title: Single cell TCR sequencing of allogeneic HSC-derived MCAR-engineered NKT cells

first: Lili

address: 610 Charles E. Young Dr. East

summary: Ovarian cancer (OC) poses a significant challenge due to frequent recurrence linked to tumor heterogeneity and an immunosuppressive tumor microenvironment (TME). Targeting both OC cells and TME simultaneously holds promise for effective treatment. This study comprehensively analyzed 17 chemonaive and 18 refractory/recurrent OC samples, identifying mesothelin (MSLN) and natural killer receptor (NKR) ligands as tumor targets and CD1d as an OC TME target. Leveraging hematopoietic stem cell (HSC) gene engineering and feeder-free differentiation culture, we generated allogeneic MSLN-targeting CAR (MCAR)-engineered invariant natural killer T (MCAR-NKT) cells, demonstrating high-yield and high-purity production, potent antitumor efficacy, multiple tumor targeting mechanism, and significant in vivo expansion and persistence. Notably, these cells selectively deplete immunosuppressive TAMs and MDSCs, counteract tumor immune evasion, display a favorable safety profile with low risks of GvHD and CRS, and exhibit a stable “hypoimmunogenic” phenotype attributed to epigenetic and signaling regulations. These findings underscore the feasibility and therapeutic potential of allogeneic MCAR-NKT cell products for OC, laying a foundation for further translation and clinical development.

overall_design: Sngle cell TCR sequencing of allogeneic HSC-derived MCAR-engineered NKT cells, compared with those of PBMC-derived conventioanl T and NKT cells

first: Yan-Ruide

first: Zhe

first: Miao


title: Pre-receptor regulation of 11-oxyandrogens differs between normal and cancerous endometrium and across endometrial cancer grades and molecular subtypes

status: Public on Jul 26 2025

city: Ljubljana

first: Marija

last: Gjorgoska

state: Outside North America

address: Vrazov trg 2

country: Slovenia

institute: Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana

type: Expression profiling by high throughput sequencing

summary: Background: Endometrial cancer (EC) is a prevalent gynecological malignancy globally, with a rising incidence trend. While classic androgens have been implicated with EC risk, the role of their 11-oxygenated metabolites is poorly understood. Here, we studied 11-oxyandrogen formation from steroid precursors in EC for the first time. Methods: We performed in vitro studies on a panel of four EC cell lines of varying differentiation degree and molecular subtype and a control cell line of normal endometrium to assess 11-oxyandrogen formation from steroid precursors. We also characterized the transcriptomic effects of dihydrotestosterone (DHT) and 11-keto-DHT on Ishikawa and RL95-2. Key molecular players in 11-oxyandrogen metabolism and action were explored in endometrial tumors using public transcriptomic datasets. Results: We discovered that within endometrial tumors, the formation of 11-oxyandrogens does not occur from classic androgen precursors. However, we observed distinct regulatory mechanisms at a pre-receptor level in normal endometrium compared to cancerous tissue, and between low- and high-grade tumors. Specifically, in vitro models of low-grade EC formed higher levels of bioactive 11-keto-testosterone from 11-oxyandrogen precursors compared to models of noncancerous endometrium and high-grade, TP53-mutated EC. Moreover, the potent androgen, DHT and its 11-keto homologue induced mild transcriptomic effects on androgen receptor (AR)-expressing EC model, Ishikawa. Finally, using public transcriptomic datasets, we found HSD11B2 and SRD5A2, coding for key enzymes in steroid metabolism, to be associated with better disease-specific survival, whereas higher intra-tumoral AR expression correlated with lower recurrence in TP53-wt tumors. Conclusions: The intra-tumoral metabolism of 11-oxyandrogen precursors is characteristic for low-grade EC of non-TP53-alt molecular subtypes. Our findings support further exploration of circulating 11-oxyandrogens as prognostic biomarkers in EC.

overall_design: RNA-seq profiling of wild type Ishikawaa and RL95-2 cells after incubation with classic androgens (10 nM dihydrotestosterone) and 11-oxyandrogens (10 nM 11-keto-dihydrotestosterone) for 48h.

first: Lea

last: Šturm

first: Tea

last: L. Rižner


title: Targeting c-Jun orchestrates heat stroke induced myocardial injury and reveals its biomarker potential

city: chongqing

first: Fating

last: Zhou

state: chongqing

address: No. 1 Jiankang Road, Yuzhong District

department: Department of Emergency Medicine, Chongqing Emergency Medical Center

country: China

institute: Chongqing University Central Hospital

summary: These experiments aim to detect changes in the transcript (mRNA) of cardiac tissue when animals are exposed to high temperatures and heat stroke occurs due to the increase in environmental temperature. The research objectives include: 1) detecting changes in transcripts (mRNA) of heart tissue during heat stroke caused by elevated environmental temperatures; 2) Detecting transcripts that can serve as biomarkers for heat stroke induced myocardial injury.

overall_design: This study used 6–8 weeks C57BL/6N male mice (body weight: 20–25 g). All mice were acclimated for 1 week under standard housing conditions: 22–25°C with a 12-hour light/dark cycle, and free access to food and water.The sham group was maintained in a normal environment (22–25°C, 60–65% humidity) with fasting and water deprivation. The HS group was exposed to high temperature intervention in a climate controlled chamber, with the temperature set to 40±0.5°C and humidity maintained at 60–65%. During this period, the mice were fasted and water-deprived. Rectal temperature was measured every 30 minutes using a rectal thermometer until the core body temperature reached 42°C, at which point the mice were immediately transferred to a recovery environment (22–25°C, 60–65% humidity).After confirming the successful modeling, we collected mouse heart tissue for further experiments.


title: Expression of IMPACT curtails metabolic plasticity and augments NK cell killing to abrogate metastatic growth [RNA-Seq 2]

status: Public on Jul 25 2025

city: Bethesda

first: Jonathan

last: Hernandez

state: MD

address: Building 37

country: USA

institute: NCI/NIH

summary: To form overt metastases, disseminated tumor cells must simultaneously acquire nutrients, circumvent oxidative stress, and evade organ-specific innate immune surveillance upon arrival. Given the propensity of aggressive epithelial tumors to form hepatic metastases, we performed an in vivo cDNA screen using the mouse liver and KRASG12D/TP53R273H pancreatic cells to identify the RNA binding protein general control of amino acid synthesis 1-like 1 (GCN1) as integral component of hepatic outgrowth. RNAi experiments reveal that GCN1 triggers the integrated stress response (ISR) to activate serine, folate, and methionine biosynthetic pathways together with amino acid transporters, which act in concert to facilitate acquisition of critical metabolites and to restore redox homeostasis. Alongside activation of the ISR, we found that GCN1 also functions in the nucleus where it interacts with an RNA binding protein (HNRNPK) to suppress the expression of MHC-I, antigen-presentation pathway molecules, and natural killer (NK) ligands. Intriguingly, we identified IMPACT as an endogenous competitive inhibitor of GCN1 that blocks both ISR-dependent metabolic control and disrupts HNRNPK interaction. In doing so, IMPACT enhances tumor immunogenicity to unleash robust NK cell killing, in addition to sensitizing metastatic tumor cells to immune checkpoint blockade (ICB). Analysis of patient tumors demonstrates that elevated expression of GCN1 and HNRNPK with concomitant loss of IMPACT correlates with poor immunogenicity, aggressive behavior, and abbreviated survival. These studies provide novel insights linking tumor metabolism, immunity, and metastasis.

overall_design: KPC177669 cells with and without GCN1 knockdown were grown in DMEM containing either 4mM or 0pt5mM Glutamine for 24 hr and RNA isolated from the cells were subjected to bulk RNAseq.

first: Surajit

last: Sinha

first: Vishal

last: Koparde


title: DDX6 undergoes phase separation to modulate metabolic plasticity and drug resistance in AML

status: Public on Jul 27 2025

city: Duarte

first: Rui

last: Su

state: CA

address: 1500 E Duarte Rd

institute: City of Hope

summary: DDX6 is a member of the DEAD-box helicase and it is highly expressed in acute myeloid leukemia (AML). The Knockout (KO) of DDX6 in AML cells significantly suppressed their growth, reduced their mitochondrial oxidative phosphorylation (OXPHOS) in vitro, and substantially delayed leukemogenesis in vivo. To delineate the molecular mechanism through which DDX6 exerts its biological functions in AML, we conducted transcriptome-wide RNA sequencing with Mono-mac-6 AML cells following DDX6 KO.

overall_design: We introduced the single-guide RNAs (sgRNAs) targeting DDX6 (sgDDX6-1 and sgDDX6-2) or the control sgRNA (sgNS) into Cas9 single-clone of Mono-mac-6 AML cells via lentivirus transduction. The transduction-positive AML cells were selected with blasticidin (10 μg/ml; Cat #: ant-bl-1, InvivoGen) and hygromycin B (200 μg/ml; Cat #: ant-hg-5, InvivoGen) for 1-2 weeks. DDX6 KO efficacy was confirmed by Western blot. Then, the total RNAs were extracted from each group with QIAzol and the poly(A)+ RNAs were enriched from total RNAs for library construction and sequencing. For each group, we included 2 replicates.

first: Lei

last: Dong

first: Hongjie

last: Bi


title: Differential infection tolerance mediates sex-biased illness severity in sepsis

status: Public on Jul 28 2025

city: Calgary

first: Braedon

last: McDonald

state: Alberta

address: 2500 University Drive NW

country: Canada

institute: University of Calgary

summary: Sepsis impacts males and females differently.  Males have higher incidence, illness severity and mortality in sepsis than females.  In this study, we use mouse models of fecal-induced peritonitis (FIP) to study sex disparities in sepsis.  Male mice show higher illness severity, physiological derangement and end-organ dysfunction compared to females.  Sex-biased outcome was driven by gonadal sex but not chromosome-linked gene effects.  The results of this study indicate that male-biased sepsis severity is driven by impaired infection tolerance in males due to sex-biased mechanisms of mitochondrial function.  We did not find differences in infection resistance or canonical immune/inflammatory pathways between males and female mice.  Here we performed RNA-sequencing on mouse liver hepatocytes of uninfected and septic males and females.

overall_design: RNA-seq profiling of hepatocytes from SPF C56/Bl6 mice with induced sepsis or controls.

first: Breena

last: Dobson

first: Kathryn

last: Strayer

first: Ayesha

last: Wijesinghe

first: Jared

last: Schlechte

first: Diana

last: Changirwa

first: Nicole

middle: A

last: Cho

first: Ian-ling

last: Yu


title: Expression data from RH30 IκBα SR cells and RH30 IkBa SR MyoD Crispr cells

city: Charleston

first: Denis

middle: C

last: Guttridge

state: SC

address: 173 Ashley Ave

department: Pediatrics

institute: Medical University of South Carolina

summary: Classical NF-κB activity can be inhibited by overexpression of the IκBα super repressor (SR). To determine the role of MyoD in rhabdomyosarcoma cells with NF-kB inhibited, ablated MyoD expression with CRISPR/cas9 editing and clonal selection of RH30-SR cell lines to compare differences in expression following deletion

overall_design:
RH30-SR cells were used as a control compared to RH30-SR MyoD CRISPR cells
Triplicates of each group were cultured. Total RNA was isolated by Trizol extractions (Invitrogen, Carlsbad, CA). Analysis used Affymetrix Human Transcriptome 2.0 Array

first: Alexander

last: Oles

first: Peter


title: KRAS-mediated upregulation of CIP2A promotes suppression of PP2A-B56a to initiate pancreatic cancer development [RNA-Seq]

city: West Lafayette

first: Brittany

middle: L.

