title: Polycomb Repressive Complex 1 Primes Non-Growing Oocytes for Growth and Early Embryogenesis [CUT&Tag]

city: Davis

first: Satoshi

last: Namekawa

address: One Shields Avenue

institute: UC Davis

summary: Ovarian reserve defines the female reproductive lifespan, which in humans spans decades due to the robust maintenance of meiotic arrest in non-growing oocytes residing in primordial follicles. Dynamic epigenomic reprogramming and programming occur during mammalian germline and early embryonic development. However, the chromatin-based mechanisms that underlie the establishment and maintenance of ovarian reserves are poorly defined. Here, we report a comprehensive epigenomic landscape of mouse perinatal oocytes and unravel Polycomb-based mechanisms underlying ovarian reserve development. By quantitatively profiling key histone modifications, including the Polycomb-mediated repressive marks H2AK119ub and H3K27me3, we identified two major epigenomic transitions: one for ovarian reserve formation from meiotic prophase I to dictyate-arrested non-growing oocytes, and another for ovarian reserve activation from non-growing to growing oocytes. Combining conditional loss-of-function mouse models for Polycomb Repressive Complex 1 or 2 (PRC1/2), we show that PRC1-H2AK119ub and PRC2-H3K27me3 undergo differential dynamics during perinatal oogenesis and have distinct biological functions in ovarian reserve formation and maintenance. Notably, PRC1-H2AK119ub presets the epigenetic states in non-growing oocytes and provides a blueprint for the PRC2-H3K27me3 profile, which is globally reprogrammed as oocytes exit the ovarian reserve and grow. Our study determines a comprehensive epigenomic roadmap of perinatal oogenesis, shedding light on how the ovarian reserve is formed, maintained, and activated, emphasizing a critical window of epigenetic programming during female germline development.

overall_design: Chromatin profiling analysis of quantitative CUT&Tag data for (1) WT perinatal oocytes; (2) PRC1ctrl and PRC1cKO non-growing oocytes and early growing oocytes; (3) PRC2ctrl and PRC2cKO non-growing oocytes.

first: Mengwen

last: Hu


title: Transcriptome-wide mapping reveals an RNA-dependent mechanism of platinum cancer drugs

status: Public on Feb 23 2026

city: Washington

first: Sreejith

last: Nair

country: USA

institute: Georgetown University

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Transcriptome-wide mapping reveals an RNA-dependent mechanism of platinum cancer drug [Plat-RNAseq cPDS]

summary: Clinically used small molecules has been predicted to off-target to RNAs. However, the extend of this interaction is small molecule cancer therapeutics has not been characterized. Here, we screened for anticancer smalll molecules for their RNA interactions and uncovered widespread RNA off-targeting. Cisplatin was found to be one among the RNA binders. We used it as a model agent to identify the specific transcripts it interact with. We developed Plat-RNAseq, a click-chemistry-mediated transcriptome-wide assay to map transcriptome-wide interaction of cisplatin. Our results revealed that cisplatin binding was enriched at guanine-rich regions capable of forming RNA G-quadruplexes (rG4s). We use an rG4 ligand, carboxy-Pyridostatin (cPDS), to block access of platin-drug to rG4. This experiment test whether cPDS blocked platinum drug accumulation on cellular RNAs.

overall_design: Cells were treated with cPDS (5 µM) or DMF for 6 hours followed by 1,3-platin (30 µM). The cells were harvested 18 hours after 1,3-platin treatment and proecessed according to the Plat-RNAseq protocol described below. The goal of the experiment is to test whether rG4 ligands can influence the RNA binding of platinum drugs.

first: Weiyi

last: Guo

first: Richi

last: Thakral


title: Transcriptome-wide mapping reveals an RNA-dependent mechanism of platinum cancer drugs [Plat-RNAseq A2780]

summary: Small molecules developed to target proteins and DNA may also bind RNA, but the extent and biological significance of these interactions remain poorly defined. Here, we systematically profiled RNA interactions of clinically approved chemotherapeutics and uncovered widespread RNA off-targeting. Cisplatin, a frontline chemotherapeutic for solid tumors, emerged as a prominent RNA-binding drug. To map these interactions in vivo, we developed Plat-RNAseq, a click-chemistry-mediated transcriptome-wide assay. Cisplatin binding was enriched at guanine-rich regions capable of forming RNA G-quadruplexes (rG4s) and preferentially accumulated at the 5′ ends of nascent transcripts that exhibited rG4 enrichment and R-loop formation. Cisplatin stabilized pre-formed rG4s while interfering with their de novo assembly, thereby altering RNA structure and function. The recruitment of cisplatin to rG4s contributed to its cytotoxicity, revealing a noncanonical mechanism of action for this widely used chemotherapeutic agent. Consistent with this mechanism, the expression level of rG4 cisplatin-RNA targets predicted the platinum sensitivity in ovarian cancer patients.  Collectively, these findings broaden platinum pharmacology by revealing RNA interactions as a functionally relevant, non-canonical component of cisplatin’s mechanism of action. Our study highlights the importance of incorporating RNA interactions into drug design and establishes a framework for considering RNA as a functionally relevant target in small-molecule therapeutics.

overall_design: Cells were treated with Cisplatin (10 µM) or DMF for 6 hours followed by 1,3-platin (30 µM). The cells were harvested 18 hours after 1,3-platin treatment and proecessed according to the Plat-RNAseq protocol described below. The goal of the experiment is to identify RNAs bound specifically by the chemotherapeutic drug cisplatin.


title: Degron models: a toolbox for rapid in vivo depletion of essential proteins regulating mRNA metabolism

city: Warsaw

first: Wiktor

last: Antczak

address: Trojdena 4

country: Poland

institute: IIMCB

summary: Due to their essentiality, studying proteins involved in fundamental processes in vivo  is challenging. PROTAC-based systems offer time-controlled protein depletion, but their characterization in vivo remains limited. Here, with an efficient direct zygote editing protocol, we generated degron-tag models (dTAG/FKBP or BromoTag) for seven genes involved in therapeutic and endogenous mRNA metabolism (Cnot1, Pan2, Tent5a, Tent4b, Dcp2, Rnasel, Tsg101). Degron tags occasionally caused phenotypes that were often mitigated by tag position or tagging system change. In cells, both approaches yielded rapid and sustained degradation. In mice, dTAG depletion was effective but varied by protein and administration route, whereas BromoTag showed no in vivo activity. We showcase the utility of these models through an analysis of CNOT1's roles in cell division, immunity, and poly(A) tail maintenance. We present a valuable toolbox for studying mRNA metabolism in mammalian models, while providing a benchmark for applying degron-tag models to study other biological processes.

overall_design: This study includes mouse liver and primary cell (BMDM) samples derived from genetically engineered mouse lines expressing FKBP-tagged proteins (CNOT1, TENT5A, TENT4B, RNASEL, PAN2, DCP2). Experimental conditions include treatment with small-molecule degrader (dTAGV-1) versus vehicle controls (DMSO). Samples were collected at multiple time points after treatment. Control samples include wild-type littermates and vehicle-treated tagged mice or cells. Biological replicates were included for each experimental condition.


title: Transcriptome-wide mapping reveals an RNA-dependent mechanism of platinum cancer drugs [Plat-RNAseq A549]

summary: Clinically used small molecules has been predicted to off-target to RNAs. However, the extend of this interaction is small molecule cancer therapeutics has not been characterized. Here, we screened for anticancer smalll molecules for their RNA interactions and uncovered widespread RNA off-targeting. Cisplatin was found to be one among the RNA binders. We used it as a model agent to identify the specific transcripts it interact with. To accomplish this, we developed Plat-RNAseq, a click-chemistry-mediated transcriptome-wide assay. Our results revealed that cisplatin binding was enriched at guanine-rich regions capable of forming RNA G-quadruplexes (rG4s) .We found that the recruitment of cisplatin to rG4s partially contributed to its cytotoxicity, revealing a noncanonical mechanism of action for this widely used chemotherapeutic agent.

overall_design: Cells were treated with Cisplatin (10 µM) or DMF for 6 hours followed by 1,3-platin (30 µM). The cells were harvested 18 hours after 1,3-platin treatment and proecessed according to the Plat-RNAseq protocol described below. The goal of the experiment is to identify RNAs bound specifically by the chemotherapeutic drug cisplatin in A549 cells.


title: Transcriptome-wide mapping reveals an RNA-dependent mechanism of platinum cancer drugs [RIP-seq]

summary: Clinically used small molecules has been predicted to off-target to RNAs. However, the extend of this interaction is small molecule cancer therapeutics has not been characterized. Here, we screened for anticancer smalll molecules for their RNA interactions and uncovered widespread RNA off-targeting. Cisplatin was found to be one among the RNA binders. We used it as a model agent to identify the specific transcripts it interact with. We developed Plat-RNAseq, a click-chemistry-mediated transcriptome-wide assay to map transcriptome-wide interaction of cisplatin. Our results revealed that cisplatin binding was enriched at guanine-rich regions capable of forming RNA G-quadruplexes (rG4s). We employed BG4-RIP-seq to identify the rG4 harboring RNAs in cisplatin-treated A2780 cells.

overall_design: Cells were treated with Cisplatin (10 µM) 6 hours followed by 1,3-platin (30 µM). The rG4 enriched RNAs were pull down using BG4 antibody that recogning G-quadruplexes. The goal of the experiment was to catalogue RNAs that harbor rG4 in cisplatin treated A2780 cells.


title: The LMO2-LDB1-TAL1 complex regulates transcription networks in AML [ChIP-Seq]

city: Charlottesville

first: Francine

middle: E.

last: Garrett-Bakelman

state: VA

address: 1340 Jefferson park Ave.

department: Medicine and BMG

institute: University of Virginia

summary: Relapsed acute myeloid leukemia (relAML) remains a clinical challenge. We have shown that epigenetic heterogeneity may contribute to transcriptional dysregulation and disease progression in AML, but the specific transcriptional programs have not been identified. To characterize relAML transcriptional landscapes, we analyzed molecular profiles from patient-matched diagnostic and relapse AML specimens. A subset of differentially expressed genes (DEGs) that were disparate in direction of expression change identified two patient subtypes, but were not associated with specific molecular events. We predicted transcriptional regulators (TRs) that might regulate the expression patterns observed. The expression patterns of the top TRs predicted for the disparate genes associated with clinical outcomes in independent AML patient cohorts. The top TRs predicted included members of the LMO2 multi-subunit complex (TAL1 and LDB1).  LMO2/LDB1/TAL1 complex members were also identified as potential TRs of DEGs in a patient derived xenograft mouse model of relapse.  Analysis of DepMap data identified LMO2-dependent cells with a subset highly expressing TAL1, suggesting coordinated regulation. TAL1 co-purified in immunoprecipitation for LMO2 and LDB1 followed by tandem mass spectrometry analysis in HEL and K562 cells. Loss of function experiments targeting LMO2/LDB1/TAL1 in AML cell lines associated with reduced cell growth, downregulation of cell cycle genes, and a negative association with gene expression patterns observed in relapsed patients with increased TAL1 expression. Data from primary AML specimens and functional analyses of AML cell lines supports an essential role for the LMO2/LDB1/TAL1 complex in relAML. Targeting the complex or downstream effectors could provide novel therapeutic considerations for relAML patients.

overall_design: K562 cells were crosslinked and chromatin was isolated. 4 ug of LDB1 antibody was incubated for every 20 ug of chromatin. LDB1 incubated chromatin was compared to input samples.


