findings demonstrate the importance of PerR to S. aureus in providing an additional level of regulation of iron homeostasis beyond Fur-dependent iron sensing.

overall_design: RNA-seq profiling of S. aureus USA300-LAC wild-type and isogenic perR transposon mutant strains grown in iron-replete and deplete liquid media.

middle: A

middle: E

last: Heinrichs


title: In vivo CRISPR knockout screen reveals Polr1a as a key driver and a potential therapeutic target for melanoma metastasis.

city: Hershey

first: Vladimir

last: Spiegelman

state: PA

address: 500 University Drive Hershey, Pennsylvania

department: Pediatrics

institute: Penn State University

summary: Identification and characterization of novel mechanisms driving melanoma metastases and ways to target them are paramount for the development of effective treatment modalities. We demonstrated that higher Polr1a levels correlate with increased metastasis and reduced survival in patients. In this study, we evaluated the effect of Polr1a knockdown on gene expression in melanoma cells.

overall_design: custom CRISPR library screen comparing cells', tumor, and metastasis samples

first: Anna

middle: F

last: Fajardo

first: Chethana

last: Gowda

first: Emily

last: Johnson

first: Ricardo

last: Petroni

first: Vivek

middle: S

last: Tomar

first: Zhenqiu

last: Liu

first: M

last: Blanco

first: Jacob

last: Janssen

first: Irina

last: Elcheva

first: Matthew

last: Lanza

first: Serge

middle: Y

last: Fuchs


title: RNA-seq analysis of PAPD5 inhibitor effects in expanded human induced pluripotent stem cell-derived cardiomyocytes

city: Matsumoto

first: Shin

last: Kadota

address: 3-1-1 Asahi

department: Regenerative Science and Medicine

country: Japan

institute: Shinshu University

summary: Human induced pluripotent stem cells (hiPSCs) were differentiated into cardiomyocytes using a conventional monolayer protocol to generate non-expanded cardiomyocytes (N-CMs). A subset of cardiomyocytes was further replated and cultured in the presence of CHIR99021 to generate expanded cardiomyocytes (E-CMs). During the expansion phase, E-CMs were treated with the PAPD5 inhibitor BCH001 (E-CM-B) or RG7834 (E-CM-R) to prevent cellular senescence. RNA sequencing was performed to characterize transcriptional differences associated with senescence and mitochondrial maturation. Treatment with BCH001 during cardiomyocyte expansion attenuated the expression of senescence-associated markers and promoted gene expression profiles consistent with mitochondrial maturation. This dataset provides transcriptomic insights into the molecular effects of PAPD5 inhibition on expanded hiPSC-derived cardiomyocytes.

overall_design: Human iPSC-derived cardiomyocytes were generated using a monolayer differentiation protocol. Non-expanded cardiomyocytes (N-CMs) were collected directly after differentiation, with or without treatment with the PAPD5 inhibitor BCH001 (N-CM-B). For expansion, cardiomyocytes were replated and cultured with CHIR99021 to generate expanded cardiomyocytes (E-CMs). During the expansion phase, E-CMs were treated with BCH001 (E-CM-B) or RG7834 (E-CM-R). Total RNA was extracted from all groups and subjected to RNA sequencing to compare transcriptional profiles.

first: Yuji

last: Shiba

first: Jian

last: Zhao


title: Amyloid-beta aggregates induce vasculopathy via ferroptosis in brain endothelial cells

city: Daegu

first: Do-Geun

last: Kim

address: Cheomdan-ro 61

department: Dementia Research Group

country: South Korea

institute: Korea Brain Research Institute

summary: Amyloid-beta (Aβ) plaque is the pathological hallmark of Alzheimer's disease (AD) and a target of various therapeutic agents for affected patients. Recent studies have demonstrated the dysfunction of the blood-brain barrier (BBB) in AD; however, how Aβ plaque induces BBB dysfunction, particularly in brain endothelial cells (ECs), remains elusive. This study investigates the lipid peroxidation-mediated ferroptosis pathway induced by Aβ by conducting RNA sequencing, phosphorylation analysis, metabolite analysis, western blotting, and immunofluorescent staining both in vitro and in vivo. Here, we found that Aβ is associated with lipid metabolic pathways following Aβ exposure in brain ECs. Additionally, Aβ aggregates induce the formation and accumulation of peroxidized lipid droplets. Lastly, Aβ is significantly reduced in brain ECs and 5xFAD mice by the inhibition of the lipid metabolic pathway associated with lipid peroxidation and ROS formation. Our findings from in vitro and in vivo both suggest that Aβ plays a causative role in the process of lipid peroxidation and might provide a potential target for the development of therapeutic interventions for AD.

overall_design: Primary human brain microvascular endothelial cells (HBMVECs) were cultured and treated with amyloid beta oligomer (OAβ) for 1, 4 or 12 hours. After treatment, RNA was extracted for transcriptomic analysis to investigate gene expression changes.

first: Suhyeon

last: Son

first: Suji

first: Min-Tae

last: Jeon

first: Moonseok

last: Choi

last: Lee

first: Kyu-Sung

first: Seung-Yeol

last: Nah


title: The challenges of single cell transcriptomics on difficult human tissue: the placenta

first: Theodoros

last: Xenakis

summary: Demand for the application of single cell transcriptomics on difficult tissues, processed and stored in disparate conditions, has led to the development of various single cell modalities. We focus on the placenta, a challenging tissue to transcriptomically interrogate due to senescence, intermittent hypoxia, high levels of RNase activity and tissue trauma at delivery. We performed single cell and nuclei transcriptomics on two samples with probe-based and native molecule transcript capture, droplet based and in situ plate based cell isolation. We explored sample and storage variations, including freshly dissociated tissues, fixed cells, snap frozen and FFPE processing. We find that variations in sample processing and storage have much larger effect on cell type proportions than differences in chemistry, impacting the biology that can be learned or the identification of disease markers. Further, the transcriptomic output of in situ combinatorial indexing consistently overlaps, with single nucleus transcriptomics, sharing little with other modalities. This may limit combinatorial indexing for sampling cytoplasmstic mRNAs. Our comprehensive analysis of the varying effect of single cell transcriptomic modalities, including their sample management strategies, provides novel and essential considerations for the experimental design and analysis of single cell transcriptomics applicable to challenging tissues, offering actionable guidance for future experiments.

overall_design: We processed two placental samples, which included the maternal decidua using 5 different single cell modalities. These two samples where from late preterm deliveries, delivered at 37 and 36 gestational weeks respectively.    The PE patients are:  F1950PYI F1958NS


title: Chromatin profiling following FASN knockdown in UMUC3 bladder cancer cell lines treated under cigarette smoke media and regular media conditions.

city: Houston

first: H. Courtney

last: Hodges

state: TX

address: 1 Baylor Plaza, BCM 229

department: Department of Molecular & Cellular Biology

institute: Baylor College of Medicine

summary: To assess the genome-wide chromatin effect of FASN knockdown under cigarette smoke treated conditions in UMUC3 bladder cancer cell lines. ChIP-seq was performed by pulling down with H3K18Ac antibody in Control and FASN KD cells upon 10%CSM treatment.

overall_design: H3K18Ac chromatin occupancy profiling in FASN knockdown cells in UMUC3 Bladder cancer cell line.

first: Chandra

last: Amara

first: Yuen

last: Chan

first: H

middle: C

first: Nagireddy

last: Putluri


title: Real-time quantitative PCR analysis of mature 3T3-L1 adipocytes treated with citrate capped gold nanoparticles

city: Cape Town

first: Anelisiwe

last: Hyera

state: Western Cape

address: Robert Sobukwe Rd, Bellville,

department: Biotechnology

country: South Africa

institute: University of the Western Cape

summary: 3T3-L1 pre-adipocytes were differentiated into mature adipocytes over 10 days using MDI induction and insulin supplementation. Differentiated adipocytes were treated with 12.5 nM citrate-capped gold nanoparticles for 24 hours. Total RNA was extracted and analyzed using the Mouse Adipogenesis RT² Profiler PCR Array (Qiagen) to quantify gene expression changes in adipogenesis, lipid metabolism, and related pathways. Untreated differentiated 3T3-L1 cells served as controls.