last: Allen-Petersen

state: IN

address: 201 S. University St., HANS 215

institute: Purdue University

summary: Oncogenic mutations in KRAS are present in approximately 95% of patients diagnosed with pancreatic ductal adenocarcinoma (PDAC) and are considered the initiating event during the development of pancreatic intraepithelial neoplasia (PanIN) precursor lesions. While it is well established that KRAS mutations can drive the initiation of pancreatic oncogenesis, the effects of oncogenic KRAS signaling on regulation of phosphatases during this process is not fully appreciated. Protein Phosphatase 2A (PP2A) has been implicated in suppressing KRAS-driven cellular transformation. However, low PP2A activity is observed in PDAC cells compared to non-transformed cells, suggesting that suppression of PP2A activity is an important step in the overall development of PDAC. In the current study, we demonstrate that KRASG12D induces the expression of both Cancerous Inhibitor of PP2A (CIP2A), an endogenous inhibitor of PP2A activity, and the PP2A target, c-MYC. Consistent with these findings, KRASG12D sequestered the specific PP2A subunit responsible for c-MYC degradation, B56a, away from the active PP2A holoenzyme in a CIP2A-dependent manner. During PDAC initiation in vivo, knockout of B56a promoted KRASG12D tumorigenesis by accelerating acinar-to-ductal metaplasia (ADM) and the formation of PanIN lesions. The process of ADM was attenuated ex vivo in response to pharmacological re-activation of PP2A utilizing direct small molecule activators of PP2A (SMAPs). Together, our results suggest that suppression of PP2A-B56a through KRAS signaling can promote Myc-driven initiation of pancreatic tumorigenesis.

overall_design: 5-6W old PDX1-Cre; LSL-KRASG12D (KC) mice or KC mice with B56a loss (KCB) were used for experiment. Pancreata were harvested and then isolated using the Fleming-Martinez and Storz JOVE 2019 protocol. Isolated acinar clusters were plated in a collagen matrix and cultured at 37*C and 5% O2 for 24, 48, or 72H. Structures were digested out of collagen using collagenase, washed in PBS, and then resulting cell pellets after final centrifgation were resuspended in 10%DMSO/90%FBS and stored at -80*C until used for ATAC-seq processing.

first: Samantha

middle: L

last: Tinsley

first: Alisha

last: Dhiman

first: Emily

last: Dykhuizen


title: Unraveling Resistance Mechanisms to the Novel Nucleoside Analog RX-3117 in lung cancer: Insights into DNA Repair, Cell Cycle Dysregulation and Targeting PKMYT1 for Improved Therapy

city: Amsterdam

first: Elisa

last: Giovannetti

address: De Boelelaan 1117

country: Netherlands

institute: Amsterdam University Medical Center

summary: Background. Nucleoside analogues are crucial in treating non-small cell lung cancer (NSCLC), but resistance hampers patient outcomes. RX-3117—a cytidine analogue— shows promise in gemcitabine-resistant cancers, yet mechanisms underlying acquired resistance to this drug remain unexplored. This study includes a comprehensive investigation into RX-3117 resistance mechanisms by leveraging new preclinical models and cutting-edge genomic tools, including a genome-wide CRISPR-Cas9 knockout screen and transcriptomics. Methods. NSCLC cell lines A549 and SW1573 were exposed to stepwise increasing concentrations of RX-3117 to establish stable resistant subclones, confirmed by SRB and clonogenic assays. Intracellular RX-3117 nucleotide levels were measured via LC/MS-MS, prompting the evaluation and modulation of the expression of key metabolic enzymes by Western blot and siRNA. A CRISPR-Cas9 screen identified genes whose loss increased RX- 3117 sensitivity, while RNA-sequencing with differential expression analyses revealed resistance-related pathways, further investigated through cell cycle distribution, knock-out, and ELISA assays. Results. Resistant clones exhibited decreased accumulation of RX-3117 nucleotides, which however, was not associated to reduced expression of activation enzymes (UCK2, UMPK, CMPK, NME1/NDPK, RR1 and RR2). Instead, increased expression was observed in certain DNA repair and deactivation enzymes (NT5C3) but pharmacological inhibition and silencing of the latter did not circumvent resistance. Remarkably, a comprehensive approach with CRISPR-Cas9 screen highlighted DNA-repair and cell cycle determinants as key sensitizing genes. XL-PCR and RNA-sequencing confirmed aberrations in DNA-repair and pathways involved in cell cycle regulation. Knock-out and pharmacological inhibition validated the role of PKMYT1, a protein kinase involved in G2/M transition and genomic stability. RX-3117- resistant A549 cells showed enhanced sensitivity to the PKMYT1 inhibitor lunresertib and its synergism with RX-3117, suggesting further studies, especially in patients with high PKMYT1 expression who have significantly shorter survival rates, as observed in public databases and validated in an internal cohort of NSCLC patients. Conclusion. By integrating CRISPR-Cas9 technology with functional assays and transcriptomics, our study established a framework for decoding resistance mechanisms and highlights potential therapeutic strategies to enhance RX-3117 efficacy in NSCLC. We demonstrated for the first time that aberrant DNA repair and cell cycle dysregulation led resistance, identifying PKMYT1 as a promising target.

overall_design: RNA-seq profiling of A549/H460/SW1573 cells and their RX-3117 resistance derivatives.

first: Mahrou

last: Vahabi

first: Geng

last: Xu

first: Dzjemma

last: Sarkisjan

first: Btissame

last: El Hassouni

first: Giulia

last: Mantini

first: Valentina

last: Donati

first: Bing

last: Wang

last: Lencioni

first: Richard

last: J. Honeywell

first: Dongmei

last: Deng

first: Sabrina

last: Strano

first: Godefridus

last: J. Peters

first: Giovanni

last: Blandino


title: IFNG production by self-reactive CD4 T cells drives the adrenal autoimmune pathology in the mouse model of Addison’s disease

city: Prague

first: Juraj

last: Michalik

address: Vídeňská 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the Czech Academy of Sciences

summary: Autoimmune Addison’s disease (AD) is a rare, life-threatening endocrine disorder caused by immune-mediated destruction of the adrenal cortex. AD frequently occurs in patients with APS-1, a monogenic autoimmune syndrome caused by AIRE deficiency. The pathogenesis of AD remains poorly understood  due to the lack of suitable animal models. Here, we establish a mouse model of autoimmune adrenalitis by targeting the adrenal self-antigen CYP11A1. Immunization with CYP11A1-derived peptides elicits clonal expansion of CYP11A1-specific clones and the adrenal infiltration of CD4+ and CD8⁺ T cells and myeloid cells. Inflammation progresses to granulomatous lesions and, in Aire-deficient mice, culminates in adrenal insufficiency. A modified model using adoptive transfer of polyclonal, CYP11A1-stimulated CD4⁺ T cells into Rag2- or Cd3e-deficient hosts accelerates adrenal dysfunction and does not require Aire-deficiency. In contrast, IFNG-deficient CD4⁺ T cells induce only mild granulomatous inflammation and fail to cause overt adrenal insufficiency. These findings establish a tractable mouse model for dissecting AD pathogenesis and identify CD4⁺ T cell–derived IFNG as a key effector of adrenal autoimmunity, providing a preclinical platform for testing targeted immunotherapies.

overall_design: The samples from spleen and adrenals of untreated samples and samples treated by CYP11A1 peptide of C57BL6/J mice.

first: Arina

last: Andreyeva

first: Veronika

last: Cimermanova

last: Niederlova

first: Ondrej

last: Stepanek

first: Ales

last: Neuwirth


title: Chromatin status of rhabdomyosarcoma (RMS) cell line RH30 in repsonse to MyoD CRISPR/Cas9 deletion [RMS ATAC-seq]

first: Denis

last: Guttridge

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To study the role of MyoD in RMS biology, we examined chromatin status changes in the absence of MyoD by CRISPR/Cas9 targeted gene editing

overall_design: Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) in rhabdomyosarcoma (RMS) cell line RH30 following the CRISPR/Ca9 mediated ablation of MyoD expression compared to cells transduced with sgRNA scramble controls

first: Alexander

last: Oles


title: cGAS-STING activation promotes innate and adaptive immunity crosstalk and enhances anti-tumor response

city: Shanghai

first: Zhichao

last: Ai

state: Shanghai

address: 371 Lishizhen Road

department: Oncology

institute: China Innovation Center of Roche (CICoR)

summary: The cancer-immunity cycle is regulated by a series of stimulatory and inhibitory factors. The Stimulator of Interferon Genes (STING) pathway, a key stimulator of type I interferon production, bridges innate and adaptive immunity to promote anti-tumor responses. Using a syngeneic pancreatic tumor model, we characterized the single-cell landscape changes induced by STING stimulation. Our findings revealed that STING agonist treatment reprograms transcription across multiple cell lineages, boosting innate immune responses and lymphocyte activation, thereby enhancing tumor killing. Single-cell transcriptome sequencing identified significant increases in monocytes, neutrophils, macrophages, and CD8 T cells, indicating augmented tumor inflammation. Differential gene expression analysis highlighted upregulated genes related to immune cell effector mechanisms and antigen presentation. Functional assays confirmed that STING activation enhances T cell-mediated tumor killing through myeloid cell activation. These results underscore the potential of STING agonists in reprogramming the tumor microenvironment to potentiate anti-tumor immunity, although clinical translation remains challenging due to pharmacokinetic limitations and potential systemic toxicity. Further research is needed to optimize STING agonist delivery and dosage for effective cancer immunotherapy.

overall_design: There are 4 mouse samples, consisting of tumour samples collected from tumour bearing mouse treated with vehicle or STING agonist EX-AC01, with whole tissue single cell sequencing.

first: Zhichao(Eric)


title: MyoD is Essential in Rhabdomyosarcoma by Promoting Survival Through Differentiation and CYLD

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

overall_design: Refer to individual Series


title: Identification of double-stranded RNAs modulated by ADAR1

city: Fort Collins

first: Cali

middle: Madison

last: McEntee

state: CO

address: 910 Moby Dr

department: Health and Exercise Science

institute: Colorado State University

summary: Endogenous double-stranded RNA (dsRNA) triggers pro-inflammatory signaling and has been shown to accumulate in Alzheimer’s disease (AD), but the origins of this dsRNA are incompletely understood. Transposable elements (TEs), which are non-coding DNA sequences capable of forming dsRNA, are a potential endogenous source of dsRNA in AD. We generated dsRNA immunoprecipitation (J2 dsRNA antibody) data on astrocytes treated with or without a siRNA to knock down the dsRNA editing enzyme ADAR1. We analyzed TE transcripts enriched in dsRNA pools when ADAR1 was knocked down, and we identified putative dsRNA-prone TEs, which were also present in secondary analyses of datasets profiling RNAs bound to PKR, MDA5, and the p110 isoform of ADAR1.

overall_design: RNA-seq of J2 immunoprecipitated RNAs (RIP), and control RNAs (input), in ADAR1 and scramble siRNA treated primary human astrocytes

middle: M

first: Thomas

middle: J

last: LaRocca


title: Downregulation of NF-κB and NLRP3 in aging wildtype and amyloid β transgenic mice

summary: Neuroinflammation is a key component of Alzheimer's disease (AD), and it may be driven by the activation of NFκB and NLRP3 signaling pathways. AD pathology, like amyloid-β, may exacerbate the activation of these pathways. We used a nucleic acid therapeutic (nanoligomer) cocktail targeting NFκB and NLRP3 to reduce inflamamtory signaling in aged wildtype mice and a transgenic mouse model of amyloid-β pathology (APP/PS1). Short-term (3 days) treatment reversed age- and amyloid-β-related gene sigantures, supporting the idea that this nanoligomer cocktail may have the potential to improve AD-related neuroinflammation and cognitive dysfunction.