title: Canonical transcription termination mechanisms explain a minority of operons in cyanobacteria

city: Cambridge

first: Jennifer

last: Cascino

state: MA

address: 31 Ames Street

department: Biology

institute: Massachusetts Institute of Technology

summary: Cyanobacteria are the most abundant phototrophs and hold potential as a carbon-negative platform for bioengineering applications. However, these efforts have been hampered by limited mechanistic understanding of their gene expression, including transcription termination. Unlike most bacteria, cyanobacteria lack the transcription termination factor Rho, raising the speculation that all transcription ends with intrinsic terminators. Here we show that most transcription units (TUs) in Synechococcus elongatus PCC 7942 are not terminated by known termination pathways. Although many TUs (52%) have unique, well-defined 3' ends, only a small fraction have features that resemble canonical intrinsic terminators (30%). The noncanonical 3' ends (22%) broadly lacked strong secondary structure, leaving it unclear how these ends are protected against 3'-5' exonucleolytic decay, but a dinucleotide motif was observed. Furthermore, many TUs (46%) have diverse positions of mRNA 3' ends, suggesting a potentially diffuse termination signal. Finally, we provide evidence that the transcription-repair coupling factor Mfd reduces transcriptional readthrough at the well-defined 3' ends, suggesting that Mfd-dependent termination may be prevalent in this species. Together, our work reveals unique end architectures of the cyanobacterial transcriptome and suggests that undescribed transcription termination mechanisms are active in the phylum.

sample_organism: Synechococcus elongatus PCC 7942 = FACHB-805

overall_design: Rend-seq mapping of transcription unit architectures including RNA 3' ends at single-nucleotide resolution in the wild-type (WT) freshwater cyanobacterium Synechococcus elongatus PCC 7942 and a mutant deleted for the transcription-repair coupling factor Mfd (Mfd_KO). Rend-seq libraries for two technical replicates of WT (cells collected from the same flask) and two biological replicates of Mfd_KO (separate flasks) were prepared.

first: K. Julia

last: Dierksheide

first: Gene-Wei

last: Li


title: Transcriptome-wide mapping reveals an RNA-dependent mechanism of platinum cancer drugs [ChIP-seq]

overall_design: A2780 ovarian cancer cells were treated with cisplatin (12.5 µM) 1 hour. Chromatin Immunoprecipitation was performed  to assess the chromatin distribution of RNA Polymerase II in response to cisplatin treatment.

first: Siva Bala

last: Subramaniyan


title: Brillouin Microscopic Assessment of Retinal Stiffness During Reactive Müller Gliosis

city: Houston

first: Kamryn

last: Gerner-Mauro

state: Texas

address: 1 Baylor Plz

institute: Baylor College of Medicine

summary: Increased retinal stiffness can indicate reactive gliosis, fibrosis, or ECM remodeling – all hallmarks of early retinal damage due to diseases such as age-related macular degeneration (AMD), glaucoma, and diabetic retinopathy. Here, we demonstrate that Brillouin microscopy can detect increased stiffness within the damaged mouse retina coincident with reactive Müller gliosis.

overall_design: ROSA26R-Ai9+/ki and Glast-CreERT2+/tg mice (both on a C57BL6/J background). Glast-CreERT2+/tg; ROSA26R-Ai9+/ki mice were induced with intraperitoneal (IP) injections of tamoxifen (Sigma, T5648) (75 mg/kg body weight) were given for five consecutive days. For intravitreal NMDA injections, mice were anesthetized using Isoflurane. One drop of Proparacaine Hydrochloride (0.5%) was placed on to the eye to be injected. The anesthetized mouse was positioned on its side under a dissecting microscope while on a warming plate and a sterile 28G hypodermic needle in inserted in the post-limbus region, with the bevel of the needle facing upwards to avoid the lens. The puncture needle was then carefully removed, and a small amount of vitreous fluid was wicked away from the puncture site using a twisted Kimwipe. Then, using a Hamilton syringe, a sterile blunt needle (33G) was gently inserted into the hole, pass the lens, and into the vitreous chamber where 2 microliters of NMDA (100 mM) (Sigma: M3262) was injected. The contralateral eye served as an un-injected control. After 24 hours, eyes were processed for FACs and subsequent scRNA-seq.

first: Sajedeh

last: Saeidifard

first: Irina V.

last: Saltykova

first: Kamryn N.

first: Kirill V.

last: Larin

first: Ross A.

last: Poché


title: CBP-IDRs regulate acetylation and gene expression [CUT&Run]

city: Sheffield

first: Daniel

middle: Arun

last: Bose

state: South Yorkshire

address: University of Sheffield, Firth Court, Western Bank

department: Biosciences

country: United Kingdom

institute: The University of Sheffield

summary: Intrinsically disordered regions (IDRs) have emerged as crucial regulators of protein function, allowing proteins to sense and respond to their environment. Creb binding protein (CBP) and EP300 (p300) are transcription coactivators that regulate gene expression in multicellular organisms, following their recruitment to cis-regulatory elements. CBP and p300 contain large IDRs, however little is known about how these different IDRs work together to regulate CBP function. Here, we show that CBP-IDRs cooperate to control different aspects of CBP behaviour in the nucleus, by regulating the properties of fluid-like condensates formed by endogenous CBP. We show how IDRs with different sequence properties make unique contributions to CBP behaviour by establishing a balance between positive and negative regulation of CBP condensates. These conflicting interactions are functionally important, shaping CBPs response to factors such as lysine acetylation, that influence condensate formation. When disrupted, regulatory CBP-IDRs change how CBP interacts with chromatin, alter patterns of CBP-dependent histone acetylation and change gene expression. Together, our work highlights how IDRs with different sequences, spatially segregated in the same protein, can cooperate to shape protein function.

overall_design: Cleavage Under Targets and Release Using Nuclease (CUT&RUN) for doxycycline inducible GFP epitope-tagged Crebbp binding protein (CBP) in HEK293T cells. Doxycycline was added to induce GFP expression while not altering overall levels of tagged and untagged CBP. Control ChIP-seq for endogenous CBP was done in parental HEK293T cells stably expressing Tet3G transactivator protein. The same system was used to generate datasets for H3K27ac CUT&RUN and total RNAseq, following induction of CBP-GFP expression. Please note that the processed data files generated from both replicates are linked to the corresponding Rep1 sample records.

first: Katie

middle: L

last: Gelder

first: Nicola

middle: A

last: Carruthers

first: Grace

last: Gilbert

first: Laura

middle: J

last: Harrison

first: Thomas

last: Evans

first: Sophie

last: Ball

first: Mark

last: Dunning

first: Timothy

middle: D

last: Craggs

first: Alison

middle: E

last: Twelvetrees


title: Prevotella intermedia culture supernatant impairs alveolar macrophage function and promotes Mycobacterium avium persistence

city: Nagasaki

first: Naoki

last: Iwanaga

address: Sakamoto, 1-7-1

country: Japan

institute: Nagasaki University

summary: In NTM-PD, P.int sup. may modulate the functions of alveolar macrophages by suppressing autophagy, type 1 interferon responses, and anti-mycobacterial protein production, thereby promoting M. avium survival in the lung microenvironment

overall_design: In vitro, total RNA was extracted from the AMLCs, which were infected with M. avium for 4 h, followed by treatment with P. int. sup. (or GAM broth) for an additional 4 h.

first: Koki

last: Fukushima


title: Multifactorial Azole Resistance, Widespread Emergence and Clonal Transmission of Fluconazole-Resistant Candida tropicalis in Indian Hospitals

city: New Delhi

first: Anuradha

last: Chowdhary

state: Delhi

address: M6R5+7X4 University of Delhi, Vijay Nagar Marg, Art Faculty, University Enclave

department: Medical Mycology

country: India

institute: Vallabhbhai Patel Chest Institute

summary: Candida tropicalis is a leading cause of invasive candidiasis in the Asia-Pacific region, with mortality rates exceeding 50%. The rising prevalence of azole resistant clinical strains, particularly in this region, presents a significant clinical challenge. In this study, we analyzed 1,032 C. tropicalis isolates, including 1,016 clinical isolates collected over nine years from 27 hospitals across India, as well as 16 environmental isolates. Fluconazole resistance was detected in 5.1% of clinical isolates, with more than half also exhibiting cross-resistance to voriconazole and itraconazole. Multilocus sequence typing (MLST) and phylogenomic analysis of 1,571 global isolates, confirmed the clonal emergence and persistence of azole- resistant MLST clade 4 strains in Indian hospitals. Genomic analysis revealed that Indian isolates cluster closely with azole resistant strains from China, Singapore, and Taiwan. Azole resistance was found to be multifactorial, involving well-characterized hotspot mutations in the ERG11 gene (Y132F, S154F), ERG11 gene amplification (2–7.5 copies), and significant overexpression of ERG11. Transcriptomic profiling showed significant up regulation of virulence-associated genes in the fluconazole-resistant isolate. Notably, ALS7, a member of the agglutinin-like sequence (ALS) family involved in cell adhesion along with Secreted Aspartyl Proteinases (SAP) genes SAP7 and SAP9, were significantly upregulated in fluconazole-resistant isolates. Additionally, fluconazole-resistant isolates exhibited significantly enhanced biofilm formation compared to fluconazole-susceptible strains, indicating a higher virulence potential. Furthermore, fluconazole-resistant isolates exhibited reduced β-glucan exposure, a trait linked to immune evasion, and showed greater survival in both neutrophil and macrophage killing assays.  Together, our findings provide comprehensive genomic and phenotypic evidence supporting the emergence, persistence, and increased pathogenic potential of azole-resistant C. tropicalis  clade 4 in Indian hospitals. A deeper understanding of the epidemiological trends and molecular mechanisms driving drug resistance in C. tropicalis is essential for improving diagnostic accuracy, optimising antifungal susceptibility testing, and informing effective clinical management strategies.

overall_design: RNA-Seq expression profiling of Fluconazole resistant and susceptible isolates

first: Jain

last: Kusum

first: Shukla

last: Nityendra

first: Kaur

last: Amtoj

first: Kalita

last: Barsha

first: Srivastava

last: Shriya

first: Yadav

last: Suhani

first: Rani

last: Preeti

first: Kagra

last: Poornima

first: Singh

last: Ashutosh

last: Hardeep

first: Patel

last: Jenish

first: Chauhan

last: Manju

first: Narayan

last: Jitendra

last: Neeraj

first: Chowdhary

last: Anuradha


title: CBP-IDRs regulate acetylation and gene expression [RNA-Seq]

first: Daniel

last: Bose

overall_design: RNA-seq for doxycycline inducible GFP epitope-tagged Crebbp binding protein (CBP) in HEK293T cells. Doxycycline was added to induce GFP expression while not altering overall levels of tagged and untagged CBP. Control ChIP-seq for endogenous CBP was done in parental HEK293T cells stably expressing Tet3G transactivator protein. The same system was used to generate datasets for H3K27ac CUT&RUN and total RNAseq, following induction of CBP-GFP expression. Please note that the processed data files generated from both replicates are linked to the corresponding Rep1 sample records.

first: Katie

last: Gelder

first: Nicola

last: Carruthers

first: Grace

last: Gilbert

first: Laura

last: Harrison

first: Thomas

last: Evans

first: Sophie

last: Ball

first: Mark

last: Dunning

first: Timothy

last: Craggs

first: Alison

last: Twelvetrees


title: CCL8-mediated recruitment of cytotoxic lymphocytes by P16-positive cells promotes adverse post-ischemic cardiac remodeling

city: Shanghai

first: Jialei

last: Zheng

state: 上海

address: 393 Middle Huaxia Road

country: China

institute: ShanghaiTech University

summary:
BACKGROUND: Ischemic heart disease remains a leading cause of mortality worldwide, with adverse remodeling post-myocardial infarction (MI) driven by inflammation and cardiomyocyte loss. While cytotoxic lymphocytes exacerbate injury, and p16 marks cellular senescence in diseased hearts, the cell-type-specific roles of P16+ populations remain undefined.