overall_design: qPCR gene expression profiling of treated and untreated 3T3-L1 adipocytes. Three biological replicates were used for each condition and averages where used for the results.

first: Jyoti

last: Rajan Sharma

first: Adewale

last: Oluwaseun Fadaka

first: Kwazikwakhe

last: Bethuel Gabuza

first: Zanele

last: Mganto Khuselo

first: Abram

last: Madimabe Madiehe

first: Mervin

last: Meyer

first: Nicole

last: Remaliah Samantha Sibuyi


title: Spatial tumour-immune ecosystems shape the efficacy of anti-PD1 immunotherapy in primary cutaneous melanoma [snRNAseq]

status: Public on Jun 23 2026

city: LYON

first: Julie

last: CARAMEL

address: 28 Rue Laennec

country: France

institute: Cancer Research Center of Lyon

summary: Intra-tumoral heterogeneity in melanoma arises from dynamic cancer cell plasticity and underlies various mechanisms of immune escape. Here, we combined high-plex immunofluorescence imaging with spatially resolved transcriptomics to map the architecture of melanoma cell states and their interactions with the immune microenvironment in primary cutaneous tumours prior to adjuvant anti-PD1 immune checkpoint inhibitor (ICI) treatment. Computational analyses showed that melanoma cells organise into spatially restricted patches, with a preferential organisation of undifferentiated cells associated with poor ICI efficacy. Neighbouring immune cell composition varied according to cancer cell states, with a crucial involvement of specific subsets of tumour-associated macrophages, driven by signalling pathways involving tumour-derived and microenvironmental cues such as IFN-γ and hypoxia. Integrated spatial analyses further revealed tumour-immune ecosystems that stratify patient outcomes, delineating configurations either associated with ICI efficacy or metastatic relapse. These results uncover the spatial landscape of tumour ecosystems and identify signalling pathways as potential targets for improving the efficacy of ICI in melanoma.

overall_design: to study the resistance to immunotherapy anti PD1, we perfomed bulk RNAseq sequencing of 57 pre treatment samples of patients with stage III melanoma, as well as snRNA sequencinf of 2 metastases and visium sequencing for 4 primary tumors..

first: Pham

last: Félix

first: Dufeu

last: Marion

first: Benboubker

last: Valentin

first: Grimont

last: Maxime

first: Lhorisson

last: Amélie

first: Berthet

last: Justine

first: Donzel

last: Marie

first: Schneider

last: Raphael

first: Tonon

last: Laurie

first: Doffin

last: Anne-Claire

first: Boivin

first: Durand

last: Simon

first: Dubois

last: Bertrand

first: Lopez

last: Jonathan

first: Caux

last: Christophe

first: Valladeau-Guilemond

last: Jenny

first: Eberhardt

last: Anaïs

first: Dalle

last: Stéphane

first: Caramel

last: Julie


title: Transcriptomics profiling in mouse xenografts derived from UMUC3 Control and FASNKD cells treated with 10%CSM (Cigarette smoke media) and regular media conditions.

first: Karthik Reddy

last: Kami Reddy

email: karthikr@bcm.edu, amara@bcm.edu, putluri@bcm.edu, piyarath@bcm.edu

state: Texas

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

summary: To assess transcript levels changes in FASN knockdown under CSM conditions in UMUC3 BLCA cell lines. RNA-seq was performed.

overall_design: Transcriptomics in UMUC3 Control and  FASN knockdown derived xenografts under control and smoke conditions

first: Chandra

last: Amara

first: Nagireddy

last: Putluri


title: BMAL1 and YAP cooperate to hijack enhancers and promote inflammation in the aged epidermis [ChIP-Seq 2]

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

institute: IRB Barcelona

summary: Ageing is characterised by persistent low-grade inflammation that is linked to impaired tissue homeostasis and functionality. However, the molecular mechanisms driving age-associated inflammation remain poorly understood. The mammalian skin is a clinically relevant target of age-driven inflammation associated with compromised barrier function, inefficient wound healing, elevated oxidative stress, and DNA damage accumulation. Here, we show that upon ageing a previously uncharacterised BMAL1–YAP transcriptional complex is hijacked from chromatin regions associated with homeostatic genes in adult epidermis and redirected to inflammation-related enhancers, amplifying the transcription of their target genes. Independently of its known role as a core circadian clock component, BMAL1 partners with the mechanosensitive transcriptional cofactor YAP at enhancer regions to regulate epidermal identity genes. In contrast, in aged skin, BMAL1–YAP complexes bind to enhancers of inflammation-related genes, co-regulated by NF-κB. Interestingly, aged pro-inflammatory signals from the IL-17 pathway activate YAP in a Hippo-independent manner. These findings unveil a transcriptional mechanism underlying epidermal ageing, linking chromatin dynamics to inflammatory transcriptional programs through BMAL1–YAP-bound enhancer rewiring. By elucidating how ageing reprograms transcriptional networks, our work highlights potential strategies to counteract chronic inflammation and restore tissue homeostasis across age-related loss of functionality.

overall_design: ChIP-seq of YAP of adult (18-25 weeks old) and aged (80-90 weeks old) WT mouse epidermis, and of 47 weeks old ColXIV KO and ColXIV WT mouse epidermis, at Zeitgeber time 4 (ZT4).

first: Camile

first: Guiomar

last: Solanas

first: Júlia

last: Bonjoch


title: RNA-Seq assay identifies potential regulon and downstream targets of Msd1 under mating-inducing and -repressing conditions in a global basidiomycete pathogen

city: Nanchang

first: Fanglin

last: Zheng

state: Jiangxi

address: 1519 Dongyue Avenue, Nanchang County, Jiangxi Province

department: The First Affiliated Hospital of Nanchang University

institute: Nanchang University

summary: Meiosis is a hallmark of sexual reproduction. Although the core meiotic machinery is evolutionarily conserved from unicellular yeasts to higher eukaryotes, the key regulators responsible for initiating meiosis vary across species. Except for the well-studied model species, such key regulators remain largely unidentified in many major eukaryotic lineages, including those in the phylum Basidiomycota of the Kingdom Fungi. The basidiomycete fungus Cryptococcus neoformans is a clinically important pathogen and a model organism for studying sexual reproduction. As in many other eukaryotes, sexual reproduction in this haploid basidiomycete requires spatiotemporal coordination of multi-step cellular differentiation events and nuclear cycles, including meiosis. However, the transcription factor that governs the initiation of meiosis in this fungus remains elusive. Here, we identified a novel transcription factor, Msd1, that plays a crucial role in activating meiosis in C. neoformans. Deletion of MSD1 abolished pre-meiotic diploidization, basidial differentiation, meiosis and the subsequent sporulation. Conversely, overexpression of MSD1 is sufficient to drive meiosis and the formation of meiotic spores in the absence of the external mating-inducing cues or the internal genetic factors of the mating pathway. Consistently, multiple evolutionarily conserved meiosis-specific genes are transcriptionally regulated by Msd1. Furthermore, Msd1 targets two downstream RNA binding proteins, Csa1 and Csa2, to ensure successful meiosis and sporulation in this species. Collectively, our findings establish this novel transcription factor as the master regulator of meiotic entry in this basidiomycete fungus.

overall_design: RNA-seq profiling of wild type Cryptococcus neoformans  serotype D strain XL280 and its knockout derivative (msd1  mutant) at 24, 48 and 48 hours of mating induction on V8 medium, and the MSD1 overexpression strain under mating suppressing condition on YPD.

first: Yanli

last: Cao

first: Xinping

last: Xu

first: Xiaorong

last: Lin


title: Transcriptional interference drives intronic polyadenylation at the endogenous H13/Mcts2 locus

first: James

middle: A.

last: Cain

address: Guy's Hospital, Great Maze Pond

department: Infectious Diseases

institute: King's College London

summary:
ABSTRACT:
Over a tenth of mammalian genes are organised as nested within distinct host genes, questioning how both can be expressed when concurrent transcription can collide in the same genetic space. DNA methylation-mediated silencing of nested genes can prevent such conflict. Alternatively, transcriptional interference can occur, but this has not been mechanistically demonstrated independently of DNA methylation outside of artificial systems. We demonstrate transcriptional interference at an endogenous mammalian host/nested locus, the imprinted H13/Mcts2 pair. Here, active nested gene (Mcts2) transcription promotes host gene (H13) intronic polyadenylation, while Mcts2 silencing through promoter DNA methylation, favours distal 3′UTR polyadenylation. Using dCas9:KRAB-mediated silencing we establish that this effect depends on transcription itself, independently of DNA methylation. Moreover, nested gene transcription interferes with host gene elongation even when the upstream intronic polyadenylation site is ablated. Nested gene transcriptional interference can thus stimulate intronic termination of their host gene with implications for hundreds of loci.

