title: RNA-seq data of Hepatic Insulin Response  in Young and Aged Mice

city: New Haven

first: Jessica

middle: Yuki

last: Kasamoto

state: CT

address: 300 George Street

department: Computational Biology and Bioinformatics

institute: Yale University

summary: To investigate age-related differences in hepatic insulin response at the transcriptomic level, we profiled RNA sequencing in liver tissue from young (6-month-old) and old (20-month-old) male C57BL/6J mice following a hyperinsulinemic-euglycemic clamp. Mice underwent detailed metabolic phenotyping, including body composition analysis and indirect calorimetry, followed by surgical catheterization and a standardized insulin clamp procedure with stable isotope tracer infusions.  Liver tissue was collected immediately after the clamp, and RNA was extracted. The tracer studies enabled quantification of hepatic fluxes through pyruvate dehydrogenase, fatty acid oxidation, citrate synthase, and pyruvate carboxylase.

overall_design: This study investigates age-related differences in hepatic RNA sequencing in response to insulin stimulation using methylation array profiling. Male C57BL/6J mice aged 6 months (young) and 20 months (old) were obtained from The Jackson Laboratory (stock number: 000664). Mice were maintained under standard housing conditions and underwent comprehensive metabolic phenotyping.  Body composition was assessed using Bruker’s Minispec Whole Body Composition Analyzer. Mice were acclimated to single housing before being placed in metabolic cages (Columbus Instruments CLAMS) for measuring. Following phenotyping, mice underwent jugular vein catheterization and recovery. After a 14-hour overnight fast, a 150-minute hyperinsulinemic-euglycemic clamp was performed, during which [2H7]glucose was infused to maintain euglycemia (~115 mg/dL), along with continuous infusion of metabolic tracers [3-13C]lactate and [U-13C]palmitate to assess substrate flux (results contained in metadata).  After the clamp, mice were euthanized, and liver tissues were collected and snap-frozen. Bulk RNA paired-end sequencing was performed on the liver tissue using NovaSeq 6000 (Illumina) according to the manufacturer’s protocols.  The design comprises two biological groups: young (6-month-old, n=8) and old (20-month-old, n=10) insulin-stimulated mice.

first: John

middle: T

last: González

first: Olivia

middle: H

last: Scharfman

first: Zhu

last: Wanling

first: Kasamoto

last: Jessica

first: Gould

last: Victoria

first: Rachel

middle: J

last: Perry

first: Albert

last: Higgins-Chen


title: Inhibiting TGFβ-1 pathway reduces the aggressiveness of intrahepatic CCA HuCCT1 CD90 positive cells

status: Public on Jun 18 2025

city: Castellana Grotte (BA)

first: Grazia

last: Serino

address: Via Turi, 27

country: Italy

institute: National Institute of Gastroenterology “S. de Bellis”, Research Hospital

type: Expression profiling by high throughput sequencing

summary: Molecular mechanisms responsible for the poor prognosis in patients with intrahepatic cholangiocarcinoma (CCA) are still unknown, however, the stem cell marker cluster differentiation 90 (CD90), has been reported to be associated with a more aggressive cancer phenotype. In this scenario, TGFβ1 signaling pathway likely has a role as master gene regulator. Aim of the study is to investigate the role of CD90 in iCCA aggressiveness. The molecular profile of HuCCT1/CD90+ and HuCCT1/CD90- cells was obtained through transcriptomic analysis (NGS). Bioinformatic data were confirmed in both cell lines by qRT-PCR and western blot. Cells were treated with Gemcitabine in monotherapy or in combination with Galunisertib, a selective TGFβRI inhibitor in 2D and 3D models.  HuCCT1 CD90 positive cells are more proliferative, less migratory, and resistant to Gemcitabine treatment. Next, HuCCT1/CD90+ express lower levels of TGFβ1 compared to /CD90- cell lines. Finally, HuCCT1/CD90+ are resistant to Gemcitabine, while the combination of both Gemcitabine and Galunisertib displays a synergistic effect on HuCCT1/CD90+ cell proliferation. These results underline that CD90 inducing Gemcitabine resistance can be overcome by adding a TGFβ1 inhibitor such as Galunisertib, thereby moving further toward a precision medicine approach in patients with iCCA.

overall_design: We used RNA sequencing technology to understand the molecular changes of CD90 increase in iCCA cell line

first: Emanuele

last: Piccinno

first: Elena

last: Pizzuto

first: Gianluigi

last: Giannelli


title: Targeting TBK1 potentiates oncolytic virotherapy via RIPK1-ICAM1 mediated NK killing in chemo-resistant colorectal cancer [scRNA-seq]

city: Guangzhou

first: Xin

last: Guo

address: No. 106 Zhongshan Second Road, Yuexiu District, Guangzhou

country: China

institute: Guangdong Provincial People's Hospital

summary: Acquired chemo-resistance poses a significant challenge in cancer therapy and is a leading cause of cancer mortality. To address this issue, we explored the therapeutic potential of using oncolytic viruses (OVs) to combat chemo-resistant colorectal cancer (CRC). However, the sensitivities to different OVs, including VSVΔ51 and HSV-1, were significantly reduced in chemo-resistant CRC. Our investigation revealed that elevated TANK-binding kinase 1 (TBK1) expression in chemo-resistant CRC mediated the activation of the type I interferon pathway, which impaired viral replication and oncolysis. Inhibition of TBK1 enhanced viral replication and the antitumor efficacy of VSVΔ51 by amplifying RIPK1-mediated necroptosis both in vitro and in vivo. Analysis of immune cell profiles demonstrated that the combination treatment reshaped the tumor microenvironment and increased the influx and functional activity of natural killer (NK) cells. Immune cell depletion studies indicated that NK cells were essential for the synergistic therapeutic activity of the combination treatment. Mechanistically, TBK1 inhibitors synergized with VSVΔ51 to increase ICAM1 expression in a RIPK1-dependent manner, promoting NK cell-mediated killing. This study presents a promising approach for treating chemo-resistant CRC by combining OVs and TBK1 inhibitors.

overall_design: Four groups, 8 samples from murine subcutaneous tumor, and two replicates in each group.

first: Huolun

last: Feng

first: Yong

last: Li

first: Fan

last: Xing


title: The impact of metformin on placental ageing in humans and mice

city: Cambridge

first: Grace

middle: Jennifer

last: Hattersley

address: Hills Road

country: United Kingdom

institute: University of Cambridge

summary: Placental ageing refers to the physiological accumulation of a senescent phenotype over healthy pregnancy. In pregnancies affected by complications such as pre-eclampsia and fetal growth restriction, placental ageing is notably accelerated and observed at an earlier gestational age. Metformin is used during pregnancy for an increasing variety of indications, including treatment of gestational diabetes and may have a role in slowing cellular ageing. It is therefore essential to understand the potential impact of metformin on placental ageing. Placental samples (n=105) were obtained from women with BMI ≥30kg/m2 randomised to treatment with metformin or placebo during pregnancy. Ageing was assessed by measuring telomere length, histological examination, and using array-based technologies to investigate gene expression and methylation. Results were validated using isolated human trophoblasts treated in vitro with metformin, and in a complementary mouse model. There were no differences between metformin-exposed and control placentas in terms of telomere length, fibrosis, or calcification. There were no differences in placental gene expression or methylation patterns by metformin status. In our mouse model, no genes classically associated with cellular ageing were differentially expressed and no senescence pathway showed evidence of enrichment with metformin treatment. There was no evidence that metformin either slows or accelerates placental ageing pathways in the complementary models that we investigated. Our findings are reassuring with regards to the safety of metformin used to treat gestational diabetes, but do not support a role for metformin in the prevention of adverse pregnancy outcomes in non-diabetic women.

overall_design: Wild-type C57BL/6J mice obtained from Charles River Laboratories were bred in house. Female mice were ad libitum fed a well-established obesogenic diet (no. 824053, Special Dietary Services) (Fernandez-Twinn et al., 2012) supplemented with condensed milk (no. 12029969, Nestlé) from weaning (3 weeks of age). A first pregnancy was commenced at 6 weeks of age, and mating for the second pregnancy was commenced when the mice achieved a body weight of ≥35g (~18 weeks of age). The day of the plug was considered embryonic day 0.5 (E0.5) and fetuses were culled at E18.5. Mice were randomized to receive metformin (0215169-CF, MP Biomedicals) in the condensed milk one week before mating and throughout the subsequent pregnancy to a dose of 300mg/kg/day (equivalent to 1.7g in a 70kg man) (Salomäki et al., 2014). We calculated that a sample size of 12 per group would be sufficiently powered to detect differential gene expression using a log 2-fold change of 1, mean coefficient of variation of 0.4 and mean depth of coverage of 50. 35-45mg of placental tissue was isolated from 12 control and 12 metformin treated placentas. RNA was extracted using the miRNeasy micro kit (QIAGEN), with DNA contamination removed using the DNAse kit (QIAGEN). Both steps were performed according to the manufacturer’s instructions. RNA quality and concentration was assessed by nanodrop analysis. RNA integrity (RIN) of > 8 for all samples was confirmed by analysis with the Agilent Bioanalyser 2100 system (Agilent RNA 6000 Nano Kit). 400ng of total RNA was used for library construction (TruSeq Stranded mRNA Library Pre Kit; Illumina). Indexed libraries were normalized, pooled and sequenced on a NovaSeq 6000 (50bp paired-end).

first: Liu

last: Yang

first: Jane

middle: L

last: Tarry-Adkins

first: Antonia

last: Hufnagel

first: Kwun Kiu

last: Wong

first: Denise

middle: S

last: Fernandez-Twinn

first: India

middle: G

last: Robinson

first: Amanda

last: Drake

first: Rebecca

middle: M

last: Reynolds

first: Susan

middle: E

last: Ozanne

first: Catherine

last: Aiken


title: Replicative and irradiation-induced senescence of endothelial cells

city: Vienna

first: Johannes

middle: A.