overall_design: RNA-seq data was generated from hippocampus samples of young C57BL/6, old C57BL/6, old nanoligomer treated C57BL/6, APP/PS1, APP/PS1 nanoligomer treated, and "non-carrier" littermate controls

first: Devin

last: Wahl


title: Allosteric and Energetic Remodeling by Protein Domain Extensions

city: Barcelona

first: cristina

last: Hidalgo-Carcedo

address: Dr. Aiguader 88

country: Spain

institute: CRG

summary: Many functions of proteins are performed by independently folding structural units called domains. The structures of domains are conserved during evolution but they are not identical. For example, the >270 human PDZ domains vary in the number of secondary structure elements and in the length of loops. An important but largely unexplored question is the impact of these extensions on protein energy landscapes: beyond any immediate functional effects, do extensions also alter the consequences of perturbations elsewhere in the domain, altering the potential for regulation and evolvability? Here we perform massively parallel energetic measurements on a model human PDZ domain to directly and comprehensively answer this question. In total we quantify the binding to a ligand and abundance of ~190,000 protein variants to quantify free energy changes for mutations throughout the canonical domain fold and ~7,000 energetic couplings between these mutations and the two domain extensions, both alone and in combination. We find that both extensions—one structured and one more dynamic—substantially and specifically re-shape the energy landscape of the domain, with the removal of an ɑ-helix altering the energetic consequences of 424 mutations in 54 sites on fold stability and 420 mutations in 56 sites on binding to a ligand. These changes to the energy landscape alter the effects of 330 allosteric mutations, including at solvent-accessible surface sites. Extending or pruning the domain therefore reshapes its energetic and allosteric landscape, adding and removing opportunities for the allosteric control of protein function.

overall_design: DNA-seq of PCR amplicon; 3 biological replicates from Saccharmocyes cerevisiae

first: Cristina

first: Andre

last: Faure

first: Aina

last: Martí-Aranda

first: Taraneh

last: Zarin

first: Ben

last: Lehner


title: SOX2 utilizes FOXA1 as a heteromeric transcriptional partner to drive proliferation in therapy-resistant prostate cancer

city: Maywood

first: Steven

last: Kregel

state: IL

address: 2160 S. First Avenue

department: Cancer Biology

institute: Loyola University Chicago

summary: Treatment options and diagnostic outlook for men with advanced, therapy resistant prostate cancer (PCa) are extremely poor; this is primarily due to the common lack of durable response to androgen receptor (AR) targeted therapies and phenotypic transdifferentiation into a particularly lethal subtype known as neuroendocrine prostate cancer (NEPC). In this study, we mechanistically determine that SOX2 (a transcription factor originally repressed by AR) physically binds and acts in a concerted manner with FOXA1 (a key AR pioneering cofactor) to regulate a subset of genes which promote cell cycle progression and lineage plasticity in AR-refractory prostate cancers. Our findings assert the SOX2/FOXA1 interaction as an important mediator of resistance to AR-targeted therapy and a driver of NEPC and lineage plasticity; their coordinated action and downstream signaling offers a potential novel therapeutic opportunity in late-stage PCa.

overall_design: ChIP-sequencing experiemnts in CWR-R1, NCI-H660, NCCIT, and PrEC for AR, FOXA1, and SOX2 proteins. In CWR-R1 we performed ChIP-seq under whole media, 20 uM Enzalutamide, CSS, and 1nM R1881

first: Phoenix

last: John T

first: Kregel

last: Steven


title: Somatic IRF4 mutations drive disease-defining expression signatures and thymic tropism in primary mediastinal large B-cell lymphoma [ATAC-seq]

city: Vancouver

first: Gerben

last: Duns

state: BC

address: 675 West 10th Ave

department: Lymphoid Cancer Research

institute: BC Cancer

summary: Disease-defining signatures in lymphomas, driven by intricate molecular mechanisms, have advanced molecular taxonomies, refined classification, and may guide clinical management; however, the role of these signatures in driving disease hallmarks including subtype-specific organotropism remains largely unexplored. Primary mediastinal large B-cell lymphoma (PMBCL) is an exemplary lymphoma characterized by disease manifestations in the thymic niche, unique genetic alterations and immune escape. Here, we identified IRF4-C99R mutations uniquely occurring in PMBCL through mutational meta-analysis of large-scale datasets. Our functional studies, integrating multi-omics approaches with genome editing in PMBCL cells, revealed that IRF4-C99R contributes to a differentiation block phenotype. Specifically, we showed that IRF4-C99R reduces its binding to the ISRE motif within PRDM1, which encodes a key transcriptional regulator of B-cell differentiation, resulting in decreased PRDM1 expression. Additionally, IRF4-C99R suppresses TNIK, a key IFNγ pathway regulator, by impairing ISRE motif binding, thereby reducing IFNγ signaling and increasing thymus and activation-regulated chemokine (TARC) expression, which drives TARC-mediated chemotaxis of T regulatory cells. We also revealed that IRF4-C99R upregulates Ephrin Type-B Receptor 1 (EPHB1) through non-canonical AICE motif binding, and showed that overexpression of EPHB1 in an immunocompetent syngeneic lymphoma model influenced organotropism to favor thymic localization, without affecting tumor burden in other organs. IRF4-C99R mutation-induced phenotypes were validated in primary PMBCL tissues using single-nuclei RNA sequencing, confirming that the molecular mechanisms observed in vitro align with the pathophysiology of PMBCL in patients. Together, these findings demonstrate how a single genetic mutation orchestrates the coordinated regulation of hallmark traits including thymus-specific tropism in PMBCL.

overall_design: Bulk ATAC-seq profiling of IRF4-C99R-mutated  and IRF4-WT PMBCL-derived cell line Karpas-1106p.

first: Shinya

last: Rai

first: Fabian

last: Frontzek

first: Jasper

last: Wong

first: Yifan

last: Yin

first: Michael

last: Li

first: Makoto

last: Kishida

first: Manabu

last: Fujisawa

first: Shannon

last: Healy

first: Elena

last: Vigano

first: Aixian

last: Jiang

first: Bruce

last: Woolcock

first: Adele

last: Telenius

first: Susana

last: Ben-Neriah

first: Barbara

last: Meissner

first: Merrill

last: Boyle

first: Hisae

last: Nakamura

first: Luke

last: O'Brien

first: Claudia

last: Cassidy

first: Andrew

last: Lytle

first: Pedro

last: Farinha

first: Graham

last: Slack

first: Laura

last: Hilton

first: Ryan

last: Morin

first: Leandro

last: Venturutti

first: Tomohiro

last: Aoki

first: Nicole

last: Wretham

first: Jonathan

last: Bush

last: Evgin

first: Kerry

last: Savage

first: David

last: Scott

first: Christian

last: Steidl


title: Expression of IMPACT curtails metabolic plasticity and augments NK cell killing to abrogate metastatic growth

last: Hernandez

overall_design: RNA isolated from human pancreatic KLM1 control and GCN1 knockdown cells were subjected to RNA sequencing.

first: Surajit

last: Sinha

first: Vishal

last: Koparde


title: TrAEL-seq with WRN inhibitors in sensitive and resistant cells

city: Cambridge

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

summary: Werner helicase inhibitors (WRNi) show promise for treating patients with microsatellite-unstable (MSI) tumors characterized by defective DNA mismatch repair. Multiple WRNi recently entered Phase 1 clinical trials. Here, we investigate the impact of cancer cell evolutionary adaptation on WRN pharmacological inhibition with implications for understanding drug selectivity and potential clinical resistance.  Coupling genome-wide CRISPR screens with WRN gene knockout, no suppressors of WRN dependency were identified, underscoring WRN’s essential non-redundant function in MSI cells. Pharmacogenomic screens pinpointed modulators of WRNi sensitivity, including SMARCAL1, linking WRN-MSI synthetic lethality with chromatin remodelling and DNA repair pathways. Semi-saturation mutagenesis of WRN and prolonged drug treatment identified on-target WRN mutations driving spontaneous secondary resistance to multiple WRNi in vitro and in vivo. Specific resistance mutations preserve sensitivity to alternative WRNi, whereas others induce cross-resistance. Our work guides next-generation strategies for targeting MSI cancers, enabling cross-resistance studies to evaluate current and novel WRNi efficacy and informing future clinical trial design.

overall_design: We employed Transferase-Activated End Ligation sequencing (TrAEL-seq), a method that captures single-stranded DNA 3′ ends genome-wide and with base pair resolution, to identify the genomic sites of DNA double-strand breaks (DSBs) in MSI cells treated with WRN inhibitors. We used SW48 cells with or without SMARCAL1, which confers resistance to WRN inhibitors

first: Kieron

last: May

first: Gabriele

last: Picco

first: Angham

last: Al Saedi

first: Shriram

last: Bhosle

first: Samantha

last: Walker

first: Mathew

last: Garnet

last: Houseley


title: Frontal cortex pyramidal neuron expression profiles differentiate the prodromal stage from progressive degeneration across the Alzheimer’s disease spectrum

city: Orangeburg

first: Stephen

middle: D.

last: Ginsberg

state: New York

address: 140 Old Orangeburg Road

department: Centre for Dementia Research

institute: Research Foundation for Mental Hygiene

summary: Alzheimer's disease (AD) is an irreversible, progressive neurodegenerative disorder affecting an estimated 6.9 million Americans. There is no current treatment to prevent the onset or progression of dementia. Therefore, it is imperative to identify molecular and cellular mechanism(s) underlying the pathobiology of AD onset and progression. We employed laser capture microdissection (LCM) to isolate layer III pyramidal neurons from postmortem human prefrontal cortex Brodmann area 9 (BA9) tissue. Single population RNA-sequencing was conducted utilizing tissue from subjects across the AD spectrum, including individuals with no cognitive impairment (NCI), mild cognitive impairment (MCI), and AD. Differentially expressed genes (DEGs) were compared and contrasted across groups. The number of DEGs increased from Prodromal (MCI versus NCI; 1,306 DEGs) to Progression (AD versus MCI; 2,505 DEGs) to Frank AD (AD versus NCI; 3,259 DEGs). Bioinformatic inquiry revealed alterations in key pathways during disease progression including oxidative phosphorylation, mitochondrial dysfunction, and immune responses suggesting dysfunctional bioenergetics in vulnerable corticocortical projection neurons. The majority of DEGs and pathways shared between Prodromal and Progression exhibited a change in the direction of dysregulation, termed ‘directionally divergent’. In contrast, the majority of common DEGs and pathways between the later stage Progression and Frank AD remained in the same direction, termed ‘directionally convergent’. Candidate genes and pathways were identified that demarcate early-stage AD onset (Prodromal) differentially from AD progression (Progression and Frank AD) providing a roadmap to study cortical cellular vulnerability and key targets for intervention at early stages of AD.

overall_design: BA9 tissue from NCI, MCI, and AD subjects was obtained. Layer III excitatory pyramidal neurons (600-800 cells) were isolated via laser capture microdissection. RNA was isolated, converted to a cDNA library, and submitted for RNA-sequencing. RNA-sequences were analysed and differentially expressed genes (DEGs) were identified.

