title: Loss of insulin signaling in microglia impairs cellular uptake of Aβ and neuroinflammatory response exacerbating AD-like neuropathology

city: Boston

first: Wenqiang

last: Chen

address: 1 Joslin Pl, Room 610

department: Joslin Diabetes Center

institute: Harvard Medical School

summary: Insulin receptors are present on cells throughout the body, including the brain. Dysregulation of insulin signaling in neurons and astrocytes has been implicated in altered mood, cognition, and the pathogenesis of Alzheimer’s disease (AD). To define the role of insulin signaling in microglia, the primary phagocytes in brain critical for maintenance and damage repair, we created mice with an inducible microglia-specific insulin receptor knockout (MG-IRKO). RiboTag profiling of microglial mRNAs revealed that loss of insulin signaling results in alterations of gene expression in pathways related to innate immunity and cellular metabolism. In vitro, loss of insulin signaling in microglia results in metabolic reprograming with an increase in glycolysis and impaired uptake of Aβ. In vivo, MG-IRKO mice exhibit alterations in mood and social behavior, and when crossed with the 5xFAD mouse model of AD, the resultant mice exhibit increased levels of Aβ plaque and elevated neuroinflammation. Thus, insulin signaling in microglia plays a key role in microglial cellular metabolism and the ability of the cells to take up Aβ, such that reduced insulin signaling in microglia alters mood and social behavior and accelerates AD pathogenesis. Together these data indicate key roles of insulin action in microglia and the potential of targeting insulin signaling in microglia in treatment of AD.

overall_design: IP samples of RiboTag profiling, using microglia-specific ribosome-bounded mRNA from whole brain extracts.

first: Xiangyu

first: Vitor Rosetto

last: Munoz

first: C

last: Kahn


title: Catalytic inhibition of KAT6/KAT7 enhances the efficacy and overcomes primary and acquired resistance to Menin inhibitors in acute myeloid leukaemia [mouse RNA-seq]

status: Public on Jun 16 2025

city: Hannover

first: Florian

last: Perner

address: Carl-Neuberg-Str. 1

department: Hematology, Hemostasis, Oncology and Stem Cell Transplantation

country: Germany

institute: Hannover Medical School

type: Expression profiling by high throughput sequencing

summary: Understanding the molecular pathogenesis of MLL fusion oncoproteins (MLL-FP) has spawned epigenetic therapies that have improved clinical outcomes in this and other molecular subtypes of acute myeloid leukaemia (AML). Using genetic and pharmacological approaches, we define the individual and combined contribution of KAT6A, KAT6B and KAT7, in range of AML models. Whilst inhibition of KAT6A/B is efficacious in some pre-clinical models, simultaneous targeting of KAT7, with the novel inhibitor PF-9363, increases the therapeutic efficacy. KAT7 interacts with Menin and the MLL complex and is co-localised at chromatin to co-regulate the oncogenic transcriptional program. Focussing on MLL-FP AML, we show that inhibition of KAT6/KAT7 provides an orthogonal route to targeting Menin to disable the transcriptional activity of the MLL-FP. Consequently, combined inhibition rapidly evicts the MLL-FP from chromatin, potently represses oncogenic transcription and overcomes primary resistance to Menin inhibitors. Moreover, PF-9363 or genetic depletion reveals that KAT7 remains an important targetable dependency in acquired genetic/non-genetic resistance to Menin inhibition. These data provide the molecular rationale for rapid clinical translation of combination therapy, particularly in MLL-FP AML.

overall_design: RNAseq of MLL-AF9 (KMT2A::MLLT3) transformed murine hematopoietic stem- and progenitor cells after CRISPR-Cas9 mediated knockout of Kat6a (Moz), Kat6b (Morf), Kat7 (Hbo1), KMT2A (Mll1)or Luciferase (LUC) as control.

first: Charlie

last: Hatton


title: Catalytic inhibition of KAT6/KAT7 enhances the efficacy and overcomes primary and acquired resistance to Menin inhibitors in acute myeloid leukaemia [human RNA-seq]

overall_design: RNAseq of Menin inhibitor sensitive and resistant human leukemia cell lines MV4;11 and OCI-AML2 under treatment with the Menin inhibitor revumenib (SNDX-5613) or the KAT6/7 inhibitor PF-9363


title: Selective GSK3α Inhibition Promotes Self-Renewal Across Different Stem Cell States [scRNA-seq]

city: Durham

first: Brian

last: Bennett

address: 111 T.W. Alexander Drive

country: USA

institute: NIEHS

summary: Mouse embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs) represent the naïve and primed pluripotent states, respectively, each requiring distinct culture conditions. In this study, we show that BRD0705, a selective GSK3α inhibitor, significantly enhances the self-renewal of both ESCs and EpiSCs. When combined with IWR1, BRD0705 sustains long-term maintenance of ESCs in a naïve state and EpiSCs in a primed state, even preserving their unique identities under long-term co-culture. Single-cell RNA sequencing and histone mark profiling confirm that this regimen maintains distinct gene expression and epigenetic signatures corresponding to each pluripotent state. Importantly, unlike pan-GSK3 inhibitors CHIR-99021 (CHIR), BRD0705 acts independently of β-catenin signaling, unveiling a novel mechanism for supporting pluripotency. Finally, BRD0705/IWR1 also supports the maintenance of the formative pluripotent stem cells and neural stem cells. Collectively, we propose that GSK3α inhibition may preserve diverse stem cell states by insulating stem cells from differentiation cues and promoting their intrinsic self-renewal capacity. We believe our findings lay the foundation for universal stem cell culture methods with significant regenerative medicine applications.

overall_design: Co-cultured cells were trypsinized and dissociated into the single-cell suspension in DMEM supplemented with 10% FBS. According to the manufacturer's instructions, single-cell RNA sequencing was performed with the 10x Genomics Chromium Next GEM Single Cell 3' Kit v3.1. ESC- and EpiSC-derived cells were separated based on GFP and RFP fluorescence by FACS sorting. Sequencing was carried out on Illumina sequencers.

first: Duo

last: Wang

first: Xiukun

first: Shuling

first: Kai-xuan

last: Shi

first: Yanpui

last: Chan

first: Chao

last: Zhang

first: Xi

first: Guang

last: Hu

first: Qi-Long

last: Ying


title: Selective GSK3α Inhibition Promotes Self-Renewal Across Different Stem Cell States [CUT&Tag]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Co-cultured cells were trypsinized and dissociated into the single-cell suspension in DMEM supplemented with 10% FBS. According to the manufacturer's instructions, single-cell RNA sequencing was performed with the 10x Genomics  2x105 cells were used for Cut&Tag for H3K4me3, H3K27me3, H3K27ac using the Epicypher CUTANA CUT&Tag Kit. Sequencing was carried out on Illumina sequencers.


title: Selective GSK3α Inhibition Promotes Self-Renewal Across Different Stem Cell States [RNA-seq]

overall_design: ESCs cultured in different medium were trypsinized and dissociated into the single-cell. Total RNA was extracted using the GeneJET RNA purification kit. For RNA-seq library preparation, 1 g total RNA was used to prepare the RNA-seq library with the Truseq RNA Library Prep Kit V2 with RiboZero (Illumina).


title: Cocaine-Induced Gene Regulation in D1 and D2 Neuronal Ensembles of the Nucleus Accumbens Revealed by Single-Cell RNA Sequencing

city: New York

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

summary: Cocaine use disorder is characterized by persistent drug-seeking behavior and a high risk of relapse, driven in part by lasting molecular and circuit adaptations in the nucleus accumbens. To explore the transcriptomic changes underlying these alterations, we employed fluorescence-activated nucleus sorting coupled with single-nucleus RNA sequencing to analyze D1 and D2 medium spiny neurons in this brain region of male mice subjected to acute cocaine exposure or to prolonged withdrawal from repeated cocaine exposure without or with an acute cocaine rechallenge. This approach allowed us to precisely delineate and contrast transcriptionally distinct neuronal subpopulations─or ensembles─across various treatment conditions. We identified significant heterogeneity within both D1 and D2 MSNs, revealing distinct clusters with unique transcriptional profiles. Notably, we identified a discrete D1 MSN population characterized by the upregulation of immediate early genes, as well as another group of D1 MSNs linked to prolonged withdrawal, uncovering novel regulators of withdrawal-related transcriptome dynamics. Our findings provide a high-resolution transcriptomic map of D1 and D2 MSNs, illustrating the dynamic changes induced by cocaine exposure and withdrawal. These insights into the molecular mechanisms underlying cocaine use disorder highlight potential targets for therapeutic intervention aimed at preventing relapse.

overall_design: To explore the transcriptomic changes underlying these alterations, we employed fluorescence-activated nucleus sorting (FANS) coupled with single-nucleus RNA sequencing to analyze D1 and D2 medium spiny neurons in this brain region of male mice subjected to acute cocaine exposure or to prolonged withdrawal from repeated cocaine exposure without or with an acute cocaine rechallenge.

first: Philipp

last: Mews

first: Autumn

last: Mason

first: Emily

middle: G

last: Kirchner

first: Eric

middle: J

last: Nestler


title: Catalytic inhibition of KAT6/KAT7 enhances the efficacy and overcomes primary and acquired resistance to Menin inhibitors in acute myeloid leukaemia [CUT&Tag]

first: Florian

overall_design: Cut&Tag sequencing of KAT6A, KAT6B, KAT7, MLL1 and IgG as control in MOLM13 cells (human KMT2A::MLLT3 rearranged AML cell line)


title: Let-7b-5p loaded Mesenchymal Stromal Cell Extracellular Vesicles reduce Pseudomonas-biofilm formation and inflammation in CF Bronchial Epithelial Cells

city: Hanover

first: Sharanya

last: Sarkar

state: NH

address: Dewey Field Road, HB 7550

department: Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth

summary: Chronic Pseudomas aeruginosa infection in the lung is a common in people with cystic fibrosis (CF). Current therapies for CF fail to eliminate persistent bacterial infections, chronic inflammation, or irreversible lung damage. Our group engineered mesenchymal stromal cell (MSC)-derived extracellular vesicles (EVs) to carry the microRNA let-7b-5p as a dual anti-infective and anti-inflammatory treatment. In a preclinical CF mice model, we found that let-7b-5p-loaded MSC EVs reduced P. aeruginosa burden, immune cells and proinflammatory cytokines in the lungs. This research hypothesized two mechanisms of the observed effects in the mouse model: anti-inflammatory properties of the let-7b-5p-loaded MSC EVs and inhibition of antibiotic-resistant P. aeruginosa biofilm formation in CF airways. Primary human broncial epithelial cells (pHBECs) were exposed to P. aeruginosa and treated with differet MSC EV conditions. The results demonstrated that MSC EVs engineered to contain let-7b-5p effectively blocked the formation of P. aeruginosa biofilms on pHBECs while also reducing P. aeruginosa-induced inflammation by CF-pHBECs.

overall_design: pHBECs from 3 different CF donors (22F, 32G, 29H) were cultured in a monolayer. P. aeruginosa was exposed to the apical side for 1 hour, after which the culture was given 1 of 4 different conditions for 5 hours: process control (PC), negative control (NC) MSC Evs, let-7b-5p-loaded MSC EVs, or  no EVs. Additionally, one sample from each donor was not exposed to P. aeruginosa or EVs (untreated, UT).