last: Schmid

address: Schwarzspanierstr. 17

department: Vascular Biology and Thrombosis Research

country: Austria

institute: Med. Univ. Wien

summary: This research investigates cellular senescence in human umbilical vein endothelial cells (HUVECs), focusing on their implications for cardiovascular diseases. We employed RNA sequencing to analyze gene expression changes in HUVECs subjected to replicative- or stress-induced senescence via ionizing radiation. Our findings reveal that both senescence types exhibit significant upregulation of genes associated with epithelial-mesenchymal transition (EMT) and inflammatory pathways, indicating a shared molecular response.  Experimental validation confirmed reduced proliferation and increased secretion of pro-inflammatory cytokines (IL-6 and IL-8) in senescent cells and substantiated the upregulation of EMT marker genes. Additionally, we observed impaired wound healing capacity in senescent cells, highlighting the functional consequences of these cellular state. Our study underscores the critical role of senescence-related changes, contributing to the understanding of age-related cardiovascular pathologies.

overall_design: RNAseq profiling of early passage ("control" = young), replicative senescent ("senescent" = old) and gamma-irradiated ("irradiated") human umbilical vein endothelial cells (HUVECs) performed in technical triplicates,

first: Barbora

last: Belakova

first: José

last: Basílio

last: Breuss

first: Pavel

last: Uhrin

middle: A


title: Long-term exposure to secondary polyethylene terephthalate nanoplastics induces carcinogenesis in vitro

city: Bellaterra

first: Alba

last: Hernández

state: Barcelona

address: Campus UAB, s/n

department: Genetics and Microbiology

country: Spain

institute: Universitat Autònoma de Barcelona

summary: Micro and nanoplastics (MNPLs) are contaminants originated mainly from plastic waste degradation that pose potential health risks. Inhalation is a major exposure route, as evidenced by their detection in human lungs, with polyethylene terephthalate (PET) among the most abundant particles in respiratory airways. However, the harmful effects of particle bioaccumulation remain unclear, as chronic effects are understudied. To assess the long-term effects, specifically the carcinogenic effects, BEAS-2B cell line was exposed to PET-NPLs for 30 weeks. Genotoxicity, carcinogenic phenotypic hallmarks, and a panel of genes and pathways associated with cell transformation and lung cancer were examined and compared across three exposure durations. No significant effects were observed after 24 hours or 15 weeks of exposure. However, 30-week exposure led to increased genotoxic damage, anchorage-independent growth, and invasive potential. Transcriptomic analysis showed upregulation of several oncogenes and lung cancer-associated genes at the end of the exposure. Further analysis revealed an increase in differentially expressed genes over time and a temporal gradient of lung cancer-related genes. Altogether, the data suggest PET-NPLs' potential carcinogenicity after extended exposure, highlighting serious long-term health risks of MNPLs. Assessing their carcinogenic risk under chronic, real-life conditions is crucial to address knowledge gaps and eventually develop preventive policies.

overall_design: RNA-seq profiling of BEAS-2B chronic exposure to PET-NPLs during 24h, 15 weeks and 30 weeks.

first: Javier

last: Gutiérrez

first: Raquel

last: Egea

first: Irene

last: Barguilla

first: Penny

last: Nymark

last: García-Rodríguez

first: Boris

last: Guyot

first: Veronique

last: Maguer-Satta

first: Ricard

last: Marcos

first: Laura

last: Rubio


title: Transcriptomic analyses of ovarian clear cell carcinoma sphe-roids reveal distinct proliferative phenotypes and therapeutic vulnerabilities

city: London

first: Gabriel

last: DiMattia

state: ONTARIO

address: 750 Base Line Rd E

department: Biochemistry

country: Canada

institute: Western University

summary: Cancer cell spheroids autonomously form in the ascites fluid and are considered a conduit for epithelial ovarian cancer metastasis within the peritoneal cavity. Spheroids are homotypic, avascular, 3D structures that acquire resistance to anoikis to remain viable after cellular detachment. We used in vitro spheroid model systems to interrogate pathways critical for spheroid cell proliferation, distinct from those driving monolayer cancer cell proliferation. Using the 105C and KOC-7c human ovarian clear cell carcinoma (OCCC) cell lines, which have distinct proliferative phenotypes as spheroids but the same prototypical OCCC gene mutation profile of constitutively activated AKT signaling with loss of ARID1A, we revealed therapeutic targets that efficiently kill cells in spheroids. RNA-seq analyses compared the transcriptome of 3-day monolayer and spheroid cells from these lines and identified the characteristics of dormant spheroid cell survival which included the G2/M checkpoint, autophagy, and other stress pathways induced in 105C spheroids, in sharp contrast to the proliferating spheroid cells of the KOC-7c cell line. Next, we assessed levels of various G2/M checkpoint regulators and found a consistent reduction in steady-state levels of checkpoint regulators in dormant spheroid cells but not proliferative spheroids. Our studies showed that proliferative spheroid cells were sensitive to Wee1 inhibition by AZD1775, but the dormant spheroid cells showed a degree of resistance to AZD1775, both in terms of EC50 values and spheroid reattachment abilities.  In doing so, we have identified biomarkers of dormant spheroids, including the G2/M checkpoint regulators Wee1, Cdc25c, and PLK1, and showed that, when compared to proliferating spheroid cells, the transcriptome of dormant OCCC spheroids is a source for therapeutic targets.

overall_design: Cell lines were cultured in monolayer or suspension and collected on day 3 for bulk RNA-sequencing

first: Bart

last: Kolendowski

first: Sylvia

last: Cheng

first: Yudith

middle: R

last: Valdes

first: Trevor

last: Shepherd


title: Expression profiling and function analysis identified new cumulus cells-expressed genes and miRNAs predictive of oocyte developmental potential

city: TaiAn

first: min

last: zhang

state: ShanDong

address: 61 Daizong Street

department: College of Animal Science and Technology

institute: ShanDongAgricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: Although studies have identified cumulus cells (CCs)-expressed genes/miRNAs that regulate cumulus expansion and/or CC apoptosis and may be used as markers for selection of competent oocytes/embryos, CCs-expressed genes/miRNAs whose expression levels are directly correlated with oocyte developmental potential (DP) are urgently needed. To identify CCs-expressed DP-directly-related genes/miRNAs, we first established CC models from mouse cumulus-oocyte-complexes that showed significantly different DP after maturation in vitro or in vivo. By conducting mRNA/miRNA sequencing and functional analysis using such in vitro and in vivo CC models, we identified and validated new sets of CCs-expressed genes/miRNAs, whose expression levels were directly correlated with oocyte DP. Thus, we identified and validated Spp1, Fn1, Sdc1 and Ngf as DP-beneficial genes, Fos and Jun as DP-detrimental genes, and miR-7686-5p, miR-133a-3p, novel-miR-239, novel-miR-193 and miR-339-5p as DP-detrimental miRNAs. Furthermore, the close similarities in top KEGG pathways among 4 different experiments suggest that CCs-expressed genes and/or miRNAs regulate oocyte DP mostly indirectly through regulating cumulus expansion and/or CC apoptosis. The new genes/miRNAs identified can be used as markers for selection of competent oocytes/embryos, and the data will contribute to elucidating oocyte maturation mechanisms.

overall_design: Mouse COCs were cultured for 18 h in good (GMS) or poor maturation system (PMS) before harvesting CCs for isolation of mRNAs and miRNAs (Fig. 1). The isolated mRNAs and miRNAs were subjected to RNA- and miRNA-seq to identify differentially expressed (DE) genes and miRNAs, respectively. To select genes, the DE genes were subjected to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment and the top enriched genes obtained were subjected to protein–protein interaction (PPI) analysis to obtain the top degree genes. Candidate genes were selected from the top degree genes. To select miRNAs, target genes were predicted from the DE miRNAs and were overlapped with the DE genes identified by RNA-seq to determine the potential genes. The potential genes were subjected to KEGG to obtain the top enriched genes, which were subjected to PPI to get the top degree genes. Candidate miRNAs were predicted from the top degree genes. The candidate genes and miRNAs were subjected to an in vivo COC validation before functional analysis. For functional analysis, COCs were transfected with siRNA or gene overexpression (GOE) vectors of the candidate genes, or with mimics (MM) or inhibitors (IN) of the candidate miRNAs, and the transfected COCs were cultured in GMS before assessment of DP to determine the DP-related (DPR) genes or miRNAs, respectively.

first: Jing-He

last: Tan

first: Jie

last: Zhang

first: Min

first: Mengmeng

last: wang

last: HE

first: Shuai

last: Gong

first: Fali


title: Mitochondrial dysfunction charachterizes the multigenerational effects of maternal obesity on MASLD

city: Ghent

first: Yannick

last: Gansemans

address: Ottergemsesteenweg 460

department: Pharmaceutical Sciences

country: Belgium

institute: Ghent University

summary: Although maternal obesity is an independent risk factor for metabolic dysfunction-associated steatotic liver disease (MASLD), the pathogenesis remains unclear. We aimed to evaluate the effect and mechanisms of multigenerational maternal western diet (WD) on MASLD progression, and test drug candidates in a preclinical model. Female mice were fed WD from 8 weeks before breeding initiation with a normal chow (NC)-fed male, throughout pregnancy and lactation. Male offspring were weaned onto NC or WD and assessed at the age of 16 weeks. Maternal WD feeding aggravated body weight gain, insulin resistance, steatosis and inflammation. Fibrosis was only observed in offspring exposed to maternal WD. Mechanistically, the latter exhibited reduced OXPHOS activity. Maternal WD aggravates MASLD in male offspring, with mitochondrial dysfunction contributing to disease severity.

overall_design: 8-week-old female C57BL/6J mice were fed either Western diet (WD) or normal chow (NC) control for 8 weeks before breeding to a NC-fed male. Diet was maintained during breeding and lactation. Female offspring were weaned onto NC and used to produce the next generation in the same way as the first generation. Offspring from the second generation were weaned onto WD or NC. In this way, four groups of offspring were generated: NC-fed offspring without maternal obesity (healthy controls, NC/NC), WD-fed offspring without maternal obesity (NC/WD), and WD-fed offspring with one or two generations of maternal obesity (WD/WD and WD/WD/WD respectively).