first: Amanda

last: Labuza

first: Melissa

last: Alldred

first: Harshitha

last: Pidikiti

first: Michael

middle: H

last: Malek-Ahmadi

first: Adriana

last: Heguy

first: Paul

middle: D

last: Coleman

first: Gabriela

last: Chiosis

first: Elliot

last: Mufson


title: Somatic IRF4 mutations drive disease-defining expression signatures and thymic tropism in primary mediastinal large B-cell lymphoma [RNA-seq]

first: Gerben

last: Duns

overall_design: RNA-seq profiling of DLBCL-derived cell line DOHH2 ectopically expressing WT IRF4 or IRF4-C99R, and IRF4-C99R-mutated PMBCL-derived cell lines U-2940 and Karpas-1106p, untreated or stimulated with Ephrin-B2.

first: Shinya

last: Rai

first: Fabian

last: Frontzek

first: Jasper

last: Wong

first: Yifan

last: Yin

last: Li

first: Makoto

last: Kishida

first: Manabu

last: Fujisawa

first: Shannon

last: Healy

first: Elena

last: Vigano

first: Aixian

last: Jiang

first: Bruce

last: Woolcock

first: Adele

last: Telenius

first: Susana

last: Ben-Neriah

first: Barbara

last: Meissner

first: Merrill

last: Boyle

first: Hisae

last: Nakamura

first: Luke

last: O'Brien

first: Claudia

last: Cassidy

first: Andrew

last: Lytle

first: Pedro

last: Farinha

first: Graham

last: Slack

first: Laura

last: Hilton

first: Ryan

last: Morin

first: Leandro

last: Venturutti

first: Tomohiro

last: Aoki

first: Nicole

last: Wretham

first: Jonathan

last: Bush

last: Evgin

first: Kerry

last: Savage

first: David

last: Scott

first: Christian

last: Steidl


title: Effect of exposing worms to FUDR on gene expression at the L4 stage

city: Riverside

first: Anusha

last: Iyengar

address: 900 University Ave

department: Biochemistry

institute: University of California, Riverside

summary: FUDR is a well-studied anti-cancer agent.  It is known to inhibit the enzyme thymidylate synthetase, which ultimately interferes with DNA synthesis.  In C. elegans, FUDR is used in longevity experiments to induce sterility and avoid transferring worms often.  The effect of FUDR on the lifespan of wild-type worms is negligible, however certain genotypes show an extension of lifespan when exposed to FUDR. The mechanisms behind this phenomenon is unclear whether FUDR acts on DNA or RNA.  Our data provides the gene expression profile characteristic of wild-type worms exposed to FUDR in comparison to worms grown on regular OP50-seeded plates.

overall_design: To investigate the transcriptional changes that occur when worms are exposed to 50µM FUDR compared to worms on regular OP50-seeded plates.  We then performed RNA-seq on whole worms at the L4 stage in triplicate.

first: Adam

last: Norris


title: Enhanced Media Optimize Bovine Myogenesis in 2D and 3D Models for Cultivated Meat Applications [in vivo scRNA-Seq]

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

summary: Livestock farming and conventional meat production pose significant environmental, health, and animal welfare challenges. In seeking sustainable alternative solutions, cultivated meat technology typically utilizes differentiation of myogenic progenitor cells (MPCs) into muscle cells for in vitro meat production. However, understanding the molecular determinants governing MPC differentiation into muscle cells, and the potential enhancement of this process through modulation of signaling pathways, remains limited. Herein, we characterized the molecular landscape associated with bovine MPC differentiation in vitro by employing multiomics, and explored its augmentation by small molecules, together leading to identification of media that enhanced myogenic differentiation compared with conventional methods in both 2D cultures and tissue‐engineered 3D skeletal muscle constructs. Through bulk and single‐cell transcriptomics and proteomics, we compared conventional and enhanced differentiation media, demonstrating that the enhanced media gave rise to unique progenitor‐like cell populations, while simultaneously promoting differentiation into myocytes and contractile myotubes expressing a wide array of myogenic markers that more closely resemble bovine muscle cells in vivo. The improved method for promoting myogenic differentiation in 2D and 3D formats, together with the corresponding molecular roadmap, may prove valuable for cultivated meat applications.

overall_design: In vivo bovine skeletal muscle tissue from two muscle types - M. abdominis and M. Masseter - were mechanically minced and subjected to enzymatic digestion to dissociate individual cells. The resulting cell suspension was then subjected to fluorescence-activated cell sorting (FACS) to isolate viable cells. Cells were then analyzed using scRNA-Seq.

first: Christine Ling Li

last: Trautmann

first: Adhideb

last: Ghosh

first: Kalkan

last: Ali

first: Falko

last: Noé

first: Ori

last: Bar-Nur


title: Gene expression profiles of brain injury at single cell level from aged mice treated with or without microglial replacement

city: Chengdu

first: Xiao-Yi

last: Xiong

address: 37 Shierqiao Road, 610075, Chengdu, China

institute: Chengdu University of Traditional Chinese Medicine

summary: We used single cell RNA sequencing (scRNA-seq) to analysis the gene expression profile of myeloid cells of brain injury influenced by microglial replacement in aged mice.

overall_design: Neural cells and myeloid cells from perihematomal brain tissues of aged intracerebral hemorrhage (ICH) mice treated with or without microglial replacement were analyzed by scRNA-seq.

first: Peng-Fei

last: Wang


title: Immune Landscape of RA from Synovial Biopsy Before and After DMARD Treatment

city: Chicago

first: Deborah

middle: R

last: Winter

address: 240 E. Huron Street, M300

institute: Northwestern University

summary: Synovial biopsy was performed on RA patients with active synovitis prior to starting a new DMARD treatment and 6 weeks following.

overall_design:
Synovial tissue was processed to a single-cell suspension and sorted for live CD45+ immune cells.

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

first: Harris

last: Perlman


title: Aberrant Transitional Alveolar Epithelial Cells Promote Pathogenic Activation of Lung Fibroblasts in Preclinical Fibrosis Modeling (Bulk RNA-Seq)

city: Philadelphia

first: Jeremy

last: Katzen

state: PA

address: 3450 Hamilton Walk, Stemmler Hall 216

institute: University of Pennsylvania Perelman School of Medicine

summary: CD44+ and CD44- negative Alveolar type 2 cells (AT2) represent distinct populations in lung fibrosis. To charecterize these cells, we isolated CD44+/- AT2s from WT mice and from fibrotic Sftpc muant lungs and performd RNA sequencing no these populations

overall_design: To determine the transcriptional distinctions between CD44+ and CD44- alveolar type 2 (AT2) cells during fibrosis we isolated AT2 by FACS from lungs of control (n=4)  and Sftpc mutant lungs (n=4). Lungs were harvested from control and Sftpc mutant lungs, single cells suspension was prepared by mehcanical and enzymatic digetsion.  CD45+ and CD31+ cells were depleted using biotinylated antibodies followed by surface staining with antibody mix to identify CD44+ and CD44- AT2s. AT2 cells were identified as CD45-CD31-Epcam+CD104-CD200hi and then CD44+ or CD44-.

first: Evan

middle: T

last: Hoffman

first: Willy

last: Roque Barboza

first: Luis

last: Rodriguez

first: Rachna

last: Dherwani

first: Kasey

last: Minakin

first: Yaniv

last: Tomer

first: Dakota

last: Jones

first: Aditi

last: Murthy

last: Bennett

first: Ana

last: Nottingham

first: Pushpinder

middle: S

last: Bawa

first: Feiya

first: Apoorva

last: Babu

first: Katrina

last: Chavez

first: Charlotte

last: Cooper

first: Maria

last: Basil

first: Micha

last: Brickman Raredon

first: Darrell

middle: N

last: Kotton

first: Konstantinos-Dionysios

last: Alysandratos


title: Aberrant Transitional Alveolar Epithelial Cells Promote Pathogenic Activation of Lung Fibroblasts in Preclinical Fibrosis Modeling (scRNAseq)

first: Jeremy

last: Katzen

overall_design: To enrich for EPCAM+ cells and mesenchymal cells , a single cell suspension was prepared by physical and enzymatic dissociation (Collagenase, DNase, Dispase) from Sftpc mutation firbosis lungs (n=2) and control lungs (n=2) followed by MACS sorting by LS columns with CD45+ and CD31 cell removal using CD45 and CD31 micobeads followed by EPCAM+ cell enrichment using EPCAM microbeads. CD45-/CD31-/EPCAM- cells were considered lung mesenchymal cells. EPCAM+ and mesenchymal cells were prepared in 50/50 concentration for sequencing.

first: Evan

last: Hoffman

first: Willy

last: Roque Barboza

first: Adam

last: Wang


title: Enhanced Media Optimize Bovine Myogenesis in 2D and 3D Models for Cultivated Meat Applications [in vitro scRNA-Seq]

first: Genome

last: Informatics

overall_design: Analysis of myoblast- and differentiated myoblast- cultures using base media (myoblast medium and iMPC medium) and three different differentiation media (conventional differentiation medium, iFR_hi and iFRC) on a transcriptome level. Cultures were analyzed at day 2 or day 10.

first: Christine

last: Trautmann

first: Adhideb

last: Ghosh

first: Falko

last: Noé

first: Ori

last: Bar-Nur


title: Single-cell transcriptomic analysis reveals that inflammation drives the unfolded protein response during endocrine aging in mice

city: Beijing

first: Ran

last: Wei

address: Haidian District, Beijing Summer Palace Road No. 5

institute: Peking University

summary: The endocrine system severely impacts individual aging. However, its cellular signatures and underlying mechanisms have not been comprehensively elucidated. Here, we present a comprehensive single-cell transcriptomic atlas of six endocrine tissues from young and aged mice. Multiple aging-related pathways are disrupted in endocrine tissues, and the unfolded protein response (UPR) emerged as a key pathway related to endocrine aging. We found significant age-related expansion of exhausted GZMK+CD8+ T cells within endocrine tissues. Additionally, granzyme K (GZMK) signaling enhances the UPR and accelerates cellular senescence through the modulation of MHC-I expression in functional endocrine cells, revealing a novel regulatory axis of aging. Moreover, the inhibition of the GZMK receptor counteracts the UPR and endocrine aging. These findings establish an interplay between inflammation and the UPR in endocrine aging, offering profound insights into the underlying mechanisms of endocrine aging.

overall_design: We isolated the hypothalamus, pituitary glands, thyroid glands, adrenal glands, pancreas islets, and pineal glands from aged mice and young mice.

first: Zhehao

last: Du

first: Wei

last: Tao

first: Chen

last: Zhang


title: Harnessing proximal T cell signaling molecules for enhanced CAR T cell activity

city: New York

first: Caleb

last: Lareau

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

summary: Chimeric antigen receptor (CAR) T cells mediate durable complete responses in patients with certain hematologic malignancies, but antigen downregulation is a common mechanism of resistance. While the native TCR can respond to very low levels of peptide presented in MHC, engineered CARs are incapable of responding to antigen-low targets, likely due to a disorganized immune synapse and poor recruitment of proximal signaling molecules. We developed a platform that endows CARs with the ability to kill antigen-low cancer cells, consisting of a membrane tethered version of the signaling molecule SLP-76 (MT-SLP-76). MT-SLP-76 can be expressed alongside any CAR to lower its threshold for activation and overcomes antigen low escape in multiple xenograft models. While SLP-76 is natively in the cytosol, only the engineered membrane tethered version can adequately amplify CAR signaling, a process that is mediated through recruitment of ITK and PLC1. MT-SLP-76 was designed based on biologic principles to render CAR T cell therapies less susceptible to antigen downregulation and is poised for clinical development to overcome this common mechanism of resistance.