first: Lily

last: Taub

first: Bruce

middle: A

last: Stanton

first: Barnaby

last: Roxanna


title: Kaiso Mediates Transcription and RNA splicing in Colorectal Carcinoma: Role of BRCA1 in the Kaiso Enhanceosome

city: NASHVILLE

first: Marisol

last: Ramirez

state: TENNESSEE

address: 2220 Pierce Avenue, 571 Preston Research Building

department: Center for Quantitative Sciences, Department of Biostatisticss

institute: Vanderbilt University Medical Center

summary: Kaiso (ZBTB33) is a transcription factor involved in mitotic clonal expansion and tumorigenesis in association with APC loss of heterozygosity. ENCODE data show strong overlap of the Kaiso promoter binding cite (eKBS) and many other transcription factors, including BRCA1.  Here we sought to determine whether BRCA1 is a component of the Kaiso enhanceosome that regulates gene transcription.  Using proximal ligation assays (PLA), immunoprecipitation followed by mass spectrometry, luciferase assays, and ChIP-seq experiments we evaluated the association between BRCA1 and Kaiso. Kaiso nuclear extract immunoprecipitation experiments revealed that Kaiso associates strongly with genes involved in RNA splicing and processing. When Kaiso was not cross linked to DNA, BRCA1 was not detected among Kaiso binding proteins. However, overexpression of BRCA1 increased Kaiso-mediated gene transcription in luciferase assays in a Kaiso-dependent manner. Comparison of BRCA1 ChIP-seq and Kaiso ChIP-seq data from HCT116 cells revealed both BRCA1 and Kaiso commonly bind to the promoters of 379 genes. The most enriched term associated with these genes where BRCA1 and Kaiso bind their promoters is metabolism of RNA. Disease processes associated with these BRCA1/Kaiso gene promoters indicate that BRCA1 is functionally linked to a Kaiso-directed program of RNAP2-mediated gene transcription and likely associated with colorectal cancer development and maintenance.

overall_design: ChIP-seq of BRCA1 in HCT116 cells

first: Weifeng

last: Luo

first: Manish

last: Tripathi

first: Qi

last: Liu

first: Lei

last: Chen

first: Robert

middle: W

last: Cowan

first: Juliet

middle: M

last: Daniel

first: Chi

last: Yan

first: Ann

last: Richmond

first: Albert

middle: B

last: Reynolds


title: Noncanonical PRC1.1 Targets BTG2 to Retain Cyclin Gene Expression and Cell Growth in Neuroblastoma [microarray]

city: Kita-adachi-gun

first: Shunpei

last: Satoh

state: Saitama

address: Komuro 818, Ina

department: Research Institute for Clinical Oncology

country: Japan

institute: Saitama Cancer Center

summary: To explore the common and specific targets of RING1A and RING1B, we conducted microarray analyses on NGP and SK-N-BE cells transduced with shRING1, shRNF2, or their combination.

overall_design: shRNAs were packaged in HEK293T cells. Subsequently, neuroblastoma (NB) cell lines were infected wirh8 μg/mol of polybrene. Four days after the transduction, extracted total RNAs were subjected to microarray analysis.

first: Miki

last: Ohira

first: Takehiko

last: Kamijo


title: Inhibition of Virally-Induced TFEB Proteasomal Degradation as a Host-Centric Therapeutic Approach for Coronaviral Infection

city: Pittsburgh

first: Jason

middle: R

last: Kennerdell

state: PA

address: 100 Technology Drive

department: Aging Institute

institute: University of Pittsburgh

summary: The endo-lysosomal pathway plays an evolutionarily conserved role in pathogen clearance, and both bacteria and viruses have evolved complex mechanisms to evade this host defense system. Here, we describe a novel aspect of coronaviral infection, whereby the master transcriptional activator of lysosomal homeostasis – TFEB – is targeted for proteasomal-mediated degradation upon viral infection. Through mass spectrometry analysis and an unbiased siRNA screen, we identify that TFEB protein stability is coordinately regulated by the E3 ubiquitin ligase subunit DCAF7 and the PAK2 kinase. In particular, viral infection triggers marked PAK2 activation, which in turn, phosphorylates and primes TFEB for ubiquitin-mediated protein degradation. Deletion of either DCAF7 or PAK2 blocks virally-stimulated TFEB degradation and protects against virally-induced cytopathic effects. We further derive a series of novel small molecules that interfere with the DCAF7-TFEB interaction. These agents inhibit virus-induced TFEB degradation and demonstrate broad anti-viral activities including attenuating SARS-CoV-2 infection in two animal models. Together, these results delineate a virally-triggered pathway that impairs lysosomal homeostasis in the host. Small molecule E3 ubiquitin ligase DCAF7 inhibitors that restore lysosomal function represent a novel class of host-directed, anti-viral therapies useful for current and potentially future coronaviral variants.

overall_design: Gene expression profiling of Beas-2B cells treated with either vehicle control or 3µM BC18630 for 18 hours.

first: Travis

last: Lear

first: Mads

last: Larsen

first: Bo

last: Lin

first: Benjamin

last: Treat

first: Qing

last: Cao

first: Áine

middle: N

last: Boudreau

first: Karina

middle: C

last: Lockwood

first: Irene

last: Alfaras

first: Laura

last: Salminen

first: Daniel

middle: P

last: Camarco

first: Jing

last: Ma

first: Jie

first: Jay

middle: X

last: Tan

first: Ferhan

last: Tuncer

first: John

last: Villandre

first: Lucas

last: Hertzel

first: Michael

last: Myerburg

first: Yanwen

first: Claudette

last: St Croix

first: Yusuke

last: Sekine

last: Evankovich

first: Simon

last: Barratt-Boyes

first: Toren

last: Finkel

first: Bill

first: Yuan


title: CNOT6L regulates energy metabolism in the ovarian granulosa cells associated with polycystic ovary syndrome.

city: Jinan

first: Shan

last: Han

address: Wenhua West road

country: China

institute: Shandong University

summary: As somatic cells surround the oocyte, the endocrine functions exerted by ovarian granulosa cells (GCs) are crucial factors in maintaining follicle development, as oocyte development relies on the provision of energy substrates and cytokines by ovarian granulosa cells. The mRNA deadenylase level of granulosa cells precisely regulates the transcription processes of key molecules involved in oocyte maturation. In this study, we detect the expression level of the deadenylase CNOT6L in  PCOS patients' granulosa cells and mouse models' ovaries. We found that the CNOT6L significantly upregulated in the ovarian granulosa cells of both PCOS patients and mouse models. Subsequently, we overexpressed CNOT6L granulosa cells to explore the alternations by which CNOT6L regulates ovarian granulosa cell function. We also found that overexpression of CNOT6L in granulosa cells significantly inhibited the glycolytic pathway, activated the mitochondrial oxidative phosphorylation pathway, led to a reduction in the generation of the intermediate product lactate, and resulted in impaired energy supply to the oocyte. Subsequently, we performed Full-length transcriptome sequencing on the granulosa cells and investigated the impact of mRNA poly(A) level differences on granulosa cell dysfunction in PCOS. This study offers new insights into the role of Cnot6l in regulating energy metabolism homeostasis and its involvement in follicular developmental disorders related to polycystic ovary syndrome.

overall_design: Analysis of comparative gene expression and poly(A) tail lengths in RNA-seq data from granulosa cells of individuals with polycystic ovary syndrome (PCOS) and control subjects.


title: Large-Scale Genomic Analysis of CpG-Mediated Immunogenicity in Bacteriophages and a Novel Predictive Risk Index

city: San Diego

first: Dwayne

last: Roach

state: CA

address: 5500 Campanile Dr

department: Biology

institute: San Diego State University

summary: Bacteriophage (phage) therapy is a promising alternative to antibiotics, yet phage-induced immune responses can affect treatment efficacy. However, current methods for assessing phage immunogenicity are limited, hindering the development of safer, more effective therapies. Here, we introduce the Bacteriophage Risk Index (BRI), a novel metric that quantifies phage immunogenic potential based on CpG dinucleotide frequency, motif spacing, and sequence context, key factors influencing Toll-like receptor 9 (TLR9) activation. Applying the BRI to 7,011 phage genomes, we classified them into five risk tiers, revealing substantial immunogenic variability, even among phages targeting the same bacterial host. BRI scores correlated with immune responses in human lung epithelial cells, validating its predictive power. Experimental testing further confirmed this, as exposure of lung epithelial cells to two phages from distinct risk tiers showed that the high-risk phage (Category 4) induced a strong pro-inflammatory response, upregulating CXCL1, CXCL8, IRF7, and TNFAIP3, while the low-risk phage (Category 2) triggered minimal immune activation with limited cytokine expression. These findings confirm that higher BRI scores predict stronger immune responses, providing a robust tool for evaluating phage immunogenicity. By enabling the selection of phages with lower immunogenic potential, the BRI enhances the safety and efficacy of phage therapy while offering a standardized framework for regulatory agencies, clinical researchers, and biologic drug development, with applications extending beyond phage therapy to other immunogenic biologics.

overall_design: To investigate the effect of bacteriophages and lung epithelial cells (A549), we purified DNA from bacteriophage P1A and bacteriophage KPS64 to compare epithelial cells' sensing of and response to phage. We performed gene expression analysis using data obtained from RNA-seq of 2 types of DNA treatment at 2 time points. Comparive gene expression analysis was conducted for A549 cells treated for 2 h or 6 h using PAK_P1 (phage) or KPS64 (phage) DNA.

first: Lukeman

last: Kharrat

first: Camillo

last: Garcia

first: Julian

last: Casas-Sierra

first: Wade

last: Ingersoll

first: Tiffany

last: Luong

first: Alejandro

last: Reyes


title: Dysregulation of cell migration by matrix metalloproteinases in geleophysic dysplasia

city: Miami

first: Mustafa

last: Tekin

state: FL

address: 1501 NW 10th Ave

institute: University of Miami

summary: Geleophysic dysplasia (GD) is characterized by short stature, brachydactyly, joint limitations, a distinctive facial appearance, as well as cardiac and respiratory dysfunction that can be life-threatening. GD is caused by pathogenic variants in the ADAMTSL2, FBN1, or LTBP3 genes. While dermal fibroblasts derived from affected individuals have shown poor organization of the extracellular matrix (ECM), it remains elusive how the disorganized ECM contributes to GD pathogenesis. To understand the molecular mechanisms in GD, we isolated and characterized primary human dermal fibroblasts from affected individuals with ADAMTSL2 and FBN1 variants. We found that the secretion of ECM proteins including ADAMTSL2, FBN1, and Fibronectin were impaired in GD fibroblasts. Increased cell migration was observed in GD fibroblasts carrying ADAMTSL2 or FBN1 variants, which was associated with up-regulation of MMP-1 and MMP-14, two proteases related to cell mobility. The enhanced cell migration and up-regulation of MMP-1 and MMP-14 were corroborated in mouse primary dermal fibroblasts carrying pathogenic variants in Adamtsl2 and in lung and heart tissues from Adamtsl2-knockout mice. A pan MMP inhibitor, GM6001, inhibited the migration of GD fibroblasts. Overall, our results suggest that MMP-1/-14 up-regulation play a role in the development of GD and may be utilized as a treatment target.

overall_design: RNA-Seq profiling of 11x human dermal fibroblasts, including 3x WT, 2x ADAMTSL2 variants (geleophysic dysplasia-1), 4x FBN1 variants (geleophysic dysplasia-2) and 2x FBN1 variants (Marfan syndrome)

first: Alejo

last: Morales

first: Vladimir

last: Camarena

first: LéShon

last: Peart

first: Katherina

last: Walz

first: Gaofeng

last: Wang


title: Endocardial primary cilia and blood flow regulate EndoMT during endocardial cushion development [Single Nuc-RNAseq_NCX]

city: New Haven

first: Kathryn

last: Berg

state: Connecticut

address: 333 Cedar St.