first: Anneleen

last: Heldens

first: Milton

last: Antwi

first: Louis

last: Onghena

first: Tim

last: Meese

first: Joél

last: Smet

first: Ellen

last: Dupont

first: Xavier

last: Verhelst

first: Sarah

last: Raevens

first: Hans

last: Van Vlierberghe

first: Arnaud

last: Vanlander

first: Filip

last: Van Nieuwerburgh

first: Lindsey

last: Devisscher

first: Ruth

last: De Bruyne

first: Anja

last: Geerts

first: Sander

last: Lefere


title: Charting the single cell transcriptional landscape governing visual imprinting

status: Public on Jun 19 2025

city: Thuwal

first: Vincenzo

last: Lagani

address: 4700 King Abdullah University of Science and Technology

country: Saudi Arabia

summary: We investigated transcriptional changes associated with memory formation in the avian brain by performing single-nucleus RNA sequencing of the intermediate medial mesopallium (IMM) in imprinted and untrained chicks.

overall_design: Trained, good learner chicks contrasted versus untrained chicks. In short, Twenty-four hours post-hatching, chicks were exposed to a rotating red cuboid light while positioned in a running wheel, followed by a preference test conducted ten minutes later to assess memory strength. Individuals scoring above 80—indicating a strong preference for the training stimulus over an alternative—were classified as good learners. After an additional 24 hours, these chicks were sacrificed and their left intermediate medial mesopallium (IMM) was dissected for analysis. Untrained, stimulus-naive chicks served as controls.

first: Lela

last: Chitadze

first: Lia

last: Tsverava

first: Revaz

last: Solomonia


title: Fibrogenic gene signature as early prediction for the efficacy of pharmacological interventions for MASH-associated fibrosis, part2

city: Leiden

first: Anita

last: van den Hoek

state: Zuid-Holland

address: Zernikedreef 9

department: MHR

country: Netherlands

institute: TNO

summary: Background and aims: The incidence of metabolic dysfunction-associated steatohepatitis (MASH) and associated liver fibrosis is rapidly increasing, while pharmacological treatment options remain limited. Despite great efforts in developing novel MASH therapeutics, many investigative therapeutics that reduced fibrosis in preclinical models ultimately lacked efficacy in clinical trials. Therefore, we explored the possibility to predict the efficacy of investigative therapeutics on fibrogenic drive in the early stages of disease development and before effects on pathology become evident.  Methods: Ldlr-/-.Leiden mice were fed a high-fat diet (HFD) to induce obesity and MASH. Mice were subsequently treated for four weeks with various therapeutics with established efficacy (obeticholic acid) or lack of efficacy (cenicriviroc, pioglitazone) to study their anti-fibrotic potential. Next, expression of a fibrogenic gene signature was evaluated, which predicts profibrotic processes preceding histopathologic fibrosis. The predictions were validated in parallel with a long-term experiment reaching histological fibrosis endpoints.  Results: Cenicriviroc and pioglitazone did not affect HFD-induced fibrosis signature, indicative of no effect of these treatments on active fibrosis processes. Consistently, in the long-term treatment study, both cenicriviroc and pioglitazone did not affect HFD-induced histologically measured fibrosis. In contrast, obeticholic acid improved the early fibrogenic gene signature indicating a less fibrotic state compared with untreated HFD controls. These early gene expression changes aligned with long-term histological fibrosis endpoints and clinical data on these investigative therapeutics.  Conclusions: This study highlights the potential of using short-term studies and applying a fibrogenic gene signature as an early screening tool to investigate the efficacy of investigative drugs on MASH-associated fibrosis. This signature, which is based on the active fibrosis processes in humans, may allow rapid screening of therapeutics and their combinations in translational mouse models to save time and resources.

overall_design: Ldlr-/-.Leiden mice were fed a high-fat diet (HFD) to induce obesity and MASH. Control mice were continuously fed on standard Chow diet (C). Mice were subsequently treated for four weeks with various therapeutics with established efficacy (obeticholic acid = OCA; at either 10 or 20 mg/kg/day) or lack of efficacy (cenicriviroc = Ce, pioglitazone = Pi) to study their anti-fibrotic potential. Next, liver expression of a fibrogenic gene signature was evaluated. Note that this GEO entry (title, part2) only deals with a set of Chow, HFD, cenicriviroc and pioglitazone fed mice that were analysed in sequencing run 105831-001. Another GEO entry (title, part1) deals with a set of Chow, HFD and OCA fed mice that were analysed in sequencing run 104930-001.

first: José

last: Inia

first: Martine

middle: C

last: Morrison

first: Arianne

last: van Koppen

first: Eveline

last: Gart

first: Martien

middle: P

last: Caspers

first: Aswin

last: Menke

first: Nicole

last: Worms

first: Robert

last: Kleemann

first: Lars

last: Verschuren

first: J

middle: W

last: Jukema

last: Princen

first: Roeland

last: Hanemaaijer


title: Differential susceptibility and role for senescence in CART cells based on costimulatory domains

city: Rochester

first: Saad

last: Kenderian

state: MN

address: 200 1st St SW

country: USA

institute: Mayo Clinic

summary: Despite the success of chimeric antigen receptor T (CART) cell therapy in hematological malignancies, durable remissions remain low. Here, we report CART senescence as a potential resistance mechanism in 41BB-costimulated CART cell therapy. To mimic cancer relapse, we utilized an in vitro model with repeated CART cell activation cycles followed by rest periods. Using CD19-targeted CART cells with costimulation via 4-1BB-CD3ζ (BBζ) or CD28-CD3ζ (28ζ), we showed that CART cells undergo functional, phenotypical, and transcriptomic changes of senescence, which is more prominent in BBζ. We then utilized two additional independent strategies to induce senescence through MYC activation and irradiation. Induction of senescence impaired BBζ activity but improved 28ζ activity in preclinical studies. These findings were supported by analyses of independent patient data sets; senescence signatures in CART cell products were associated with non-response to BBζ but with improved clinical outcomes in 28ζ treatment. In summary, our study identifies senescence as a potential mechanism of failure predominantly in 41BB-costimulated CART cells.

overall_design: RNA-seq profiling of T cells (T_cell_D0) collected from three different normal donors and chimeric antigen receptor T (CART) cell generated from those T cells. T cells are divided into three groups to generate Day 8 (D8) untransduced control (UTD_D8), D8 CD19 targeting 4-1BB costimulated CART cells (CART19-4-1BB_D8) and D8 CD19 targeting CD28 costimulated CART cells (CAR19-CD28_D8). D8 CART cells are recurrently activated/rested to generate UTD_D15, CART19-4-1BB_D15 and CAR19-CD28_D15.

first: Ismail

last: Can


title: VimR is a conserved transcription regulator controlling virulence and metabolism in Pseudomonas syringae

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

summary: Pseudomonas syringae, a highly destructive plant bacterial pathogen causing severe disease and significant yield losses in agriculture globally, has complex regulatory systems involving many transcriptional factors (TFs). Although the LysR-type transcriptional regulator (LTTR) family proteins are a well-known group of TFs involved in diverse physiological functions, the roles of LTTRs in P. syringae are still largely unknown. In this study, we characterised a LysR-type TF, PSPPH4638, which is a virulence and metabolism regulator (VimR) with multiple functions. Genome-wide identification of VimR using chromatin immunoprecipitation sequencing revealed 1,032 binding sites in the genome, of which 85% were in intergenic regions. Transcriptomic analysis showed altered expression of 454 and 82 genes in response to vimR deletion in King’s B medium (KB) and minimal medium, respectively. Conjoint analysis showed that 99 genes were directly affected by VimR in KB. VimR was identified as a repressor of the type III secretion system, oxidative stress response and key metabolic pathways such as the tricarboxylic acid cycle. In addition, we found that VimR was positively involved in the type VI secretion system and alanine, aspartate and glutamate metabolism. Taken together, our findings identified a new TF VimR and revealed its important functions in P. syringae. This is the first time to describe a transcription factor that regulates both type III secretion system and type VI secretion system and multiple metabolic pathways in Pseudomonas syringae.

sample_organism: Pseudomonas savastanoi pv. phaseolicola 1448A

overall_design: RNA-seq profiling of P. savastanoi pv. phaseolicola 1448A (Psph) and vimR deletion derivative in KB and MM , and  P. aeruginosa PAO1(PAO1) and PA3565 overexpressing derivative in LB

first: Fang

last: Chen

first: Yue

last: Sun

first: Jiadai

last: Huang

first: Tianmin

last: Li

first: Zhe

last: He

first: Jingwei

first: Tianqi

last: Wang

first: Haiyan

last: Hu

last: Deng


title: Gene expression analyses in mouse sensory ganglia determine a crucial role of NGF/TrkA in knee osteoarthritis chronification

city: Salamanca

first: Juan Carlos

last: Arevalo

address: C/ Pintor Fernando Gallego, 1

department: INCyL

institute: University of Salamanca

summary: Objective: Osteoarthritis (OA) can be experimentally induced by injecting mono-iodoacetate (MIA) in the knee capsule of mice. Our aim was to assess the role of NGF/TrkA axis in OA identifying differentially expressed genes (DEGs) and functional pathways in knee-innervating dorsal root ganglia (DRG) from WT and hypersensitive TrkAP782S (KI) mice after MIA injection. Method: We performed saline or MIA-injection in knee joints of WT and KI mice and harvested L3-L5 DRGs at 5 and 21 days after injection, pooling males and females (n = 4/group). RNA was extracted and microarray analysis was performed. Upon comparisons between different groups, identification of DEGs was defined as adjusted P < 0.01. Gene ontology, pathway analysis and protein interactions were conducted using Gene Set Enrichment Analysis over Gene Ontology and REACTOME databases, and STRING database. Results: For each comparison regarding genotype (WT vs KI), numerous DEGs were identified but with limited overlap, being Lingo1, Socs2, and Slc4a4 already related to pain, OA and/or NGF/TrkA axis. Regarding comparisons of early vs late OA (D5 vs D21), many more DEGs were revealed including genes previously implicated in OA such as Gal, Gja1, and Lep. Moreover, we found enriched pathways in the KI_MIA group such as gene expression, neuronal system and signal transduction, in which NTRK1 and MAPK pathways indicate specificity in the NGF/TrkA axis and in the transition from early to late OA pain. Conclusions: Our results identify new mouse DEGs and pathways that demonstrate the relevance of the NGF/TrkA system in the chronification of OA pain.