overall_design: Human CAR T cells were co-cultured with and without MTSLP76 engineering. CAR T cells were either left or restimulated and compared against other CARs. Two donors were mixed per run. A CD22-targeted CAR was used for each Experiment

first: Maria

last: Rotiroti

first: Robbie

last: Majzner


title: Single-cell analysis of testicular bacterial microbiome changes during aging and effect on reproductive capacity

city: xuzhou

first: Jianteng

last: zhou

state: JiangSu

address: Tongshan road 209, Xuzhou Medical University, Xuzhou, China

department: College of Life Sciences

institute: Xuzhou Medical University

summary: Recent studies have highlighted connections between bacterial microbiome (BM) of the gut and seminal fluid and male reproductive health. However, knowledge regarding the BM within the testis—the site of spermatogenesis—remains notably limited. Here, we employed INVADEseq, an improved single-cell RNA sequencing technology, to explore the testicular BM in terms of its composition, distribution, age-related changes, host-microbiome interactions and impact on reproductive capacity. Our analyses unveiled a widespread yet sparse distribution of BM across diverse testicular cell types. Notably, we identified significant spatial heterogeneity in BM load, with somatic cells and early-stage germ cells located outside the blood-testis barrier (BTB) exhibiting relatively higher BM abundance. Additionally, we observed an age-dependent increase in BM load, potentially attributable to compromised BTB integrity in aged testes. Functionally, the presence of BM induced distinct transcriptional responses across testicular cell types. Specifically, it enhanced testosterone production in Leydig cells, promoted endocytosis and autophagy functions in M2 macrophages, and reshaped the ligand-receptor interaction network. Collectively, our study presents the first single-cell resolution atlas of host-microbiome interactions in the testis. These findings not only deepen our understanding of testicular microbiome biology but also hold promise for the discovery of novel diagnostic biomarkers and therapeutic targets for BM-related and age-associated male subfertility.

overall_design: C57BL/6 male mice at 5 months (young) and 20 months (older) were used, with 3 biological replicates per group.

last: Zhou

first: Ying

last: Li

first: Tao

last: Zhu

first: Conghui

last: Han

first: Zuobin


title: Efficient mouse embryo models from stem cells for environmental studies

city: Stanford

first: Laura

last: Amaya

address: 269 Campus Drive

institute: Stanford University

summary: Blastoids are stem cell-derived structures that mimic natural blastocysts, including formation of the trophectoderm, epiblast, and primitive endoderm lineages. However, current methods often produce incomplete structures that do not cavitate or form sufficient primitive endoderm. We developed a new approach to enhance blastoid formation by aggregating embryonic stem cells (ESCs) with ESCs transiently expressing Gata4 (iG4-ESCs) to promote the primitive endoderm fate, followed by addition of trophoblast stem cells (TSCs). This method achieved an ~80% efficiency in forming cavitated blastocyst-like structures, termed iG4-blastoids. Single-cell RNA sequencing revealed that iG4-blastoids resemble day 4.5 blastocysts. iG4-blastoids cultured in media lacking FGF4 showed improved specification of the invasive mural trophectoderm. iG4-blastoids underwent post-implantation remodeling, with ~12% forming an egg cylinder-like structure. Notably, blastoid formation was affected by caffeine, alcohol, nicotine, and amino acid levels. Thus, iG4-blastoids are a robust model for screening diverse environmental factors for their consequences on embryogenesis.

overall_design: Blastoids derived from embryonic stem cells were sequenced with Chromium Single Cell Gene Expression.

first: Victoria

last: Jorgensen

first: Min

last: Bao

first: Sergi

last: Junyent


title: Label-free melanoma phenotype classification using AI-based morphological profiling

first: Mitchell

last: Levesque

address: Wagistrasse 18

institute: University of Zurich

summary:
Melanomas are the deadliest skin cancers, in part due to cellular plasticity and heterogeneity. Within tumors, cells coexist in different mutable phenotypes that exhibit differential functional properties and drug responses. The definition of these phenotypic states has been challenging to rigorously define with conventional marker-based methods, and more high-parameter molecular methods are cell-destructive, labor-intensive, and can take days to weeks to obtain a readout. To overcome these technical and practical limitations, we utilized the Deepcell platform to perform real-time classification of unlabeled melanoma cells into Melanocytic and Mesenchymal phenotypes.
We used 19 patient-derived cell lines with known Melanocytic or Mesenchymal transcription scores to develop the ‘Melanoma Phenotype Classifier’ to phenotype melanoma cells based on morphology alone. A Classifier accuracy of >88% was achieved, and morphology analysis of the images revealed distinct morphotypes for each phenotype, highlighting distinct morphological differences. To further link phenotypic state with multi-dimensional morphological profiles, we performed genetic and chemical perturbations known to shift the phenotypic state. The AI Classifier successfully predicted shifts in phenotype driven by the perturbations. These results further demonstrate how phenotype is linked to distinct morphological changes that are detectable by AI. Lastly, we applied the Melanoma Phenotype Classifier to dissociated biopsy samples, which revealed phenotypic heterogeneity that was confirmed by single cell RNASeq.
This work establishes a link between morphology and Melanoma phenotype, and lays the groundwork for the use of morphology as a label-free method of phenotyping viable melanoma cells combined with additional analyses.

overall_design: Cell line samples and dissociated biopsy samples were processed with the Deepcell device and analyzed using scRNA-sequencing

first: Evelyn

last: Lattmann

first: Andreja

last: Jovic

first: Julie

last: Kim

first: Aizhan

last: Tastanova

first: Tiffine

last: Pham

first: Christian

last: Corona

first: Kiran

last: Saini

first: Zhouyang

last: Lian

first: Manisha

last: Ray

first: Vivian

last: Lu

first: Stephane

last: Boutet

middle: P


title: Somatic IRF4 mutations drive disease-defining expression signatures and thymic tropism in primary mediastinal large B-cell lymphoma [ChIP-seq]

first: Gerben

last: Duns

overall_design: Chip-seq profiling of IRF4-C99R-mutated  and IRF4-WT PMBCL-derived cell line Karpas-1106p using anti-IRF4 antibody.

first: Shinya

last: Rai

first: Fabian

last: Frontzek

first: Jasper

last: Wong

first: Yifan

last: Yin

first: Michael

last: Li

first: Makoto

last: Kishida

first: Manabu

last: Fujisawa

first: Shannon

last: Healy

first: Elena

last: Vigano

first: Aixian

last: Jiang

first: Bruce

last: Woolcock

first: Adele

last: Telenius

first: Susana

last: Ben-Neriah

first: Barbara

last: Meissner

first: Merrill

last: Boyle

first: Hisae

last: Nakamura

first: Luke

last: O'Brien

first: Claudia

last: Cassidy

first: Andrew

last: Lytle

first: Pedro

last: Farinha

first: Graham

last: Slack

last: Hilton

first: Ryan

last: Morin

first: Leandro

last: Venturutti

first: Tomohiro

last: Aoki

first: Nicole

last: Wretham

first: Jonathan

last: Bush

last: Evgin

first: Kerry

last: Savage

first: David

last: Scott

last: Steidl


title: Enhanced Media Optimize Bovine Myogenesis in 2D and 3D Models for Cultivated Meat Applications [RNA-Seq]

first: Genome

last: Informatics

overall_design: Analysis of myoblast- and differentiated myoblast- cultures using base media (myoblast medium and iMPC medium) and three different differentiation media (conventional differentiation medium, iFR_hi and iFRC) on a transcriptome level. Cultures were analyzed at day 2 or day 15.

first: Christine

last: Li Trautmann

first: Adhideb

last: Ghosh

first: Falko

last: Noé

first: Ori

last: Bar-Nur


title: H9c2 cells with or without lactate

city: Salt Lake City

first: Jordan

last: Berg

state: UT

address: 15 N Medical Drive East, Rm 5520

institute: University of Utah

summary: H9c2 cardiomyoblast cells grown in DMEM or HPLM in the presence and absence of lactate. 4 unique conditions.

overall_design: H9c2 rat cardiomyoblast cells were grown in either DMEM or HPLM, in the presence or absence of lactate for 24 hours. RNA was then extracted from each condition and sequenced.

first: Ahmad

last: Cluntun

first: Zsanett

last: Buko

first: Jared

last: Rutter


title: Histone deacetylase HDA-5 regulates lipid metabolism through H4K5 and H4K8 acetylation in Caenorhabditis elegans

status: Public on Jul 24 2025

city: kunming

first: meng

last: zhou

state: yunnan

address: tuanjiexiang

institute: Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, China;

summary: To identify genes were involved in hda-5 regulation. The C. elegans N2 were subjected to hda-5 RNAi and empty vector RNAi until reach to adult. Then the worms were collected and washed by M9 buffer for three times following re-suspended in PBS, and frozen immediately in liquid nitrogen for RNA sequencing. RNA sequencing was carried out by Biomarker Technologies (BMK) GmbH (Beijing, China). Total RNA of worms were extracted by using RNeasy Plus Mini Kit (Qiagen) and assessed for quality by NanoDrop, Qubit 2.0 and Agilent 2100. mRNA was enriched via Oligo(dT) magnetic beads, fragmented, and reverse-transcribed to cDNA with random hexamers. After end repair, A-tailing, adapter ligation and PCR amplification, libraries were qualified by Qubit 2.0, Agilent 2100 and Q-PCR, then sequenced on Illumina NovaSeq 6000 (PE150).

overall_design: The C. elegans N2 were subjected to hda-5RNAi and empty vector RNAi until reach to adult. Total RNA from C. elegans was extracted with RNeasy Plus Mini Kit (Qiagen), assessed for quality by NanoDrop, Qubit 2.0 and Agilent 2100. mRNA was enriched via Oligo(dT) magnetic beads, fragmented, and reverse-transcribed to cDNA with random hexamers. After end repair, A-tailing, adapter ligation and PCR amplification, libraries were qualified by Qubit 2.0, Agilent 2100 and Q-PCR, then sequenced on Illumina NovaSeq 6000 (PE150). Raw reads were trimmed with trim_galore, mapped to hg38 using HISAT 2.2.1, and counted in genes by featureCounts. Normalized to CPM, differential expression was analyzed with DESeq2 (≥10 reads in at least one condition; adjusted P<0.01, |log2FC|≥1)

first: Qin-Yi

last: Wu

first: Yi-Cheng

last: Ma

first: Meng

last: Zhou

first: Rui

last: Zhu

first: Cheng-Gang

last: Zou


title: Transcriptomic profiling of day 194 patient-specific pluripotent stem cell-derived alveolar epithelial type 2 cells expressing the SFTPCC121Y mutation and their gene-edited corrected counterparts

city: Boston

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

summary: We performed transcriptomic profiling of cells derived from human induced pluripotent stem cells (iPSCs) using our previously described distal lung directed differentiation protocol to generate alveolar epithelial type 2 cells (iAT2s). We used the SPC8 human iPSC line and specifically the SPC8-ST-Corr (SFTPCtdT/WT) and SPC8-ST-Mut (SFTPCC121Y/tdT) clones containing a SFTPCtdTomato knock-in reporter. SFTPCtdTomato+ cells were sorted on days 45, 87 and 182 of differentiation. iAT2s were single-cell passaged in self-renewing 3D alveolosphere cultures approximately every 10-14 days through day 194. On day 194, all live cells were sorted and encapsulated for scRNA-seq using the 10X Chromium System. We find that a subset of mutant (SFTPCC121Y/tdT) iAT2s develops an aberrant transitional cell state.