Allelic CUT&RUN was utilised to assay H3K36me3 to track elongation and H3K4me3 to assay promoters at the H13/Mcts2 locus within this study

overall_design: CUT&RUN analysis to assay chromatin was performed in hybrid mouse neural stem cells for H3K4me3 (Abcam, ab8580) and H3K36me3 (EpiCypher, 13-0058). This was performed in WT and modified NSCS: dCas9:KRAB mediated Mcts2 repressed NSCs and CRISPR mediated H13d poly(A) deletion cell lines.

first: Chuying

last: Yang

first: Hallgerdur

last: Kolbeinsdottir

first: Anne-Valerie

last: Gendrel

first: Hannah

last: Mischo

first: Bertille

last: Montibus

first: Rebecca

middle: J

last: Oakey


title: Mechanical stress suppressed miR-330 in the development of osteoarthritis and its protection from osteochondral degeneration

first: luxiang

last: zou

state: SHANGHAI

address: No.639, Zhizaoju Road, Shanghai

institute: shanghai ninth hospital

summary: Abnormal mechanical stress plays a crucial role in the progression of osteoarthritis (OA). However, more key factors regulating mechanical response remain to be explored. This study harvested temporomandibular joint synovium fluids from 96 patients and revealed that miR-330 is significantly reduced under abnormal mechanical stress. Similarly, the expression of miR-330 is also decreased in cartilage and subchondral bone tissue from clinical specimen and animal models. Global knock out of miR-330 aggravated osteoarthritis development in both temporomandibular joint and knee joint. Conditional knock out of miR-330 in either chondrocytes or osteoclasts exhibited similar phenotype in both mechanical instable and aging animal models, suggesting the importance of miR-330 in both types of cells. Further molecular mechanism exploration unveiled that miR-330 can regulate the catabolism of chondrocytes and osteoclasts via suppressing CTGF, FGFR1 and EPOR as well as key inflammatory cytokines such as IL-1β and TNF-α. More importantly, intra-articular supplement of miR-330 exerts a therapeutic effect by mitigating the detrimental impacts of abnormal mechanical stress, where inhibition of chondrocytes apoptosis, osteoclasts activation and inflammation were further confirmed via single-cell RNA sequencing analysis. In conclusion, this study for the first time revealed that miR-330 is a mechanical responsive, osteoarthritis protective micro RNA. We provide evidence that miR-330 has potential diagnostic and therapeutic value for both temporomandibular and knee osteoarthritis.

overall_design: All the animal study procedure conformed to the ARRIVE Guideline as required. 24 SD Rats were randomly divided into 3 groups, and the sham groupswere treated with Vector AAV injection without UAC establishment. The other two groups were treated with Vector AAV injection or miR-330 AAV injection with UAC establishment. The 16 condyles in each group were freshly collected for the single cell RNA sequecing.

first: Dongmei

last: He

first: Luxiang

last: Zou

first: Cong

last: Li

first: Kaiwen

first: Yeke

last: Yu


title: HIF1 Counteracts FOXO1/Bim-associated Follicle Atresia in Mouse Ovaries by Promoting Bcl-XL Expression

city: Beijing

first: Ming

last: Hao

address: Shuangqing Rd.

institute: Tsinghua Univ

summary:
Background
In mammalian ovaries, the majorities of developing follicles (up to 95% in human) undergo atresia. A considerable part of follicle atresia is initiated by granulosa cell (GCs) apoptosis. Our previous work identified hypoxia-inducible factors 1 (HIF1) pathway induced by follicle-stimulating hormone as a protective factor against atresia, yet the molecular mechanism of follicles’ “norm” death, and how HIF1 pathway protect follicles has not been fully delineated.
Methods
We employed a single-follicle, multi-dimensional profiling strategy based on serial sectioning, to dissect the signaling logic underlying physiological follicle fate decisions.
Results
HIF1 and forkhead box protein O1 (FOXO1) pathway show complementary activation patterns in GCs of healthy versus atretic mouse follicles. In growing mouse follicles, HIF1 pathway activity is associated with increased reactive oxygen species (ROS)-related signals, likely through enhanced granulosa-cell metabolic activity. Under the physiological conditions, ROS-related signals appear to help maintain HIF1 pathway activity in mouse granulosa cells during follicle growth, and are not by themselves associated with follicle atresia. HIF1 pathway appears to promote Bcl-XL expression, which may counterbalance FOXO1-associated atretic pressure.
Conclusion
In mouse ovaries, follicular fate appears to be associated with the dynamic balance between the pro-survival HIF1/Bcl-XL axis and the pro-apoptotic FOXO1/Bim axis.

overall_design: 3w C57B6/J female mice were intraperitoneal injected with 150 mg/kg N-acetyl-l-cysteine for 3 consecutive days, with 3w C57B6/J female mice injected with normal saline as control group. Their ovaries were harvested at the 4th day after the first injection. Granulosa cells were collected from those ovaries via laser micro dissection. mRNA was extracted, reverse transcripted and amplified as GEO-seq protocol.

first: Longping

last: Liu

first: Jianbin

last: Wang


title: Decoupling oxidative resilience from reprogramming to rejuvenate the RPE and restore vision [GSTA4_RNA-seq_3]

city: Cambridge

first: Yuancheng Ryan

last: Lu

state: MA

address: 455 Main St

institute: Whitehead Institute for Biomedical Research

summary: OCT4, SOX2, and KLF4 (OSK) Yamanaka factors can reverse age-related epigenetic changes, yet alternate mechanisms by which they promote tissue resilience remain poorly understood. Oxidative stress contributes to retinal pigmented epithelium (RPE) degeneration in age-related macular degeneration. Here, we show that OSK expression in RPE promotes Tet2-independent oxidative resilience through acute, memory-free transcriptomic changes, and restores visual function in aged mice. Integrative functional genomics helped identify GSTA4, a detoxifying enzyme that clears the lipid peroxidation byproduct 4-HNE, as a key OSK downstream effector. OSK directly and dynamically activates GSTA4, recapitulating a stem cell-derived stress resilience program. GSTA4 overexpression alone enhances oxidative resilience, rejuvenates the aged RPE transcriptome, and reverses visual decline while avoiding OSK’s pleiotropic effects. GSTA4 is upregulated across diverse lifespan-extending interventions suggesting a broader pro-longevity role. These findings uncover a previously unrecognized protective axis directly regulated by OSK, that can be decoupled from reprogramming, providing a framework for developing more precise rejuvenation therapies.

overall_design: Transgenic OSK mouse ear fibroblasts were induced with doxycycline (DOX) for 6 days, with or without a 4-day DOX withdrawal. This dataset was used in Fig. 3 to identify shared differentially expressed genes (DEGs) and nominate candidate genes, and in Fig. 4 to demonstrate the dynamic and reversible activation of Gsta4 by OSK.


title: Decoupling oxidative resilience from reprogramming to rejuvenate the RPE and restore vision [GSTA4_RNA-seq_5]

overall_design: RNA-seq of stable ARPE-19 cells after four days of ORF expression. This dataset was used for ploting Fig. 4A heatmap showing induction of candidate oxidative effectors upon ectopic expression of Oct4, Sox2, Klf4 or OSK in ARPE-19 cells.


title: Decoupling oxidative resilience from reprogramming to rejuvenate the RPE and restore vision [GSTA4_RNA-seq_6]

overall_design: Aged mouse RPE cells, collected 12 weeks after AAV-GFP or AAV-GSTA4 treatment, were first preserved in RNAprotect Cell Reagent and subsequently processed with TRIzol for RNA extraction.