overall_design: We performed saline or MIA-injection in knee joints of WT and KI inbreed litermates mice and harvested L3-L5 DRGs at 5 and 21 days after injection (n = 4/group, a total of 32 animals). Experimental groups were block randomized, and an equal number of 3-5 months old-male and -female mice was used and the data combined because no differences were found in previous results (sousa-Valente et al. 2018). Researchers who performed behavioral experiments and microarray analyse were blind to genotype and treatment.

first: Daniel

last: Cañada-Garcia

first: Laura

last: Calvo

first: Silvia

last: Lisa

first: Joao

last: Sousa-Valente

first: Marta

last: López-García

first: Ivan

last: Arisi

first: Mara

last: D'Onofrío

first: Carlos

last: Prieto

first: Juan

last: Arévalo


title: Physiological changes in maternal glucose levels in pregnancies complicated by diabetes impact the human placental transcriptome

city: Leeds

first: Abigail

middle: Rose

last: Byford

address: Clarendon Way

institute: University of Leeds

summary: Recent continuous glucose monitoring (CGM) studies have revealed that in pregnancies complicated by maternal diabetes, fluctuations in maternal glucose are linked to complications of fetal growth. The underlying mechanisms are unclear but likely involve the placenta. We cultured ex vivo human placental explants from term uncomplicated pregnancies with medium changes every 6-18 hours in variable (5/5.5 mM; normoglycaemia), or constant 5 mM (mild hypoglycaemia) or 7 mM glucose (mild hyperglycaemia) for 48 hours to recapitulate in vivo maternal glucose profiles and performed RNA sequencing. Additional placental explants were also exposed to 5.5 mM glucose.

overall_design: RNA sequencing of human term placental explants from uncomplicated pregnancies exposed to either constant 5-, 5.5- 7-mM glucose, or fluctuating 5/5.5 mM glucose for 48 hours.

first: Byford

last: Abigail

first: Walsh

last: Katy

first: Wang

last: Dapeng

first: Baird-Rayner

last: Chloe

first: Pensabene

last: Virginia

first: Scott

last: Eleanor

first: Forbes

last: Karen


title: Novel prognostic biomarkers in central neurocytoma

city: Berlin

first: Leonille

last: Schweizer

address: Charitépl. 1

country: Germany

institute: Charité - Universitätsmedizin

type: Methylation profiling by genome tiling array

summary: Central neurocytomas (CN) are intraventricular brain tumors predominantly occurring in young adults. Although prognosis is usually favorable, tumor recurrence is common, particularly following subtotal resection (STR). Currently, the risk of progression is evaluated using histopathological criteria, such as atypical features and elevated Ki67 proliferation index. However, these markers lack consistent definitions and application. Genome-wide DNA methylation profiles were examined in 136 tumors histologically classified as CN. Clinical and histopathological characteristics were assessed in 93 and 90 cases, and whole-exome sequencing was conducted in 12 cases. Clinical and molecular characteristics were integrated into a survival model to predict progression-free survival (PFS). A diagnosis of CN was epigenetically confirmed in 125 of 136 cases (92%). No DNA methylation subgroups associated with risk were identified, but global DNA hypomethylation emerged as a hallmark feature of CN. Hypomethylation at the FGFR3 locus, accompanied by increased FGFR3 protein expression, was observed in 97% of cases. Exome-sequencing revealed BCR frameshift mutations in 3/12 cases. Gross total resection was associated with significantly improved PFS compared to subtotal resected tumors (STR), while patients undergoing STR benefited from adjuvant radiotherapy (p = 0.00088). Younger patients were identified as having a higher risk of recurrence (p = 0.026). Patient age and treatment strategy were key factors influencing survival outcomes in this cohort. These findings underscore the importance of closer follow-up for younger patients and recommend radiotherapy for STR cases. Furthermore, FGFR3 represents a hallmark feature and potential therapeutic target warranting further investigation.

overall_design: The  cohort (125 cases) comprises 111 primary and 22 recurrent samples (of which 8 were matched with primary samples, including 2 samples from second recurrence).

first: Amos

last: Muench


title: Splenic CD169+Tim4+ Marginal Metallophilic Macrophages Are Essential for Wound Healing After Myocardial Infarction

city: St Louis

first: Sumanth

last: Prabhu

state: MO

address: 1 Brookings Dr

department: Department of Cardiology

institute: Washington University in St Louis

summary: Fidelity of wound healing after myocardial infarction (MI) is an important determinant of subsequent adverse cardiac remodeling and failure. Macrophages derived from infiltrating Ly6Chi blood monocytes are a key component of this healing response; however, the importance of other macrophage populations is unclear. Here, using a variety of in vivo murine models and orthogonal approaches, including surgical myocardial infarction, splenectomy, parabiosis, cell adoptive transfer, lineage tracing and cell tracking, RNA sequencing, and functional characterization, we establish in mice an essential role for splenic CD169+Tim4+ marginal metallophilic macrophages (MMMs) in post-MI wound healing. Splenic CD169+Tim4+ MMMs circulate in blood as Ly6Clow monocytes expressing macrophage markers and help populate CD169+Tim4+CCR2-LYVE1low macrophages in the naïve heart. After acute MI, splenic MMMs augment phagocytosis, CCR3 and CCR4 expression, and robustly mobilize to the heart, resulting in marked expansion of cardiac CD169+Tim4+LyVE1low macrophages with an immunomodulatory and pro-resolving gene signature. These macrophages are obligatory for apoptotic neutrophil clearance, suppression of inflammation, and induction of a reparative macrophage phenotype in the infarcted heart. Splenic MMMs are both necessary and sufficient for post-MI wound healing, and limit late pathological remodeling. Liver X receptor-a agonist-induced expansion of the splenic marginal zone and MMMs during acute MI alleviates inflammation and improves short- and long-term cardiac remodeling. Finally, humans with acute ST-elevation MI also exhibit expansion of circulating CD169+Tim4+ cells, primarily within the intermediate (CD14+CD16+) monocyte population. We conclude that splenic CD169+Tim4+ MMMs are required for pro-resolving and reparative responses after MI and can be manipulated for therapeutic benefit to limit long-term heart failure.

overall_design: Naive mouse peripheral blood underwent erythrocyte lysis and leukocytes were centrifuged and collected immediately. Cells were stained with  DAPI and  Draq5  for 5 min. Cells were diluted to 4 mL for sorting, and viability was verified by ethidium homodimer (EtHD) staining.

first: Mohamed Ameen

last: Ismahil

first: Guihua

last: Zhou

first: Shreya

last: Rajasekar

first: Min

last: Gao

first: Shyam

last: Bansal

first: Bindiya

last: Patel

first: Nita

last: Limdi

last: Xie

first: Sergey

last: Antipenko

first: Gregg

last: Rokosh

first: Tariq

last: Hamid

middle: D


title: METTL3 mediated m6A modification of HKDC1 promotes renal injury and inflammation in lead nephropathy via binding to ATPB

city: Hefei

first: guo

middle: Xiao

last: Suo

address: No. 81 Meishan Road, Shushan District, Hefei City, Anhui Province

institute: anhui medical university

summary: Environmental and industrial Pb exposure poses a major public health problem. Acute exposure to high Pb concentrations can result in renal injury. Here, we reveal that N6-methyladenosine (m6A) RNA methylation is significantly upregulated in lead nephropathy and is mainly mediated by the methyltransferase METTL3. Functionally, METTL3 knockout in renal tubular epithelial cells or AAV9 mediated METTL3 silencing alleviated renal injury and inflammatory response induced by lead acetate. METTL3 silencing in HK2 cells reduces m6A RNA methylation and inflammatory responses following lead acetate treatment. We identified hexokinase domain-containing 1 (HKDC1), which is known to function in the glycolytic pathway, as a direct METTL3 target. Moreover, HKDC1 was upregulated at both mRNA and protein levels after lead acetate treatment, promoting kidney injury and inflammation. Mechanistically, HKDC1 binds to ATPB and antagonises the ubiquitinase Murf1, thereby increasing ATPB expression. Therefore, excessive ATP is generated to activate the NF-κB signalling pathway and promote renal inflammation. We further confirmed that STM2457, a novel inhibitor of METTL3, protects against renal injury and inflammation induced by lead acetate. Collectively, our study demonstrates that the METTL3/HKDC1 axis is a potential target for the treatment of lead nephropathy, and STM2457 is expected to be a protective agent against renal injury caused by lead acetate.

overall_design: This study was designed to investigate the underlying mechanism impact of m6A RNA modifications in heavy metal lead-induced renal diseases and find effective treatment, we performed m6A-RIP-seq and RNA-seq analyses in  lead acetate-exposed mice with or without METTL3 cKO

first: Xiao guo

first: Xiao ming

last: Meng


title: Cardiomyocyte mitochondrial mono-ADP-ribosylation dictates cardiac tolerance to sepsis by configuring bioenergetic reserve

city: xiamen

first: XiaoQiang

last: Chen

address: 2999 Jinshan Road,Huli District,Xiamen,Fujian Province

institute: Xiamen Cardiovascular Hospital, Xiamen University School of Medicine

summary: The metabolic flexibility of tissues dictates the extent and reversibility of organ damage during inflammatory challenges. However, there are currently no countermeasures for myocardial metabolic breakdown in the treatment of septic cardiomyopathy (SCM). Nicotinamide adenine dinucleotide (NAD+) signaling is crucial for maintaining cellular metabolic homeostasis and modulating inflammatory responses. Through the use of single-cell sequencing technology, specifically the 10x Genomics scRNAseq approach, we have investigated the role of NAD+ signaling-related genes in SCM. Our findings reveal that both genetic and pharmacological inhibition of the mono-ADP-ribosyl hydrolase MacroD1, which is highly expressed in cardiomyocytes, can effectively counteract the myocardial metabolic impairment, inflammation, dysfunction, and mortality risk triggered by lipopolysaccharide exposure and cecal ligation and puncture in mice.

overall_design: We applied lipopolysaccharide via intraperitoneal injection in mice to establish a septic cardiomyopathy model, and harvested the hearts 18 hours post-administration. The cardiac tissues were enzymatically digested into a single-cell suspension and subjected to single-cell sequencing.