METHODS: Using p16-CreER;R26-tdT reporter mice, we mapped P16+ cellular heterogeneity post-MI. Senolytic effects were assessed via combination of dasatinib and quercetin (DQ) administration. Transcriptomic profiling (bulk/scRNA-seq) of sorted P16+ cells identified secreted factors, validated by in silico predictions and qPCR. Intercellular communication was analyzed using CellChat. Functional roles were tested via CCL8 neutralization, genetic Ccl8 ablation in P16+ cells, lymphocyte depletion, and intersectional genetic ablation of P16+ fibroblasts/macrophages using dual-recombinase systems (p16-DreER;Pdgfra-CreER;R26-lr-tdT-DTR and p16-DreER;Cx3cr1-CreER;R26-lr-tdT-DTR).

RESULTS: P16 was induced in fibroblasts, macrophages, coronary endothelial cells, and cardiomyocytes post-MI. DQ treatment selectively eliminated P16+ macrophages and fibroblasts, improving cardiac function. Transcriptomics revealed P16+ macrophages and fibroblasts as primary CCL8 sources. CCL8 blockade reduced infiltration of cytotoxic lymphocytes (CD8+ T cells and NK cells), decreased cardiomyocyte apoptosis, and improved repair. Genetic Ccl8 ablation in P16+ cells replicated these benefits. Crucially, intersectional genetic ablation of P16+ fibroblasts, but not macrophages, reduced fibrosis and enhanced function, whereas CD8+ T cell (not NK cell) depletion attenuated remodeling.

CONCLUSIONS: P16+ cells orchestrate adverse post-MI remodeling via CCL8-dependent recruitment of cytotoxic lymphocytes, expecially CD8+ T cells, driving cardiomyocyte apoptosis. Precision targeting of P16+ fibroblasts or CCL8 blockade represents a promising therapeutic strategy for ischemic heart disease.

overall_design: p16-2A-CreER;R26-mTmG mice underwent myocardial infarction (MI) surgery, received tamoxifen via oral gavage 5 days post-MI. Non-cardiomyocyte cells were harvested from the cardiac infarct zone on day 7 to prepare a single-cell suspension. GFPhiPDGFRahi，GFPloPDGFRahi and GFPhiF4/80hi，GFPloF4/80hi cells were subsequently isolated by flow cytometry sorting (FACS) and analyzed using RNA sequencing (RNA-seq).

first: Lei

last: Yan

first: Anqi

last: Zhu

first: Min

last: Ye

first: Jufeng

last: Meng

first: Zhengkai

last: Lu

first: Juan

last: Tang

first: Hui

last: Zhang


title: The membrane-associated ubiquitin ligase MARCHF8 promotes cancer immune evasion by degrading MHC class I proteins

city: Detroit

first: Qing-Sheng

last: Mi

address: 1 Ford Place, 1D

institute: Henry Ford Health

summary: The current immunotherapy is effective, but many cancer patients do not respond. The loss of major histocompatibility complex class I (MHC-I) molecules has been proposed as a mechanism by which cancer cells evade tumor-specific T cells in Immune Checkpoint Inhibitor (ICI)-refractory patients. Nevertheless, how cancer cells downregulate MHC-I is poorly understood. We report here that membrane-associated RING-CH-type finger 8 (MARCHF8), upregulated by human papillomavirus (HPV), ubiquitinates and degrades MHC-I proteins in HPV-positive head and neck cancer (HPV+ HNC). MARCHF8 knockdown restores MHC-I levels on HPV+ HNC cells. We further reveal that Marchf8 knockout significantly suppresses tumor growth and increases the infiltration of natural killer (NK) and T cells in the tumor microenvironment (TME). Furthermore, Marchf8 knockout markedly increases the cytotoxic NK cells and CD8+ T cells and their crosstalk with macrophages and enhances the tumor cell-killing activity of CD8+ T cells. CD8+ T cell depletion in mice abrogates Marchf8 knockout-driven tumor suppression and NK and T cell infiltration. Interestingly, Marchf8 knockout, in combination with anti-PD-1 treatment, synergistically suppresses tumor growth in mice bearing ICI-refractory tumors. Taken together, our finding suggests that MARCHF8 could be a promising target for novel immunotherapy for HPV+ HNC patients.

overall_design: We performed  scRNA-seq on tumor samples harvested from the C57BL/6J mice injected with mEERL/Marchf8-/- (sgR-Marchf8-2 and sgR-Marchf8-3) or mEERL/scr cells .

first: Mohamed I.

last: Khalil

first: Jie

last: Wang

first: Canchai

last: Yang

first: Lexi

last: Vu

first: Smriti

last: Chadha

first: Harrison

last: Nabors

first: Daniel

last: Vocelle

first: Danielle

last: May

first: Kyle

last: Roux

first: Matthew

last: Bernard

first: Dohun

last: Pyeon


title: RNA Sequencing of Liver Samples from UM-HET3 Mice Exposed to Various Compounds from the ITP Study

city: Boston

first: Alexander

last: Tyshkovskiy

state: Massachusetts

address: 77 Avenue Louis Pasteur

institute: Brigham & Women's Hospital, Harvard Medical School

summary: This dataset contains liver gene expression profiles of aged UM-HET3 male and female mice subjected to long-term treatment with various compounds from ITP studies, along with age-matched and young control mice of the same strain. It is part of a broader dataset used to identify gene expression signatures of aging, mortality, and lifespan, as well as to develop rodent and multi-species transcriptomic clocks of chronological age and expected mortality.

overall_design: Male and female UM-HET3 mice were treated with various compounds in food as part of the ITP program until sacrifice at 22 months. Canagliflozin group: 7 biological replicates per sex; other compounds: 3 biological replicates per sex; old (22-month-old) control group: 24 biological replicates per sex; young (4-6-month-old) control group: 6 biological replicates per sex.

first: Vadim

middle: N

last: Gladyshev


title: Single-nucleus RNA Sequencing of Kidney and Brain Samples from Young WT and Klotho KO Male Mice

summary: This dataset includes single-nucleus gene expression profiles from kidney and cerebral cortex samples of a young male C57BL/6J mouse with α-klotho gene knockout, along with the age-matched wild-type control. This short-lived model was used to validate transcriptomic clocks and to comprehensively characterize the molecular hallmarks of mortality associated with this genetic modification.

overall_design: Young (8-week-old) male wildtype (WT) and α-klotho knockout (Klotho KO) C57BL/6J mice. 4 biological replicates: 1 kidney and 1 brain sample per genotype.

first: Tomoko

last: Kasahara

first: Yoshiyasu

last: Tongu

first: Takaaki

last: Abe


title: RNA Sequencing of Kidney and Skeletal Muscle Samples from Young WT and Klotho KO Male Mice

summary: This dataset includes gene expression profiles from kidney and skeletal muscle samples of young male C57BL/6J mice with α-klotho gene knockout, along with age-matched wild-type controls. This short-lived model was used to validate transcriptomic clocks and to comprehensively characterize the molecular hallmarks of mortality associated with this genetic modification.

overall_design: Young (8-week-old) male wildtype (WT) and α-klotho knockout (Klotho KO) C57BL/6J mice. 24 biological replicates: 6 kidney and 6 skeletal (gastrocnemius) muscle samples per genotype.


title: Transcriptomic Hallmarks of Mortality Reveal Universal and Specific Mechanisms of Aging, Chronic Disease, and Rejuvenation

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

overall_design: Refer to individual Series


title: Dissociated human cerebral organoids on micro-electrode arrays develop neuronal networks

city: London

first: Adam

last: Pavlinek

address: Maurice Wohl Clinical Neuroscience Institute 5 Cutcombe Road

department: Basic and Clinical Neuroscience

institute: King's College London

summary: Microelectrode arrays (MEAs) are increasingly used to profile the development of synchronised network activity in neural organoids, yet no organoid study has investigated the consistency of electrophysiological development across multiple cell lines. Here, we used dissociated neural organoids derived from six cell lines on MEAs to characterise functional synapse development using multiple parameters across time. The dissociated organoids had increasing functional connectivity and network activity over time across all cell lines and plasticity in response to synaptic-like stimulation. Like the organoids they were derived from, dissociated organoid cultures contained a diverse mixture of cell types, including neurons and glia. Variability in activity parameters was associated with differences in cell type composition and regional identity, which in turn were affected by donor cell line and batch effects. Cell type composition and regional identity in dissociated organoid cultures grown on MEAs was investigated using bulk RNA-seq.

overall_design: Bulk RNA-seq profiling of control dissociated cerebral organoid cultures at 37 days post dissociation (82-84 days in vitro including culture time as 3D organoids) across six donor cell lines: KOLF2.1J, SCTi003-A, H1, H9, 59XY and 272XX. Two independent batches are included for the H9, KOLF2.1J and SCTi003-A lines. Three batches are included for 59XY and 272XX. Each sample represents RNA pooled from six wells.

first: Deepak

middle: P

last: Srivastava


first: Jialei

last: Zheng

overall_design: p16-2A-CreER;R26-mTmG mice underwent myocardial infarction (MI) surgery, received tamoxifen via oral gavage 5 days post-MI. Non-cardiomyocyte cells were harvested from the cardiac infarct zone on day 7 to prepare a single-cell suspension. GFPhi and GFPlo non-cardiomyocyte cells were subsequently isolated by flow cytometry sorting (FACS) and analyzed using single-cell RNA sequencing (scRNA-seq).

first: Lei

last: Yan

first: Anqi

last: Zhu

first: Min

last: Ye

first: Jufeng

last: Meng

first: Zhengkai

last: Lu

first: Juan

last: Tang

first: Hui

last: Zhang


title: RNA binding regulation is a new dimension in the type I IFN response

city: Glasgow

first: Louisa

last: Iselin

state: Lanarkshire

address: 464 Bearsden Road

institute: University of Glasgow

summary: The type I interferon (IFN-I) response shapes the intracellular environment to supress virus infection. Historically, this remodelling has been linked to the transcriptional induction of interferon stimulated genes (ISGs). However, whether IFN-I alters the activity of proteins already present in the cell remains largely unexplored. Here, we profiled the activity of cellular RNA-binding proteins (RBPs), which are key players in antiviral immunity. Using RNA interactome capture (RIC), we identified hundreds of RBPs whose association with RNA is regulated by IFN-I (IR-RBPs). Among these IR-RBPs are known antiviral proteins, as well as novel antiviral candidates, identified through functional assays. By modifying RIC to study IR-RBPs' phosphorylation states, we identified several putative instances of IFN-I-driven phospho-regulation of RNA binding. We experimentally confirmed that MATR3’s IFN-regulated S188 phosphosite modulates its RNA-binding activity, speaking to an exciting new layer of regulation. Altogether, our results reveal a new dimension of the cell’s antiviral programme, in which the cellular RNA-bound proteome is remodelled by IFN-I.

overall_design: iCLIP of WT MATR3-GFP and two mutants, S118A and S118D, in mock conditions. All samples were generated as biological triplicates. Size matched input samples derived from the parental HEK293 FITR line were used as a control for all three lines.

first: Natasha

last: Palmalux

first: Alfredo

last: Castello


title: RNA-seq analysis of the human SC1 lymphoma cell line after bryostatin treatment

city: San Francisco

first: Huimin

last: Geng

state: CA

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

summary: RNA-seq analysis was performed on a CD72 antigen-low human lymphoma cell line (SC1) to examine gene expression changes after bryostatin treatment compared to DMSO

overall_design: RNA-seq profiling of total RNA transcript levels in human SC1 lymphoma cell line treated with bryostatin or DMSO (vehicle), with three samples per condition.

first: Adila

last: Izgutdina

first: Arun

last: Wiita


title: Transcriptome analysis in skeletal muscle conditional Phf2 KO gastrocnemius muscle in male mice

city: Nagakute

first: Taku

last: Fukushima

state: Aichi

institute: Aichi Medical University

summary: To evaluate the role of PHF2 in  skeletal muscle, we generated  skeletal muscle conditional Phf2 KO mice and analyzed the transcriptome by CUT&RUN-sequencing.