title: Decoupling oxidative resilience from reprogramming to rejuvenate the RPE and restore vision [GSTA4_RNA-seq_2]

overall_design: RNA-seq of stable ARPE-19 cells after four days of ORF expression. This dataset was used in Fig. 3 to identify shared differentially expressed genes (DEGs) and nominate candidate genes.


title: Effect of latrunculin A on gene expression in human skin dermal fibroblasts

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

summary: The purpose of the study was to determine the relationship between dermal fibroblast size and mechanical force and expression of extracellular matrix-related gene expression (matrisome).

overall_design: Primary human dermal fibroblasts were treated with latrunculin A, which inhibits actin polymerization, thereby reducing fibroblast size and mechanical force. Total mRNA was prepared following latrunculin A treatment, and global gene expression was determined by RNA sequencing.

first: Gary

last: Fisher

first: Taihao

last: Quan


title: Decoupling oxidative resilience from reprogramming to rejuvenate the RPE and restore vision [GSTA4_RNA-seq_4]

overall_design: RNA-seq of stable ARPE-19 cells after four days of ORF expression. This dataset was used in Fig. S4 to display the Gene set enrichment analysis (GSEA).


title: In vivo CRISPR knockout screen reveals Polr1a as a key driver and a potential therapeutic target for melanoma metastasis [Ribo-Seq]

first: Vladimir

last: Spiegelman

summary: Identification and characterization of novel mechanisms driving melanoma metastases and ways to target them are paramount for the development of effective treatment modalities. We demonstrated that higher Polr1a levels correlate with increased metastasis and reduced survival in patients. In this study, we evaluated the effect of Polr1a knockdown on gene translation in melanoma cells.

overall_design: Ribo-seq profiling of mouse melanoma SW1 cells with Polr1a constitutive knockdown or non-targeting control

first: Anna F.

last: Fajardo

first: Chethana P.

last: Gowda

first: Emily

last: Johnson

first: Ricardo

last: Petroni

first: Vivek S.

last: Tomar

first: Zhenqiu

first: M. Andres

last: Blanco

first: Jacob

last: Janssen

first: Irina A.

last: Elcheva

first: Matthew

last: Lanza

first: Serge Y.

last: Fuchs

first: Vladimir S.


title: A systemic role of macrophage-derived BMP2/4 homolog Dpp in controlling sterol hormone synthesis under dietary stress

city: Barcelon

first: Lidia

last: Mateo

address: C/ Baldiri Reixac 10

institute: Institute for Research in Biomedicine (IRB Barcelona)

summary: High-caloric diets, prevalent in Western societies, are characterized by their affordability, yet they hinder overall development and compromise adult physiological performance. Unfortunately, children consuming diets rich in sugar are prone to developing insulin resistance, chronic low-grade inflammation, and delayed developmental transitions, such as puberty, which collectively lead to adverse systemic outcomes. In metazoans, these critical developmental transitions are tightly regulated by steroid hormones. These deleterious effects underscore the vital role of nutritional sensing organs in orchestrating inter-organ communication, which is indispensable for maintaining physiological and metabolic homeostasis. For instance, macrophages are capable of detecting metabolic perturbations and subsequently secreting growth factors to restore equilibrium. Whereas macrophages have been shown to modulate steroid hormone synthesis in Drosophila melanogaster under conditions of inanition, it remains unclear whether high-sugar diets (HSDs) influence macrophage behavior and steroid hormone synthesis. Using Drosophila melanogaster, we report that macrophage-derived Decapentaplegic (Dpp) mediates the biosynthesis of the steroid hormone ecdysone during HSD consumption, thereby impacting development and growth. Mechanistically, macrophage-derived Dpp interacts with Thickveins (Tkv) in the prothoracic gland, leading to the activation of the BMP pathway. This activation subsequently downregulates ecdysone synthesis (the only sterol hormone in flies), ultimately extending developmental time to ensure adult viability.

overall_design: Hemocytes from five larvae at 96 hours AEL were bled into 120 μl of FACS buffer (PBS, 0.5% bovine serum albumin, and 2 mM EDTA) containing 1 nM phenylthiourea (Sigma-Aldrich, St. Louis, MO, USA) to prevent melanization. We used two forceps to make an incision from the posterior and pull to the anterior ends of the larvae. We allow larvae to bleed for a few seconds, and, later, we carefully scrape the lateral cuticle to avoid the lymph gland disruption71. We counted the macrophage numbers by quantify the number of GFP-positive hemocytes [40,6-diamidino-2-phenylindole (DAPI) negative], using hmlΔ>2xeGFP, in on an BD FACSARIA III (BD Biosciences). Cells were selected based on their size with a FSC-A from 2.5K to 250K and their granularity with a SSC-A from 2.5K to 150K. Later, we gated for singlets (FSC-H vs FSC-A). For fluorescent hemocytes, we used BlueC (530_30) RB-A laser (GFP). Flowcytometry plots were obtained with FlowJo 9.9. Total RNA from a total of 4 replicates of 20000 GFP+ sorted macrophages were then purified at the IRB Barcelona Functional Genomics Core Facility, as described in González et al., 2010. mRNA was isolated from total RNA using the kit NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). NGS libraries were prepared from the purified mRNA using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs). 18 cycles of PCR amplification were applied to all libraries. The final libraries were quantified using the Qubit dsDNA HS assay (Invitrogen) and quality controlled with the Bioanalyzer 2100 DNA HS assay (Agilent). An equimolar pool was prepared with the twenty libraries and submitted for sequencing at the Centro Nacional de Análisis Genómico (CNAG). A final quality control by qPCR was performed by the sequencing provider before paired-end 150 nt sequencing on a NovaSeq6000 S4 (Illumina). More than 275 Gbp of reads were produced, with a minimum of 39 million of paired-end reads per sample.

first: Sergio

last: Juarez-Carreño

first: Marco

last: Milán


title: Decoupling oxidative resilience from reprogramming to rejuvenate the RPE and restore vision [GSTA4_ATAC-seq_1]

first: Yuancheng Ryan

last: Lu

overall_design: ATAC-Seq of mouse ear fibroblasts derived from young and old transgenic Rosa26-M2rtTA/Col1a1-tetOP-OKS-mCherry mice; OSK, OSK induced with Doxycycline for 6 days; OSKonoff, OSK induced with doxycycline for 4 days, then withdrawn for 4 days.

first: Yan

last: Hu


title: Distinct roles of COPI proteins attenuated with cell senescence

city: Baltimore

first: Supriyo

last: De

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Cellular senescence is characterized by persistent cell cycle arrest, apoptosis resistance, and widespread changes in gene expression.  Although the functional alterations in organelles like mitochondria and lysosomes are well characterized, senescence-associated changes in the structure and function of the Golgi apparatus remain poorly understood.  The Golgi apparatus orchestrates intracellular transport processes that rely heavily on the coating of vesicles with Coatomer Protein Complex I (COPI) proteins (COPA, COPB1, COPB2, COPD, COPE, COPG1, and COPZ1).  Based on an earlier RNA interference (RNAi) screen showing that silencing COPI subunits reduced extracellular vesicle (EV) uptake in human diploid WI-38 fibroblasts, and that EV uptake was diminished in senescent WI-38 cells, we sought to functionally analyze COPI proteins in senescent cells.  In proliferating cells, individually silencing COPA, COPB1, COPB2, or COPD induced ATF4 production and disrupted autophagy, apoptosis, and cytokine signaling—hallmarks of impaired Golgi-to-ER transport—while individually silencing COPG1, COPE, or COPZ1 altered extracellular matrix organization and GTPase activity.  Silencing of any COPI subunit reduced mitochondrial respiration and EV uptake.  Proteomic analysis revealed that individual COPI proteins associate with both Golgi and endosomal components, supporting their role in vesicular trafficking.  Importantly, the phenotypic effects observed in proliferating cells were not observed in senescent cells, which appeared refractory to further COPI reduction.  Our findings underscore the distinct, multifunctional actions of individual COPI proteins and suggest that they are key factors in the intracellular transport networks that sustain homeostatic responses, which become attenuated during senescence.