first: Xiaoqiang


title: Fibrogenic gene signature as early prediction for the efficacy of pharmacological interventions for MASH-associated fibrosis, part1

first: Anita

last: van den Hoek

overall_design: Ldlr-/-.Leiden mice were fed a high-fat diet (HFD) to induce obesity and MASH. Control mice were continuously fed on standard Chow diet (C). Mice were subsequently treated for four weeks with various therapeutics with established efficacy (obeticholic acid = OCA = O; at either 10 or 20 mg/kg/day) or lack of efficacy (cenicriviroc = Ce, pioglitazone = Pi) to study their anti-fibrotic potential. Next, liver expression of a fibrogenic gene signature was evaluated. Note that this GEO entry (title, part1) only deals with a set of Chow, HFD and OCA fed mice that were analysed in sequencing run 104930-001. Another GEO entry (title, part2) deals with another set of Chow, HFD, cenicriviroc and pioglitazone fed mice that were analysed in sequencing run 105831-001.

first: José

last: Inia

first: Martine

last: Morrison

first: Arianne

last: van Koppen

first: Eveline

last: Gart

first: Martien

last: Caspers

first: Aswin

last: Menke

first: Nicole

last: Worms

first: Robert

last: Kleemann

first: Lars

last: Verschuren

first: J

last: Jukema

first: Hans

last: Princen

first: Roeland

last: Hanemaaijer


title: Toxicity and absorption of polystyrene micro-nanoplastics in healthy and Crohn's disease human duodenum-chip models

city: Piscataway

first: Michael

last: Verzi

state: NJ

address: 145 Bevier Road,

department: Department of Genetics

institute: Rutgers University

summary: Micro and nanoplastics (MNPs) are widespread contaminants of our environment and food web that can be absorbed by the intestine and distributed to most or all organs, and may cause significant toxicity and dysfunction. In our recent study, we investigated the toxicity and mechanisms underlying uptake and translocation of 26 nm carboxylated polystyrene MNPs (PS26C) using a combination of simulated digestion and a static, immortalized cell-based, three cell type (triculture) small intestinal epithelial model. Results revealed that PS26 caused minimal toxicity, and inhibitor studies revealed that uptake mechanisms included passive diffusion, phagocytosis, clathrin-mediated endocytosis (CME), and fast endophilin-mediated endocytosis (FEME). However, the triculture model is somewhat lacking in physiological relevance, and studies in a more relevant and accurate model are required to validate and expand upon those results. In the current study, we therefore employed a microfluidic intestine-on-a-chip model developed using primary human intestinal epithelial organoids from both healthy and Crohn’s disease donors, and primary human microvascular endothelial cells to evaluate the toxicological impacts and mechanisms effectuating uptake and translocation of 25 nm polystyrene shell-gold core tracer (quantifiable by ICP-MS) MNPs (AuPS25). As in our previous study, AuPS25 caused minimal toxicity after 24 h exposure in either the healthy or Crohn’s IOC model. RNAseq analysis of epithelial cell lysates identified only 9 dysregulated genes, which notably included downregulation of IFI6 (interferon alpha-induced protein 6), which has antiviral and negative innate immune regulatory  functions in the intestine. Inhibitor studies revealed that AuPS25 uptake occurred by both passive and active mechanisms, including phagocytosis and/or macropinocytosis, and CME and/or FEME. Interestingly, uptake and translocation of AuPS25 was greater in healthy than in unstimulated Crohn’s disease epithelium.

overall_design: RNAseq of epithelial channel cells after 24 h exposure to digested AuPS25 at an effective oral 25 nm PS concentration of 5.25 µg/mL (final intestinal concentration of 0.44 µg/mL)

first: Davood

last: Kharaghani

first: Glen

last: DeLoid

first: Ping

last: He

first: Ben

last: Swenor

first: Trung Huu

last: Bui

first: Nubia

last: Zuverza-Mena

first: Carlos

last: Tamez

first: Craig

last: Musante

first: Jason

last: White

first: Philip

last: Demokritou


title: Alteration in expression and subcellular localization of the androgen receptor-regulated FAM111A

city: Davis

first: Maria

last: Mudryj

state: CA

address: 1 Shields Ave.

department: Medical Microbiology and Immunology

institute: University of California, Davis

summary: The androgen receptor (AR) is a pivotal regulator of growth and proliferation of prostate cancer (PCa) and the majority of lethal castration-resistant prostate cancers (CRPC) remain reliant on AR signaling. PCa exhibits variability in progression and responses to treatment suggesting genetic heterogeneity.  Two independent studies identified PCa predisposing single nucleotide polymorphisms (SNPs) within the FAM111A protease gene, but the mechanistic basis of this association remained elusive. Our in vitro and in vivo studies uncovered that AR represses FAM111A in castration sensitive and resistant cells via an AR binding site within the FAM111A gene. Consistent with AR-dependent FAM111A repression, the two transcripts are reciprocally regulated in metastatic lesions, FAM111A levels are significantly lower in matched castration-resistant than in castration-sensitive LuCaP patient-derived xenograft (PDX) tumors, and lower in metastatic lesions than in primary tumors. We uncovered that FAM111A subcellular localization changes dramatically with acquisition of castration resistance, where in castration sensitive cells FAM111A is predominantly in the nucleoli, but with castration resistance it becomes more dispersed in the nucleus and in the cytoplasm. FAM111A depletion in castration sensitive and resistant cells enhances the efficacy of PARP1 inhibitors olaparib and niraparib consistent with its role in DNA repair. Moreover, FAM111A depletion reduces AR target gene PSA and TMPRSS2 transcription, indicating that FAM111A modulates AR-dependent gene expression and forms a FAM111A-AR co-regulatory loop in PCa. Our studies argue that AR-dependent FAM111A regulation modulates PCa gene expression, acquisition of castration resistance, and sensitivity to agents that target DNA damage repair.

overall_design: RNA-seq profiling of two cell lines 22Rv1 and LNCaP-AI , AR signaling was reduced by AR-targeting siRNA (siAR) in cells proliferating in steroid depleted media. Non-targeting siRNA (siC) served as a control

last: Malvina Tsamouri

first: Stephen

last: Libertini

first: Salma

last: Siddiqui

first: Maitreyee

middle: K

last: Jathal

first: Blythe

last: Durbin-Johnson

first: Clifford

last: Tepper

first: Eva

last: Corey

first: Jun

last: Luo

first: Paramita

last: Ghosh


title: DNA methylation patterns in breast cancer, paired benign tissue from ipsilateral and contralateral breast, and healthy controls

city: Chicago

first: Saya

last: Dennis

state: IL

address: 680 N. Lake Shore Dr.

department: Preventive Medicine

institute: Northwestern University

summary:
Epigenetic changes, particularly DNA methylation, are crucial to breast cancer development. Tumor-adjacent normal (AN) tissue frequently serves as a reference for characterizing genomic alterations but is reported to share some characteristics with tumors. However, it is unclear whether AN’s epigenetic profiles reflect a predisposition to cancer or a response to the presence of the tumor. We address this gap by systematically comparing methylation profiles of tumor, AN, and matched-benign tissues from both breasts, as well as to healthy donated breast tissue.     We studied four different samples from 69 cancer cases: tumor (TU), AN, ipsilateral opposite quadrant (OQ), and contralateral unaffected breast (CUB); and healthy donated breast (HDB) tissue from 182 cancer-unaffected donors. These constitute a “tumor proximity axis” (TPxA): HDB→CUB→OQ→AN→TU. Methylation profiles were assayed using Illumina’s Infinium Methylation EPICv1.0 BeadChip. Differential methylation (DM) analysis was conducted, and the significantly DM CpGs were analyzed for enrichment of transcription factor binding sites (TFBS) and other features.     Following data processing and quality control, there were 69 TU, 60 AN, 67 OQ, 68 CUB, and 182 HDB samples for analysis. DM analysis showed distinct methylation profiles of TU relative to benign tissues, whereas case-benign tissues were similar to each other but distinct from HDB. Hypomethylated sites in case-benign versus HDB were enriched for TF binding sites of TP63, GATA3, ESR1, PR, AR, NR3C1, and GREB1. TU hypermethylation events were enriched for Polycomb-repressive complex 2 (PRC2) binding, including EZH2, SUZ12, and JARID2, with hypermethylation enrichment for PRC2-related binding motifs in both ER+ and ER- tumors. TU methylation profiles were otherwise highly distinct by ER status: TFBS enrichment of hypomethylation events for hormone receptor-related pathways in ER+ tumors and for hematopoiesis/immune-related pathways in ER- tumors. We found no differential methylation between benign tissues from patients with ER+ vs. ER- tumors.      DNA methylation profiles differ profoundly at two points: tumor to case-benign and case-benign to HDB, with clear distinction between ER+ and ER- tumors. Case-benign tissues are not epigenetically “normal”, are similar across both breasts, and do not differ by ER status of paired tumors.
Epigenetic changes, particularly DNA methylation, are crucial to breast cancer development. Tumor-adjacent normal (AN) tissue frequently serves as a reference for characterizing genomic alterations but is reported to share some characteristics with tumors. However, it is unclear whether AN’s epigenetic profiles reflect a predisposition to cancer or a response to the presence of the tumor. We address this gap by systematically comparing methylation profiles of tumor, AN, and matched-benign tissues from both breasts, as well as to healthy donated breast tissue.
We studied four different samples from 69 cancer cases: tumor (TU), AN, ipsilateral opposite quadrant (OQ), and contralateral unaffected breast (CUB); and healthy donated breast (HDB) tissue from 182 cancer-unaffected donors. These constitute a “tumor proximity axis” (TPxA): HDB→CUB→OQ→AN→TU. Methylation profiles were assayed using Illumina’s Infinium Methylation EPICv1.0 BeadChip. Differential methylation (DM) analysis was conducted, and the significantly DM CpGs were analyzed for enrichment of transcription factor binding sites (TFBS) and other features.
Following data processing and quality control, there were 69 TU, 60 AN, 67 OQ, 68 CUB, and 182 HDB samples for analysis. DM analysis showed distinct methylation profiles of TU relative to benign tissues, whereas case-benign tissues were similar to each other but distinct from HDB. Hypomethylated sites in case-benign versus HDB were enriched for TF binding sites of TP63, GATA3, ESR1, PR, AR, NR3C1, and GREB1. TU hypermethylation events were enriched for Polycomb-repressive complex 2 (PRC2) binding, including EZH2, SUZ12, and JARID2, with hypermethylation enrichment for PRC2-related binding motifs in both ER+ and ER- tumors. TU methylation profiles were otherwise highly distinct by ER status: TFBS enrichment of hypomethylation events for hormone receptor-related pathways in ER+ tumors and for hematopoiesis/immune-related pathways in ER- tumors. We found no differential methylation between benign tissues from patients with ER+ vs. ER- tumors.
DNA methylation profiles differ profoundly at two points: tumor to case-benign and case-benign to HDB, with clear distinction between ER+ and ER- tumors. Case-benign tissues are not epigenetically “normal”, are similar across both breasts, and do not differ by ER status of paired tumors.