overall_design: Examination of the role of PHF2 in skeletal muscle.

first: Iori

last: Sakakibara


title: Human TSLP administration promotes homeostatic maturation of human cDC2 in humanized mice

city: Wuhan

first: Harris

last: Han

state: Hubei

address: No. 115, East Lake Road, Wuchang District

department: Medical Research Institute

institute: Wuhan University

summary: To test whether TSLP triggers homeostatic maturation of human cDC2s in vivo, we administrated human TSLP to humanized mice and performed scRNA-seq. We found that TSLP administration increased the proportion of homeostatically matured DC (DC2hm) subtype in cDCs.

overall_design: Humanized mice (male or female, 7 weeks old). At Day 0, human TSLP (1mg/kg) was injected intraperitoneally, and then every 2 days. The control group mice were injected intraperitoneally with the same volume of PBS. On the 6th day, the mouse spleen was taken out and ground into a single-cell suspension. hCD3+, hCD19+ and hCD14+ cells were firstly deleted from splenocytes using MACS, and then purified hCD45+cells from the effluent were collected for scRNA-seq or flow cytometry.

first: Runpeng

first: Mengmeng


title: Single-cell RNA-seq analysis of PDX (Patient-Derived Xenograft) tumors isolated from mouse spleens, treated with Empty CAR, anti-CD72 H24 nanoCAR or anti-CD72 NbD4.13 nanoCAR.

summary: Single-cell RNA-seq analysis was performed on human mantle cell lymphoma PDX (Patient-Derived Xenograft) tumors isolated from mouse spleens to examine gene expression changes after treatment of Empty CAR, humanized anti-CD72 nanobody-based CAR-T (“H24 nanoCAR”) or NbD4.13-based anti-CD72 nanoCAR-T.

overall_design: Human mantle cell lymphoma PDX tumor (DFBL44685) was implanted at 1 e6 cells/mouse, mice were then treated with Empty, H24 or NbD4.13 CAR at 5e6 CAR+ cells per mouse on day 10. Spleens were collected at day 70 after tumor implantation. Tumor cells were isolated from mouse spleens and sorted with gating on human CD45+ positive cells. The samples were processed using 10X chromium platform (Chromium Next GEM Immune Profiling 5'HT kit v2, 1000374). Illumina sequencing was performed on the PDX tumor samples using Illumina NovaSeq X 1.5B platform with paired-end 150 bp reads.

first: Bonell

last: Patino Escobar


title: STAT5 inhibition abrogate TSLP-induced homeostatic maturation of human cDC2s

summary: It has been reported that TSLP activates several downstream signalings including STAT5. To test whether TSLP triggers the homeostatic maturation program of human splenic cDC2 (DC2hm program) in a STAT5-dependant manner, we administrated TSLP to in-culture human splenic cDC2 with or without STAT5 inhibitor and performed RNA-seq. The results showed that TSLP-induced DC2hm-like profile was abrogated by STAT5 inhibition.

overall_design: Purified cDC2s were treated with TSLP (50 ng/ml) without the presence of STAT5 inhibitor (100µM) for 12 hours. UID RNA-seq which incorporating unique identifiers to improve sensitivity and remove PCR-ampliaction bias was then performed on TSLP-cDC2s, Med-cDC2s  and purified cDC2s.


title: Transcriptome analysis in skeletal muscle conditional Phf2 KO gastroceiumus and soleus muscles in male mice

summary: To evaluate the role of PHF2 in  skeletal muscle, we generated  skeletal muscle conditional Phf2 KO mice and analyzed the transcriptome by RNA-sequencing.


title: The metabolic signature of inflammatory skin-imprinted eosinophils accounts for the chronicity of Leishmania mexicana infections [Day14]

city: Erlangen

first: David

last: Barinberg

address: Wasserturmstraße 3/5

department: Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene

country: Germany

institute: Universitätsklinikum Erlangen and Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg

summary: Eosinophils exert antimicrobial, cytotoxic and immunoregulatory effects, but their function in cutaneous tissue still remains poorly understood. Here, we used a mouse model of chronic cutaneous leishmaniasis caused by the protozoan parasite Leishmania (L.) mexicana to investigate the functional role and transcriptomic signature of eosinophils in the skin. In C57BL/6 wild-type mice, L. mexicana induced local and systemic eosinophilia that was dependent on type 2 innate lymphoid cells and interleukin-5. Genetic and pharmacological depletion of eosinophils led to clinical resolution of disease, which was accompanied by a more pronounced Th1 and M1-like macrophage response. Bioinformatic analyses revealed a novel inflammatory and tissue-specific transcriptional trajectory in skin-infiltrating eosinophils. Skin-imprinted eosinophils strongly expressed the high-affinity glucose transporter 3 (Slc2a3), deprived the environment of glucose and directly impeded the function of Th1 cells. Together, our results demonstrate that the chronicity of L. mexicana infection is linked to inflammatory eosinophils and their metabolic signature

overall_design: 10x C57BL/6N mice were infected subcutaneously in the skin of both hind feet with 3 x 106 Leishmania mexicana (MNYC/BZ/62/M379) in 50 µl of PBS for 14 days. A scRNA-Seq was performed on total viable foot skin, bone marrow  and blood using BD Rhapsody.

first: Dominik

last: Lerm

first: Christian

last: Bogdan

first: Ulrike

last: Schleicher


title: Polycomb Repressive Complex 1 Primes Non-Growing Oocytes for Growth and Early Embryogenesis [RNA-Seq]

city: Davis

first: Satoshi

last: Namekawa

institute: UC Davis

summary: Ovarian reserve defines the female reproductive lifespan, which in humans spans decades due to the robust maintenance of meiotic arrest in non-growing oocytes residing in primordial follicles. Dynamic epigenomic reprogramming and programming occur during mammalian germline and early embryonic development. However, the chromatin-based mechanisms that underlie the establishment and maintenance of ovarian reserves are poorly defined. Here, we report a comprehensive epigenomic landscape of mouse perinatal oocytes and unravel Polycomb-based mechanisms underlying ovarian reserve development. By quantitatively profiling key histone modifications, including the Polycomb-mediated repressive marks H2AK119ub and H3K27me3, we identified two major epigenomic transitions: one for ovarian reserve formation from meiotic prophase I to dictyate-arrested non-growing oocytes, and another for ovarian reserve activation from non-growing to growing oocytes. Combining conditional loss-of-function mouse models for Polycomb Repressive Complex 1 or 2 (PRC1/2), we show that PRC1-H2AK119ub and PRC2-H3K27me3 undergo differential dynamics during perinatal oogenesis and have distinct biological functions in ovarian reserve formation and maintenance. Notably, PRC1-H2AK119ub presets the epigenetic states in non-growing oocytes and provides a blueprint for the PRC2-H3K27me3 profile, which is globally reprogrammed as oocytes exit the ovarian reserve and grow. Our study determines a comprehensive epigenomic roadmap of perinatal oogenesis, shedding light on how the ovarian reserve is formed, maintained, and activated, emphasizing a critical window of epigenetic programming during female germline development.

overall_design:
Comparative gene expression analysis of RNA-seq data for PRC2ctrl and PRC2cKO non-growing oocytes.

Comparative gene expression analysis of RNA-seq data for PRC1ctrl and PRC1cKO growing oocytes.

first: Mengwen

last: Hu

middle: H


title: Combining CD33-Targeted Chimeric Antigen Receptor T cells with Decitabine for Acute Myeloid Leukemia

city: Duarte

first: Hung-Ping

last: Shih

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

summary: Background: Relapsed and/or refractory (r/r) acute myeloid leukemia (AML) is a challenging disease with poor prognosis and limited treatment options. CD33, a cell surface antigen expressed on over 85% of AML blasts, is a promising target for chimeric antigen receptor (CAR) T-cell therapy. Decitabine (DAC), a hypomethylating agent (HMA), is a well-tolerated treatment for AML patients. Combining anti-CD33 immunotherapy with HMAs has shown benefits in AML patients unfit for intensive chemotherapy. Our goal is to develop optimal CD33-CAR T cells and combine them with DAC to provide an effective treatment for AML. Methods: Flow cytometry and antibody-binding capacity analysis were used to measure cell surface marker expression. Degranulation, intracellular cytokine expression, and tumor cell killing assays were used to assess CAR-T cell function in vitro. In vivo antileukemic activity was examined in AML xenografted NSG mice, with leukemic burden monitored via bioluminescence imaging. colony-forming-unit assay assessed the impact of CD33-CAR T cells on normal hematopoiesis. Public dataset analysis assessed correlation between two variables, such as CD33 mRNA expression and DNA methylation. Pairwise Controlled Manifold Approximation (PaCMAP) was used to visualized T cell-patient AML blast microenvironment after killing assay. Bulk RNA-seq analyzed mRNA and signaling pathways changes in AML cells after exposure to DAC. Results: We generated CD33-CAR T cells using a humanized anti-CD33 scFv and found that the CD8H version was more potent than the IgG4(EQ) variant against CD33⁺ AML cell lines. The CH8H CAR T cells exhibited strong effector functions and significantly reduced AML tumor burden in NSG mice, without impairing HSPC colony formation. In silico analysis revealed an inverse correlation between CD33 methylation and gene expression. DAC pretreatment upregulated CD33 expression, enhancing AML cell elimination by CD33-CAR T cells in vitro and in vivo, especially under conditions with limited CAR T-cells. DAC upregulated the proteasome inhibition-induced apoptosis pathway and downregulated DNA repair and MYC oncogenic pathways, which, together with enhanced CD33 expression, primed AML cells for more effective CAR T-cell targeting.   Conclusions: This study demonstrates the preclinical efficacy and safety of CD33-CAR T cells in treating AML and shows that DAC pretreatment boosts their antileukemic activity. This strategy holds promise for improving clinical outcomes and overall survival in r/r AML patients.

overall_design: RNA-seq profiling of KG-1A cells treated with Decitabine (DAC) for 2 days. KG-1A cells treated with DMSO for 2 days were used as control.

first: Tongyuan

last: Xue

first: Marissa

last: Del Real

first: Jonas

last: Wu

first: Elizabeth

last: Budde


title: The metabolic signature of inflammatory skin-imprinted eosinophils accounts for the chronicity of Leishmania mexicana infections [Day50]

overall_design: 7x 4get C57BL/6N and 7x 4get dblGATA-1 C57BL/6N mice were infected subcutaneously in the skin of both hind feet with 3 x 106 Leishmania mexicana (MNYC/BZ/62/M379) in 50 µl of PBS for 50 days. A scRNA-Seq was performed on total viable foot skin cells using BD Rhapsody.

first: Barinberg

last: David

first: Lerm

last: Dominik

first: Bogdan

last: Christian

first: Schleicher

last: Ulrike


title: Maternal antibodies orchestrate the establishment of salivary and oral mucosal immunity

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

summary: The establishment of mucosal homeostasis after birth involves mutual development of the microbiota and the immune system, with each mucosal barrier has specific mechanisms. Here, we show that in utero-delivered maternal IgG antibodies are translocated to the salivary glands and secreted to the neonatal saliva. As a result, the microbial burden of the neonate oral cavity and salivary glands is reduced. In the absence of maternal antibodies, oral dendritic cells migrate in higher frequencies to the salivary glands resulting in elevated activation of T and B cells, while dampening T regulatory cells. The IgG/IgA balance in the adult saliva was also dysregulated. The absence of maternal antibodies further regulates the adult gingival immunity, a key oral barrier, increasing alveolar bone loss during experimental periodontitis. This work reveals the importance of the salivary-oral axis during neonatal life via maternal antibodies, orchestrating local mucosal immunity and protecting against pathological damage in adulthood.