overall_design: Transcriptomic analysis of WI-38 fibroblasts silenced with individual subunits of the COPI complex.

first: Krystyna

last: Mazan-Mamczarz

first: Eleanor

last: Wind

first: Apala

last: Pal

first: Kyoung-Mi

last: Kim

first: Rachel

last: Munk

first: Chang-Hoon

last: Shin

first: Jennifer

middle: L

last: Martindale

first: Jixiang

last: Lang

first: Qiong

last: Meng

first: Martina

last: Rossi

first: Marika

last: Oksanen

first: Sarah

last: Buchman

first: Braden

last: Daugherty

first: Yulan

last: Piao

first: Jinshui

last: Fan

first: Lu

last: Chen

first: Madhu

last: Lal-Nag

first: Myriam

last: Gorospe


title: In vivo CRISPR knockout screen reveals Polr1a as a key driver and a potential therapeutic target for melanoma metastasis [RNA-Seq]

first: Vladimir

last: Spiegelman

summary: Identification and characterization of novel mechanisms driving melanoma metastases and ways to target them are paramount for the development of effective treatment modalities. We demonstrated that higher Polr1a levels correlate with increased metastasis and reduced survival in patients. In this study, we evaluated the effect of Polr1a knockdown on gene expression in melanoma cells.

overall_design: RNA-seq profiling of mouse melanoma SW1 cells with Polr1a constitutive knockdown or non-targeting control

first: Anna F.

last: Fajardo

first: Chethana P.

last: Gowda

first: Emily

last: Johnson

first: Ricardo

last: Petroni

first: Vivek S.

last: Tomar

first: Zhenqiu

last: Liu

first: M. Andres

last: Blanco

first: Jacob

last: Janssen

first: Irina A.

last: Elcheva

first: Matthew

last: Lanza

first: Serge Y.

last: Fuchs

first: Vladimir S.


title: Transcript profiling of human prostate tumor cell lines [2]

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: Prostate tumor cell line mRNA transcript levels assessed by RNA sequencing.

overall_design: RNA sequencing 5 prostate cancer cell lines using Illumina stranded mRNA TruSeq Library prep and sequenced on Illumina NovaSeq 6000.

first: Peter

last: Nelson


title: Scalable expansion and hepatic zone maturation of hepatic progenitor cells from human pluripotent stem cells

city: Toronto

first: Jeff

address: 101 College Street, RM 4-601

department: Princess Margaret Cancer Center

institute: University Health Network

summary: We devised a method for large-scale manufacturing of hepatocytes derived from human pluripotent stem cells by modulating levels of FGF19, TGFβ and NOTCH. We further employed WNT inhibitor and agonist to enhance differentiation efficiency. These differentiation strategies produce hepatocytes cells with improved in vivo functionality and enable their application in 3D bioprinted liver tissue constructs.

overall_design: FGF19 induced hepatic progenitors were treated with either 1: WNT inhibitor (XAV939) or 2: WNT agonist (CHIR99021) which directs hepatocyte differentiation to Zone1 and Zone3, respectively. The hepatocytes were subjected to scRNA analysis for characterization.

first: Ogawa

last: Mina

first: Liu

last: Jeff C.

first: McGilvray

last: Ian

first: MacParland

last: Sonya

first: Bader

last: Gary

last: Shinichiro


title: A Novel LMX1A Frameshift Variant Underlies Familial Phenotypic Heterogeneity in DFNA7

city: Lanzhou

first: Chenyang

last: Xu

address: Cuiying 88

institute: Lanzhou University

summary: Hereditary hearing loss (HHL) exhibits significant genetic heterogeneity, with mutations in LMX1A related to autosomal dominant non-syndromic hearing loss (DFNA7). Here, we report a novel heterozygous frameshift variant, LMX1A c.405delT (p. Phe135LeufsTer3) in a three-generation Chinese family with progressive and asymmetric sensorineural hearing loss (ASNHL). Clinical evaluations revealed variable severity (mild-to-profound) and onset (infancy to mid-adulthood), with cochlear aperture stenosis observed in the proband. Whole exon sequencing (WES), Sanger sequencing and segregation analysis confirmed the novel mutation and its cosegregation with the phenotype. Structural modeling predicted that truncation within the conserved LIM2 domain disrupts protein function. Functional studies demonstrated reduced transcriptional activity, supporting haploinsufficiency as the pathogenic mechanism. RNA sequencing (RNA-seq) of HEI-OC1 cells revealed dysregulation of neurodevelopmental, synaptic and mitochondrial pathways, implicating neurodegeneration and metabolic dysfunction in LMX1A-related hearing loss. This study highlights the role of LMX1A in auditory homeostasis, provides insights into genotype-phenotype correlations and underscores structural cochlear anomalies as potential contributors to ASNHL.

overall_design: Transcriptome analysis of HEIOC1 from LMX1A mut vs wild-type to identify mechanisms of LMX1A mutation leads to hearing loss.

first: Zhipeng

last: Nie

first: Suyang

last: Wang

first: Yiming

last: Zhu

first: Xiaowen

first: Yufen

last: Guo


title: Clonal dynamics reveal cancer resistance arises from adaptive programs [CROP-Seq]

city: Philadelphia

first: Yeqing

last: Chen

address: 3601 Spruce Street

institute: The Wistar Institute

summary: Most advanced cancers initially respond to targeted therapies but eventually relapse1. Rather than acquiring new mutations, resistance is driven by drug-tolerant persister cells (DTP) that enter a reversible drug-refractory state and sustain minimal residual disease2. Here, we developed MeRLin, a high-resolution barcoding platform combining single-cell RNA sequencing, RNA fluorescence in situ hybridization, and computational analyses to track clonal and transcriptional dynamics of melanoma cells during targeted therapy. Clonal tracking reveals that dominant resistant clones arise from minor pre-treatment subpopulations. The pre-treatment melanoma populations diversify into phenotypically distinct DTP subpopulations, marked by stress-like, lipid metabolism, PI3K signaling, and extracellular matrix remodeling programs associated with adaptive resistance. Spatial transcriptomics revealed the co-localization of lipid metabolism and PI3K signaling programs near the tumor boundaries, and a complex network of autocrine and paracrine interactions among DTP subpopulations. Using barcoded RNA fluorescence in situ hybridization, we identified a dominant persister subpopulation in resistant tumors marked by SLC2A1 expression. Thus, MeRLin provides a robust framework to dissect melanoma heterogeneity and uncover vulnerabilities in persister populations to improve long-term treatment efficacy.

overall_design: To systematically identify key epigenetic drivers of melanoma resistance, we performed a custom CRISPR screen using a restricted library targeting 235 epigenetic regulators that were expressed in melanoma and considered potentially druggable genes. WND238_Cas9-GFP cells were transduced with the lentiviral epigenetic regulator gRNA library, expanded and sorted at MOI < 0.4. Cells were expanded and split into control and BRAFi/MEKi treatment groups. Depletion of sgRNAs targeting top candidate genes was used to identify hits that sensitize melanoma cells to BRAFi/MEKi treatment.

first: Haiyin

last: Li

first: Jessica

last: Kaster

first: Maggie

last: Dunne

first: Min

last: Xiao

first: Ling

first: Monzy

last: Thomas

first: Nazifa

last: Promi

first: Dylan

last: Fingerman

first: Gregory

last: Brown

first: Xingyue

first: Meenhard

last: Herlyn


title: Engineering a Lipid Nanoparticle with Atypical Calcium Crystal Structure for Enhanced IFNβ-mediated Immunotherapy [BMDC]

first: yujie

last: luo

state: Beijing

address: xueyuan road 38

institute: peking university

summary: We have employed RNA sequencing (RNA-seq) to investigate the effects of NanoCa on the activated innate immune response. Our results indicate that NanoCa activates the innate immune response by inducing interferon beta (IFNβ). To examine the transcriptional changes of its associated cytokines, dendritic cells derived from bone marrow were isolated and analyzed using RNA-seq.

overall_design: RNA-seq profiling of dendritic cells derived from bone marrow treated with NanoCa.