department: Genetics

institute: Yale University

summary: Blood flow is critical for heart valve formation, and cellular mechanosensors are essential to translate flow into transcriptional regulation of development.  Here, we identify a role for primary cilia in vivo in the spatial regulation of cushion formation, the first stage of valve development, by regionally controlling endothelial to mesenchymal transition (EndoMT) via modulation of Kruppel-like Factor 4 (Klf4). We find that high shear stress intracardiac regions decrease endocardial ciliation over cushion development, correlating with KLF4 downregulation and EndoMT progression. Mouse embryos constitutively lacking heart contractility do not upregulate KLF4 or undergo EndoMT. snRNA-seq revealed that Ncx1-/- embryos failed to transition to early-EndoMT and have reduced mesenchymal markers.

overall_design: Whole hearts of e9.5 mouse embryos (Ncx1+/+ (wildtype), Ncx1+/-, Ncx1-/-) were microdissected and flashfrozen. Five flashfrozen hearts of each genotype were pooled and prepared for single nuclei RNA-sequencing, 1 technical replicate per genotype.

first: Faith

last: Lundt

first: Joshua

last: Gorham

first: Jonathan

last: Seidman

first: Martina

last: Brueckner


title: Selective GSK3α Inhibition Promotes Self-Renewal Across Different Stem Cell States

first: Brian

last: Bennett

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

overall_design: Refer to individual Series


title: LEADR ncRNA dampens interferon signalling in bladder cancer

city: Rome

first: Artem

last: Smirnov

address: Via Montpellier 1

department: Dept. of Exper. Medicine

country: Italy

institute: University of Rome "Tor Vergata"

summary: Bladder cancer affects over half a million people worldwide each year. Recent advances in early detection allowed a successful management of non-aggressive cancers, yet the recurrence rate remains high. Aggressive muscle-invasive bladder tumours are life-threatening and challenging to cure. Therefore, understating of key molecular pathways involved in cancer progression is critical for developing of new personalised targeted therapies. Recently, non-coding RNAs (ncRNAs) have emerged as key regulators orchestrating complex biological processes in cancer, yet their function is not fully understood. Here, we compare non-muscle invasive and muscle invasive cell lines and identify a ncRNA gene MIR205HG and its transcript LEADR among the top ncRNAs lost in muscle invasive urothelial tumours. We show that LEADR expression is epigenetically regulated by master transcription factor p63. LEADR is localised in the nuclei of non-muscle invasive bladder cancer cells where it dampens hyperactivation of interferon stimulated genes possibly increasing sensitivity of bladder cancer cells to interferon signalling. These findings uncover an anti-tumoral role of non-coding RNA LEADR in mediating immune response in bladder cancer.

overall_design: The RT4 bladder cancer cells were silenced with scramble or LEADR siRNAs for 48h and the RNA was used for a poly(A) RNA sequencing.


title: Caloric restriction mimetic 2-deoxyglucose alters metabolic and transcriptomic phenotype in association with changes in chromatin accessibility in human astrocytes [RNA-Seq]

city: La Jolla

first: Johannes

last: Schlachetzki

address: 9500 Gilman Drive

institute: UCSD

summary: Caloric restriction and ketogenic diets may modify the progression of neurological disorders, including HIV-associated neurological disorders and Alzheimer’s disease, in part by influencing astrocyte function. This study examines how metabolic substrate availability affects metabolic processes and gene expression in human astrocytes. We exposed astrocytes to the glycolysis inhibitor 2-deoxyglucose (2-DG) prior to stimulation with interleukin-1β and measured extracellular flux using the Seahorse ® platform. We next analyzed gene expression and chromatin accessibility changes using RNA-sequencing and ATAC-sequencing, respectively. Finally, we tested the effects of glucose deprivation and the ketone body β-hydroxybutyrate (BHB) on inflammatory gene expression. 2-DG reduced oxygen consumption rate and extracellular acidification rate in the presence of IL-1β, while concomitantly decreasing expression of pro-inflammatory cytokines TNF, IL-6, and C3. These changes were linked to altered chromatin structure. The metabolic substrate β-hydroxybutyrate was associated with reduced cytokine expression compared to glucose. Inhibition of glycolysis attenuated IL-1β-induced inflammation and gene expression changes and altered chromatin architecture. Both glucose deprivation and BHB treatment reduced inflammatory cytokine expression, with additive effects when combined with 2-DG. These results suggest that targeting glycolysis could provide therapeutic strategies for treating neurological diseases through modulation of astrocyte-driven inflammation.

overall_design: Primary astrocytes,  2replicates per group (control, 2-DG, IL1B, IL1B+2DG)

first: Adam

last: Fields

first: Sydney

last: O'Brien

first: Mathew

last: Spencer

first: Jacqueline

last: Kulbe

first: Vikram

last: Venkatesh

first: Anna

last: Laird

first: Mary

last: Ford

first: Ali

last: Boustani


title: Genome-wide DNA methylation analysis of hippocampal tissue in a murine model of Attention Deficit-Hyperactivity Disorder

city: SANTIAGO

first: RODRIGO

last: VIDAL

state: METROPOLITANA

address: Avenida Libertador Bernardo O'Higgins nº 3363.  Estación Central

department: BIOLOGY

country: Chile

institute: UNIVERSIDAD DE SANTIAGO

summary: Attention Deficit-Hyperactivity Disorder (ADHD) is a neurodevelopmental disorder with a prevalence around 5% in children and adolescents and 2.5% in adults. Recent reports using GWAS approaches have identified several genetic risk loci for this disorder. However, the epigenetic influence of extrinsic factors during pregnancy or the exposure to environmental factors during childhood, on the onset of the disorder remains unclear. This question has been addressed by analyzing blood or saliva samples from ADHD patients or by postmortem analysis. The aim of this study was to determine differential patterns in DNA methylation in fresh hippocampal samples using a murine model of ADHD. We analyzed the genome-wide pattern of differentially methylated CpG sites using the Illumina Infinium Mouse Methylation BeadChip in fresh hippocampal samples from the prenatal nicotine exposure (PNE) mouse model of ADHD and control animals. Our analysis revealed 218 DMPs including genes associated with growth factors signaling, such as adhesion G protein-coupled receptor B2 (ADGRB2), leukemia inhibitory factor receptor (LIFR) and erb-b2 receptor tyrosine kinase 3 (ERBB3) involved in synaptogenesis, proliferation, and differentiation of neural stem cells. The functional gene enrichment analysis of differentially methylated positions (DMPs) revealed the nervous system development as the biological process with highest enrichment factor. In addition, the GO and KEEG enrichment analysis of 113 differentially methylated regions (DMR) revealed several loci associated with the positive regulation of Hippo signaling (involved in neuronal development) in PNE samples. In addition, our results revealed a DMP previously associated to ADHD patients supporting the PNE murine model of ADHD. These results are relevant in terms of the validation of PNE model of ADHD and for the identification of epigenetic markers of the disorder in humans. In addition, our results are relevant for the characterization of the cellular and molecular mechanisms underlying the ADHD, currently unknown.

overall_design: Attention Deficit-Hyperactivity Disorder (ADHD) is a neurodevelopmental disorder with a high prevalence (approximately 5%) among children worldwide. We analyzed the genome-wide pattern of differentially methylated CpG sites using the Illumina Infinium Mouse Methylation BeadChip in fresh hippocampal samples from the prenatal nicotine exposure (PNE) mouse model of six ADHD (3 males and 3 females) and six control animals (3 males and 3 females).

first: S

last: Rodrigo Vidal


title: Choline metabolism drives metastasis in BRCA1-deficient ovarian cancers by activating FAM3C [ChIP-seq]

city: Nanjing

first: Cong

last: Wang

address: 639, Longmi Avenue

institute: China Pharmaceutical University

summary: BRCA1 mutations are a hallmark of hereditary ovarian cancer, strongly linked to deficiencies in homologous recombination (HR) DNA repair and impaired DNA replication fork protection. However, its roles in cancer progression beyond maintaining genomic integrity remain poorly understood. Through metabolomics approaches, we found BRCA1-deficiency strikingly increased choline metabolism. Loss of BRCA1 promotes choline uptake through upregulating choline transporter-like protein 4 (CTL4). BRCA1 directly binds and recruits EZH2-mediated H3K27Me3 deposition to CTL4 promoter. CTL4 was therefore overexpressed in ovarian cancer tissues with BRCA1 mutations. Furthermore, BRCA1-deficiency significantly promotes ovarian cancer invasion, while inhibition of CTL4 reverses the high metastatic potential of BRCA1-deficient ovarian cancer cells, suggesting the functionality and specificity of CTL4 as a therapeutic target. Additionally, we discovered that phosphocholine, the choline metabolite increased by CTL4 overexpression, interacted with and stabilized the epithelial-to-mesenchymal transition inducer FAM3C in BRCA1-deficient ovarian cancer cells. Importantly, we identified a potent CTL4 inhibitor, DT-13, which significantly reduces choline metabolism and effectively suppresses metastasis in BRCA1-deficient ovarian cancers. Therefore, our study uncovers a mechanism underlying metastasis in BRCA1-deficient cancers and identifies CTL4 as a therapeutic target for metastatic ovarian cancer patients with BRCA1 mutations.

overall_design: CHIP-seq of BRCA1 in A2780 ovarian cancer cell to analysis genomic distribution of BRCA1-binding peaks in A2780 cells.

first: Xuexia

last: Xie

first: Jiahuang

last: Li

first: Jiawei

last: Zhu

first: Binghe

last: Sun

first: Dake

first: Guo

last: Chen


title: Caloric restriction mimetic 2-deoxyglucose alters metabolic and transcriptomic phenotype in association with changes in chromatin accessibility in human astrocytes [ATAC-Seq]

first: Johannes

last: Schlachetzki

first: Adam


title: A pathogenic CD4 T cell phenotype in experimental uveitis shares common features with other immune mediated inflammatory diseases [EAU]

city: Bristol

first: Lindsay

last: Nicholson

address: Biomedical Sciences Building

department: Cellular and Molecular Medicine

country: United Kingdom

institute: University of Bristol

summary: Experimental autoimmune uveoretinitis, a mouse model of ocular autoimmunity, was induced by the transfer of allelically marked T cells. Thirteen days after transfer, CD4 cells were sorted from spleens and individual eyes and processed using the SMART-Seq v4 Ultra Low Input RNA kit. Samples were classified as: transferred cells from the eye, transferred cells from the spleen, endogenous cells from the eye, endogenous cells from the spleen. Analysis of differential gene expression revealed an extended pathogenic phenotype that shared common features with other models of autoimmunity.

overall_design: Data from 24 samples obtained from two experiments (ASS03 & ASS04) and classified as transferred CD4 cells from single eyes (e4T), transferred CD4 cells from the spleen (s4T), endogenous cells from the eye (e4E) and endogenous cells from the spleen (s4E). Cells numbers were in the range 18-100 cells.