overall_design: B cell-deficient (JhT-/- ) females were crossed with wild-type (WT) males to generate offspring with intact B cells that were not exposed to mIg.

first: Reem

last: Naamneh

first: Avi-Hai

last: Hovav

first: Yasmin

last: Netanely

first: Shahd

last: Yacoub

last: Jaber


title: The combination of IL-7Ra and CCR7 is a highly specific marker to identify and purify homeostatically matured cDC2s (DC2hm).

first: Harris

last: Han

summary: To explore whether co-expression of CCR7 and IL7R can better define DC2hm (homeostatically matured cDC2) than either marker alone.  We sorted IL7R-CCR7+, IL7R+CCR7-, IL7R+CCR7+ DCs as well as CD141+ cDC1 and CD1c+ cDC2 from Lin-CD11c+HLA-DR+ splenocytes of 4 healthy donors and performed bulk RNA-seq. The results showed that the IL7R+CCR7+ double-positive subset showed the highest expression of DC2hm markers among the five subpopulations, supporting the hypothesis that combining CCR7 and IL7R better defines DC2hm.

overall_design: IL7R-CCR7+, IL7R+CCR7-, IL7R+CCR7+ DCs as well as CD141+ cDC1 and CD1c+ cDC2 were sorted from Lin-CD11c+HLA-DR+ splenocytes of heathy donors and performed bulk RNA-seq.

first: Runpeng

first: Mengmeng

last: Lu


title: ISG induction differs immunogenical human splenic cDC2 activation from homeostatic ones

summary: To assess the commonalities and differences in the transcriptomic reprogramming involved in immunogenic and homeostatic (DC2hm) human cDC2 activation, we conducted a comparison of gene regulation programs between DC2hm and immunogenically activated cDC2s (Generated using TLR-agonist cocktails or LPS+IFN-γ) by RNA-seq and found that though both programs upregulate common DC maturation markers like CCR7, CD80, CD40, and LAMP3, several transcription modules including ISG induction distinguish immunogenically activated cDC2s from DC2hm.

overall_design: Human splenic cDC2s was stimulated in U-bottom 96-well plates for 12 h in complete medium with the combination of TLR-agonist including polyinosinic-polycytidylic acid [poly(I:C); 10 µg/ml], R848 (1 µg/ml), and LPS (4 µg/ml) or LPS (4 µg/mL) plus IFN-γ (100 ng/mL).


title: TSLP administration promotes homeostatic maturation of human cDC2

summary: To test whether TSLP triggers the homeostatic maturation program of human splenic cDC2 (DC2hm program) in vitro, we administrated TSLP to in-culture human splenic cDC2 and performed RNA-seq. The results showed that TSLP induced DC2hm-like profile including the upregualtion of genes related to DC maturation, migration, immunoregulation, Treg induction and did not induce drastic ISG upregulation compared to either freshly isolated or cDC2s cultured in medium.

overall_design: Purified cDC2s were treated with TSLP (50 ng/ml) or complete medium (Med) for 12h . UID RNA-seq which incorporating unique identifiers to improve sensitivity and remove PCR-ampliaction bias was then performed on TSLP-cDC2s, Med-cDC2s  and purified cDC2s.


title: Effects of blood criculating extracellular vesicles on social behaviors in mice: blood miRNA analysis

city: Birmingham

first: Shinichi

last: Kano

state: AL

address: 1720 7th Ave South

department: Psychiatry

institute: University of Alabama at Birmingham

type: Non-coding RNA profiling by high throughput sequencing

summary: Extracellular vesicles (EVs) are cell-derived membrane vesicles that circulate throughout the body. Accordingly, circulating EVs and their associated molecules, such as RNAs and proteins, are regarded as promising sources of molecular biomarkers for various disorders. Cell culture-derived EVs have also drawn substantial attention as possible delivery tools for therapeutic molecules. Nevertheless, the biological impact of circulating EVs on in vivo physiology and pathology remains elusive. Here we report that systemic exposure to blood circulating EVs from wild-type (WT) mice attenuates sociability deficits in Rag1-/- mice. Intravenously injected WT mouse blood EVs reach the brain and restore postsynaptic inhibitory signals in the Rag1-/- medial prefrontal cortex (PFC) pyramidal neurons. Mechanistically, WT EV-associated microRNAs, miR-23a-3p and miR-103-3p, reduce PKCε expression, increasing postsynaptic GABAA receptors in the mPFC pyramidal neurons. Our findings reveal a sociability-promoting effect of blood circulating EVs and associated miRNAs with therapeutic potential for sociability deficits.

overall_design: We compared the miRNA expression profiles of the sear colelcted from Rag1-/- mice with or without adoptive T cell transfer by miRNA-seq.

first: Shin-ichi

first: David

middle: K

last: Crossmann

first: Eisuke

last: Dohi

first: Norimichi

last: Ito

first: Ken

last: Matoba


title: CBP-IDRs regulate acetylation and gene expression [ChIP-Seq]

first: Daniel

last: Bose

summary: Intrinsically disordered regions (IDRs) have emerged as crucial regulators of protein function, allowing proteins to sense and respond to their environment. Creb binding protein (CBP) and EP300 (p300) are transcription coactivators that regulate gene expression in multicellular organisms, following their recruitment to cis-regulatory elements. CBP and p300 contain large IDRs, however little is known about how these different IDRs work together to regulate CBP function. Here, we show that CBP-IDRs cooperate to control different aspects of CBP behaviour in the nucleus, by regulating the properties of fluid-like condensates formed by endogenous CBP. We show how IDRs with different sequence properties make unique contributions to CBP behaviour by establishing a balance between positive and negative regulation of CBP condensates. These conflicting interactions are functionally important, shaping CBPs response to factors such as lysine acetylation, that influence condensate formation. When disrupted, regulatory CBP-IDRs change how CBP interacts with chromatin, alter patterns of CBP-dependent histone acetylation and change gene expression. Together, our work highlights how IDRs with different sequences, spatially segregated in the same protein, can cooperate to shape protein function.

overall_design:
Chromatin immunoprecipitation sequencing (ChIP-seq) for doxycycline inducible GFP epitope-tagged Crebbp binding protein (CBP) in HEK293T cells. Doxycycline was added to induce GFP expression while not altering overall levels of tagged and untagged CBP. Control  ChIP-seq for endogenous CBP was done in parental HEK293T cells stably expressing Tet3G transactivator protein.
The same system was used to generate datasets for H3K27ac CUT&RUN and total RNAseq, following induction of CBP-GFP expression. Please note that the processed data files generated from both replicates are linked to the corresponding Rep1 sample records.

first: Katie

last: Gelder

first: Nicola

last: Carruthers

first: Grace

last: Gilbert

first: Laura

last: Harrison

first: Thomas

last: Evans

first: Sophie

middle: S

last: Ball

first: Mark

last: Dunning

first: Timothy

last: Craggs

first: Alison

last: Twelvetrees


title: CSF1R inhibition plus chemotherapy induces systemic anti-tumor immune responses in triple negative breast cancer and sensitizes tumors to anti-PD-1 therapy by relieving resident memory T cell dysfunction [luminex]

city: Portland

first: Lisa

last: Coussens

state: OR

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

summary: Triple-negative breast cancer (TNBC) is a heterogeneous and aggressive disease where limited therapeutic options are available. A significant correlation exists between presence of intratumoral macrophages, tumor progression, and poor outcomes in TNBC. Preclinical in vivo studies revealed that inhibition of myelomonocytic colony stimulating factor 1 (CSF1) or its receptor (CSF1R), plus cytotoxic therapy decreases primary tumor growth kinetics and pulmonary metastases by CD8+ T cell-dependent mechanisms. To evaluate safety and tolerability of this immune-based therapeutic strategy, we conducted a phase Ib/II clinical trial evaluating Pexidartinib (PLX3397), a small molecule CSF1R inhibitor plus Eribulin chemotherapy in patients with heavily pretreated metastatic TNBC. Correlate analyses from baseline revealed increased leukocyte activation biomarkers, increased presence of CD8+ and CD4+ T central memory cells, and increased PD-1 expression on CD4+ T cells in patients experiencing a partial response or stable disease, together providing evidence of enhanced anti-tumor immunity. We hypothesized that addition of either PD-1 and PD-L1-blockade following CSF1R inhibition and chemotherapy would lead to a further enhanced anti-tumor T cell response. To test this, we evaluated tumor-bearing MMTV-PyMT transgenic mice comparing addition of PD-1- or PD-L1-blockade to Pexidartinib/Paclitaxel therapy. This revealed tumor regression in ~60% of transgenic mice with combined PD-1, but not PD-L1-blockade. Analysis of mammary tumors from mice treated with the PD-1 combination revealed activation and expansion of short-lived effector and memory T cells, and unique clonally-expanded T cells not observed with the PD-L1-blockade combination. These clinical and preclinical findings together provide rationale for addition of CSF1/CSF1R inhibitors to chemotherapy and PD-1-blocakde to further improve outcomes for patients with BC.

overall_design:
The Luminex platform was used to measure the abundance of 65 analytes in human blood plasma of women with metastatic triple-negative breast cancer
NOTE: characteristics: sourceID' id  indicates same sample source across timepoints
NOTE: 'characteristics: Timepoint' variable indicates which timepoint from sample source the data is from

first: Hope

last: Rugo

first: Amanda

last: Poissonnier

first: Eivind

middle: V

last: Egeland

first: Wesley

last: Horton

first: Tiziana

last: Cotechini

first: Brian

last: Ruffell

first: Cecil

last: Gomes

first: Shamilene

last: Sivagnanam

first: Nicky

last: Belen

first: Dhaarini

last: Murugan

first: Nell

last: Kirchberger

first: Courtney

last: Betts

first: Motomi

last: Mori

first: Shivaani

last: Kummar

first: K

last: Blackwell

first: E

last: Mayer

first: Shelley

last: Hwang


title: Identification of a human cDC2 homeostatic maturation program by scRNA-seq

first: Harris

last: Han

summary: To explore the homeostatic maturation program of human cDCs, we exploited the nature of the spleen where DC maturation leads to migration from the red pulp and marginal zone to the white pulp of the spleen. Therefore, all steps of DC maturation are present and can be studied in the same organ. We first used single-cell RNA-seq (scRNA-seq) to profile lineage- (lin-) CD11c+ HLA-DR+ cells from spleens of 3 healthy human donors and identified a homeostatic maturation of the cDC2 subtype with 3 stages (cDC2, DC2pre-hm, DC2hm).

overall_design: Single-cell transcriptomics of lineage- (lin-) CD11c+ HLA-DR+ cells from spleens of 3 healthy donors were obtained using MACS and FACS. 10 × Chromium single-cell libraries were prepared according to the manufacturer’s instructions. Sequencing was performed using Illumina NovaSeq 6000.