first: Yujie

first: Chuanda

first: Yu

last: Sun

first: Dan

last: Lu

first: Yufei

last: Xia

first: Zhiqiang

last: Lin

first: Fuping

last: You


title: Curcumin Attenuates Liver Fibrosis and Inflammation by Modulating Slamf8-Mediated TNF/NF-κB Signaling

city: Hangzhou

last: Liu

address: No. 261 Huansha Road

institute: Hangzhou First People's Hospital Affiliated to Medical School of Westlake University

summary: Liver fibrosis (LF) is characterized by inflammation and fibrosis following liver injury. Curcumin has anti-inflammatory, antioxidant, and cytoprotective properties, with benefits in managing liver diseases. However, the specific mechanisms underlying these effects remain obscure. This work aims to probe into the potential mechanism of curcumin treating LF.We used CCL4 to construct a liver fibrosis model and treated with low, medium, and high concentrations of curcumin. Subsequently, we collected liver tissues and performed RNA sequencing to identify potential targets and associated signaling pathways affected by curcumin treatment. The results showed that curcumin significantly reduced liver damage in mice induced with carbon tetrachloride. RNA sequencing results indicated that Slamf8 was a likely target and the Slamf8 expression was notably decreased in the curcumin group. According to in vivo and vitro results, curcumin inhibited the TNF/NF-κB pathway via Slamf8 modulation, reducing release of pro-inflammatory cytokines (IL-6, IL-17A, MCP-1). Curcumin also suppressed the expression of LF-associated proteins, including α-SMA, COL1A1 and FN. In summary, curcumin exerts potent anti-fibrotic and anti-inflammatory effects by modulating Slamf8 to influence the TNF/NF-κB pathway, thus protecting the liver.

overall_design: Six-week-old C57BL/6J mice received a 200 μL intraperitoneal injection of a 7.5% carbon tetrachloride (CCl4) olive oil solution twice weekly for six consecutive weeks. Different concentrations of curcumin were administered via gavage, with mice assigned into groups: control (CCl4), low-concentration (25 mg/kg, Low), medium-concentration (50 mg/kg, Med), and high-concentration (100 mg/kg, High), with daily treatments for two weeks.

first: Ye

last: Wang

first: Jintao

last: Zheng

first: Lixin

last: Zhou

first: Chenao

last: Yang

first: Jiachen

last: Zhang

first: Yuqiang

last: Shan


title: Loss of endothelial ALK1 signaling induces the emergence of a KIT+ angiogenic endothelial cluster driving brain arteriovenous malformations

city: Montréal

first: Gael

last: Cagnone

state: QC

address: 3175 Chemin de la Côte-Sainte-Catherine

department: The Montreal single-cell Academy

institute: CHU Sainte Justine

summary: Background Hereditary Hemorrhagic Telangiectasia type 2 (HHT2) is a genetic disorder caused by mutations in the Alk1 (Acvrl1) gene, encoding a receptor for Bone Morphogenetic Proteins 9 and 10 (BMP9/BMP10). HHT2 patients frequently develop brain arteriovenous malformations (bAVMs), abnormal connections between arteries and veins. Currently, surgical resection is the only treatment, associated with significant risks and complications. Despite evidence suggesting endothelial cell (EC) heterogeneity in bAVMs, it remains poorly characterized, limiting our ability to identify new therapeutic avenues. Methods We employed endothelial cell-specific and inducible Alk1 knockout mice (Alk1iECKO) with tamoxifen-induced deletion at postnatal day 6 (P6). We separately analyzed the perineural (PNVP) and intraneural (INVP) vascular plexuses, which differ in vessel composition and flow dynamics, at P8. Single-cell RNA sequencing (scRNAseq) was performed to characterize EC heterogeneity and identify transcriptomic changes in both vascular plexus of mutant mice. Results Loss of endothelial ALK1 signaling triggered bAVM formation predominantly in PNVP vascular network. scRNAseq revealed that Alk1 deletion promoted brain capillaries differentiation into angiogenic-1 ECs, whereas it drove PNVP venules EC proliferation and the emergence of the unique angiogenic-2 cluster. The latter shares transcriptomic features with human AVM ECs, including angiogenic tip cell markers and a strong glycolytic signature. Among its defining markers, Kit emerged as a direct downstream target of BMP9-ALK1 signaling. Pharmacological KIT inhibition using Masitinib, Imatinib, or KIT-blocking antibodies prevented bAVM formation in Alk1iECKO mice. Conclusion Our study uncovers a previously unrecognized EC population, the angiogenic-2 cluster, as a key contributor to bAVM development. We identify Kit as a central regulator of this cluster, establishing it as a promising therapeutic target for preventing bAVMs in HHT2.

overall_design: In 2 replicates, brain from mutant mice and littermate controls (Alk1l/l P8 N=2; Alk1iECKO P8 N=2) were collected and directly immersed and digested using the Neural Tissue Dissociation Kit (P) (Miltenyi Biotec, 130-092-628). Each brain was digested at 37°C for 30 minutes. During the enzymatic reaction, gentle flushing of the brain tissue was performed to separate the PNVP from the rest of the brain. The reaction was stopped by adding DMEM containing 5% fetal bovine serum (FBS), and the enzymatic solution containing the PNVP was filtered through a 40 μm cell strainer (Falcon, 352340). The remaining brain tissue was rinsed with PBS, mechanically dissociated, and subjected to a second round of enzymatic digestion. After further homogenization by pipetting, digestion was stopped with 5% FBS in DMEM, and the suspension was again passed through a 40 μm cell strainer. Myelin and cell debris were removed using the Debris Removal Solution (Miltenyi Biotec, 130-109-398), which separates components into distinct phases. Red blood cells were lysed with Red Blood Cell Lysis Solution (Miltenyi Biotec, 130-094-183). The resulting cell suspension was washed with a FACS buffer (PBS containing 1% FBS and 0.2% EDTA). Cells were stained for 30 minutes at room temperature with PE anti-mouse CD140b Antibody (Biolegend, 136006); APC-conjugated anti-mouse CD31 antibody (BD Biosciences, 551262) and FITC-conjugated anti-mouse CD45 antibody (BioLegend, 103108) in Fc block solution (5 µg/mL CD16/CD32 Fc Block, eBioscience, 16-0161-82). After washing, cells were stained with Live/Dead Fixable Aqua Dead Cell Stain (ThermoFisher Scientific, L34957) for 20 minutes at room temperature. Stained cells were washed and resuspended in PBS. The gating strategy was defined using unstained and single-stained controls. Dead cells and doublets were excluded, and endothelial cells (CD45⁻ CD31⁺) were sorted using a BD FACS Aria Fusion. Cells were resuspended in PBS containing 0.04% BSA. Cells from WT PNVP/brain and mutant PNVP/brain sample were then subjected to single-cell RNAseq aiming at a yield of 5 000 cells per condition.

first: Elise

last: Drapé

first: Alexandre

last: Dubrac


title: Dysbiosis-induced expansion of AXL-positive inflammatory type 3 dendritic cells triggers pre-clinical autoimmunity

city: Bethesda

first: Grozdan

last: Cvijetic

state: Maryland

address: 30 Convent Dr, Building 30, Room 332

institute: NIH/NIDCR

summary: Conventional dendritic cells (cDC) are key sentinels at epithelial barriers, regulating immunity to microbial pathogens and commensals while preserving tissue integrity. NOTCH2 deficiency in CD11c-expressing cells (Notch2cKO) disrupts type 2a DC (cDC2a) development, impairs intestinal TH17 immunity, and increases susceptibility to enteropathogenic bacteria. This lead to persistent dysbiosis within our Notch2cKO colony, characterized by low-grade inflammation and systemic autoimmune features, including elevated autoantibody titers and renal immune-complex deposition. Dysbiosis preceded expansion of highly inflammatory AXL-expressing type 3 DC (AXL+inf-DC3), promoting chronic inflammation and tertiary lymphoid structures driving adaptive immune responses. Notably, dysbiosis was defined by three dominant pathobionts and was transferable to WT mice, recapitulating the autoimmune features observed in Notch2cKO mice. Collectively, these findings identify a microbiota–DC axis linking intestinal pathobionts to systemic autoimmunity, establishing inflammatory DC3 as the cellular bridge between dysbiosis, chronic inflammation and autoimmune pathogenesis.