first: Amy

last: Ward

first: Oliver

middle: H

last: Bell

first: Luis

last: Martinez-Robles

first: Phillip

last: Lait

first: Colin

last: Chu

first: David

last: Copland

first: Andrew

middle: D

last: Dick


title: A novel cardiomyopathy phenotype linked to missense mutation of CHD7

city: Houston

first: Maria

middle: Elisa

last: Ruiz Echartea

state: Texas

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: Loss-of-function of the chromatin remodeler CHD7 causes CHARGE syndrome, characterized by variable penetrance and diverse abnormalities.  However, establishing genotype-phenotype correlations has been challenging, as most CHD7 inactivating mutations are null alleles.  Through CHD7 missense variant analysis at potential phosphorylation sites, we identified T730 (T720 in mice) as a critical residue associated with pathogenesis.  Using a CHD7 T730 missense mutation (Chd7T720A) and a frameshift null allele (Chd7fs) in a mouse model, we found that Chd7fs/fs mice were non-viable, while Chd7fs/+ mice exhibited haploinsufficiency-related circling behavior.  Notably, Chd7fs/T720A mice died before postnatal day 2, indicating the Chd7T720A allele is hypomorphic.  Micro-CT analysis at E18.5 revealed heterozygous mice primarily exhibited hypertrophic cardiomyopathy (HCM), while homozygous mice developed both HCM and dilated cardiomyopathy (DCM).  RNA-seq analysis of neonatal Chd7T720A/T720A hearts revealed a disrupted transcriptome, which in males and females was characterized by downregulation of mitochondrial energy metabolism genes and enrichment of ETS family transcription factor targets.  We further identified GSK3β, GSK3α, HIPK1, and DYRK2 as candidate kinases for this site, suggesting a regulatory role in CHD7.  This missense mutation causing developmental heart abnormalities establishes the first genotype-phenotype correlation for CHD7, and offers new insights into CHARGE syndrome pathogenesis.

overall_design: Mouse hearts from neonatal mice at postnatal day 0 (P0) were immediately processed for total RNA extraction.  The study included three biological replicates for each experimental group, encompassing male and female hearts of Chd7+/+, Chd7T720A/+, and Chd7T720A/T720A mice.

first: In-Young

last: Park

first: Cheryl

middle: L

last: Walker

first: Cristian

last: Coarfa

first: Sandra

last: Grimm


title: Human iPSC-cardiomyocyte models of insulin resistance demonstrate metabolic and contractile dysfunction that recapitulates diabetic cardiomyopathy

city: Oxford

first: Ryan

middle: Daniel

last: Carter

address: Sherrington Building, Sherrington Rd

department: DPAG

institute: University of Oxford

summary: In type II diabetes (T2DM), the heart is exposed to hyperglycaemia, hyperlipidaemia, and hyperinsulinaemia, leading to insulin resistance and metabolic dysfunction, culminating in diabetic cardiomyopathy (DbCM). Human-centric models of DbCM are needed to provide mechanistic insights and therapeutic targets in a translationally relevant setting. We hypothesised that culturing human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) in an “insulin resistance” (IR) media, and assessing this using a systems biology approach, would offer a comprehensive evaluation of dysregulated pathways, establishing their suitability as a model of DbCM.  Culturing 2D hiPSC-CMs in IR media induced insulin resistance and activated pathways implicated in DbCM, including metabolic remodelling, mitochondrial dysfunction, and endoplasmic reticulum stress. Adaptation to hypoxia, a key component of post-ischaemic remodelling, was blunted in the 2D IR hiPSC-CMs, highlighting impaired cellular responses to low oxygen conditions. Proteomic and transcriptomic analyses revealed significant enrichment of DbCM-related pathways, particularly those involved in metabolic dysregulation.  In conclusion, 2D hiPSC-CMs cultured in IR media recapitulate key features of DbCM, including impaired adaptation to hypoxia, providing a valuable model for studying diabetic cardiomyopathy.

overall_design: RNA-seq profiling of control of insulin-resistant hiPSC-CMs in normoxia or hypoxia.

first: Ujang

last: Purnama

first: Marcos

last: Castro-Guarda

first: Claudia

last: Montes-Aparicio

first: Anandhakumar

last: Chandran

first: Richard

last: Mbasu

first: Maxwell

last: Ruby

first: Charlotte

last: Daly

first: Francesca

last: Buffa

first: Lisa

last: Heather

first: Carolyn

last: Carr


title: A pathogenic CD4 T cell phenotype in experimental uveitis shares common features with other immune mediated inflammatory diseases

first: Lindsay

last: Nicholson

summary: Experimental autoimmune uveoretinitis, a mouse model of ocular autoimmunity, was induced by immunization with the uveitogenic peptide IRBP1-20. 26 days after disease induction, CD4 T cells were purified by cell sorting for RNAseq.

overall_design: Data from 12  samples obtained from C57BL/6 mice immunised with the uveitogenic peptide IRBP 1-20 and adjuvants. CD4+ T cells were obtained 26 days after disease by sorting from individual eyes (8 samples) or from the spleens of animals with disease (2 mice, A2S&B3S) or naïve (2 mice, A3S&B1S).

first: Amy

last: Ward

first: Oliver

last: Bell

first: Colin

last: Chu

first: David

last: Copland

first: Andrew

last: Dick


title: Choline metabolism drives metastasis in BRCA1-deficient ovarian cancers by activating FAM3C [RNA-seq]

first: Cong

last: Wang

overall_design: RNA-seq profiling of BRCA1 knockout UWB cells and BRCA1 WT cells.

first: Xuexia

last: Xie

first: Jiahuang

last: Li

first: Jiawei

last: Zhu

first: Binghe

last: Sun

first: Yue

last: Wu

first: Wanying

last: Zhang

first: Dake

first: Guo

last: Chen


title: p21, ccng1, foxo3b and fbxw7 contribute to p53-dependent cell-cycle arrest [MPNP 18hpf]

city: Birmingham

first: John

last: Parant

state: AL

address: 1670 University Blvd

institute: University of Alabama at Birmingham

summary: p53 is a transcription factor that plays a critical role in cancer prevention. However, the mechanisms by which p53 exerts its tumor-suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53-dependent apoptosis, and p21/CDKN1A is crucial for p53-dependent cell-cycle arrest, we demonstrate that zebrafish lacking puma, noxa, and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53-dependent cell-cycle arrest, we provide evidence that p53 can still induce cell-cycle arrest in the absence of p21, following DNA damage or loss of mdm2 (p53 activation in the absence of stress). This implies the involvement of other p53 transcriptional targets in mediating p53-dependent cell-cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species, we conducted a cross-species comparative analysis of p53-dependent transcriptional profiles to identify a conserved set of 136 p53-upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species, since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally, we performed a CRISPR/Cas9 G0 “crispant” screen in a genetic background lacking mdm2, puma, noxa, and p21 to identify key components involved in p53-dependent cell-cycle arrest. Our findings revealed that ccng1, fbxw7, and foxo3b play an important role in this process.

overall_design: RNA sequencing was performed on zebrafish quadruple knockouts of mdm2, puma, noxa, and p21 at 18 hours post-fertilization. Sibling controls from the same batch, including mdm2+/- (or mdm2+/+); puma-/-; noxa-/-; and p21-/- embryos, were also harvested to extract RNA for comparison.

first: Parant

last: John M.

first: Wang

last: Jun

first: Li


title: p21, ccng1, foxo3b and fbxw7 contribute to p53-dependent cell-cycle arrest [MPNP timecross]

overall_design: RNA-sequencing was performed on zebrafish of un-genotyped progeny from mdm2+/-; pnp-/-intercrosses at various developmental stages (8, 10, 12, 14, 16 hpf) as the mutant group (N=~50 embryos for each group, referred to as MPNP). While this approach generated a dilution of RNA transcripts, since only approxmiately ¼ of the embryos were mpnp-/-, it nonetheless allowed us to glimpse at the dynamics of p53 target gene induction in mpnp-/- animals. Same-stage progeny from pnp-/- intercrosses were harvested to extract RNA for comparison, referred to as PNP.


title: p21, ccng1, foxo3b and fbxw7 contribute to p53-dependent cell-cycle arrest [PNP IR]

overall_design: RNA sequencing was performed on zebrafish triple knockouts of puma, noxa, and p21, at 1, 2, and 3 hours post-30-Gy IR irradiation, administered at 30 hours post-fertilization. Untreated controls were included at the same developmental stage. p53 wild-type zebrafish embryos were only sampled at 3 hpi and in the untreated condition. Zebafish p53 knockout embryos were samples at 1 hpi, 3 hpi and in the untreated condition.


title: Transcriptomic signature of frailty in elderly patients with cardiovascular disease

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

summary: Frailty in elderly cardiovascular disease (CVD) patients is linked to declining functional capacity and procedural complications. This study investigated the transcriptomic signature of frailty in patients ≥70 years undergoing cardiac surgery or TAVI. Frailty was assessed using mobility, gait speed, and handgrip strength. Muscle samples were collected during surgery for RNA sequencing, and gene expression was analyzed. Transcriptomic analysis identified 10 frailty-associated genes, with S100A1 showing the strongest association. Functional studies confirmed S100A1’s role in muscle function, and higher blood S100A1 levels correlated with handgrip strength in a second cohort. S100A1 is a potential target for addressing frailty in elderly CVD patients and offers insights into genetic factors contributing to frailty.

overall_design: Patients aged ≥70 undergoing elective cardiac surgery or TAVI were recruited. Frailty was assessed using impaired mobility (Timed Up-and-Go ≥10 or ≥20 sec), low gait speed (5-meter Walk Test ≥6 sec), or reduced handgrip strength (male ≤27, female ≤16 kg). Muscle specimens (quadriceps femoris) collected during surgery were used for RNA sequencing. Differential gene expression and regression analyses explored associations between frailty and gene expression levels.

first: Markus

last: Jähnert

first: Simon

last: Sündermann


title: p21, ccng1, foxo3b and fbxw7 contribute to p53-dependent cell-cycle arrest [Mouse IR]

overall_design: RNA-sequencing profiling of mouse p53 wild-type and p53 knockout embryos at 1 and 3 hours post 30-Gy IR irradiation at the E9.5 stage, along with untreated controls at the same developmental stage.


title: Nucleus-localized S100A9 triggers senescence of human amnion fibroblasts as a heterochromatin buster at parturition - CUT&Tag

city: Shanghai

first: Wangsheng

state: Please Select

address: 845 Lingshan Rd.

institute: Shanghai Jiao Tong University

summary: Aging in the amnion is considered to trigger and intensify inflammation for the initiation of labor. However, the inducers of amnion cell senescence await to be identified. Here, we unexpectedly observe that S100A9, a classical cytokines, also localizes in the nucleus of human amnion fibroblasts (hAFs), and reveal that nucleus-localized S100A9 (nS100A9) abundance in hAFs increases at parturition and that nS100A9 triggers hAFs senescence. Mechanistically, nS100A9 interacts with heterochromatin proteins, preventing them from binding and maintaining condensed heterochromatin, resulting in heterochromatin erosion, LINE1 de-repression, and type I interferon response activation via the cGAS-STING pathway. Moreover, we demonstrate that dephosphorylation of S100A9 at Thr 113 is required for its nuclear translocation. Mouse studies show that intra-amniotic injection of nS100A9 induces preterm birth along with LINE1 activation, which is blocked by reverse-transcriptase inhibitor. Together, these findings highlight a novel role for S100A9 as a heterochromatin buster that triggers hAFs aging at parturition.