first: Runpeng

first: Mengmeng

last: Lu

first: Qiu-Chen

last: Zhao


title: CSF1R inhibition plus chemotherapy induces systemic anti-tumor immune responses in triple negative breast cancer and sensitizes tumors to anti-PD-1 therapy by relieving resident memory T cell dysfunction [tumor]

first: Lisa

last: Coussens

overall_design: genomic DNA extracted from mice from 7 treatments and two timepoints was amplified for TCRb library and sequenced

first: Hope

last: Rugo

first: Amanda

last: Poissonnier

first: Eivind

last: Egeland

first: Wesley

last: Horton

first: Tiziana

middle: M


title: Fine-tuning of ERK oscillation frequencies enables proliferation differentiation balance during mesendoderm fate specification

city: HangZhou

first: WeiKang

last: Meng

state: ZheJiang

address: A4 Floor, Teaching Building, School of Medicine, Zijingang Campus, Zhejiang University

institute: ZheJiangUniversity

summary: It is well documented that differentiation of stem cells is generally associated with and facilitated by an elongated cell cycle. However, for lineage specification requiring high ERK activity, which also promotes proliferation, it is unclear how stem cells simultaneously negotiate the “proliferation-differentiation” decision. Here we investigate this question using multiplex quantitative live-cell imaging to track embryonic stem cells (ESC) differentiation into mesendoderm (ME) lineage with high ERK activity. We show that ERK activity increase manifested by a heightened ERK oscillation frequency drove robust ME differentiation accompanied by a modest cell cycle acceleration. We profile the responses of ME differentiation and cell cycle length as a function of a synthetic ERK oscillatory activity gradient. Our results reveal that these two processes took place in distinct ranges of ERK oscillation frequency, with ME differentiation requiring higher level for ERK oscillation to secure efficient ME protein translation. Interactions between gastrulation morphogens recapitulated an ERK oscillation gradient, potentiating heterogeneous ME fates while maintaining a comparable level of proliferation. Our study thus provides mechanistic insights into how ERK fine-tunes proliferation and differentiation during cell fate specification

overall_design: hESCs were treated with CHIR99021 in combination with different concentrations of the Ulix inhibitor. Polysome profiling was performed by sucrose gradient ultracentrifugation, and RNA was extracted from pooled gradient fractions for RNA-seq analysis. The collected fractions included CHIR-total-RNA and gradient pools CHIR-2–3, CHIR-4–5, CHIR-6–7, and CHIR-8–11, which represent RNA populations ranging from free/lowly translated mRNAs to heavy polysome-associated mRNAs. Sample names containing labels such as “CHIR-U0_15” indicate cells treated with CHIR99021 together with 0.15 μM Ulix inhibitor; additional samples include treatments with 1.25 μM and 5 μM Ulix.

first: Chenyang

last: Ma

first: Weikang


title: Effects of blood criculating extracellular vesicles on social behaviors in mice: brain gene expression analysis

first: Shinichi

last: Kano

overall_design: We compared the gene expression profiles of the PFCs colelcted from WT mice, Rag1-/- mice, and Rag1-/- mice administered with WT blood extracellular vesicles by RNA-seq.

first: Shin-ichi

first: David

last: Crossmann

first: Eisuke

last: Dohi

first: Norimichi

last: Ito

first: Ken

last: Matoba


title: CSF1R inhibition plus chemotherapy induces systemic anti-tumor immune responses in triple negative breast cancer and sensitizes tumors to anti-PD-1 therapy by relieving resident memory T cell dysfunction [blood]

last: Cotechini

first: Brian

last: Ruffell

first: Cecil

last: Gomes

first: Shamilene

last: Sivagnanam

first: Nicky

last: Belen

first: Dhaarini

last: Murugan

first: Nell

last: Kirchberger

first: Courtney

last: Betts

first: Motomi

last: Mori

first: Shivaani

last: Kummar

first: K

last: Blackwell

first: E

last: Mayer

first: Shelley


title: CSF1R inhibition plus chemotherapy induces systemic anti-tumor immune responses in triple negative breast cancer and sensitizes tumors to anti-PD-1 therapy by relieving resident memory T cell dysfunction [nanostring]

first: Lisa

last: Coussens

overall_design: Expression of 750 genes from the nCounter Mouse PanCancer IO360 Nanostring panel was assessed for 5 different treatments, minimum two replicates per treatment.

first: Hope

last: Rugo

first: Amanda

last: Poissonnier

first: Eivind

last: Egeland

first: Wesley

last: Horton

first: Tiziana

last: Hwang


title: RNA-seq of fresh apheresis human platelets and freeze dried platelets (Thrombosomes)

first: Huimin

last: Geng

summary: To determine the transcriptomic (mRNA and microRNA) content present in fresh apheresis platelets and freeze dried platelets (Thrombosomes) we used RNA-Seq approach. The goal was to determine if the freeze drying process maintained the transcriptomic cargo of the fresh platelets.

overall_design: Genome-wide profiling of total RNA transcript levels in human Pletlet and Thrombosomes

first: Alpa

last: Trivedi

first: Shibani

last: Pati


title: Multi-dimensional characterization of a human cDC2 homeostatic maturation program by single-cell multi-omics

first: Harris

last: Han

summary: To gain insights into the homeostatic maturation program of human cDCs at multiple dimensions, we exploited the nature of the spleen where DC maturation leads to migration from the red pulp and marginal zone to the white pulp of the spleen. Therefore, all steps of DC maturation are present and can be studied in the same organ. We utilized the Chromium Single Cell Multiome ATAC + Gene Expression technique to depict the chromatin accessibility and nucleic mRNA profiles of lineage- (lin-) CD11c+ HLA-DR+ cells from the spleen of a healthy human donor and characterized a homeostatic maturation of the cDC2 subtype with 3 stages (cDC2, DC2pre-hm, DC2hm) at both transcription and epigenetic levels.

overall_design: Single-cell multi-omics (scATAC-seq+snRNA-seq) of lineage- (lin-) CD11c+ HLA-DR+ cells from the spleen of a healthy donor were obtained by MACS and FACS. 10 × Chromium Next GEM Single Cell Multiome ATAC + Gene Expression libraries were prepared according to the manufacturer’s instructions. Sequencing was performed using Illumina NovaSeq 6000.

first: Runpeng

first: Mengmeng

last: Lu

first: Qiu-Chen

last: Zhao


title: Hypoxia Promotes an Adrenergic to Mesenchymal Transcriptional Program Transition in Neuroblastoma

city: Chicago

first: Mark

last: Applebaum

state: IL

address: 900 E 57th St

department: Pediatrics, Section of Hematology/Oncology

institute: University of Chicago

summary: Purpose: Neuroblastoma is the most common extracranial solid tumor in childhood. We previously showed that circulating cell-free DNA (cfDNA) and tumor biopsy derived 5-hydroxymethylcytosime (5-hmC) profiles identified patients with neuroblastoma who experienced subsequent relapse. Here, we hypothesized that 5-hmC modifications selectively enriched in cfDNA compared with tumor biopsy samples would identify epigenetic changes associated with aggressive tumor behavior and identify novel biomarkers of outcome in patients with high- risk neuroblastoma.  Methods: 5-hmC profiles from cfDNA (n = 64) and tumor biopsies (n = 48) were compared. Two neuroblastoma cell lines underwent chromatin immunopre- cipitation followed by sequencing (ChIP-Seq) for H3K27me3, H3K4me3, and H3K27ac; kethoxal-associated single-stranded DNA sequencing; hmC-Seal for 5-hmC; and RNA-sequencing (RNA-Seq). Genes enriched for both H3K27me3 and H3K4me3 in the included cell lines were defined as bivalent. Using bivalent genes defined in vitro, a bivalent signature was established in three publicly available cohorts of patients with neuroblastoma through gene set variation analysis. Differences between tumors with high or low bivalent signatures were assessed by the Kaplan-Meier method and Cox proportional hazards models.  Results: In cfDNA compared with tumor biopsy derived 5-hmC profiles, we found in- creased 5-hmC deposition on Polycomb Repressive Complex 2 target genes, a finding previously described in the context of bivalent genes. We identified 313 genes that bore bivalent chromatin marks, were enriched for mediators of neuronal differentiation, and were transcriptionally repressed across a panel of heterogeneous neuroblastoma cell lines. In three distinct clinical cohorts, low bivalent signature was significantly and independently associated with worse clinical outcome in patients with high-risk neuroblastoma.  Conclusion: Low expression of bivalent genes is a biomarker of worse outcome in patients with high-risk neuroblastoma.

overall_design: RNA-Seq performed in 8 neuroblastoma cell lines that were incubated in hypoxic conditions for 48 hours.

first: Mohansrinivas

last: Chennakesavalu

first: Kelley

last: Moore

first: Gepoliano

last: Chaves

first: Sahil

last: Veeravalli

first: Rachel

last: TerHaar

first: Tong

last: Wu

first: Ruitu

last: Lyu

first: Alexandre

last: Chlenski

first: Chuan

last: He

first: Andrea

last: Piunti


title: CSF1R inhibition plus chemotherapy induces systemic anti-tumor immune responses in triple negative breast cancer and sensitizes tumors to anti-PD-1 therapy by relieving resident memory T cell dysfunction [lymph node]

first: Lisa

last: Coussens

first: Hope

last: Rugo

first: Amanda

last: Poissonnier

first: Eivind

last: Egeland

first: Wesley

last: Horton

first: Tiziana

last: Cotechini

first: Brian

last: Ruffell

first: Cecil

last: Gomes

first: Shamilene

last: Sivagnanam

first: Nicky

last: Belen

first: Dhaarini

last: Murugan

first: Nell

last: Kirchberger

first: Courtney

last: Betts

first: Motomi

last: Mori

first: Shivaani

last: Kummar

first: K

last: Blackwell

first: E

last: Mayer

first: Shelley

last: Hwang


title: Human pluripotent stem cell–derived A10 dopaminergic neurons specifically integrate into host circuits and relieve depression

first: Yuejun

last: Chen

state: Shanghai

address: 320 Yueyang Road

institute: Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences

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

overall_design: Refer to individual Series


title: CSF1R inhibition plus chemotherapy induces systemic anti-tumor immune responses in triple negative breast cancer and sensitizes tumors to anti-PD-1 therapy by relieving resident memory T cell dysfunction [lung]

first: Lisa

last: Coussens

first: Hope

last: Rugo

first: Amanda

last: Poissonnier


title: AtDEK2, a dual histone mark reader regulates plant immunity [RNA-seq]

city: Gif Sur Yvette

first: Xiaoning

last: HE

address: 630,Rue Noetzlin

country: France

institute: universite-paris-saclay

summary: Arabidopsis DEK2, a nuclear protein involved in multiple chromatin-related processes, was found to be phosphorylated in response to flg22 treatment suggesting a role in plant immunity to bacterial pathogens. dek2 loss of function mutants were susceptible to bacterial as well as fungal pathogens. Transcriptome data of the dek2-1 mutant shows that AtDEK2 is a transcriptional repressor of defense related genes, hormone synthesis & signaling genes. ChIP-Seq analysis indicates that DEK2 binds to motifs of several families of transcription factors (TFs) and to class I TCP binding motif regions with the highest affinity. We determined that DEK2 is recruited to specific regions on the chromatin by transcription factors. Our data suggests that DEK2 is a reader of the dual histone mark, H3K4me3K27me3. Finally, based on our data we postulate a hypothetical working model for the function of DEK2 as a transcriptional repressor and targets regions with H3K4me3K27me3 marks.

overall_design: WT (col-0) and dek2-1 mutant plans were either mock treated or with the bacteria Pst DC3000 hrcC- strain. For each sample 3 biological replicates were used.

first: Hanna

last: Alhoraibi

first: Santiago

last: Alejandro-Martinez

first: David

last: Latrasse

first: Papita

last: Mandal

first: Léa

last: Faivre

first: Deborah

last: Manza

first: Aala

last: Abulfaraj

first: Siba

last: Alharbi

first: Kiruthiga

last: Mariappan

first: Olga

last: Artyukh

first: Fatimah

last: Abdulhakim

last: Aljedaani

first: Stefan

last: David

first: Marilia

last: Almeida-Trapp

first: Jean

last: Bigeard

first: Delphine

last: Pflieger

first: Wolfgang

last: Fischle

last: Arold

last: Colcombet

first: Daniel

last: Schubert

first: Moussa

last: Benhamed

first: Ikram

last: Blilou

first: Heribert

last: Hirt

first: Naganand

last: Rayapuram


title: RNA Sequencing Study to Investigate the Role of LITAF in Regulating Gene Expression Profiles of H9C2 Cells Exposed to Hypoxia/Reoxygenation

status: Public on Feb 22 2026

city: Chongqing

first: Guo

last: Yang

state: Chongqing

address: No. 1 Jiankang Road, Yuzhong District.