overall_design: Global transcriptomic profiling of day 194 patient-specific induced pluripotent stem cell (iPSC)-derived alveolar epithelial type 2 cells (iAT2s) expressing the SFTPCC121Y mutation and their gene-edited corrected counterparts by scRNA-seq

first: Konstantinos-Dionysios

last: Alysandratos

first: Darrell

last: Kotton


title: Enhanced Cell-Cell Contact and Planarian Tissue Extract increase DNA replication and cell viability for neoblast cultivation

city: Hang Zhou

first: Wenya

last: Zhang

address: No. 600 Dunyu Road

institute: Westlake University

summary: The development of an in vitro culture system for planarian neoblasts remains at an early stage. Although modified neoblast enrichment method and basic culture conditions have been established, it is still unclear whether mimicking the in vivo micro- and macro-environments can functionally improve neoblast behavior in vitro. Neoblasts tend to aggregate in culture, but when cultured as aggregates in the U-bottom plate or on feeder layers, they show increased DNA replication, potentially due to improved cell-cell interactions that mimic the in vivo microenvironment. At the macroenvironment level, the addition of planarian extract to the culture medium reduces cell death, increases lipid droplet formation, and decreases the intracellular reactive oxygen species (ROS) levels. An optimized culture condition has thus been established using U-bottom plates supplemented with planarian extract for the first three days, effectively recapitulating aspects of both the in vivo microenvironment and macroenvironment. Although the culture period remains limited, this system enabled gene knockdown via dsRNA in culturing neoblasts. By modulating both micro- and macro-environmental factors, this study provides a foundation for further optimization at the metabolic and genetic levels in subsequent studies.

overall_design: RNA seq profiling of planarian SiRNeoblasts cultured in different test conditions. 5 experiments are included: experiment1,  compare cultured cells in aggregates&non-aggregating cells at2 days, 3 replicates per group; experiment2,  compare SiRNeoblasts cultured in aggrewell & flat conditions at 1 day, 3 replicates per group; experiment3, compare cells without culture and cultured in U-bottom plate & 100Pa PA gel & flat conditions at 1 day & 2 days & 3 days, 3 replicates per group except for PA_3d group (2 replicates); experiment4, compare cells without culture and cultured in HFF1 feeder & MEF feeder & flat conditions at 1 day & 3 days, 3 replicates per group; experiment5, compare cells without culture and cultured in U-bottom plate-extract & U-bottom plate+extract  & flat -extract conditions at 1 day & 3 days & 7 days, 3 replicates per group.

first: Ling

last: Yang

last: Li

first: Kai

last: Lei


title: Defining a NK cell-enriched molecular rejection-like state in lung transplant transbronchial biopsies

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

institute: University of Alberta

summary: In lung transplantation, antibody-mediated rejection (AMR) diagnosed by ISHLT criteria is uncommon compared to other organs, and previous studies failed to find molecular AMR (ABMR) in lung biopsies. However, understanding of ABMR has changed with the recognition that ABMR in kidney transplants is often DSA-negative and associated with NK cell transcripts. After optimizing rejection-selective transcript sets (RSTS) in a training set (n = 488), the resulting algorithms separated an NK cell-enriched rejection-like state (NKRL) from TCMR/Mixed in a test set (n = 488). Applying this approach to all 896 TBBs distinguished three groups - No rejection; TCMR/Mixed; and NKRL. Like TCMR/Mixed, NKRL had increased expression of all-rejection transcripts, but NKRL had increased expression of NK cell transcripts, whereas TCMR/Mixed had increased effector T cell and activated macrophage transcripts. NKRL was usually DSA-negative and not recognized as AMR clinically. TCMR/Mixed was associated with CLAD, reduced FEV1, and short-term graft failure, but NKRL was not. Thus, some lung transplants manifest a molecular state similar to DSA-negative ABMR in kidney and heart transplants, but its clinical significance must be established.

overall_design: We therefore searched for a similar molecular ABMR-like state in transbronchial biopsies (TBBs) using gene expression microarray results from the INTERLUNG study (#NCT02812290).


title: Immune profiling in subclinical secondary dengue-infected cases

city: Paris

first: Sebastien

last: Mella

address: 28 rue du Dr Roux

department: Immunology

country: France

institute: Institut Pasteur

summary: To define adaptive immune signatures associated to protection from hospitalized dengue, we performed in depth immunoprofiling, single cell T cell receptor (TCR) and B cell receptor (BCR) analysis and quantified DENV-specific T cells in Cambodian children with subclinical infection or hospitalized dengue.

overall_design: T and B cells were isolated from PBMC by fluorescence-activated cell sorting (FACS) and analyzed using 10X Genomics scRNA-seq, paired with T cell receptor and B cell receptor repertoire sequencing.

first: Giorgio

last: Gonnella

first: Valentina

last: Libri

first: Emanuele

last: Gioacchino

first: Sébastien

first: Sotheary

last: Sann

first: Sopheak

last: Sorn

first: Sreymom

last: Ken

first: Valerie

last: Seffer

first: Leangyi

last: Heng

first: Chantana

last: Yay

first: Anavaj

last: Sakuntabhai

first: Sowath

last: Ly

first: Philippe

last: Dussart

first: Veasna

last: Duong

first: Milena

last: Hasan

first: Tineke

last: Cantaert


title: Enhanced polyhydroxyalkanoates production from Mixed Microbial Culture through Short Settling Aerobic Dynamic Feeding: improved selection and bulking resilience [18S]

city: Pisa

first: Giulio

last: Petroni

address: Via A. Volta n°4/6

department: Department of Biology

country: Italy

institute: University of Pisa

summary: This study explores the use of short settling times as a strategy to enhance microbial selection and prevent bulking induced by nutrient shortage in an aerobic dynamic feeding (ADF) process using mixed microbial cultures (MMCs) for polyhydroxyalkanoate (PHA) production from fermentation digestate. A 5.0-L aerobic reactor was operated under three conditions: Long Settling (LS, 30 minutes), Short Settling (SS, 10 minutes), and Short Settling under Nutrient Shortage (SS-NS, 10 minutes with reduced nutrient load). Short settling significantly improved biomass settleability, reducing the Sludge Volume Index (SVI) from 126 to 25 mL g⁻¹, and promoted the formation of dense flocs enriched in PHA-accumulating bacteria, as confirmed by transmission electron microscopy. Process kinetics revealed enhanced substrate uptake rates and improved storage yields under SS conditions, despite an elevated C/P ratio. Notably, nutrient shortage conditions were inadvertently reached by the proliferation of Polytoma mirum in the feeding tank. Although Polytoma mirum did not affect VFA composition, its presence significantly reduced nitrogen and phosphorus concentrations. These nutrient shortage conditions were maintained for at least 30 days until the system began to exhibit stress, as demonstrated by an increased SVI (178.6 mL g⁻¹). Microbial community analyses indicated marked shifts: the eukaryotic assemblage transitioned from sessile to motile ciliates under SS, while bacterial diversity within the PHA‐accumulating fraction remained high, with key taxa such as Sphaerotilus and Neomegalonema becoming more prevalent under phosphorus-limited conditions. Overall, short settling not only improved microbial selection but also prevented bulking by retaining well-aggregated biomass, thereby mitigating nutrient shortage conditions.

overall_design: Total DNA was extracted from activated sludge and mixed microbial cultures grown under three operational conditions (LS, SS, SS-NS), then amplified for full-length 18S rRNA gene sequencing using the PacBio platform

first: Alessio

last: Castagnoli

first: Sitihaya

last: Malibo

first: Tianshi

last: Li

first: Serena

last: Falcioni

first: Letizia

last: Modeo

first: Isabella

last: Pecorini


title: Dynamic change of immune microenvironment in ovarian cancer following neoadjuvant chemotherapy [MON_RNAseq]

city: Hangzhou

first: Lv

last: Fei

address: The First People's Hospital of Hangzhou, Zhejiang Province

institute: Zhejiang Chinese Medical University

summary: Initial surgery and platinum-based chemotherapy is extensively applied to ovarian cancer. Although the majority of patients were sensitive, most relapse at later stage, highlighting the urgent need to understand the tumor microenvironment in ovarian cancer following NACT (neoadjuvant chemotherapy). Through analyzing the published scRNA-seq on human high-grade serous ovarian cancer and performing several in vitro and in vivo experiments, we found prostaglandins-mediated immunosuppressive microenvironment formation is a critical contributor to chemotherapy-resistant upon cisplatin treatment. In mechanisms, cisplatin-treated ovarian cancer cells induce the formation of MDSCs, which passivates the cytotoxicity of CD8+T cell. Moreover, we also carried out scRNA-seq on mice ovarian cancer intraperitoneal injection model to confirm our findings. Notably, Collaborative application of cisplatin and prostaglandins-specific inhibition boosts the cytotoxicity of CD8+T cell and greatly improves the effective rate compared to cisplatin monotherapy.

overall_design: We conducted in vitro co-culture experiments with ID8 cells pretreated with 40μM cisplatin and PBS and bone marrow-derived macrophages (BMDMs), and then performed RNA-seq profiling on BMDMs.

first: Shuai

last: Wang

first: Ruoyao

last: Zou

first: Fei

last: Lv

first: Yi

last: Jin

first: Xiaoye

last: Ye

first: Yongfeng

last: Wu

first: Jinyi

last: Tong


title: Enhanced polyhydroxyalkanoates production from Mixed Microbial Culture through Short Settling Aerobic Dynamic Feeding: improved selection and bulking resilience [ITS]

overall_design: Total DNA was extracted from activated sludge and mixed microbial cultures grown under three operational conditions (LS, SS, SS-NS), then amplified for full-length ITS amplicon sequencing using the PacBio platform


title: Enhanced polyhydroxyalkanoates production from Mixed Microbial Culture through Short Settling Aerobic Dynamic Feeding: improved selection and bulking resilience [16S]

overall_design: Total DNA was extracted from activated sludge and mixed microbial cultures grown under three operational conditions (LS, SS, SS-NS), then amplified for full-length 16S rRNA gene sequencing using the PacBio platform


title: Single cell transcriptomic profiling of eosinophils and airway immune cells in childhood asthma

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: To enhance granulocyte recovery in scRNA-seq, we employed nasal lavage samples from children with asthma, leveraging the 10x Genomics Flex platform combined with a customized data processing pipeline. Nasal lavage samples were processed without prior manipulation to avoid technical artifacts such as lysis or stimulation. Granulocyte recovery was optimized using fixation to preserve cell quality and advanced computational techniques to separate low RNA content cells from background noise.

overall_design: We grouped children to high-eosinophil and low-eosinophil asthma and compraed their transcriptional differences, cell composition and distinct biological pathways.

first: Naresh

last: Doni Jayavelu

first: Andrew

last: Liu

first: Daniel

last: Jackson

first: Matthew

last: Altman


title: Dynamic change of immune microenvironment in ovarian cancer following neoadjuvant chemotherapy

overall_design: We conducted in vitro co-culture experiments with ID8 cells pretreated with 40μM cisplatin and PBS and T cells, and then performed RNA-seq profiling on T cells.