overall_design: Examination of the enrichment of H3K9me3 at TE regions in human amnion fibroblasts treated with or without nS100A9 overexpression with CUT&Tag

first: Wang-sheng

first: Fan


title: Mongolian medicine Eerdun-Wurile promotes myocardial regeneration by regulating MVDA in zebrafish

city: Baotou

first: Xiaoe

last: Jia

address: 31# Jian She Road, Baotou Medical College, Baotou, 014040, Inner Mongolia Autonomous Region, China

institute: Baotou Medical College

summary: Myocardial infarction (MI) is a leading cause of death and disability worldwide. The promotion of myocardial regeneration is a promising therapeutic strategy for acute MI. Using a zebrafish ventricular ablation system, we found that the Mongolian traditional medicine Eerdun-Wurile (EW) promotes myocardial regeneration in zebrafish. EW treatment significantly accelerated proliferation of myocardial cells and improved cardiac function. Transcriptome sequencing revealed a significant decrease in mevalonate diphosphate decarboxylase a (mvda) expression in the metronidazole-induced ventricular ablation group, whereas mvda expression was restored in the EW group. mvda knockdown using morpholino oligonucleotides reversed the EW-mediated myocardial regeneration, whereas mvda overexpression enhanced the regenerative ability. In conclusion, EW may promote zebrafish myocardial regeneration, accelerate myocardial cell proliferation, and improve cardiac function by upregulating mvda expression. Our data partially revealed the molecular mechanism by which EW promotes myocardial regeneration and repair, and provides experimental data and novel insights for advancing MI treatment.

overall_design: RNA-seq profiling of zebrafish embryos in Mongolian medicine Eerdun-Wurile promotes myocardial regeneration.

first: Wei


title: Bile acids bind to exposed cavities in the glucocorticoid receptor

city: Bethesda

first: Thomas

last: Johnson

state: Maryland

address: 41 Medlars Dr. Room B307

department: CCR

institute: National Cancer Institute

summary: We propose certain bile acids bind to a highly conserved pocket in the glucocorticoid receptor ligand binding domain, interfere with receptor multimerization and modulate its transcriptional activity.

overall_design: We use crystallography along with microscopy and transcriptomics to study the effects of bile acids on the glucocorticoid receptor activity.

first: Alba

last: Jiménez-Panizo

first: Kaustubh

last: Wagh

first: Andrea

last: Alegre-Martí

first: Inés

last: Montoya-Novoa

first: Agustina

last: Lafuente

first: Ulrich

last: Eckhard

first: Martín

last: Stortz

first: Montserrat

last: Abella

first: Ido

last: Goldstein

first: Lyuba

last: Varticovski

first: Irwin

last: Arias

first: Annabel

last: Valledor-Fernández

first: Diego

last: Presman

first: Diana

last: Stavreva

first: Juan

last: Fernández-Recio

first: Pablo

last: Fuentes-Prior

first: Gordon

last: Hager

first: Eva

last: Estébanez-Perpiñá


title: Maternal exposure to ozone during implantation promotes a feminized transcriptomic profile in the male adolescent liver

city: Research Triangle Park

first: Colette

last: Miller

state: NC

address: 109 TW Alexander

institute: U.S. Environmental Protection Agency

summary: Maternal exposure to ozone during implantation results in reduced fetal weight gain in rats. Offspring from ozone-exposed dams demonstrate sexually dimorphic risks to high-fat diet feeding in adolescence. To better understand the adolescent hepatic metabolic landscape following fetal growth restriction, RNA sequencing was performed to characterize the effects of ozone-induced fetal growth restriction on male and female offspring. Pregnant Long-Evans rats were exposed to filtered air or 0.8 ppm ozone for 4 hours on both gestation days 5 and 6 (n = 6 / group). At approximately postnatal day 48, liver tissue was obtained for RNA sequencing from offspring. Peri-implantation exposure to ozone in the dam had greater effects on hepatic gene expression in male offspring than in the females. Interestingly, heatmaps of these DEGs suggested that male offspring from ozone-exposed dams had a transcriptomic pattern like that of female offspring. Using a filtered set of highly female-predominant genes (n = 390), 57% were upregulated in the male offspring from ozone-exposed dams. Upregulated canonical pathways included sirtuin and orexin signaling, estrogen receptor signaling, and integration of energy metabolism. Relatively few genes altered in the male offspring from ozone exposed dams were associated with endpoints of sexual maturity, signifying the likely source of the observed feminization was not attributed to sex hormones. This study provides initial evidence that growth restriction in utero may increase the risk of hepatic feminization in male offspring. Additional work is needed to further understand the relationship between developmental undernutrition and feminization in the male liver.

overall_design: Liver sections were collected from ~PND 48 offspring from dams exposed to either filtered air or 0.8ppm ozone at GD 5 and 6. Samples were sequenced using the Illumina NextSeq 500 platform.


title: Cannabidiol Potentiates p53-Driven Autophagic Cell Death in Non-Small Cell Lung Cancer Following DNA Damage: A Novel Synergistic Approach Beyond Canonical Pathways

city: Gangneung-si

first: Young-Joo

last: Kim

state: Gangwon-do

address: 679, Saimdang-ro

country: South Korea

institute: Korea Institute of Science and Technology

summary: The search for more effective and safer cancer therapies has led to an increasing interest in combination treatments that use well-established agents. This study explores the potential of cannabidiol (CBD), a compound derived from cannabis, to enhance the anticancer effects of etoposide in non-small cell lung cancer (NSCLC). Although CBD is primarily used to manage childhood epilepsy, its broader therapeutic applications are being actively investigated, particularly in oncology. Our results revealed that among various tested chemotherapeutic drugs, etoposide showed the most significant reduction in NSCLC cell viability when combined with CBD. To understand this synergistic effect, we conducted extensive transcriptomic and proteomic profiling, which showed that the combination of CBD and etoposide upregulated genes associated with autophagic cell death, while downregulating key oncogenes known to drive tumor progression. This dual effect on cell death and oncogene suppression was mediated by inactivation of the PI3K-AKT-mTOR signaling pathway, a crucial regulator of cell growth and survival, and was dependent on the p53 status. Interestingly, our analysis revealed that this combination therapy did not rely on traditional cannabinoid receptors or transient receptor potential cation channels, indicating that CBD exerts its anti-cancer effects through novel, non-canonical mechanisms. The findings suggest that the combination of CBD with etoposide could represent a groundbreaking approach to NSCLC treatment, particularly in cases where conventional therapies fail. By inducing autophagic cell death and inhibiting oncogenic pathways, this therapeutic strategy offers a promising new avenue for enhancing treatment efficacy in NSCLC, especially in tumors with intact p53 function.

overall_design:
RNA sequencing was performed on A549 cells in four groups: mock,  15 μM CBD,  20 μM Etoposide, and a combination of 15 μM Etoposide +  20 μM CBD, with three samples per group.
A549 cells are a human non-small cell lung cancer (NSCLC) cell line with the following genotype: TP53 (R175H), KRAS (G12S), and EGFR wild type


title: The neural stem cell gene PAFAH1B1 controls cell cycle progression, DNA integrity, and paclitaxel sensitivity of triple-negative breast cancer cells

city: Cleveland

first: Ruth

last: Keri

state: Ohio

address: 9500 Euclid Ave, ND4-52

department: Cancer Biology

institute: Cleveland Clinic

summary: Triple-negative breast cancer (TNBC) is a highly aggressive disease with limited approved therapeutic options. The rapid growth and genomic instability of TNBC cells makes mitosis a compelling target. Indeed, a current mainstay of treatment is paclitaxel (Ptx), a taxane that stabilizes microtubules during mitosis. While initially effective, acquired resistance to Ptx is common, and other antimitotic therapies can be similarly rendered ineffective due to the development of resistance or systemic toxicity, underscoring the need for new therapeutic approaches. Interrogating CRISPR essentiality screens in TNBC cell lines, we identified LIS1 (PAFAH1B1) as a potential vulnerability in this disease. LIS1 regulates mitotic spindle orientation, proliferation, and cell migration during neurodevelopment, yet little is known regarding its function in breast cancer. We found that suppressing LIS1 expression in TNBC cells reduces cell number, while non-malignant cells remain unaffected. LIS1  suppression alters cell cycle dynamics, increasing mitotic duration and accumulation of cells in the G2/M phase. DNA damage is a common inducer of mitotic delays, and the suppression of LIS1 expression increases DNA double-strand breaks, indicating a requirement for sustained LIS1 expression to maintain the genomic integrity of TNBC cells. Lastly, LIS1 silencing substantially enhances these defects in cells that are taxane-resistant and sensitizes both parental and Ptx-resistant TNBC cells to Ptx. These results indicate that LIS1 may be a novel target for the development of new anti-mitotic agents for treating TNBC, particularly in the context of paclitaxel resistance.

overall_design: RNA-seq profiling of MDA-MB-231, HCC38, and BT549 cells transfected for 6 hours with non-specific siRNA (control, NS) or siRNA targeting PAFAH1B1 (PAF) after 72 hours.

first: Parth

last: Majmudar


title: Skeletal Site-Specific Variations in CD11b+ Cells: Insights from Single Cell RNA Sequencing of the Mandible and Femur [scRNA-Seq]

city: Minneapolis

first: Kim

last: Mansky

state: MN

address: 515 Delaware St SE

institute: University of Minnesota

summary: Osteoclasts of the craniofacial region facilitate processes such as tooth eruption and jawbone development. Evidence suggests that craniofacial  osteoclasts exhibit distinct characteristics compared to their counterparts within the appendicular skeleton. A biological mechanism to explain the observable difference between craniofacial osteoclasts and osteoclasts in the long bones has not been previously explored. To further understand differences that exist between the two populations,  here we perform an unbiased genetic survey via single-cell RNA sequencing of CD11b+ cells from mandibular- and the femur-derived bone marrow of 2-month-old C57BL/6 mice to further understand differences that exist between the two populations in an unbiased genetic survey. Our results reveal transcriptomic evidence that suggests a uniquely inflammatory genetic profile of the mandibular-derived CD11b+ cells. This correlates  with an increase in select areas of open chromatin by ATAC-Sequencing and inflammatory gene expression by RT-qPCR. Further exploration into a specific upregulated genes determined KLF4 was both necessary and important for proper differentiation in mandibular derived cells. Suppression of KLF4 likewise limited gene expression of metabolic transporter MCT2. Because this transporter is well understood to impact lactate transportation into cells, we determined that concentration of intracellular lactate was increased in mandibular derived osteoclasts. Together these data suggest a potential metabolic mechanism for the observable differences seen between craniofacial and appendicular osteoclasts.

overall_design: scRNA-Seq of monocytes isolated from mouse femur long bones and mandibles.

first: Rachel

last: Clark

first: Marissa

last: Macchietto

first: Sarah

last: Munro


title: Single-nuclei RNA-seq of neural organoids generated from wildtype and FNDC4 KO iPSCs

city: Rochester

first: Duan

last: Liu

email: liud25@gmail.com, liu.duan@mayo.edu

address: 200 1st ST SW

department: MPET

institute: Mayo Clinic

summary: Large-cohort genome-wide association studies (GWAS) for alcohol use disorder (AUD) risk and drug treatment outcomes have identified significant genetic loci that are splicing quantitative trait loci (sQTLs) for the FNDC4 gene in multiple human brain regions. However, in spite of the fact that FNDC4 is highly expressed in the brain, its function and how it might contribute to AUD pathophysiology remain unknown. In the precent study, we characterized FNDC4 function using CRISPR/cas9 gene editing, the creation of human induced pluripotent stem cell (iPSC)-derived neural organoids and with single-nucleus RNA sequencing (snRNA-seq).

overall_design: Specifically, we generated FNDC4 homozygous knock-out (KO) iPSC lines and differentiated two single-colony KO iPSCs, together with wildtype (WT) iPSCs, to generate forebrain organoids. Those neural organoids were harvested at three time points of differentiation (45, 90, and 150 days) for snRNA-seq using a “split-pool” combinatorial barcoding technology (Parse Bio).