overall_design: We used bulk RNA sequencing (bulkRNAseq) to analyze the transcriptional profiles of sorted cDC2a, DC3 and cDC1 from the spleen of Notch2fl/fl and Notch2fl/fl CD11cCre+ mice.

first: Mladen

last: Mitrovic

first: Daniel

last: Martin

first: Roxane

last: Tussiwand


title: Early seed priming by closely related Bacillus strains drives distinct metabolic and defense programs in melon

city: Málaga

first: María Luisa

last: Carrégalo Ríos

state: Malaga

address: Blvr Louis Pasteur 31

institute: Universidad de Málaga

summary: Mutualistic interactions with beneficial microbes can influence plant physiology far beyond the point of initial contact, yet how host plants differentiate among microbial partners, and the consequences of that discrimination, remain poorly understood. Here, we investigate how Cucumis melo responds to early seed priming with two phylogenetically related Bacillus strains: B. subtilis NCIB3610 and B. velezensis FZB42. Despite exhibiting similar colonization patterns and persistence in the root system, these strains elicit distinct, strain-specific plant responses at the developmental, metabolic, and defensive levels. B. subtilis enhances radicle elongation and drought resilience through increased starch and L-tryptophan accumulation, while B. velezensis transiently represses early growth and reprograms host transcriptome and metabolome, including jasmonate-associated gene expression and flavonoid biosynthesis. Both treatments ultimately converge on improved performance in the phyllosphere, including enhanced resistance to Botrytis cinerea and a population of Tetranychus urticae, though via divergent physiological routes. These findings reveal that plants do not merely tolerate or benefit from microbial presence, but actively engage in partner-specific programming, even among closely related beneficial strains. This capacity for functional discrimination broadens our understanding of how mutualistic interactions are shaped and diversified in plant hosts.

overall_design: RNAseq profiling of seeds (S) and emerged radicles (R) derived from seed inoculation of Bacillus velezensis FZB42 at a high dose (ODH) and a low dose (ODL)

first: Luisa

last: Carrégalo-Ríos

first: Carlos

last: Molina-Santiago

first: Diego

last: Romero


title: Loss of SMARCAD1 mitigates tauopathy

first: Vaishnavi

last: Jadhav

address: VA Puget Sound 1660 South Columbian Way

institute: University of Washington

summary: Background  Tauopathies are neurodegenerative diseases characterized by the accumulation of misfolded tau protein in Alzheimer’s disease (AD) and related dementia disorders. Identifying new strategies to treat tauopathy remains an important gap in the field.  Methods  Using forward and reverse genetic approaches in C. elegans, we identified smrd-1 the C. elegans homolog of SMARCAD1 as a potent modifier of tauopathy phenotypes in a transgenic model of tauopathy.     Results  Loss of smrd-1 function rescues tauopathy associated neuronal dysfunction and neurodegeneration in C. elegans models of tauopathy. Loss or reduction of smrd-1/SMARCAD1 decreases phosphorylated and total tau protein levels by reducing tau mRNA transcripts in C. elegans and mammalian HEK-tau cells. Loss of smrd-1 rescues tau-driven abnormal H3K9me3 chromatin methylation. We identified mir-235 potentially acting downstream of smrd-1 in conferring tauopathy rescue. Immunohistochemistry in human postmortem AD brain tissue found SMARCAD1 depletion in a subset of cases that also exhibit depletion of MSUT2.  Conclusion  Loss of smrd-1/SMARCAD1 rescues tau mediated neurodegeneration via a tau mRNA lowering mechanism involving changes in chromatin conformation.

overall_design: RNA from stage matched day adult C.elegans worms (N2 and smrd-1 deletion) was extracted using TRIzol extraction and was sent to Novogene for PolyA enrichment bulk-RNA sequencing. 4 replicates each of wildtype N2 woms (C1-C4) and smrd-1 deletion worms (N1-N4) were sequenced.

first: Rebecca

last: Kow

first: Asia

middle: D

last: Beale

first: Misa

last: Baum

first: Pam

last: MacMillian

first: Caitlin

last: Latimer

first: Nicole

last: Liachko

first: Brian

last: Kraemer


overall_design:
We used single-cell RNA sequencing (scRNA-seq) to analyze the heterogeneity of sorted CD11c+ cells from the spleen, skin-draining lymph nodes (sLN) and mesenteric lymph nodes (mLN) of two mouse genotypes: C57BL/6 and Notch2fl/fl CD11cCre+ mice. This series includes Notch2fl/fl CD11cCre+ only. Control C57BL/6 samples used for comparison were previously submitted under the GEO accession number GSE223841.

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

last: Rodrigues

first: Robert

last: Ivanek


title: CRL2-FEM1B uses heme to recruit BACH1 for degradation and regulate ferroptosis in lung cancer

city: Marseille

first: Luca

last: Lignitto

address: 27 Boulevard Leï Roure

institute: CNRS

summary: The goal of this study is to characterize the transcriptional programs regulated by the BACH1–CRL2-FEM1B axis in mouse lung adenocarcinoma cells.

overall_design: Mouse lung adenocarcinoma KP cells, either BACH1 wild-type (KP) or BACH1 knockout (KPB), were transfected with FEM1B-targeting siRNAs for 48 hours. Knockdown efficiency was validated by western blotting and RT-qPCR. Transcriptomic analyses were conducted to investigate how the loss of BACH1 or FEM1B affects ferroptosis-related gene expression programs. In total, 12 samples were generated and analyzed by deep RNA sequencing, with three biological replicates per condition.

first: Bashir

last: Ahmed

first: Daniele

last: Salaun

first: Jack

middle: B

last: Jordan

first: Avais

last: Daulat

first: Chiara

last: Pastorello

first: Tarcísio

last: Brito

first: Yuying

last: Yang

first: Emmanuelle

last: Josselin

first: Deborah

last: Byrne

first: Stephane

last: Betzi

first: Amandine

last: Pelletier

first: Julien

last: Vernerey

first: Lorene

last: Ferreira

first: Remy

last: Castellano

last: Audebert

first: Luc

last: Camoin

first: Attilio

last: Pane

first: Cherine

last: Bechara

first: Jean-Paul

last: Borg

first: Mauro

last: Modesti


title: Prenatal exposure to particulate matter impairs behavior in offspring by reduction of NMDA receptors in hippocampus: Evidence from in vivo and ex vivo studies

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

summary: Accumulating evidences with epidemiological and experimental animal studies elicited concerns of environmental exposure to particulate matter (PM) as a risk of neurodevelopmental- and neurodegenerative disorders. Given that the susceptibility of developing brain to environmental pollutants and toxicants, exposure to PM during pregnancy cause more severe toxicity in the offspring. However, it is ambiguous whether the impairment in the brain is derived from direct or indirect effect from systemic toxicity. The deposition of PM and the subsequent activation of inflammatory responses and oxidative stress in various organs further complicate the identification of the specific toxic mechanisms of PM in the brain. This study aimed to uncover this uncertainty by investigating toxicity of PM exposure in the brain and other phenotypes. Prenatal exposure of PM (200 and 400 μg/kg) through intranasal respiration causes aberrant behaviors in offspring, including cognitive deficits, hyperactivity, and anxiety. However, exposure to 200 μg/kg of PM induces aberrant neurobehaviors, while lung functions remained unaffected. Transcriptomic analyses indicated PM dysregulate gene expression in the hippocampus related to neuronal activity and synaptic development, which may contribute to behavioral impairment in offspring. Additionally, we found that PM reduced the expression of N-methyl-D-aspartate (NMDA) receptors in the hippocampus, which are crucial glutamatergic receptors for neuronal development and activity. To further confirm the effect of PM on NMDA receptor expression, we examined the expression of NMDA receptor in ex vivo cultures of hippocampal neurons using pH-sensitive green fluorescence protein pHluorin fused to NMDA receptor subunit. Ex vivo cultures (200 μg/kg) showed that PM exposure decreased NMDA receptor expression and disrupted spontaneous neuronal activity and synaptic network, while inflammatory responses are unaffected in glial cells. Our results provide insights into the direct evidence by which vulnerability of developing brain to PM exposure and necessitate developing effective strategies for mitigating PM exposure.