first: Susan

last: Clare

first: Seema

last: Khan

first: Yuan


title: Single-cell multiomic characterization of erythroid cells (cultured human BEL-A cell line) with a panel of 118 genes and 7 surface markers on the BD Rhapsody platform

first: Stephan

last: Menzel

address: Rayne Institute, 123 Coldharbour Lane

department: Comprehensive Cancer Centre

institute: King's College London

summary: We used the BD Rhapsody multi-omics platform to perform a targeted quantification of 118 erythroid mRNA species and seven erythroid surface proteins in developing erythroid cells derived from the human erythroid cell line BEL-A. The goal of the project was to detect heterogeneity among developing human red blood cells independent of their state of maturity and relate this to their expression of fetal haemoglobin-specific globin chains. A gene-targeted approach was selected to increase the power to evaluate ranscripts of interest and to exclude alpha and beta globin mRNA, which tend to swamp experimental data in more mature precursors and reticulocytes.

overall_design: BEL-A cells were cultured and harvested during the expansion phase (mostly proerythroblasts) and on day 2 of the differentiation phase (mostly basophilic erythroblasts). The main objective of the study was to charaterise fetal-haemoglobin expressing erythroid precursors (Fcell precursors) regarding their gene expression profiles and characteristic surface markers CD71, CD36, CD45, CD44, CD34, CD235a and CD49d. Heterogeneity was observed within differentiation stages regarding the epression of the two HbF specific globin chain enes HBG1 and HBG2 and the long non-coding RNA BGL2. (Manuscript under review Rooks et al 2025).

first: Helen

last: Rooks

first: Ghulam

middle: J

last: Mufti

first: Sara

last: El Hoss


title: Induction of miR162 contributes to invasive habitat adaption of Alternanthera philoxeroides

city: shanghai

first: Qian

middle: qian

last: Hu

address: Xinjiangwancheng

department: School of Life Sciences

institute: Fudan University

summary: Rapid phenotypic changes in adaptive traits are crucial for organisms to thrive in changing environments. Alternanthera philoxeroides, originally a terrestrial plant from South America, has become an invasive weed in Asia, capable of colonizing both aquatic and terrestrial habitats. The mechanism by which this invasive habitat is rapidly achieved without genetic variation remains unknown. Here, we demonstrate that miRNA activity in A. philoxeroides plays a significant role in its high invasive capacity. Our results highlight that an intact miRNA pathway is essential for the survival of A.philoxeroides in aquatic habitats. We identified one key miRNA, Aph-miR162, that promotes rapid elongation of stem in aquatic environments. Upon water submergence, the levels of miR162 significantly increased in stems from 3 hours to 24 hours. TRV based VIGS-mediated knockdown of Aph-miR162 significantly disrupted stem elongation in water submergence condition, ultimately resulting in a failure of plants protruding from the water surface. Interestingly, miR162 was not up-regulated in the non-invasive sibling species Alternanthera pungens, which also originates from South America but has retained its original terrestrial habitats in Asia. More importantly, delivering the antisense RNA oligos complementary to Aph-miR162 via the nanoparticle method significantly impaired stem elongation upon water submergence, causing A. philoxeroides to wither after 2-3 weeks. Thus, our findings reveal that the miRNA pathway can drive rapid phenotypic variation, facilitating adaptation to aquatic environments. Importantly, miR162 has the potential as a bio-pesticide for controlling the invasive capacity of A. philoxeroides.

overall_design: Small RNA-Seq for miRNA in young stem and old stem at different time points on land or after waterlogged treatment was performed with 3 biological replicates each.

first: Qianqian

first: Binglian

last: Zheng


title: Early signaling pathways during in vitro culture of isolated primordial follicles

city: Lodi

first: Alberto Maria

last: Luciano

state: LO

address: Via dell'Università 6

department: Department of Veterinary Medicine and Animal Sciences

institute: University of Milan

summary: The ability to grow undifferentiated oocytes in vitro from primordial follicles would increase the availability of fully grown oocytes in fertility preservation programs and other downstream applications. To date, the development of living offspring in vitro from the primordial follicle reserve has only been achieved in mice, proving the principle of the potential value of these follicle cultures as a source of competent oocytes. In certain pathophysiological conditions, such as polycystic ovarian syndrome, premature ovarian failure, or in ovarian and blood cancer where the ovarian tissue cannot be reintroduced into the patient, it is essential to isolate these follicles from the surrounding tissue and culture them in vitro. However, culture systems to produce mature oocytes from the isolated primordial follicles are still experimental. Upon isolation from the ovarian microenvironment, a critical limiting factor is follicle death after a short period of culture.  Our study defines a serum-free culture system capable of sustaining bovine primordial follicles to more than 60% viability for 24 hours. Using this system as a base, we employ RNA-Seq to advance the knowledge of the main transcriptional events and molecular factors determining follicle fate in a 2D culture system and suggest the role of ferroptosis in bringing about primordial follicle death. Future ameliorations to the culture system should not only inhibit such programmed cell death mechanisms but also ensure the physiological compliance of the genes regulating primordial follicle activation and transition to the primary stage with effective supplementation media to attain isolated primordial follicle development in vitro.

overall_design: RNASeq profiling of mechanically isolated primordial follicles (3 biological replicates) that were retrieved after collection (PMF T0/PM00) or 16 hours of culture (PMF T16/PM16).

first: Pritha

last: Dey

first: Noemi

last: Monferini

first: Ludovica

last: Donadini

first: Filippo

last: Zambelli

first: Maria Belen

last: Rabaglino

first: Valentina

last: Lodde

first: Federica

last: Franciosi


title: NEXN deficiency leads to dilated cardiomyopathy in human pluripotent stem cell-derived cardiomyocytes

city: Yantai

first: Mengqi

last: Jiang

address: 346 Guanhai Road, Laishan District, Yantai City, Shandong Province, China

institute: Binzhou Medical University

summary: Dilated cardiomyopathy (DCM) constitutes a major cause of heart failure, characterized by high mortality rates and a limited availability of effective therapeutic options. A substantial body of evidence indicates that mutations in the Nexilin (NEXN) gene are significant pathogenic contributors to DCM, and we have developed a NEXN-deficient human cardiac myocyte model that faithfully replicated the pathophysiological characteristics of DCM. This model addressed the limitations associated with interspecies physiological differences and was highly suitable for further investigation into the underlying pathogenesis. We demonstrated that NEXN was one of the important components in maintaining the structure and function of cardiomyocyte JMCs, and played a key regulatory role in maintaining the normal excitation-contraction coupling of cardiomyocytes. Meanwhile, NEXN also played a critical role in maintaining the normal energy metabolism of cardiomyocytes, and the loss of its function would lead to DCM. Furthermore, Levo-carnitine and SERCA2a Activator 1 were identified as promising therapeutic agents for the treatment of DCM. Our finding reveals a critical regulatory role of NEXN in JMCs and mitochondria to prevent the development of DCM.

overall_design: To investigate the function of NEXN in  the pathogenesis of myocardial remodeling, we established a NEXN-deficient human cardiac myocyte (CM) model.  We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different cells at one time point.  Comparative gene exprission profiling analysis of RNA-seq data for cells.

first: Yun

last: Bai


title: Single-cell transcriptome reveals the reprogramming of immune microenvironment during the transition from MASH to HCC

city: Guangzhou

first: Xue-Jia

last: Lin

state: Guangdong

address: Xin Gang Xi Road 135#

institute: Sun Yat-sen University

summary: Metabolic dysfunction-associated steatohepatitis (MASH)-driven hepatocellular carcinoma (HCC) development is accompanied by the accumulation of immune cells within the hepatic microenvironment, yet its immunological networks remain obscure. Herein, we illustrate the profound reprogramming of the liver immune microenvironment during the transition from MASH to HCC by single-cell RNA sequencing (scRNA-seq).

overall_design: A well-established MASH-driven HCC mouse model, STAM model, was first constructed. Thereafter, we applied single-cell RNA sequencing (scRNA-seq) analysis of CD45+ cells sorted from livers of mice with normal chow or at MASH stage, as well as paired paracancerous and cancer tissues from mice at HCC stage.

first: Yu

last: Huang

first: Ying

last: Xie

first: Yuqing

last: Zhang

first: Zhemian

last: Liu

first: Weihua

first: Zhenhua

last: Li

first: Zhinan

last: Yin


title: Effect of PRMT1 deletion on gene expression in head and neck squamous cell carcinoma cells LIU-LSC-1

city: HeFei

first: Liu

last: Shixian

address: No. 81 Meishan Road

institute: Anhui Medical University

summary: To investigate the role of PRMT1 in head and neck squamous cell carcinoma, we established a LIU-LSC-1 cell line with PRMT1 knocked down by lentivirus technique. We then performed gene expression profiling targeting the RNA-seq data of the control and PRMT1 knockdown groups

overall_design: Gene expression profile analysis of RNA-seq data from control group (shNC) and PRMT1 knockdown group (shPRMT1) in LIU-LSC-1 cells


title: Effect of PRMT1 deletion on gene expression in head and neck squamous cell carcinoma cells FaDu with CBP treatment

summary: To investigate the role of PRMT1 in head and neck squamous cell carcinoma, we established a FaDu cell line with siPRMT1 by siRNA. We then performed gene expression profiling targeting the RNA-seq data of the control and siPRMT1 groups

overall_design: Gene expression profile analysis of RNA-seq data from control group (siSc) and PRMT1 knockdown group (siPRMT1) in FaDu cells  with CBP treatment


title: Effect of PRMT1 deletion on head and neck squamous cell carcinoma cells LIU-LSC-1