first: Xiujuan

last: Zhu

first: August

last: John

first: Ching Man

last: Wai


title: Novel effects of reverse transcriptase inhibitor supplementation in skeletal muscle of old mice

city: Fort Collins

first: Thomas

last: LaRocca

state: Colorado

address: 1582 Campus Delivery

department: Health and Exercise Science

institute: Colorado State University

summary: Aging is the primary risk factor for the development of many chronic diseases, including dementia, cardiovascular disease, and diabetes. There is significant interest in identifying novel “geroprotective” agents, including by repurposing existing drugs, but such treatments may affect organ systems differently. One current example is the nucleoside reverse transcriptase inhibitor 3TC, which has been increasingly studied as a potential gerotherapeutic. Recent data suggest 3TC may reduce inflammation and improve cognitive function in older mice; however, the effects of 3TC on other tissues in aged animals are less well characterized. Here, we use transcriptomics (RNA-seq) and targeted metabolomics to investigate the influence of 3TC supplementation on skeletal muscle in older mice. We show that 3TC: (a) does not overtly affect muscle mass or functional/health markers; (b) largely reverses age-related changes in gene expression and metabolite signatures; and (c) is potentially beneficial for mitochondrial function in old animals via increases in antioxidant enzymes and decreases in mitochondrial reactive oxygen species. Collectively, our results suggest that, in addition to its protective effects in other tissues, 3TC supplementation does not have adverse effects in aged muscle and may even protect muscle/mitochondrial health in this context.

overall_design: RNA-seq profiling (paired-end reads) of rectus femoris (skeletal muscle) from young (8 mos), old (19 mos), and old treated (19 mos) C57BL/6 mice.

first: Shelby

last: Osburn

first: Meghan

middle: E

last: Smith

first: Devin

last: Wahl


title: Insulin Resistance Increases TNBC Aggressiveness and Brain Metastasis via Adipocyte-derived Exosomes

city: Boston

first: Gerald

middle: V

last: Denis

state: MA

address: 72 East Concord Street

institute: Boston University

summary: This dataset includes mRNA sequencing data obtained from 4T1 cells, either from in vitro cell culture, or clonogenic assay from brain, or primary tumor  treated with exosomes from insulin sensitive (IS) or induslin resistant (IR) adipocytes; and 4T1 cells cultured in vitro and treated with miR-145a-3p. Exosomal small RNA from IS and IR aidpocytes derived exsomes were also included. RNA was extracted and sequenced to investigate differential gene expression and associated biological pathways. The aim of the study is to elucidate how insulin resistance in adipocytes influences gene expression, cancer aggressiveness and metastasis. Data include raw and processed mRNA sequencing files from replicates for each condition.

overall_design: Cells were treated with exosomes derived from IS or IR adipocytes. Total RNA was extracted using the RNeasy Plus Mini Kit (QIAGEN, Cat. No. 74136) following the manufacturer’s instructions. Sequencing libraries were prepared and sequenced using the Illumina platform to produce paired-end reads. Data were processed using the nf-core RNA-seq pipeline, and differential expression was analyzed using DESeq2. Low-expressed genes (fewer than 3 reads per million in at least 3 samples) were filtered out, and data were normalized for library size differences. Differentially expressed genes (DEGs) were analyzed for pathway enrichment using Gene Ontology (GO) and further correlated with survival outcomes in breast cancer patients from The Cancer Genome Atlas (TCGA). Survival analysis was conducted using Cox proportional hazards models.

first: Andrew

last: Chen

first: Yuhan

last: Qiu


title: Targeting STAT3 with Conditional Knockout or PROTAC Technology Alleviates Renal Injury by Limiting Pyroptosis [RNA-seq]

city: Hefei

first: Minglu

last: Ji

address: China

institute: Anhui Medical University

summary: The role of signal transducer and activator of transcription protein 3 (STAT3) in AKI remains controversial. Our study demonstrated an upregulation of total STAT3 protein in AKI mouse models induced by cecal ligation and puncture (CLP) or ischemia-reperfusion (I/R), correlating with patient biopsy results. This increase may be attributed to histone H3K27 acetylation. STAT3 knockout in renal tubular epithelial cells significantly reduced AKI injury and inflammation in mice. Mechanistically, STAT3 induces the transcription of tripartite motif-containing protein 21 (TRIM21), triggering a cascade that activates gasdermin D (GSDMD), resulting in pyroptosis. Administration of the novel proteolysis-targeting chimera (PROTAC) compound E034, which selectively targets STAT3 for ubiquitination and degradation, significantly alleviated renal injury in a low-dose, single-dose regimen, underscoring its substantial therapeutic potential with infrequent dosing requirements. In the context of renal injury, PROTAC emerges as a promising modality by specifically targeting the STAT3/TRIM21/GSDMD axis, which our study has identified as a potential therapeutic target, thereby potentially endowing novel and clinically significant therapeutic strategies.

overall_design: RNA-seq for the control group of mTEC cells stimulated by LPS and the STAT3 silenced group.

first: Jianan

last: Wang

first: Mingfei

last: Wu

first: Chuanhui

last: Xu


title: Targeting STAT3 with Conditional Knockout or PROTAC Technology Alleviates Renal Injury by Limiting Pyroptosis [ChIP-seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the control group of mTEC cells stimulated by LPS and the STAT3 silenced group.


title: LINE-1 transposable elements regulate the exit of human pluripotency and early brain development

city: Lund

first: Johan

last: Jakobsson

address: Sölvegatan 17

department: Wallenberg Neuroscience Center

country: Sweden

institute: Lund University

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

overall_design: Refer to individual Series


title: After stimulation by angiotensin II, changes occur in the aortic adventitial cells

first: xuelian

last: wang

address: Ruijin er road No.197

institute: Ruijin hospital

summary: Mice were stimulated with angiotensin Ⅱ, and vascular adventitial cells were extracted for single-cell sequencing analysis. Changes of DDR2 gene before and after stimulation

overall_design: The wide type mice were divided into control group and angiotensin  Ⅱ stimulation group. After 4 weeks, the samples from adventitial cells were aggregated.

first: Gaojian

last: Huang

first: Xuelian

first: Qi

last: Jia

first: Zhen

last: Li


title: Skeletal Site-Specific Variations in CD11b+ Cells: Insights from Single Cell RNA Sequencing of the Mandible and Femur [ATAC-Seq]

first: Kim

last: Mansky

overall_design: ATAC-Seq of monocytes isolated from mouse femur long bones and mandibles. Four male mice were pooled per batch to create each pair of femur and mandible monocyte samples.

first: Rachel

last: Clark

first: Marissa

last: Macchietto

first: Sarah

last: Munro


title: Knockout of all nematode-specific NSPC genes expressed exclusively in excretory gland cell results in transcriptomic signatures indicating affected insulin signaling

city: Warsaw

first: Andrzej

last: Dziembowski

address: 4 Ks. Trojdena Street

country: Poland

institute: International Institute Of Molecular And Cell Biology In Warsaw

summary: The nematode Caenorhabditis elegans is one of the best-studied model organisms in molecular biology; however, many aspects of its physiology and the functions of many genes remain poorly understood. In this study, we investigated the role of nematode-specific NSPC proteins, recently identified as primary targets of poly(A) polymerase TENT-5. Surprisingly, we found that NSPCs are exclusively expressed in the excretory gland cell, a cell with still unclear functionality. Using an optogenetic approach, we precisely ablated the excretory gland cell and observed that nematodes exhibited no transcriptomic or physiological changes in its absence. Additionally, we generated and thoroughly studied a strain with deletion of all 18 NSPC genes, which revealed that, despite previous indications, NSPCs lack antimicrobial activity. Instead, the transcriptomic analysis showed that the absence of NSPCs strongly impacts DAF-2/DAF-16 insulin signaling, suggesting that NSPCs may function as neuropeptides influencing key C. elegans signaling pathways. Although further studies are required to elucidate the physiological effects of this regulation, our findings provide new insights into this unexplored part of nematode physiology.

overall_design: We implemented Illumina RNA sequencing to investigate differences in gene expression after ablation of the excreotry gland cell or deletion of nspc genes in C. elegans (either in CRISPR knockouts or RNAi silenced worms). Moreover, we checked the potential involvement of NSPCs in TENT-5 mediated polyadenylation by using Nanopore Direct RNA Sequencing .

first: Zuzanna

last: Mackiewicz

first: Vladyslava

last: Liudkovska


title: Dual STAT3/STAT5 inhibition as a novel treatment strategy in T-prolymphocytic leukemia

city: Leipzig

first: Marco

last: Herling

address: Johannisallee 32a

department: Department for Hematology, Cell Therapy, Hemostaseology, and Infectious Diseases

institute: University Clinic Leipzig

summary: T-prolymphocytic leukemia (T-PLL) is a rare, aggressive T-cell malignancy with poor outcomes and an urgent need for new therapeutic approaches. Integrating genomic data and new transcriptomic profiling, we identified recurrent JAK/STAT mutations as a hallmark in T-PLL in an unprecedented cohort of 335 T-PLL cases, predominantly involving JAK3 and STAT5B. In line, transcriptomic and immunoblot analyses revealed constitutive JAK/STAT activation in virtually all samples. Building on these findings, we explored the therapeutic potential of dual STAT3/STAT5 non-PROTAC degraders in T-PLL treatment, with JPX-1244 as our lead substance. JPX-1244 efficiently and selectively induced cell death in primary T-PLL samples, including those resistant to conventional therapies, by blocking STAT3/STAT5 phosphorylation and inducing their degradation. The extent of STAT3/STAT5 degradation directly correlated with cytotoxicity. RNA-sequencing confirmed the downregulation of STAT5 target genes. While JAK/STAT mutations did not predict treatment responses, elevated TOX, PAK6, and SPINT1 expression was associated with drug sensitivity. In a subsequent combination screening, cladribine, venetoclax, and azacytidine emerged as most effective combination partners even in low-responding T-PLL samples, synergistically reducing STAT5 phosphorylation. These findings highlight dual STAT3/STAT5 inhibition, particularly in combination with hypomethylating agents, as a promising therapeutic approach in T-PLL, warranting further preclinical and clinical investigation.

overall_design: In total, we performed bulk RNA-sequencing of 118 primary T-PLL samples, comprising 32 samples without treatment and/or stimulation, and eleven T-PLL patients in the context of JPX-1244 treatment (compared to DMSO control) and/or IL-6 stimulation (compared to unstimulated control), resulting in 4 conditions per patient and timepoint (8h and 24h, n=86 primary T-PLL samples after exclusion of 2 samples with low RNA quality).

first: Dechow

last: Annika

first: Ianevski

last: Aleksandr

first: Aittokallio

last: Tero

first: Braun

last: Till

first: Herling

last: Marco


title: Inducible re-epithelialization of cancer cells increases autophagy and DNA damage: implications for breast cancer dormancy

city: Rehovot

first: Sima

last: Lev

address: 234 Herzl St.