institute: chongqing university

summary: This study employed H9C2 cells (a rat myocardial cell line) as the experimental model, with three experimental groups and four biological replicates per group, resulting in a total of 12 samples. The experimental design aimed to investigate the regulatory role of LITAF in H9C2 cells under hypoxia reoxygenation (H/R) injury conditions. Specifically, the control group consisted of H9C2 cells cultured under normal conditions without H/R treatment or lentiviral transfection. The hypoxia reoxygenation (H/R) group consisted of H9C2 cells transfected with an empty lentiviral vector as a control, followed by exposure to hypoxia (1 percent O2) for 8 hours and subsequent reoxygenation under normoxic conditions for 2 hours. The hypoxia reoxygenation plus LITAF overexpression group consisted of H9C2 cells transfected with a LITAF overexpressing lentiviral vector to achieve LITAF overexpression, followed by hypoxia (1 percent O2 for 8 hours) and reoxygenation (2 hours) under the same conditions as the H/R group. After completion of the treatments, total RNA was extracted from each sample using a standard RNA extraction kit, and RNA quality was assessed, including RNA integrity number (RIN) evaluation, to ensure suitability for sequencing. RNA sequencing libraries were constructed according to standard protocols. Eukaryotic mRNA was enriched using Oligo(dT) magnetic beads, fragmented into approximately 300 bp fragments, reverse transcribed into cDNA, ligated with sequencing adapters, size selected, PCR amplified, and purified to obtain the final libraries. High throughput sequencing was performed on the Illumina NovaSeq X Plus platform using a paired end 150 bp sequencing strategy. Each sample was sequenced to a depth of approximately 6 to 10 Gb to ensure sufficient coverage for downstream analyses. Bioinformatics analyses included raw data quality control, alignment of sequencing reads to the rat reference genome, gene expression quantification, identification of differentially expressed genes using DESeq2 and/or edgeR, functional annotation using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, and functional enrichment analyses. By comparing the transcriptomic profiles of the H/R group and the H/R plus LITAF overexpression group, with the control group serving as a baseline reference, this study aimed to identify LITAF-regulated differentially expressed genes, characterize enriched signaling pathways, and elucidate the molecular mechanisms by which LITAF modulates H/R-induced injury in H9C2 myocardial cells.

overall_design: Three experimental groups were set up with 4 biological replicates per group, totaling 12 H9C2 cell samples (rat myocardial cell line). Group 1 (Control group, NC_1 to NC_4): H9C2 cells cultured under normal conditions without hypoxia/reoxygenation (H/R) treatment or lentiviral transfection. Group 2 (H/R group, H_R_1 to H_R_4): H9C2 cells transfected with empty lentiviral vector, followed by 8 hours of hypoxia (1% O2) and 2 hours of normoxic reoxygenation. Group 3 (H/R + LITAF overexpression group, H_R_OE_1 to H_R_OE_4): H9C2 cells transfected with LITAF-overexpressing lentiviral vector, then treated with the same H/R conditions as Group 2. Total RNA was extracted from all samples, and RNA sequencing was performed on Illumina NovaSeq X Plus platform (paired-end 150 bp, sequencing depth 6-10 Gb per sample) to detect gene expression profiles. Raw sequencing data have been submitted to SRA with SubmissionID SUB15968871 and BioProject ID PRJNA1415685; GEO submission will link to these SRA data without duplicate upload of raw files. Downstream analyses include differential gene expression identification and functional enrichment to explore LITAF's regulatory role in H/R-induced H9C2 cell injury.


title: Human pluripotent stem cell–derived A10 dopaminergic neurons specifically integrate into host circuits and relieve depression [scRNA-seq]

city: Shanghai

first: Yuejun

last: Chen

summary: Ventral Tegmental Area (VTA) dopaminergic neuron group (A10) one of the important subtype of midbrain dopaminergic (mDA) neurons plays a crucial role in regulation of mainly brain functions and has been related into various psychiatric disorders. Despite the great achievements in generation of mDA neurons from pluripotent stem cells, the subtype-specific mDA differentiation especially A10 group still remains challenging. Here, we report an efficient differentiation paradigm for hPSCs to generate specific A10 subtype mDA neurons. The differentiation paradigm revealed that post-mitotic patterning by NOTCH inhibitor, GDNF and AA induced the specification of A10 subtype. The hPSC-derived neurons exhibited characteristic of A10 subtype from molecular expression, electrophysiological properties and neural innervation. Considering the dysfunction of A10 mDA neurons has been implicated in depression, we detected that specific activation of the grafted-A10-like-mDA-neurons induced anxiolytic and antidepressant-like phenotypes on the transplanted mice. Our approach provides deep insights into the subtype specification of mDA neurons and offers a promising clinical application of these derived cells in cell transplantation therapy for disorders related to A10 mDA neurons.

overall_design: We differentiated TH-tdTomato H9 cell line into A10-like neurons, and collected cells for scRNA-seq at the terminal stage of neural differentiation (day 46) by FAC-sorting tdTomato positive cells;

first: Wei

last: Yan

first: Qinqin

last: Gao

first: Peibo

last: Xu

first: Ziyan

last: Wu


title: Quantification of Systemic Inflammation by a Gene Score Uncovers Relevant Features on Acutely Decompensated Cirrhosis

city: Barcelona

first: Ferran

last: Aguilar Parera

state: BARCELONA

address: Avinguda Diagonal 477, 11th floor, EF CLIF

country: Spain

institute: EF-CLIF

summary: Acutely decompensated cirrhosis (ADC) is related to systemic inflammation (SI) due to activation of the innate-immune system. Acute-on-Chronic Liver Failure (ACLF) is the extreme expression of this process. We developed a gene score to quantify SI in ADC.

overall_design: Whole-blood RNA-seq was performed in 700 patients (Cohort 1) (Figure 1A), 383 from the PREDICT study and 317 from the ACLARA study, explored by whole-blood RNA sequencing (RNA-seq) within 2 days after hospital admission (time 1, T1). In 375 of these patients (Sub-cohort 1a), a second RNA-seq was performed at T2 (median duration of the T1-T2 period 7 days; 75% CI: 5- 8 days). Finally, 51 patients from Sub-cohort 1a, who were explored by one or two additional RNA-seq after T2, formed the Sub-cohort 1b. The CLF-SIG score was designed in Cohort 1. The early course of CLIF-SIG score was estimated in Sub-cohort 1a and more in detail in Sub-cohort 1b. Cohort 1 and Sub-cohort 1a included patients with and without ACLF at T1. Sub-cohort 1b included only patients without ACLF. Whole-blood RNA-seq was also performed in 25 healthy subjects as a control group.

first: F

last: Aguilar

first: J

last: Trebicka

first: A

last: Queiroz Farias

last: Lozano

first: R

last: Moreau

first: V

last: Arroyo


title: TPD52 Inhibits Aldosterone Synthesis Through Suppression of CAMKK2 Signaling

first: Ling

last: Xie

address: No. 1 Youyi St

institute: the First Affiliated Hospital of Chongqing Medical University, Chongqing, China

summary: Background: Aldosterone-producing adenomas (APA) are a major cause of primary aldosteronism. While gene mutations in APA trigger aldosterone overproduction via Calcium signaling, their precise regulatory mechanisms remain unclear. Our prior proteomic analysis identified significant upregulation of Tumor protein D52 (TPD52), an oncogene protein implicated in cancer progression, in APA. This study investigates the role of TPD52 in regulating aldosterone synthesis and its molecular mechanism. Method: TPD52 expression was validated in APA specimens. Gain- and loss-of-function studies in NCI-H295R cells were performed to assess its role in aldosterone synthesis. Mechanistic insights were obtained through transcriptomics and immunoprecipitation-mass spectrometry (IP-MS), with key results validated in NCI-H295R and HEK-293T cells. Results: TPD52 was upregulated in APA tissues. Functionally, TPD52 overexpression suppressed aldosterone synthesis in NCI-H295R cells, whereas its knockdown enhanced aldosterone production. Transcriptomics confirmed that TPD52 knockdown promoted CYP11B2 expression and aldosterone synthesis. IP-MS identified calcium/calmodulin-dependent protein kinase kinase 2 (CAMKK2) as a novel TPD52-interacting protein. This interaction suppressed phosphorylation of calmodulin-dependent protein kinase 4 (CAMK4) and CREB. Importantly, CAMKK2 overexpression rescued the TPD52-mediated suppression of CYP11B2 expression and aldosterone synthesis. Conclusion: TPD52 acts as a negative regulator of aldosterone synthesis by inhibiting the CAMKK2–CAMK4–CREB signaling axis.

overall_design: RNA-seq profiling of  NCI-H295R cells, in which TPD52 expression was knocked down by lentivirus-delivered specific shRNA compared to a non-targeting shRNA control.

first: Linqiang

last: Ma

first: Shumin

first: Qifu

last: Li

first: Chuan

last: Peng


title: Human pluripotent stem cell?derived A10 dopaminergic neurons specifically integrate into host circuits and relieve depression

overall_design: We differentiated H9 cell line into mDA progenitors with or without GAD treatment during the stage V for bulk RNA-seq


title: IL2Ra-dependent feedback control of the B-cell receptor and its oncogenic mimics

first: Huimin

last: Geng

summary: Human BCR-ABL1 ALL cells were sorted as CD25-positive and CD25-negative BCR-ABL1 ALL cells on three xenograft samples BLQ11, LAX9 and BLQ1. The expression profiles of CD25+ and CD25- BCR-ABL1 ALL cells were studied by Affymetrix Human Genome U133 Plus 2.0 Array.

overall_design: Human BCR-ABL1 ALL cells were sorted as CD25-positive and CD25-negative BCR-ABL1 ALL cells for microarray gene expression profiling.

first: Markus

last: Muschen


title: Profiling of MCM2 and phosphorylated MCM2 in MLL3/4 double mutant and control ESCs [ChIP-seq]

first: Robert

last: Blelloch

address: 35 Medical Center Way

department: Urology

summary: We performed ChIP-seq for MCM2 and phosphorylated MCM2 in MLL3/4 double mutant and MLL3 single mutant ESCs grown under naive (L2i) conditions.

overall_design: Two replicates derived from independent cultures were collected per target and cellular condition

first: Deniz

last: Goekbuget


title: Single-cell RNA sequencing reveals cellular and molecular heterogeneity and distinct immunosuppressive traits in the MMTV-R26Met syngeneic TNBC model

city: Marseille

first: Olivier

last: Castellanet

address: 27 boulevard Lei Roure

institute: Aix Marseille University, CNRS, INSERM

summary: Triple-negative breast cancer (TNBC) is an aggressive and heterogeneous subtype of breast cancer with limited targeted therapies. To model TNBC heterogeneity in an immunocompetent setting, we established syngeneic grafts derived from the TNBC MMTV-R26Met genetically engineered mouse model, which preserve both the molecular identity and immune landscape of primary tumors. These grafts recapitulate features of distinct TNBC subtypes, providing a physiologically relevant preclinical platform to investigate tumor–immune interactions and therapy response. Here, we performed single-cell RNA sequencing (scRNA-seq) on four syngeneic tumors (S34, S35, S37, and S39), generating transcriptomic profiles from 22,046 cells. Clustering identified cell populations spanning malignant epithelial, stromal, endothelial, and diverse immune subsets. Tumors displayed subtype-specific traits, including oxidative phosphorylation programs with N2-like neutrophils and epithelial–mesenchymal transition with M2-like macrophages. Despite overall low T cell infiltration, inhibitory receptors and myeloid checkpoint ligands were broadly expressed, highlighting strongly immunosuppressive microenvironments. These datasets provide a resource for dissecting TNBC subtype heterogeneity in an immunocompetent context and offer a preclinical framework to explore mechanisms of immune evasion and therapeutic response.