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To investigate the role of PRMT1 in head and neck squamous cell carcinoma, we established a LIU-LSC-1 cell line with PRMT1 knocked down by lentivirus technique. We then performed profiling targeting the ATAC-seq data of the control and PRMT1 knockdown groups

overall_design: Analysis of ATAC-seq data from control group (shNC) and PRMT1 knockdown group (shPRMT1) in LIU-LSC-1 cells


title: Effect of PBX2 on Head and neck squamous cell carcinoma cells TU177

summary: To investigate the role of PBX2 in Head and neck squamous cell carcinoma. We performed profiling targeting the CUT＆Tag data of the IgG and HA-PBX2 groups

overall_design: Analysis of CUT＆Tag data from control group (IgG) and HA-PBX2 group (HA-PBX2) in HA-PBX2-overexpressing TU177 cells.


title: The TFIID subunit Taf13 is dispensable for RNA polymerase II transcription, but essential for early embryogenesis [CUT&TAG]

city: Illkirch

first: Igor

last: Martianov

address: 1 rue Laurent Fries

country: France

institute: IGBMC

summary: RNA polymerase II (Pol II) transcription initiation requires assembly of a preinitiation complex (PIC) comprising the general transcription factors amongst which the multiprotein complex TFIID. TFIID comprises the TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs). Recent cryo-electron microscopy studies reported topological reorganization of TFIID upon promoter binding with the TAF11-TAF13 heterodimer as the last TFIID subunits directly contacting TBP prior to deposition on promoter DNA upstream of the transcription start site. To challenge the role of the TAF11-TAF13 heterodimer, we inactivated the gene encoding Taf13 both in mice and embryonic stem cells (ESCs). Taf13 inactivation in mice is embryonic lethal with null embryos implanting but surviving only until E6.5. Taf13-null ESCs are viable, but show slower proliferation and fail to form embryoid bodies and differentiate. Biochemical analyses from these ESCs show that Taf13 loss had minimal effect on TFIID integrity, and genomic profiling shows only a mild reduction of promoter recruitment of TBP and Taf4 while that of Taf1 is increased. Moreover, while TFIIH recruitment is unaffected indicating normal PIC formation, that of Pol II is globally diminished. These data indicate that the Taf11-Taf13 heterodimer is not essential for TBP/TFIID recruitment and PIC formation, but is specifically required for normal Pol II  recruitment.

overall_design: Cut and Tag experiment was performed on ESCs expressing or lacking 3XHATaf13 using anti TBP, Taf4 and Xpb antibodies

last: Martiyanov

first: Stephanie

last: Le Gras

first: Irwin

last: Davidson


title: Characterization of monocytes influence in human skin melanoma

city: Madrid

first: Rafael

last: Samaniego

address: Calle Dr Esquerdo 46

institute: Fundación para la Investigación Biomédica del Hospital Gregorio Marañón

summary: Tumor cells attract and dynamically interact with monocytes/macrophages, one of the more abundant cell types in the tumor microenvironment, to subvert their differentiation into tumor associated macrophages (TAMs), which mainly promote immunosuppression and neoplastic progression, but the mechanisms governing their protumoral activity are not completely understood. Thus, identifying molecular pathways promoted by monocytes that could be responsible for immune evasion and tumor malignicity may provide new therapeutic targets to improve the efficacy of immunotherapy of cancer.

overall_design: BLM and A375 human melanoma cell lines were coculture for 24h with CD14+ monocytes isolated from human PBMCs of three healthy donors. Also, CD14-CD3- tumor cells (TC) and CD3+ tumor infiltrated lymphocytes (TILs) were obtained skin melanoma primary tumors (CD14+ tumor-associated macrophages from the same tumors are available at GSE171277).

first: Alicia

last: Nieto-Valle

first: Celia

last: Barrio-Alonso

first: Alba

last: Gutiérrez-Seijo

first: Paloma

last: Sánchez-Mateos

first: Elena

last: García-Martínez


title: Delivery of A4GALT targeting siRNA-lipid nanoparticle rescues fabry disease phenotypes in hiPSC derived endothelial cell and podocyte models

city: Seoul

first: Yoo Jin

last: Shin

address: 222, Banpo-daero, Seocho-gu,

department: Transplantation Research Center

country: South Korea

institute: College of Medicine, The Catholic University of Korea

summary: In this study, we explore the therapeutic feasibility of globotriaosylceramide (Gb3) synthase (A4GALT)-specific siRNA-loaded polyhistidine (pHis)-incorporated lipid nanoparticles (HLNPs) for Fabry disease (FD). HLNPs were developed to deliver siRNAs targeting A4GALT using a microfluidic device, with pHis aiding in endosome escape. The therapy was tested on GLA-knockout human induced pluripotent stem cell-derived endothelial cells (GLA-KO-hiPSC-ECs) and podocytes (GLA-KO-hiPSC-PCs). GLA-KO-hiPSCs-ECs or -PCs, upon differentiation, were treated with A4GALT-siRNA-HLNP. Successful intracellular uptake of A4GALT-siRNA-HLNP was confirmed through fluorescence and electron microscopy in both cell types. A4GALT-siRNA-HLNP treatment confirmed both cell types' stability at 5 µg/mL. Increased Gb3 deposition and zebra body formation were detected in both cell types, but A4GALT-siRNA-HLNP treatment attenuated these FD phenotypes, demonstrating reduced expression of A4GALT through western blot analysis. RNA sequencing analysis revealed that the expression of transcripts associated with FD in both cell types was restored by A4GALT-siRNA-HLNP treatment. Suppression of A4GALT via siRNA/HLNP treatment significantly rescued FD phenotypes, presenting a novel therapeutic approach for FD.

overall_design: To investigate the transcriptomic alterations ensuing from A4GALT suppression via siRNA-HLNP in the context of GLA loss-of-function, RNA sequencing analysis was conducted on hiPSC-EC and hiPSC-PC.

first: Hyejung

last: Mok

first: Byung Ha

last: Chung


title: p63 and ZNF148 cooperate to regulate head and neck squamous cell carcinoma

city: Rome

first: Artem

last: Smirnov

address: Via Montpellier 1

department: Dept. of Exper. Medicine

institute: University of Rome "Tor Vergata"

summary: Head and neck squamous cell carcinoma (HNSCC) is a common and aggressive malignancy. While significant advances have been made in the management of low-grade cancer, treatment of advanced HNSCC remains challenging. Here, we used a proteomic approach to discover novel binding partners of the oncogene p63, the most frequently amplified transcription factor in HNSCC. We identified a zinc finger protein, ZNF148, which is coexpressed and physically binds p63 in carcinoma cells. Genome occupancy analyses identified a functional transcribed enhancer-derived RNA (eRNA) upstream of the CCND1 gene occupied by both factors. Mechanistically, p63 and ZNF148 control transcription of this eRNA, leading to overexpression of cyclin D1 to reinforce tumour cell proliferation. Importantly, this axis is specific for cancer cells and remains inactive in normal epithelial cells. The expression levels of these factors and the eRNA are positively correlated in cancer and associated with advanced stage and metastasis. Collectively, our data reveal a novel molecular pathway controlling HNSCC progression and identifies potential selective targets for cancer treatment.

overall_design: Here we use ChIP seq to map p63 and ZN148 occupancy on chromatin in a HNSCC cell line FaDu to understand the impact of their co-operation on tumour cell growth

first: Rosalba

last: Pecorari

first: Mara

last: Mancini

first: Corleone

last: Giacomo

first: Fanciulli

last: Maurizio

first: Gerry

last: Melino

first: Candi

last: Eleonora


title: Transforming properties of E6/E7 genes from Beta HPV80 in a fibroblast model in vitro

city: Guadalajara

first: Adriana

middle: del Carmen

last: Aguilar Lemarroy

state: Jalisco

address: Sierra Mojada #800, Colonia Independencia

department: División de Inmunología

country: Mexico

institute: Centro de Investigación Biomédica de Occidente

summary: This analysis aimed to elucidate the effect of transduced E6/E7 HPV80 genes in primary fibroblasts employing lentiviral vectors, examining their influence on the transcriptome of our cellular model and demonstrating their capacity to prolong the lifespan of the culture and lead to malignant transformation. Total RNA sequencing was performed on the Illumina NovaSeq 6000 platform by Novogene Bioinformatics Technology Co., Ltd, Beijing, China, with two independent replicate sequences for each cell model. Methodology: The execution of the bioinformatics pipeline analysis was carried out as follow: R (ver. 4.4.1), RStudio (2024.09.0+375) and Galaxy (https://www.usegalaxy.org accessed on 04 September 2024) open-source platforms were used to analyze the Illumina raw data. The Quality Control was conducted through the FastQC tool (v0.74+galaxy0). Afterward, all the reads were processed by the Rsubread package (v2.14.2); at that point, the reads were trimmed and aligned to the Human Genome Reference (GRCh38.p13 v46). The obtained output was the BAM files, of which the number of reads was counted by the FeatureCounts tool (v2.0.3); at the final step, the Differential Expression Analysis was settled by the DESeq2 package for R (ver. 1.42. 0). The differential gene expression measurements were normalized by DESeq2's median of ratios (median of ratio of gene counts relative to geometric mean per gene) method. All genes with an adjusted p-value (p-adj) minus or equal to 0.05 and fold change (Log2FC) up to 2 or less than minus 2 were selected as differentially expressed genes (DEGs). Conclusions: Our study found that E6/E7 HPV80 genes have the capacity to prolong the lifespan of the primary Fibroblasts mainly throug the disregulation of pathways related to cell cycle progression, p53-related DNA repair machinery and cell cycle arrest, apoptosis, immune evasion, cell growth, differentiation, and cell death.