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

summary: Epithelial lineage differentiation is pivotal to mammary gland development and it can pause metastasis of breast cancer (BC) by inducing tumor dormancy. To simulate this, we expressed epithelial genes in mesenchymal BC cells. Inducible expression of the epithelial OVOL genes in metastatic BC cells suppressed proliferation and migration. We found that C1ORF116, an OVOL’s target, is susceptible to genetic and epigenetic aberrations in BC. It is regulated by steroids and functions as a putative autophagy receptor that inhibits antioxidants like thioredoxin. Accordingly, boosting epithelialization lowered glutathione, elevated reactive oxygen species and increased both DNA oxidation and double strand breaks. Epithelialization also associated with redistribution of NRF2 and an altered interplay among p38, ATM, and the other kinases regulating the DNA damage response. Hence, hormonal regulation of OVOLs and chronic stress might permit epithelial differentiation and retard exit from dormancy, while altering redox homeostasis and permitting DNA damage accumulation, which may awaken dormant tumors.

overall_design: RNA was sequenced from the human breast cancer cell line MDA-MB-231 harboring over-expression of OVOL1, and compared to control MDA-MB-231 cells. Four biological replicates were performed.

first: Yosef

last: Yarden

first: Diana

last: Drago Garcia


title: Expression of lncRNA and mRNA in the cumulus-oocyte complex of rabbits exposed to ammonia

city: Handan

first: Jia

last: Cui

address: 19 Taiji Road

institute: Hebei University of Engineering

summary: Background: Ammonia (NH3) is an environmental pollutant and a potent reproductive stressor widely found in rabbit houses. Exposure to ammonia can result in follicle atresia, affect oocyte maturation and cause cumulus cell apoptosis. Long non-coding RNA (lncRNA) is an important factor in the regulation of cumulus cell development and oocyte maturation. The potential molecular mechanism of NH3 in the induction of cumulus-oocyte complex (COCs) toxicity and the regulatory role of lncRNA in COCs are currently unclear. Methods: A total of 150 female IRA rabbits (35 days old) were randomly divided into three groups, and kept in environmental control rooms for four weeks. The rabbits in the control group (CG) were kept under an NH3 concentration of < 3 ppm. The two treatment groups were kept under NH3 concentrations of 10 ppm (low ammonia concentration, LAC) and 30 ppm (high ammonia concentration, HAC). We used a combination of RNA deep sequencing, quantitative real-time polymerase chain reaction (qRT-PCR), and bioinformatic analysis to explore the regulatory mechanism of lncRNA and messenger RNA (mRNA) in COCs. Results: The results from Gene Ontology (GO) items showed that female meiosis sister chromatid cohesion and the regulation of follicle-stimulating hormone secretion were involved in the mechanism of rabbits exposed to NH3. The results demonstrated that the mammalian target of the rapamycin (mTOR) signaling pathway and the transforming growth factor-beta (TGF-beta) signaling pathway inhibits germ cell development and follicular growth in the LAC versus the CG group. LncRNAs were involved in the apoptosis of female germ cells via the hypoxia-inducible factor (HIF-1) signaling pathway in the HAC versus the CG group. Co-expression analysis found that lncRNA MAPK3 and lncRNA SHC1 were correlated with changes in cumulus cell and oocyte function after NH3 exposure. Conclusions: These results indicate that NH3 affected the development and function of COCs by influencing lncRNA expression.

overall_design: A total of 150 female IRA rabbits (35-days-old) were randomly divided into three groups, and were kept in environment control rooms for four weeks.  The rabbits in the control group (CG) were kept under NH3 concentration of < 3 ppm.  The two treatment groups were kept under NH3 concentration of 10 ppm (low ammonia concentration, LAC) and 30 ppm (high ammonia concentration, HAC).  Then we used a combination of RNA deep sequencing, quantitative real-time polymerase chain reaction (qRT-PCR), and bioinformatic analysis to explore the regulatory mechanism of lncRNA and messenger RNA (mRNA) in cumulus-oocyte complex.


title: Pioneering new enhancers by GATA3: role of facilitating transcription factors and chromatin remodeling [RNA-seq]

first: Paul

last: Wade

address: 111 TW Alexander Drive

department: Laboratory of Molecular Carcinogenesis

institute: NIEHS

summary: The mechanistic details by which pioneer transcription factors interact with partner transcription factors and chromatin modification/remodeling enzymes to activate enhancers remains an emerging area of study. Here, we utilize inducible expression of the pioneer factor GATA3 and study cofactor association and structural alterations in local chromatin.  ATAC-seq analysis and footprinting revealed co-occurrence of GATA3 with other transcription factors, including AP-1, in newly accessible chromatin. GATA3 and AP-1 co-localize at primed enhancers with p300 and BRG1 where nucleosome positioning is responsive to GATA3 location, not to AP-1. Genetic inhibition of AP-1 binding alters chromatin opening at some, but not most, GATA3-bound loci. Pharmacologic inhibition of SWI/SNF ATPase function results in loss of GATA3-dependent chromatin accessibility, binding, and alterations in local chromatin architecture. We conclude that GATA3-dependent gains in chromatin accessibility require chromatin remodeling and that accessibility at some loci is facilitated by a partner transcription factor, in this case AP-1.

overall_design: Doxycycline (dox) inducible wildtype (wt) and TA1del (ta1) GATA3 cell lines were generated in SUM159PT basal breast cancer cell line.  RNAseq was performed for comparison of gene expression in wt and ta1-GATA3 cell lines with or without dox induction.

first: Krystal

last: Orlando


title: Pioneering new enhancers by GATA3: role of facilitating transcription factors and chromatin remodeling


title: A low temperature-sensitive regulator that enhances virulence in the kiwifruit canker pathogen Pseudomonas syringae pv. actinidiae

city: Nanjing

first: Xiaolong

last: Shao

state: Jiangsu

address: Nanjing Agricultural University,  No.1 Weigang

institute: Nanjing Agricultural University

summary: Pseudomonas syringae pv. actinidiae (Psa) is responsible for causing kiwifruit canker disease, which severely impacts on the global kiwifruit industry, leading to substantial economic losses. Cooler environmental temperatures (below 20℃) are known to favor the outbreak of this bacterial disease in the field. However, the specific mechanisms that enable Psa to adapt and thrive in such conditions have remained elusive. In this study, we discovered that the gene RS16350, encoding a heat shock protein, positively regulates pathogenicity in kiwifruit leaves at low temperature (16℃), but not at room temperature (28℃). Delving into the mechanics, we found that RS16350 directly interacts with HrpL, an RpoN-dependent RNA polymerase sigma factor that serves as a master regulator of the type III secretion system (T3SS) in Psa. This RS16350-HrpL interaction enhances HrpL’s binding affinity to hrp-box, which in turn elevates the expression of downstream T3SS genes, thereby boosting virulence. Consequently, we have designated RS16350 as TspR (temperature sensitive and pathogenic regulator). Our findings shed light on how a kiwi pathogen enhances its virulence in response to low temperatures, paving the way for the development of innovative strategies to combat kiwifruit canker disease.

sample_organism: Pseudomonas syringae pv. actinidiae str. Shaanxi_M228

overall_design: To investigate the impact of low temperatures on kiwifruit canker disease, we conducted transcriptomic profiling in T3SS-inducing medium (minimal medium, MM) at low temperature (16℃) and room temperature (28℃) to mimic field conditions conducive to the disease. The wild type Psa_M228 strain was cultured in MM at 28℃ for 2 hours and then transferred to 16℃ for 5 more hours, while the control group was cultured at 28℃ for a total of 7 hours.


title: Pioneering new enhancers by GATA3: role of facilitating transcription factors and chromatin remodeling [ATAC-seq]

overall_design: Doxycycline (dox) inducible wildtype (wt; 1-444aa) and TA1del (ta1; 126-444aa) GATA3 cell lines were generated in SUM159PT basal breast cancer cell line. ATAC-seq was performed for accesible chromatin in  +/- DOX conditions and +/- inhibitiors of transcription factor binding  (AFOS) or chromatin remodeling (BRM014).


title: Multicomponent Parenteral Lipid Emulsions Do Not Protect Against Liver Injury in Neonatal Pigs with Obstructive Cholestasis

city: Hous

first: Gregory

middle: Jude

last: Guthrie

state: TX

address: 1100 Bates St

department: Pediatrics

institute: Baylor College of Medicine

summary: Biliary atresia (BA) is a pediatric liver disease that often necessitates parenteral nutrition (PN) to support growth due to impaired liver function. While soy oil lipid emulsions (SLE) are commonly used in PN, they may contribute to cholestatic liver injury. In contrast, mixed oil lipid emulsions (MLE) have shown promise in preventing cholestasis in non-BA infants, potentially by restoring bile flow. However, their effectiveness in cases of complete bile duct obstruction, as seen in BA, remains uncertain. To explore the potential benefits of MLE in BA, we utilized a neonatal pig model of bile duct ligation (BDL). Pigs underwent either BDL or sham surgery and were subsequently fed either MLE or SLE via PN, or enterally with formula. The MLE-BDL pigs exhibited significantly greater weight gain compared to those fed SLE or formula enterally. Additionally, MLE-BDL pigs showed higher serum bile acid and gamma-glutamyl transferase concentrations compared to SLE-BDL pigs. However, no significant differences in liver injury, assessed by ductular reaction or fibrosis, were observed between MLE- and SLE-BDL pigs. Based on weight gain alone, MLE may be a superior lipid emulsion for use in neonates with obstructive cholestasis.

overall_design: Piglets at day 1 of life following c-section delivery were randomly assigned to receive either sham (sham) or bile duct ligtation surgery (BDL) and implanted with jugular catheters and orogastric tubes. After surgery, piglets were assigned to one of three diet groups: enteral feeds (ENT), or parenteral nutrition containing soy-based lipid (IL) or mixed lipid (SL). Piglets were maintained on these diets for 14 days then euthanized and liver samples were collected.


title: RNA sequencing analysis identifies sex differences in transcriptional signatures in the dorsal striatum of female and male rats after withdrawal from methamphetamine self-administration

city: Baltimore

first: Jean Lud

last: Cadet

address: 251 Bayview BLVD

department: Molecular Neuropsychiatry Research Branch

institute: National Institute On Drug Abuse

summary: Significant methamphetamine (METH)-induced behavioral differences exist between the two sexes of humans and other animals. These dissimilarities may be related to sexual dimorphism in baseline molecular and biochemical mechanisms in brain reward neuroanatomical pathways. As a first step towards identifying sex-based differences in methamphetamine-induced transcriptional signatures, we used RNA sequencing analysis to measure genome-wide changes in gene expression in the dorsal striatum of rats that had self-administered METH. We trained rats to self-administer METH (0.1 mg/kg/infusion, i.v.) using two 3-hr daily sessions (with 30 minutes time out between session) for 20 days. Control rats self-administered saline under similar conditions. This was followed by drug seeking tests on withdrawal days 3 (WD3) and 30 (WD30). Behavioral results show that male rats took more METH than female rats. In both male and female rats, some animals escalated (high-takers) whereas others did not escalate (low-takers) their METH intake during the behavioral experiment.  Rats were euthanized 24 hours after the second drug seeking test. RNA was extracted from the dorsal striatum (dSTR) and used in RNA sequencing analysis. The data identified substantial baseline differences in gene expression between female and male control rats. In addition, METH use and withdrawal were associated with significant sex-related differences in changes in striatal gene expression, with minimal overlaps of altered mRNAs. Thus, the present results provide further supporting evidence for sexually dimorphic responses to METH exposure. These observations support the notion of sex-specific approaches to the treatment of patients who suffer from METH use disorder.

first: Vaibhav

last: Gujar

first: Atul

last: Daiwile


title: Permeable lung vasculature creates chemoresistant endothelial niche by producing SERPINE1 at breast cancer metastatic sites

city: Kanazawa

first: Tsunaki

last: Hongu

address: Kakuma-machi

department: Cancer Research Institute

institute: Kanazawa University

summary: Chemotherapy resistance remains a major obstacle to eradicating metastatic cancer cells in distant organs. We identified that endothelial cells (ECs) in the lungs, where breast cancer cells often metastasize, form a chemoresistant perivascular niche for disseminated breast cancer cells. By investigating the lung EC secretome activated by metastasis, we found that serine protease inhibitor family E member 1 (SERPINE1), encoded by Serpine1, is upregulated in metastasis-associated lung ECs. This upregulation shields cancer cells from paclitaxel-induced apoptosis and promotes cancer stem cell properties. Serpine1 expression appears to be driven by YAP-TEAD activation in lung ECs that lose cell-cell contact, a phenomenon associated with increased vascular permeability in lungs affected by metastasis. Crucially, pharmacological inhibition of SERPINE1 enhances the chemotherapy sensitivity of metastatic breast cancer cells in the lung. Overall, our findings underscore the pivotal role of the vascular niche, which produces SERPINE1, in conferring chemoresistance to breast cancer cells during metastatic progression in the lungs.