overall_design: Single-cell RNA sequencing was performed on four independent syngeneic tumors (S34, S35, S37, S39) derived from the MMTV-R26Met triple-negative breast cancer mouse model. Tumors were dissociated into single-cell suspensions and processed using the 10x Genomics Chromium pipeline.

first: Jean

last: Monatte

first: Paula

last: Michea

first: Julien

last: Vernerey

first: Flavio

last: Maina

first: Fabienne

last: Lamballe


title: Loss of Histone Methyltransferase Ezh2 Exacerbates Polarization of Macrophages toward M2-Like Phenotypes by Hepatocellular Carcinoma [RNA-Seq]

city: Bangkok

first: Tanapat

last: Palaga

address: Payathai Road, Pathumwan

department: Microbiology

country: Thailand

institute: Chulalongkorn University

summary: The roles of histone methytransferase Ezh2 in TAMs of liver cancer still unclear. In this study, an RNA sequencing was performed for samples from bone marrow-derived macrophages (BMDMs) of WT and Ezh2 KO mice upon exposure to conditioned media (CM) from hepatocellular carcinoma (HCC) cell line Hepa1-6. The results demonstrated that the absence of Ezh2 in BMDMs exacerbated M2-like phenotypic changes upon incubation with CM from hepatocellular carcinoma (HCC) cell line. The RNA-sequencing revealed that the M2 gene set was further upregulated in treated BMDMs Ezh2 KO compared to treated BMDMs WT WT and the hallmark of Glycolysis as enriched pathway was identified in BMDMs Ezh2 KO. Additionally, the hallmark of IL-6/JAK/STAT pathway was enriched in CM-treated BMDMs. Collectively, these findings provide evidence that JAK/STAT3 axis is critical for M2-like phenotypic changes and Ezh2 suppresses the shifts of macrophage metabolism toward glycolysis that promotes M2 polarization.

overall_design: RNA-seq profiling of bone marrow-derived macrophages WT and Ezh2 KO that treated with conditioned media of mouse liver cancer cell line Hepa1-6 for 24 hours.

first: Kittin

last: Weerasopon

first: Atsadang

last: Boonmee

first: Patipark

last: Kueanjinda

first: Benjawan

last: Wongprom

first: Thitiporn

last: Pattarakankul


title: A cytomegalovirus encoded lncRNA blocks cell cycle progression

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

institute: Weizmann Institute

summary: During HCMV infection RNA2.7 is the most highly expressed transcript in the infected cell, but its function is not well understood. We tackeled this open question utilizing methods such as RNA sequencing, ribosome profiling and SLAMseq.

overall_design: To decipher RNA2.7 functions we performed RNA sequencing following infection of the WT virus or a deletion mutant virus in two cell types. We also performed fractionation, ribosome profiling and SLAMseq on infected and uninfected cells. We also made libraries without using poly-A selection to sequence histones.

first: Tal

last: Fisher

first: Orel

last: Mizrahi

first: Julie

last: Tai-Schmiedel

first: Aharon

last: Nachshon

first: Michal

last: Schwartz

first: Meidva

last: Patrick

first: Avraham

last: Gluck

first: Sharon

last: Karniely


title: Ketogenic diet exacerbates DSS-induced colitis through a β-hydroxybutyrate -T. spiroformis-γδ17 T cell axis in mice

first: Yameng

last: Liu

address: No.555 Zuchongzhi Road, Pudong New Area

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

summary: Ketogenic diets (KD) benefit metabolic and neurological health by modulating gut microbiota, but their impact on inflammatory bowel disease, particularly ulcerative colitis (UC), remains controversial. Here, we show that KD aggravated colitis by triggering a ketogenesis-microbe-immune cascade. KD elevated luminal β-hydroxybutyrate (β-HB), which fueled the expansion of Thomasclavelia spiroformis (T. spiroformis), a pathobiont that activated mucosal γδ17 T cells potentially via peptidoglycans. These cells drived IL-17A production and inflammation; reconstitution of γδ17 T cells in Tcrd-/- mice confirmed their pathogenic role. Blocking ketogenesis or neutralizing IL-17A abolished KD-exacerbated colitis, whereas β-HB supplementation and ketogenesis activation phenocopied disease worsening. In UC patients, T. spiroformis abundance correlated with fecal β-HB and serum IL-17A levels, but not in Crohn’s disease, supporting a UC-specific β-HB-T. spiroformis-γδ17 T cell axis. These findings uncover a metabolic-microbial-immune loop linking dietary ketosis to UC, and suggest that targeting ketone metabolism or IL-17A signaling may offer new therapeutic opportunities.

overall_design: To elucidate the mechanisms of KD-driven immune dysregulation in colitis, we performed single-cell RNA sequencing (scRNA-seq) on colon tissues from DSS-treated mice fed either CD or KD.

first: Xuan

last: Wu

first: Li

last: Chen

first: Shan

last: Wang

first: Cen

last: Xie

first: Lei

first: Weiwei


title: Effect of beta-catenin (Ctnnb1) on vasopressin-responsive gene expression in mouse kidney collecting duct mpkCCDc11 cells

city: Baltimore

first: Hyun Jun

last: Jung

state: MD

address: 720 Rutland Ave, Ross Research Building 1165B

department: Medicine (Nephrology)

institute: Johns Hopkins University School of Medicine

summary: Vasopressin tightly regulates water reabsorption in renal collecting duct cells by increasing the abundance of aquaporin-2 (AQP2) through transcriptional and post-transcriptional mechanisms. We recently discovered that a complex comprising CTNNB1 (beta-catenin) and PARP1 involves Aqp2 gene transcription in response to vasopressin as a transcriptional regulator. However, the mechanistic involvement of Ctnnb1 in Aqp2 gene transcription in response to vasopressin is poorly known. To understand Ctnnb1-mediated Aqp2 gene regulation in the collecting duct cells, RNA sequencing (RNA-seq)-based transcriptomic profiling was perfomred in mouse kidney collecting duct cell line mpkCCDc11 treated with dDAVP or Ctnnb1 knockdown.

overall_design: The mpkCCDc11 cells transfected with control-siRNA (50 nM) or Ctnnb1-siRNA (50 nM) were grown on semipermeable supports (6-well transwell, 3450, Corning Costar) for 4 days and starved in serum- and hormone-free medium for an additional 24 h before dDAVP treatment. After treatment with dDAVP (1 nM) for 24 h, total RNA was extracted for RNA-Seq analysis. The experimental groups are 1) control-siRNA with vehicle treatment; 2) control-siRNA with dDAVP treatment; 3) Ctnnb1-siRNA with vehicle treatment; 4) Ctnnb1-siRNA with dDAVP treatment.

first: Hyo-Ju

last: Jang

first: Euijung

last: Park

first: Tae-Hwan

last: Kwon


title: BAFF-R Expression as a Predictive Biomarker for COVID-19 Vaccine Non-Responsiveness in Antibody-Deficient Patients

city: Leeds

first: Sinisa

last: Savic

address: St James's University Hospital

institute: University of Leeds

summary: Patients with primary and secondary antibody deficiencies exhibit variable responses to vaccination, with a substantial proportion failing to mount protective immunity to SARS-CoV-2. Mechanisms underpinning vaccine non-responsiveness in this population remain poorly defined. Our objective was to investigate B-cell-intrinsic defects underlying SARS-CoV-2 vaccine failure by assessing the capacity for plasma cell differentiation in a heterogeneous cohort of antibody-deficient patients using an in vitro model.

overall_design: Peripheral B-cells from 50 patients enrolled in the COVID-19 in Antibody Deficiency (COV-AD) study underwent a validated in vitro B-cell differentiation assay. We assessed plasmablast and plasma cell generation, immunoglobulin production, B-cell receptor repertoire diversity, and BAFF-R surface expression. RNA sequencing was performed on pre-activated B-cells to evaluate BAFF-R encoding gene, TNFRSF13C and related gene expression.

first: Eleanor

last: O’Callaghan

first: Adrian

last: Shields

first: Leon

last: Chang

first: Michelle

last: Umpierrez

first: Siobhan

middle: O

last: Burns

first: Alex

middle: G

last: Richter

first: Gina

last: Doody


title: Loss of Histone Methyltransferase Ezh2 Exacerbates Polarization of Macrophages toward M2-Like Phenotypes by Hepatocellular Carcinoma [ATAC-seq]

first: Tanapat

last: Palaga

summary: The roles of epigenetic regulator Ezh2 in TAMs of liver cancer still unclear. In this study, our results demonstrated that the absence of Ezh2 in bone marrow-derived macrophages (BMDMs) exacerbated M2-like phenotypic changes upon incubation with conditioned media (CM) from hepatocellular carcinoma (HCC) cell line Hepa1-6. The ATAC-seq revealed that the promoter regions of pyruvate metabolic process-related genes were more accessible in treated BMDMs Ezh2 KO.

overall_design: ATAC-seq profiling of bone marrow-derived macrophages WT and Ezh2 KO that treated with conditioned media of mouse liver cancer cell line Hepa1-6 for 24 hours.

first: Kittin

last: Weerasopon

first: Atsadang

last: Boonmee

first: Patipark

last: Kueanjinda

first: Benjawan

last: Wongprom

first: Thitiporn

last: Pattarakankul


title: Tim-3 Agonist Restrains ILC2 Function and Attenuates Airway Hyperreactivity via NLK Pathway

city: Los Angeles

first: Yoshihiro

last: Sakano

address: 1450 Biggy street

department: Molecular Microbiology & Immunology

institute: Unversity of Southern California

summary: Allergic asthma is driven by type 2 inflammation involving cytokines such as IL-4, IL-5, and IL-13, with group 2 innate lymphoid cells (ILC2s) playing a key pathogenic role. Here, we identify T cell immunoglobulin and mucin domain-containing protein 3 (Tim-3) as a negative regulator of ILC2 function. Tim-3 expression was upregulated in activated pulmonary ILC2s, and engagement with Tim-3 agonists inhibited ILC2 activation, proliferation, and type 2 cytokine production via the NLK signaling pathway and suppression of mitochondrial metabolism. In vivo, Tim-3 agonists alleviated airway hyperreactivity (AHR) and inflammation in both IL-33- and Alternaria alternata-induced AHR models, while ILC2-specific Tim-3 deletion exacerbated AHR. These results were confirmed in human ILC2s and humanized mice, supporting the translational relevance. Our findings establish Tim-3 as an inhibitory checkpoint for ILC2s and suggest its potential as a therapeutic target in allergic asthma and other ILC2-mediated diseases.

overall_design: mRNA profiles of mouse lung ILC2s which were cultured with isotype control or Tim3 agonist,  from CB57BL/6 mice were generated by deep sequencing, in duplicates, using a NextSeq 500.


title: The impact of Pyruvate dehydrogenase kinase 4 knockout on the function of vascular smooth muscle cells

city: Guangzhou

first: Li

last: Zhao

state: Guangdong

address: 1838 North Guangzhou Avenue,

department: Department of Cardiovascular Surgery

institute: Nanfang Hospital, Southern Medical University

summary: This study investigated the impact of pyruvate dehydrogenase kinase 4 knockout on the function of vascular smooth muscle cells.

overall_design: Vascular smooth muscle cells were extracted from the abdominal aorta of Pdk4fl/fl and Pdk4SMKO mice. The expression of pyruvate dehydrogenase kinase 4 in vascular smooth muscle cells was detected using RT-qPCR, followed by transcriptomic sequencing to investigate the impact of pyruvate dehydrogenase kinase 4 on the function of vascular smooth muscle cells.

first: Xiu

last: Liu