title: Profiling mouse exosomal RNA to understand antibiotics treatment consequences

city: Los Angeles

first: Brian

middle: George

last: Dias

address: 4650 Sunset Blvd

department: Division of Endocrinology

institute: Children's Hospital Los Angeles

summary: We isolated circulating extracellular vesicles (EVs) from plasma collected from adolescent mus musculus. RNA sequencing revealed that mouse plasma EVs contain RNA aligned to the microbiome.

overall_design: We performed total RNA sequencing of the content of extracellular vesicles purified from mouse plasma. Each sample contains 4 animals' plasma  pulled

middle: G

first: Laura

last: Korobkova

last: E. Thornton

last: Collin

first: Elyse

last: Morin

first: Had

last: j Aoued

first: Soma

last: Sannigrahi

first: Kristie

last: Garza

first: Erin

last: Siebert

first: Hasse

last: Walum

first: Nabeel

last: Bhinderwala

first: Ryan

last: Cabeen

first: Brendan

last: Grubbs

first: Mar

last: Sanchez


title: DEC1 Regulates Human β Cell Functional Maturation and Circadian Rhythm

first: Mai

last: Liu

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Stem cell-derived islet (SC-islet) organoids offer hope for cell replacement therapy in diabetes, but their immature function remains a challenge. Mature islet function requires the β-cell circadian clock, yet how the clock regulates maturation is unclear. Here, we show that a circadian transcription factor specific to maturing SC-β cells, DEC1, regulates insulin responsiveness to glucose. SC-islet organoids form normally from DEC1-ablated human pluripotent stem cells, but their insulin release capacity and glucose threshold fail to increase during in vitro culture and upon transplant. This deficit reflects downregulation of maturity-linked effectors of glucose utilization and insulin exocytosis, blunting glycolytic and oxidative metabolism, and is rescued by increasing metabolic flux. Moreover, DEC1 is needed to boost SC-islet maturity by synchronizing circadian glucose-responsive insulin secretion rhythms and clock machinery. Thus, DEC1 links circadian control to human β-cell maturation, highlighting its vitality to foster fully functional SC-islets.

overall_design: RNAseq of DEC1+/+ and DEC1-/- hPSC-islets at week 0, week 1, and week 2 of in vitro maturation by extended culture

first: Sam

last: Preza

first: Bliss

last: Zheng

first: Zihan

last: Gao

first: Akshaya

last: Biju

first: Juan

last: Alvarez-Dominguez


title: Application of machine learning (ML) / deep learning (DL) using multiple epigenetic features reveals H3K27Ac as driver of gene expression prediction across patients with glioblastoma [RNA-Seq]

city: Bronx

first: Jorge

middle: Eduardo

last: Fajardo

state: NY

address: 1301 Morris Park Avenu

department: Computational and Systems Biology

institute: Albert Einstein College of Medicine

summary: To investigate the contribution of multi epigenetic features on gene expression across glioblastoma patients

overall_design: We empolyed cross-patient prediction on gene expression by using  a combination of epigenetic features and investigated different ML/DL models for this task and build our pipeline using XGBoost.

first: Yusuke

last: Suita

first: Hardy

last: Bright Jr.

first: J. Eduardo

first: Nikos

last: Tapinos

first: Ritambhara

last: Singh


title: Application of machine learning (ML) / deep learning (DL) using multiple epigenetic features reveals H3K27Ac as driver of gene expression prediction across patients with glioblastoma [ATAC-seq]


title: A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories [snRNA_multiome_tissue]

city: Bern

first: Irene

last: Paassen

address: Murtenstrasse 28

department: Biomedical Research

institute: Universität Bern

summary: Atypical teratoid rhabdoid tumors (ATRTs), characterized by the loss of SMARCB1, are among the most lethal pediatric brain tumors. Three molecular subtypes have been identified, each defined by distinct molecular and clinical features. Still, no subtype-specific treatments are available, highlighting the need to understand their inter and intra-subtype heterogeneity. Here, we generated a single-nucleus transcriptome atlas of ATRTs, validated with single-cell ATAC-seq and spatial transcriptomics, to study subtype-specific differentiation trajectories. We identified retained brain progenitor expression profiles within unique subtype-specific differentiation lineages. A shared cycling, progenitor-like cell population, interspersed throughout tumors, was observed across all ATRT patients. Finally, we demonstrate that subtype-specific differentiation trajectories can be induced pharmacologically in ATRT tumoroids directing tumor cells towards a non-proliferative, mature phenotype. Our study reveals that ATRT subtypes exhibit signaling trajectories mirroring normal fetal brain development, potentially enabling the development of maturation therapies tailored towards ATRTs.

overall_design:
Viably frozen samples were minced into small pieces and following 10X Genomics snMultiome pipeline after a nuclei were 7ADD+ sorted

***************************************************************
Raw files for human/patient samples are being made available in EGA (https://www.ebi.ac.uk/ega/) for controlled access to the personally identifiable sequence data.
***************************************************************

first: Enrique

last: Blanco Carmona

first: I

first: Jiayou

last: He


title: A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories [snMultiome_data_organoids]

overall_design:
ATRT tumoroid samples were made single cell and sorted for intact 7AAD+ nuclei. Following 10X Genomics snMultiome pipeline cells were processed for sequencing.

***************************************************************
Raw files for human/patient samples are being made available in EGA (https://www.ebi.ac.uk/ega/) for controlled access to the personally identifiable sequence data.
***************************************************************


title: Disruption of PRC1 Components RING1A and RING1B Promotes Angiogenesis via Relieving BMP4 Repression [RNA-Seq]

city: Guangzhou

first: Jingyuan

last: Zhang

address: 190 Kaiyuan Avenue,Science Park

institute: Guangzhou National Labratory

summary: Angiogenesis is crucial for maintaining tissue homeostasis and responding to injury and disease. Epigenetic mechanisms have been elucidated to regulate the expression of pro-angiogenic factors and modulate angiogenesis. The Polycomb repressive complex 1 (PRC1) is a key epigenetic repressive complex that regulates multiple biological functions. Within this complex, RING1A and RING1B, which serve as the E3 ubiquitin ligases for PRC1, contribute to the monoubiquitylation of histone H2A on Lysine 119 (H2AK119ub), thereby repressing gene transcription. However, the role of RING1A and RING1B in regulating angiogenesis has remained elusive. In this study, we demonstrate that RING1A and RING1B suppress angiogenic capacity in vitro, although they do not inhibit migration and proliferation in endothelial cells (ECs). Furthermore, by integrating RNA sequencing data from RING1A knockdown or RING1B knockdown ECs with CUT&Tag assay results for RING1A, RING1B, and H2AK119ub in ECs, we have identified that PRC1 inhibits angiogenesis by repressing BMP4 expression, a pro-angiogenic factor known to regulate angiogenesis. Additionally, we verify that the knockdown of RING1A and RING1B enhances angiogenesis in vivo, which may provide a new therapeutic target for angiogenesis-related diseases.

overall_design: To investigate the roles of RING1A and RING1B in the regulation of angiogenesis, we developed human umbilical vein endothelial cells (HUVECs) in which both target genes were selectively knocked down using specific siRNAs. Subsequently, we conducted gene expression profiling analysis based on RNA-seq data obtained from three distinct cell lines. This involved comparing the gene expression profiles from RNA-seq data of HUVECs with those of their knockdown (KD) derivatives, specifically the RING1A KD and RING1B KD cells.

first: Xing

last: Peng


title: A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories [Xenium Spatial_Transcriptomics]

overall_design: Formalin fixed paraffin embedded ATRT tissue sections were analyzed using the Xenium in situ Gene Expression platford for performing spatial transcriptomics (10X genomics)

first: J

last: DeMartino


title: A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories [bulk RNA-Seq]

overall_design:
ATRT organoids were treated 48h with IC80 of drug compounds Entinostat, RO31-8220 mesylate, DMSO or thiostrepton and then harvested with trizol for RNA isolation

***************************************************************
Raw files for human/patient samples are being made available in EGA (https://www.ebi.ac.uk/ega/) for controlled access to the personally identifiable sequence data.
***************************************************************

last: Blanco-Carmona


title: A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories [snRNA_10Xv3]


title: Disruption of PRC1 Components RING1A and RING1B Promotes Angiogenesis via Relieving BMP4 Repression [CUT&Tag]

overall_design: Cleavage Under Targets and Tagmentation (CUT&Tag) DNA-sequencing for  H2AK119ub, RING1A, and RING1B in  human umbilical vein endothelial cells (HUVECs).


title: MSC co-culture effect on mouse ooycte

status: Public on Jul 29 2025

city: Hong Kong

first: Wing Tung

last: Lee

address: Room Y934, 9/F, Lee Shau Kee Building, The Hong Kong Polytechnic University, Hung Hom, Kowloon

department: Department of Health Technology and Informatics

country: Hong Kong

institute: The Hong Kong Polytechnic University (PolyU)

summary: We reported that MSC had positive effect on aged mouse oocyte.

overall_design: SMART-seq2 on in vivo and in vitro matured single mouse oocytes with and without overnight MSC co-culture collected from 6-week-old (6wk) and 12-month-old (12m) mice.

first: Annie

middle: W

first: Tin-Lap


title: A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories [snATAC_data_tissue]

first: E


title: Expression data from drosophila ML3 gonads, pointed aga vs. Wt (Oregon R)

city: Sevilla

first: Alicia E.

last: Rosales-Nieves

state: Sevilla

address: HUVR. Edif. IBiS. Lab 109. Av Manuel Siurot S/N

institute: Instituto de Biomedicina de Sevilla-CSIC

summary:
pointed agametic mutation give rise to adults without germline. In this microrray we compare gondas from the pointed aga mutation to Wt gonads.
We used microarrays to detail the transcription profile in the agametic gonads

overall_design: 2 larval gonads (each gonad aproximately 2000-3000 cells) per sample (pointed aga and Wt) 3 biological replicates

first: Alicia

middle: E

first: Acaimo

last: Gonzalez-Reyes


title: Zea mays B73 seedling primary and seminal root tips (0-1mm), RNA-seq, steady-state transcription data

city: Raleigh

first: Linda

last: Hanley-Bowdoin

state: NC

address: 851 Main Campus Drive, Partners III Suite 360

department: Plant and Microbial Biology

institute: North Carolina State University

summary: Conventional cellular transcriptome profiling (RNA-seq) data reports “steady-state” transcript abundance rather than actual transcription rates in the nucleus. It also lacks sensitivity to detect unstable and low-abundance RNA species. We generated these maize (Zea mays L.) B73 total cellular RNA samples, extracted directly from frozen 1-mm root tips, as a parallel experiment to compare to two other types of RNA extracted from isolated nuclei.

overall_design: To investigate the steady-state total cellular transcriptomes of primary and seminal root root tips of maize B73 seedlings.

first: Leigh

last: Mickelson-Young

first: Emily

last: Wear

first: William

middle: F

last: Thompson

first: Lorenzo

last: Concia


title: Topoisomerase II drug cleavage sites (no formaldehyde)

city: Newcastle

first: John

last: Casement

address: Framlington Place

department: Bioinformatics Support Unit

institute: Newcastle University

summary: TOP2A and TOP2B bind and cleave genomic DNA. These enzymes are targeted by some anti-cancer drugs that stabilise the enzyme complexes on the DNA. Whole genome TOP2 ChIP-seq was carried out on human KG-1 cells in the presence and absence of the topoisomerase targeting drugs Etoposide and Mitoxantrone in the absence of formaldehyde.

overall_design: Whole genome TOP2 ChIP-seq was caried out on human KG-1 cells in the presence (60 minute exposure) and absence of the topoisomerase targeting drugs Etoposide or Mitoxantrone. Input control samples were also sequenced for background detection and comparison.