overall_design: To investigate the function of SERPINE1 (PAI1) on breast cancer cells, we stimulated BT20 breast cancer cell line with recombinant PAI1 and performed gene expression profiling analysis using data obtained from RNA-seq of stilumated and unstimulated cells.

first: Noriko

last: Gotoh


title: The ferret bleomycin-induced model of lung fibrosis shares features of human idiopathic pulmonary fibrosis

city: South San Francisco

first: Ian

last: Driver

state: California

address: 486 Cabot Road

department: Bioinformatics

institute: Gordian Biotechnology

summary: In the present study, we report a bleomycin-induced ferret PF model characterized by an irreversible decrease in pulmonary compliance and increase of opacification, accompanied by “honeycomb cyst-like” structures, “proximalization” of distal lung epithelium. Cellular and molecular analysis by single-nucleus RNA sequencing analysis revealed a significant shift in distal lung epithelium towards proximal epithelial phenotype. Importantly, a histopathological pattern of bronchiolization encompassing divergent atypical epithelial cells, and KRT17+/TP63+/KRT5low “basaloid-like” cells, were present in the distal fibrotic lung lesions. Trajectory analysis revealed AT2 cells transition through multiple cell-states in bleomycin injured ferret lungs, particularly AT2 to KRT8high/KRT7low/SOX4+ to eventual KRT8high/KRT7high/SFN+/TP63+/KRT5low “basaloid-like” cells. Further, immunofluorescence analyses demonstrated KRT7 and KRT8 populations reside in close proximity to the ACTA2 positive myofibroblasts in fibrotic foci thereby driving fibrogenic phenotype in bleomycin injured ferret lungs. Collectively, our results provide evidence that the bleomycin ferrets can reproduce pathophysiological, cellular, and molecular features of human IPF disease, suggesting that they may be a reliable model for understanding mechanisms of IPF pathogenesis and for testing therapeutic strategies for treatment of IPF.

overall_design: Multiple (3x) low doses (2.5U/kg) of bleomycin were delivered to the lung of ferrets to induce a more rapidly progressive and irreversible pulmonary fibrosis. Lung structure/function studies (Pulmonary function tests and CT), cellular phenotyping by single nucleus RNA sequencing (snRNA-seq), and histopathologic cellular phenotyping were utilized to demonstrate the progressive and irreversible features of IPF that lead to honeycomb cysts and bronchiolization of the distal airspaces.

first: Engelhardt

last: John

first: Liu

last: Xiaoming

first: Shuang

last: Wu

first: Miyazaki

last: Hikaru

first: Shambhu

last: Smitha

first: Driver

last: Ian

first: Sontake

last: Vishwaraj


title: SIRT2 is a regulator of the differentiation block driven by SMARCB1 loss in ATRT [scRNA-seq]

city: AURORA

first: Etienne

last: Danis

state: CO

department: Cancer Center

institute: University of Colorado, Denver - Anschutz Medical Campus

summary: Atypical teratoid rhabdoid tumor (ATRT) is a highly aggressive brain tumor of childhood with a poor overall survival. The salient molecular feature of ATRT is the loss of SMARCB1 which results in epigenetic dysregulation of the genome. SMARCB1 loss affects lineage commitment and differentiation by controlling gene expression. We hypothesized that additional epigenetic factors co-operate with SMARCB1 loss to control cell self-renewal and drive ATRT. We identified SIRT2 as a primary dependency in ATRT. Using a combination of RNA-seq, CUT&RUN and single RNA sequencing in model systems ATRT, we observed genome-wide reorganization of active chromatin and significantly changes in genes expression in ATRT cells with genetic (with shRNA) or chemical (with Tenovin or Thiomyristoyl (TM)) SIRT2 deactivation. Single-cell RNA transcriptome analysis of xenograft tumors revealed the elimination of tumor cells expressing stem cell genes and expansion of tumor cells expressing differentiated genes in vivo. Furthermore, SIRT2 inhibition induced apoptosis, decreased tumor growth and prolonged survival in orthotopic xenograft models. In summary we demonstrated that SIRT2 inhibition is a molecular vulnerability in SMARCB1-deleted tumors with therapeutic potential.

overall_design: single-cell RNA sequencing on GFP-positive BT16ATRT cells. To study the impact of TM on differentiation in vivo, we performed single-cell RNA sequencing on GFP-positive BT16 ATRT cells. Cell were growing in mice cerebellum and treatment started when tumors were established. Mice were treated with either TM (50 mg/kg IP 3/week for 4 weeks) or DMSO(Vehichle controi).

first: Irina

last: Alimova

first: Dong

last: Wang

first: John

last: Desisto

first: Senthilnath

last: Lakshmanachetty

first: Eric

last: Prince

first: Rajeev

last: Vibhakar


title: Tumor microenvironment in the invasive and premalignant portions of early cutaneous squamous cell carcinoma (SCC)

city: Asan

first: Jeong-An

last: Gim

address: 22 Suncheonhyang-ro

institute: Soonchunhyang University

summary: Cutaneous squamous cell carcinoma (SCC) is known for its stepwise progression from healthy skin to premalignant actinic keratosis (AK), followed by malignant transformation into SCC. The main aim is to capture and compare gene expression patterns as AK progresses to SCC.

overall_design: From 17 patients, 34 ROIs (invasive and premalignant portions per patient) were selected, resulting in a total of 102 AOIs (tumor cell, immune cell, and fibroblast segments per ROI).

first: Chungyeul

last: Kim

first: Yoo Sang

last: Baek


title: Effect of FTO deletion on gene expression of HT29 and HCT116 in colon cancer cell lines

city: XIAN

first: xu

middle: chang

last: wei

address: 169 Changle West Road, Xincheng District

institute: AIR FORCE MEDICAL UNIVERSITY

summary: Colorectal cancer stands as one of the four most lethal malignancies globally, ranking second among women and third among men in terms of prevalence. The m6A RNA methylation process, mediated by various m6A regulatory genes, has been implicated in promoting the development and progression of tumors. However, the understanding of its involvement in colorectal cancer remains limited. Therefore, RNA sequencing (RNA-seq) was performed in HT29 and HCT116 cells following FTO knockout, as it functions as an oncogene and is one of the m6A erasers.

overall_design: To elucidate the role of FTO in the context of colorectal cancer,we knock out FTO in HT29 and HCT116 cells by CRISPR/Cas9 genome editing. Subsequently, we conducted gene expression profiling utilizing RNA-sequencing data derived from these cell lines.

first: Ling

last: Shen

first: Chang

last: Xu


title: Mesenchymal SLMAP coordinates with MST3 to govern gut elongation during development (scRNA-Seq)

city: Beijing

first: PAN

last: YUWEI

state: Beijing

address: 2 West Yuanmingyuan Road

department: College of biological sciences

institute: China Agriculture University

summary: Developing gut in mice undergoes rapid elongation during late embryogenesis, yet significantly slows down after birth. Precise regulatory mechanism of this dynamic morphogenetic process remains unknown. Utilizing single-cell RNA-sequencing analysis, we show that YAP activity in Cxcl13high intestinal fibroblasts is the major molecular contributor to gut elongation. To determine how mesenchymal YAP activity is controlled, we identified canonical Sarcolemma membrane-associated protein (SLMAP) as its critical regulator during embryonic gut morphogenesis. Deleting Slmap in gut mesenchyme impairs YAP activity, leading to short gut and a significant decrease in intestinal epithelial cell proliferation. Mechanistically, SLMAP activates YAP by directly regulating MST3 kinase. Physiologically, MST3 levels prominently increase over the developmental time, reaching their peak on postnatal day P14, when gut elongation in mice slows down. Depleting Mst3 in mesenchyme results in increased gut length at P14 accompanied by enhanced YAP activity. Importantly, short gut phenotype in mesenchyme-specific Slmap mutant mice is partially compensated by concomitant deletion of mesenchymal Mst3. Taken together, our findings demonstrate that SLMAP interacts with MST3 kinase to dynamically regulate mesenchymal YAP activity that governs dynamic gut elongation across its embryonic and postnatal development.

overall_design: To elucidate the cellular mechanism governing gut elongation, we performed scRNA-seq analysis on cells from mouse small intestine at E15.5, E17.5 and postnatal day 7 (P7).

first: Yuwei

last: Pan

first: Wuqi

last: Yang


title: RNA-Sequencing results of the human Gallbladder cancer (GBC) and adjacent tumor tissues (AT)

city: taiyuan

first: ming

last: gao

state: Shanxi

address: NO.56 Xinjian South Road

institute: Shanxi Medical University

summary: Here we report gene expression profiles of human gallbladder cancer (GC) and adjacent tumor (AT) tissues. This study revealed genes with significant changes in gallbladder cancer tissue, providing a basis for exploring the malignant progression of gallbladder cancer.

overall_design: Profiling of 7 GBC and 5 paired AT tissues were performed using RNA-seq. Total RNA was isolated using TRIzol reagent according to the manufacturer's protocol. RNA libraries were prepared for sequencing using standard Illumina protocols. Sequencing was performed in paired end reads using NovaSeq 6000 platform (Illumina).

first: Ming

last: Gao

first: Yutong

last: Zhang


title: Mesenchymal SLMAP coordinates with MST3 to govern gut elongation during development [RNAseq_TL]

summary: Developing gut in mice undergoes rapid elongation during late embryogenesis, yet significantly slows down after birth. Precise regulatory mechanism of this dynamic morphogenetic process remains unknown. Utilizing scRNA-seq analysis, we show that YAP activity in Cxcl13high intestinal fibroblasts is the major molecular contributor to gut elongation. To determine how mesenchymal YAP activity is controlled, we identified canonical Sarcolemma membrane-associated protein (SLMAP) as its critical regulator during embryonic gut morphogenesis. Deleting Slmap in gut mesenchyme impairs YAP activity, leading to short gut and a significant decrease in intestinal epithelial cell proliferation. Mechanistically, Slmap activates YAP by directly regulating Mst3 kinase. Physiologically, Mst3 levels prominently increase over the developmental time, reaching their peak on postnatal day P14, when gut elongation in mice slows down. Depleting Mst3 in mesenchyme results in increased gut length at P14 accompanied by enhanced YAP activity. Importantly, short gut phenotype in SlmapcKO mice is partially compensated by concomitant deletion of mesenchymal Mst3. Taken together, our findings demonstrate that Slmap interacts with Mst3 kinase to dynamically regulate mesenchymal YAP activity that governs gut elongation across its embryonic and postnatal development.

overall_design:
To test whether spliceosome-mediated alternative splicing (AS) partakes in gut elongation, we analyzed full-length bulk RNA-seq on small intestine mesenchyme between E17.5 and P14,
We conducted gene expression profiling analysis using data obtained from RNA-seq of the small intestinal mesenchyme from four wild-type E17.5 and four P14 mice


title: Mesenchymal SLMAP coordinates with MST3 to govern gut elongation during development

overall_design:
To understand the molecular mechanism underlying gut shortening caused by Slmap deletion, we performed bulk RNA-seq on small intestine tissues from control and Slmap-cKO E15.5 embryos (under C57BL6J background)
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 control embryo intestines and 4 Slmap-cKO embryo intestines