overall_design: mRNA-seq was performed on mouse hippocampus cells treated with normal saline or PM.

first: Sung Hoon


title: TREM2 plays a critical role in innate immune defense against acute Toxoplasma gondii infection by promoting macrophage antimicrobial activities

city: Irvine

first: Hannah

last: Debray

state: CA

address: 3342 McGaugh Hall

department: MBB

institute: University of California Irvine

summary: The TREM2 receptor is a well-known rheostat for inflammation and immunity, but its role in host defense against parasitic infection is only just emerging. We investigated the function of TREM2 during acute Toxoplasma gondii infection by comparing TREM2-deficient and C57BL/6 wild-type (WT) mice during intraperitoneal infection with type II (Prugniaud strain) T. gondii. Infected TREM2 knockout (KO) mice had significantly increased mortality and elevated parasite burden during acute infection, as well as increased liver pathology and higher levels of inflammatory cytokines IL-1, IL-6, and IL-17A by 7 days post-infection (dpi). Notably, we observed an early expansion and dissemination of T. gondii in infected macrophages in the omentum in TREM2 KO compared to WT mice, and this phenotype was specific to TREM2 deficiency on radiation-sensitive cells, based on bone marrow chimera experiments. In vitro, TREM2 KO macrophages were more permissive to T. gondii infection and exhibited reduced LAMP-1 upregulation and impaired phagocytotic clearance of T. gondii compared to WT macrophages. TREM2 deficiency has been previously associated with elevated ERK signaling and defective lysosomal activity, and we found that treatment of TREM2 KO macrophages with the ERK inhibitor SCH772984 rescued LAMP-1 expression and improved macrophage control of the parasites. Finally, RNA sequencing of myeloid cells isolated from the peritoneal cavity of infected mice at 3 dpi revealed increased transcripts associated with inflammation and decreased transcripts associated with cellular migration in the TREM2 KO compared to WT mice. These findings demonstrate a critical role for TREM2 in the early antimicrobial immune response to T. gondii infection by limiting parasite expansion, dissemination, and pathological inflammation in the infected host.

overall_design: Bulk RNAseq profiling of sorted monocytes from the peritoneal exudate of 4 TREM2 KO mice and 3 WT mice at 3 dpi with Toxoplasma gondii

first: Dillon

last: Cheng

first: Angel

last: Ayala

first: Toan

last: Lam

first: Ji-Hun

last: Shin

first: Dequina

last: Nicholas

first: Matthew

last: Inlay

first: Nir

last: Drayman

first: Robert

last: Edwards

first: Melissa

last: Lodoen


title: Effects of SIK3 KO on the transcriptome in CA1 region

city: Palo Alto

first: Xiao

last: Han

state: California

address: 265 Campus Drive

institute: Stanford University

summary: SIK3 is reported to regulate sleep in mice, but it's unclear how SIK3 works at the synapse in the brain. Here, to explore the potential effects of endogenous SIK3 on the global transcriptome, in-vivo deletion of SIK3 was achieved by CRISPR KO in the CA1 region of Cas9 mice. The CA1 tissues were  dissected and analyzed by bulk RNAseq. The result shows that in-vivo deletion of SIK3 induces a minor change in the transcriptome, suggesting a transcription-independent mechanism for SIK3.

overall_design: Cas9 mice were stereotaxically injected by SIK3 sgRNA AAV (2 female and 2 male) or control sgRNA AAV (2 female and 2 male). The CA1 tissues were dissected from 8 mice, and total RNAs were extracted and  subjected to RNAseq.

first: Rui

last: Lu

last: Malenka

first: Thomas

last: Südhof


title: Visible traits demonstrate that crispant founder mice can be used for phenotypic assessment

city: Edinburgh

first: Fernando

last: Bellido Molias

address: Crewe Rd S,

institute: University of Edinburgh

summary: Genes can be knocked out in model organisms by introducing a single guide RNA and Cas9 into one cell zygotes. Recently, the zebrafish and Xenopus communities have employed this method in genetic screening pipelines that assess phenotypes in founders (F0), referred to as “crispants”. In contrast, phenotyping of crispant mice has been avoided as results are believed to be confounded by genetic mosaicism, requiring that only established mouse lines undergo phenotypic assessment. Here, we targeted seven genes associated with visible recessive phenotypes. We observed the expected null phenotype in up to 100% founders per gene. Crucially, we achieved 100% editing efficiency in all but two animals. Genetic mosaicism was common, but did not confound an animal’s phenotype when comprised of mutations that all disrupt the targeted gene. Mosaicism included short in-frame mutations, but these were sufficient to disrupt function of five genes. Several founders were compound heterozygotes carrying a null and a non-null allele (short in-frame mutation or late truncation), enabling functional assessment of the non-null allele to dissect protein function. Our results set the stage for using crispant founders for initial phenotypic assessment in genetic screening, before selecting candidates for further study. This will dramatically reduce animal numbers.

overall_design: To characterize the CRISPR/Cas9 mediated deletions, we adapted ELF-CLAMP (Enrichment of Long DNA Fragments using Capture and Linear Amplification)(Chang et al., 2023) where regions of interest (up to 2 kb) are amplified from viewpoints using in vitro transcription followed by Nanopore long read RNA sequencing.

first: Rebekah

last: Tillotson

first: Marina

last: Gertsenstein

first: Li-Hsin

last: Chang

first: Julie

last: Ruston

first: Lauri G

last: Lintott

first: Christine

last: Taylor

first: Philippe

last: Gautier

first: James

last: Davies

first: Lauryl

last: Nutter

first: Monica

last: Justice


title: A protective role for APP in nuclear waste clearance via lysosomal exocytosis

city: Niigata

first: Hideaki

last: Matsui

state: Niigata

address: 1  Bancho-757 Asahimachidori, Chuo Ward

department: Brain Research Institute

institute: Niigata University

summary: Amyloid precursor protein (APP) is widely known for its role in Alzheimer’s disease (AD) pathogenesis through its proteolytic processing into amyloid-β peptides. However, its physiological function remains incompletely understood. Here, we uncover a protective role for full-length APP in facilitating the disposal of nuclear-derived debris under genotoxic stress. In both cultured cells and in vivo mouse models, loss of APP leads to nuclear waste accumulation, increased inflammation, and cell death, whereas APP overexpression mitigates these effects. Mechanistically, we show that APP supports the extracellular release of nuclear material through lysosomal exocytosis. APP mutants associated with familial AD fail to mediate this process. Consistently, human AD brain tissue exhibits abnormal nuclear morphology, accumulation of nuclear waste in the cytoplasm, and reduced APP levels per neuron. These findings highlight a conserved cellular mechanism by which APP contributes to nuclear and cellular homeostasis, and suggest that impaired nuclear waste clearance may represent an underappreciated contributor to neurodegeneration.

overall_design:
Using CRISPR-Cas9 technology, we established two HeLa cell lines harbouring APP genome mutations. One line (316-34) was knockout (KO) mutant with no detectable protein expression, and the other cell line (316-15) had a mutation with no frameshift in APP, in which most amino acids of the APP protein were translated.
We then performed gene profiling expression analysis using data obtained from RNA-seq analysis of each line and their respective control, treated with Etoposide 20 µM, 2 days.
Comparative gene profiling analysis for RNA-seq data of HeLa cells, 316-34 (APP mutant) and 316-15 (APP mutant) and each cell treated with Etoposide

first: Godfried

last: Dougnon

first: Takayoshi

last: Otsuka

first: Yuka

last: Nakamura

first: Akiko

last: Sakai

first: Tomoyuki

last: Yamanaka

first: Noriko

first: Asa

last: Nakahara

first: Ai

last: Ito

first: Atsushi

last: Hatano

first: Masaki

last: Matsumoto

first: Hironaka

last: Igarashi

first: Akiyoshi

last: Kakita

last: Ueno


title: Single-cell RNA and TCR sequencing from skin, blood and cerebral spinal fluid (CSF) samples from Degos disease patients

first: Stephen

middle: R

last: Brooks

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

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

overall_design: Refer to individual Series