first: Caroline

middle: A

last: Austin

first: Kayleigh

last: Smith

first: Zbyslaw

last: Sondka

first: Ian

last: Cowell


title: Application of machine learning (ML) / deep learning (DL) using multiple epigenetic features reveals H3K27Ac as driver of gene expression  prediction across patients with glioblastoma [ChIP-Seq]

first: Jorge

last: Fajardo

first: Yusuke

last: Suita

first: Hardy

last: Bright Jr.

first: J. Eduardo

first: Nikos

last: Tapinos

first: Ritambhara

last: Singh


title: Genetic variation in the activity of a TREM2-p53 signaling axis determines oxygeninduced lung injury

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

institute: University of California, San Diego (UCSD)

summary:
To investigate the role of Trem2 in neonatal hyperoxia induced lung injury, we exposed mice to 75% oxygen for 14 days.
We then performed gene expression profiling in whole lung and bone marrow derived macrophages using RNA-seq. We studied gene regulation using ChIP-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for lungs exposed to hyperoxia and room air controls. ChIP-seq analysis to assess p53 binding in the lung and macrophages after hyperoxia exposure.

first: Yohei

last: Abe

first: Nathanael

last: Spann

first: Wenxi

last: Tang

first: Robert

last: Huff

first: Sean

last: Jansky

first: Richard

last: John

first: Kelly

last: Chanthavixay

first: Debanjan

last: Dhar

first: Souradipta

last: Ganguly

first: Cadence

last: Seymour

first: Miguel

last: Mooney

first: Jason

last: Guo

first: David

middle: M

last: Lopez

first: Michael

last: Longaker

middle: K

last: Glass

first: Eniko

last: Sajti


title: Whole-genome mapping of 5-hydroxymethylcytosine at single-base resolution by double-stranded DNA deamination sequencing

city: Wuhan

first: Shan

last: Zhang

state: Hubei

address: 299 Bayi Road, Wuchang District

institute: Wuhan University

type: Methylation profiling by high throughput sequencing

summary: 5-Hydroxymethylcytosine (5hmC) is a crucial epigenetic mark that plays a key role in regulating various physiological and pathological processes. Although several methods have been developed to detect 5hmC, direct genome-wide mapping at single-base resolution remains highly desirable. Herein, we developed a double-stranded deamination sequencing (DDD-seq) method for genome-wide mapping of 5hmC at single-base resolution. This method utilizes the double-stranded DNA deaminase SsdAcat from Pseudomonas syringae, which efficiently deaminates cytosine (C), 5-methylcytosine (5mC), 5hmC, 5-formylcytosine (5fC), and 5-carboxycytosine (5caC) in duplex DNA, but not glycosylated 5hmC (5gmC). In DDD-seq, C, 5mC, 5fC, and 5caC in dsDNA are deaminated by SsdAcat and read as T during sequencing, while 5gmC is resistant to deamination, allowing its identification by detecting the remaining C in sequence reads. The map of 5hmC generated by DDD-seq in mouse cerebellum tissue closely aligns with results obtained from the ACE-seq method. Additionally, applying DDD-seq to cerebellum tissue of mouse subjected to chronic sleep deprivation revealed significant global changes in 5hmC distribution on genomic DNA. In contrast to previous single-stranded deaminase APOBEC3A-based mapping methods that require denaturation of dsDNA into ssDNA, DDD-seq eliminates this step, reducing risks associated with incomplete denaturation and simplifying sequencing library construction. Additionally, SsdAcat demonstrates superior thermostability and activity across a wide range of pH values and temperatures, making DDD-seq applicable in broader scenarios with more accessible conditions. Collectively, the DDD-seq method is straightforward, bisulfite-free, and eliminates the need for DNA denaturation step, making it a valuable tool for direct and quantitative detection of 5hmC in genomes at single-base resolution.

overall_design: Single-base resolution mapping of 5-hydroxymethylcytosine in mouse cerebellum tissue by DDD-seq and ACE-seq.

first: Yuan

last: Liang

first: Bifeng

last: Yuan


title: Unravelling Role of miRNA-mRNA Interactome in Pathophysiology of Arrhythmogenic Cardiomyopathy [miRNA-seq]

city: Cádiz

first: Fernando

last: Bonet

address: Plaza Falla 9

institute: University of Cádiz

type: Non-coding RNA profiling by high throughput sequencing

summary: Arrhythmogenic cardiomyopathy is an inherited entity characterized by irregular cell-cell adhesion, cardiomyocyte death, fibro-fatty replacement of ventricular myocytes, leading to malignant ventricular arrythmias, contractile dysfunction and sudden cardiac death. Pathogenic variants in genes that encode desmosome are the predominant cause of arrhythmogenic cardiomyopathy. Moreover, signalling pathways such as Wnt/ß-catenin and transforming growth factor-β have been involved in the disease progression. However, still little is known about the molecular pathophysiological mechanisms that underlie arrhythmogenic cardiomyopathy pathogenesis. We used mRNA and small RNA sequencing to analyse the transcriptome of health and arrhythmogenic cardiomyopathy autopsied human hearts. Our results showed 697 differentially expressed genes, and eight differentially expressed miRNAs. Functional enrichment revealed mitochondrial respiratory-related pathways, impaired response to oxidative stress, apoptotic signalling pathway, inflammatory response-related and extracellular matrix response pathways. Furthermore, analysis of miRNA-mRNA interactome identified eleven negatively correlated miRNA-target pairs for arrhythmogenic cardiomyopathy. Our finding revealed novel arrhythmogenic cardiomyopathy-related miRNAs with important regulatory function in disease pathogenesis highlighting their value as potential key targets for therapeutic approaches.

overall_design: To investigate the molecular pathophysiological mechanisms underlying arrhythmogenic cardiomyopathy. By employing mRNA and small RNA sequencing, we aimed to analyze the transcriptome of healthy and arrhythmogenic cardiomyopathy-affected human hearts, identifying differentially expressed genes and miRNAs. Additionally, we sought to elucidate the functional pathways and miRNA-mRNA interactions involved in the disease, with the goal of discovering novel miRNAs with regulatory functions that could serve as potential therapeutic targets for arrhythmogenic cardiomyopathy.

first: Oscar

last: Campuzano

first: José

last: Córdoba-Caballero

first: Mireia

last: Alcalde

first: Georgia

last: Sarquella-Brugada

first: Aitana

last: Braza-Boïls

first: Ramon

last: Brugada

first: Francisco

last: Hernández-Torres

first: Maribel

last: Quezada-Feijoo

first: Mónica

last: Sánchez

first: Alipio

last: Mangas

first: Juan

last: Ranea

first: Rocío

last: Toro


title: Unleashing the Potential: Myeloid-Specific STING Inhibition Mitigates Deep Vein Thrombosis

city: Nanjing

first: Zhiguang

last: Shi

state: Jiangsu

address: 101Longmian Avenue, Jiangning District

institute: Nanjing Medical University

summary: Deep vein thrombosis (DVT), the third most common cause of cardiovascular deaths, is characterized by intravascular clot formation, often accompanied by inflammation. Although the Stimulator of Interferon Genes (STING) signaling pathway has gained recognition as a central mediator of inflammation in the context of infection, cellular stress, and tissue, its intricate involvement in DVT remains enigmatic. Here, we demonstrate that STING inhibition via specific inhibitors or myeloid-specific STING deficiency ameliorated thrombus formation in murine DVT models. Furthermore, our findings uncover a direct interaction between STING and YBX1, resulting in nuclear translocation and enhanced thrombotic inflammation. A synthetic peptide, C-ST16, designed to resemble STING inhibitors, exhibits promising therapeutic potential by effectively reducing thrombus formation and diminishing inflammatory factor expression without the hepatorenal toxicity. Overall, these findings shed light on the interplay between myeloid specific STING-YBX1 and inflammation, offering novel therapeutic insights for DVT management.

overall_design: To measure the alterations in gene expression levels in inferior vena cava (IVC) ligated for 24 hours in mKO mice compared to control mice. We then pefromed gene expression profiling analysis using data obtained from RNA-seq of  thrombi containing IVCs in Stingf/f mice and Stingf/f Lyzm-Cre+/- mice. Since the thrombi was too small to extract enough RNA, three thrombi was mixed as a sample and 3 samples  were included in each group.

first: Zhiye

last: Guo

last: Lu


title: Dasatinib Overcomes Acquired Resistance to BRAF/MEK Inhibitor Therapy

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

address: 3601 Spruce Street

institute: The Wistar Institute

summary: Despite high initial activity, resistance to combination BRAF/MEK inhibitor (BRAFi/MEKi) therapy arises in virtually all patients with BRAFV600E/K melanoma. There remains a critical unmet need to identify strategies to overcome acquired BRAFi/MEKi resistance. To better personalize therapy in cancer patients and address therapy relapse, umbrella trials have commenced whereby genomic sequencing of a panel of potentially actionable targets guide therapy selection for patients. However, the superior efficacy of such approaches remains to be seen. We here test the robustness of the umbrella trial rationale by analyzing relationships between genomic status of a gene and the downstream consequences at the protein level of related pathways, and find poor relationships between mutations, copy number amplification, and protein expression and activation.  To profile candidate therapeutic strategies that may offer clinical benefit in the context of acquired BRAFi/MEKi resistance, we utilized a repository of patient-derived xenograft models from heavily pretreated patients with resistance to BRAFi/MEKi and/or immunotherapy (R-PDX). With these R-PDXs, we executed in vivo compound repurposing screens using 11 FDA-approved agents from an NCI-portfolio with pan-RTK, non-RTK and/or PI3K-mTOR specificity. We identify dasatinib as capable of restoring sensitivity to BRAFi/MEKi in ~70% of R-PDX models tested. Elevated baseline protein expression of canonical drivers of therapy resistance (e.g., AXL, YAP, HSP70, phospho-AKT) predicts BRAFi/MEKi plus dasatinib treatment sensitivity. We therefore propose that dasatinib plus BRAFi/MEKi combination therapy may restore antitumor efficacy in patients that have relapsed to standard-of-care therapy by broadly targeting proteins critical in melanoma therapy escape. Further, we submit that this experimental PDX paradigm could potentially improve preclinical evaluation of therapeutic modalities and augment our ability to identify biomarker-defined patient subsets that may respond to a given clinical trial. Furthermore, the aged patient population has suboptimal responses to SARS-CoV-2 vaccine antigens. Here, we characterize vaccine-induced responses to SARS-CoV-2 synthetic DNA vaccine antigens in 18-month-old mice and interrogate protection. Aged mice have altered cellular responses, including decreased IFNγ secretion and increased TNFα secretion as compared to young mice. Aged mice had significantly decreased binding and neutralizing antibodies in their serum compared to their young counterparts. Co-immunization with the plasmid-encoded molecular adjuvant adenosine deaminase-1 (pADA) enhanced cellular responses and expanded the breadth of humoral responses in aged mice. pADA co-delivery also altered the gene expression profiles of lymph node lymphocytes in aged animals. Upon challenge pADA co-immunization modestly decreased age-associated morbidity and mortality in ACE2 transgenic and mouse-adapted SARS-CoV-2 challenge models. These data support the use of aged mice as a model for age-associated decreased vaccine immunogenicity and infection-mediated morbidity and mortality in the context of SARS-CoV-2 and provide further support of the use of adenosine deaminase as a molecular adjuvant.

first: Rebecca

last: Vito

first: Herlyn

last: Mennhard