overall_design: Primary Fibroblasts that constitutively expressed E6/E7 HPV80 genes (transduced with lentiviral vectors harboring E6/E7 HPV80 genes) underwent total  RNA extraction (process was addressed in duplicate). After that, the replicates were compared vs. the controls (pLVX vector alone) for the development of the differential expression analysis.

first: Francisco

middle: I

last: Renteria-Flores

first: Andrea

last: Molina-Pineda

first: Alejandra

middle: N

last: Vega-Magaña

first: Mariel

last: García-Chagollan

first: Ruben

last: Piña-Cruz

first: Luis

middle: F

last: Jave-Suárez

last: Aguilar-Lemarroy


title: Catalyzing Early Ovarian Cancer Detection: Platelet RNA-Based Precision Screening

city: Pohang

first: Sarah

last: Kim

address: 558, Handong-ro, Buk-gu

institute: Handong Global University

summary: Early detection of ovarian cancer is crucial for successful treatment, yet most cases are diagnosed at advanced stages due to a lack of effective screening. Recent advancements in RNA technology from platelets aid in early tumor detection. Here, we proposed our two-step method for assessing the existence of pelvic mass either located at ovaries or uterus with more than 99% specificity by utilizing exon-exon junction features with a sampling invariant normalization technique; then next our model finds the malignancy of detected mass with more than 99% negative predictive value to practically assist clinicians’ further investigation via combined features of exon-exon junctions, and hematology parameters. We diverged from traditional methods by employing ISR counts rather than gene expression levels to use splice junctions as features in our models. If integrated with current screening methods, our algorithm holds promise for identifying ovarian or endometrial cancer in its early stages.

overall_design: In this study, platelet RNA samples were analyzed to assess the presence of ovarian and uterine tumors, as well as to determine malignancy, utilizing exon-exon junction features and a sampling-invariant normalization technique.


title: CaB34 –a spontaneously immortalized prostate cancer cell line from a Black Caribbean patient, and its radioresistant subline, as novel research models

city: Toronto

first: Jessica

last: Wright

state: Ontario

address: 2075 Bayview Ave

institute: Sunnybrook Research Institute

summary: Prostate cancer cell lines are particularly racially and clinically homogenous, and while there has been significant work in the development of additional models, few have been created without oncogenic transformation. Here we describe the derivation of a spontaneously immortalized primary prostate cancer cell line from a Black Caribbean patient with Gleason 7 prostate cancer – designated CaB34 - which presents a novel model for pre-clinical study of localized prostate cancer. From CaB34, a paired radioresistant subline CaB34-CF was generated using a clinically relevant fractionated radiotherapy schedule. Both CaB34 and CaB34-CF express prostate-specific markers including CK18, NKX3.1, and AMACR. Multi-omic analyses using RNAseq and shotgun proteomics identified NNMT as the most significantly dysregulated target in CaB34-CF. Bioinformatic analysis determined that NNMT was more abundant within prostate tumors compared to benign prostate, supporting a role in tumor progression. Knockdown studies of NNMT demonstrated significant radiosensitization of both CaB34-CF cells, which was largely a result of increased radiation-induced cellular senescence. Our findings present NNMT as a potential therapeutic target for sensitization of radioresistant disease. Together, our research provides a paired model of treatment naive and radioresistant disease to address mechanisms of therapy resistance, while expanding the racial diversity of prostate cancer cell lines for the research community.

overall_design: Samples from primary prostate cancer cell line, and paired radiation resistant subline run in biological triplicate.

first: Stephanie

last: White

first: Stanley

last: Liu

first: Shahbaz

last: Khan

first: Thomas

last: Kislinger


title: Differential Effect of Electrical stimuli on a 3D bioprinted model of inflamed skin

first: Christine

last: Nardini

address: Via dei Taurini 9

institute: PICB

summary:
To investigate the effects of direct and alternate current on a 3D bioprinted construct containing fibroblasts and keratinocytes in a collagen matrix
We then performed gene expression profiling analysis using data obtained from RNA-seq of constructs in physiological and inflamed conditions, using direct or alternate current, at 3 time points

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 3D bioprinted constructs at time 0, 1, and 48 hours after culture, perfused with TNF-α or in physiological conditions, stimulated with direct current (DC) at 1 or 5V, or alternate current (AC) at 10 or 100 Hz, or without stimuli

first: Anna

last: Plaksienko

first: Yuanhua


title: Cholesterol-Modified MIR29B Induces Fetal Hemoglobin via targeting DNMT3A in Townes Sickle Cell Mice

city: Memphis

first: Athena

last: Starlard-Davenport

state: TN

address: 71 S Manassas Street

department: Genetics, Genomics and Informatics

institute: University of Tennessee Health Science Center

summary: MicroRNA (miRNA) molecules hold promise as potential therapeutics capable of silencing target gene expression through RNA interference. The delivery of miRNAs without degradation has posed a significant challenge to their clinical use. However, cholesterol-conjugated miRNA has emerged as a promising delivery approach thanks to its low toxicity and high efficiency. We previously showed that MIR29B by 28-day continuous infusion using subcutaneous mini osmotic pump delivery, MIR29B induces HbF. The present study delves into evaluating intermittent delivery of a cholesterol-conjugate of MIR29B (Chol-MIR29B), to induce fetal hemoglobin (HbF) in Townes sickle cell mice. Therefore, we conducted additional in vivo studies to test intermittent dosing of Chol-MIR29B in Townes sickle cell mice. Blood was processed for complete blood count with differential and reticulocytes at weeks 0, 2, and 4, and γ-globin gene reactivation was determined by RT-qPCR. The percentage of HbF-positive cells was measured by flow cytometry. RNA seq was performed on the peripheral blood of mice treated with MIR29B. Mice treated with Chol-MIR29B exhibited normal behavior and weight gain. While there was no direct effect of Chol-MIR29B on γ-globin reactivation, delivery of Chol-MIR29B after 4 weeks of treatment significantly increased the percentage of HbF positive cells by up to 15-fold. Additionally, there were no toxic effects on complete blood counts and differential or activation of oncogenes as determined by RNA seq, supporting the safety of Chol-MIR29B while inducing HbF expression.  Our results provide the first evidence of the ability of Chol-MIR29B to induce HbF in sickle cell disease transgenic mice.

overall_design: To investigate intermittent dosing of MIR29B to induce HbF and evaluate its effects on global gene expression in Townes sickle cell mice

first: Xueyuan

last: Cao

first: Betty

middle: S

last: Pace


title: Transcriptomic alterations including p53 pathway dysregulation prime DNMT3A mutant cells for transformation

city: Parkville

first: Connie

middle: S. N.

last: Li-Wai-Suen

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

summary: DNMT3A mutations are prevalent in haematologic malignancies. Our mouse model introduced the murine homologue (R878H) of the human ‘hotspot’ R882H mutation into the mouse Dnmt3a locus, resulting in globally reduced DNA methylation in all tissues. Mice with heterozygous R878H mutations developed g-radiation induced thymic lymphoma more rapidly than control mice, suggesting a vulnerability to stress stimuli in Dnmt3aR878H/+ cells. In competitive transplantations, Dnmt3aR878H/+ Lin-Sca-1+Kit+ (LSK) cells had a competitive advantage over WT cells, indicating a self-renewal phenotype at the expense of differentiation. RNA-sequencing of Dnmt3aR878H/+ LSKs exposed to low dose g-radiation showed downregulation of the p53 pathway. Accordingly, reduced PUMA expression was observed by flow cytometry in the bone marrow of g-irradiated Dnmt3aR878H/+ mice due to altered p53 signalling. These findings provide new insights as to how DNMT3A mutations cause subtle changes in the transcriptome of LSK cells which contribute to their increased self-renewal and propensity for malignant transformation.

overall_design: To investigate the transcriptomic changes taking place in response to g-irradiation in Dnmt3aR878H/+ mutant LSK cells, we utilised RNA-seq. The RNAseq samples included in this submission were taken from bone marrow LSK cells of 4-week-old female mice in the following conditions: 4 replicate Dnmt3aR878H/+ untreated samples, 4 replicate WT untreated samples,  3 replicate Dnmt3aR878H/+ irradiated samples, and 2 replicate WT irradiated samples.

first: Amali

last: Cooray

first: Erin

middle: M

last: Lawrence

first: Marco

last: Herold


title: Expression data from the adipose-derived mesenchymal stem cell (ASCs) line

city: Linköping

first: Mouna

last: Tababi

state: Östergötland

country: Sweden

institute: Linköping University

summary:
We investigated the differentiation of adipose-derived stem cell line (ASCs) into keratinocyte-like cells in the presence of the competitive Rab7 inhibitor, CID-1067700
We utilized microarrays to pinpoint distinct categories of genes that are either up-regulated or down-regulated, and to clarify the regulatory pathways affected by Rab7 inhibition in ASCs.

overall_design: We differentiated ASCs into KLCs and subsequently with the Rab7 inhibitor, CID-1067700, at a concentration of 40 μM. RNA was extracted and hybridized using Affymetrix microarrays (Clariom S Human). The analysis compared three groups: CID-treated ASCs, differentiation media (DM)-treated ASCs, and vehicle (DMSO)-treated ASCs. Each group had three biological replicates

first: Raghad

last: Alghazali

last: Tabebi

first: Moustafa

last: Elmasry

first: Ahmed

last: Elserafy


title: PARP inhibitor augments anti-tumor efficacy of DNMT inhibitor in cholangiocarcinoma

first: Jianfeng

last: Chen

address: 651East Dongfeng Road

institute: SYSUCC

summary: Cholangiocarcinoma (CCA) is a dismal, heterogeneous malignancy with limited treatment options. One of the key epigenetic dysregulations in CCA is aberrant DNA methylation, suggesting that targeted DNA methylation is a promising therapeutic strategy for this disease. However, the clinical utility of DNA demethylation reagents is not well documented. Here, we established patient-derived CCA cell lines and demonstrated that the demethylating agents decitabine and 5-azacytidine had minimal effects on antitumor proliferation of CCA cells. A combinatorial drug screen using a kinase inhibitor library identified PARP inhibitors as sensitizers that synergistically enhanced the antitumor effects of decitabine. The combination of DNMT inhibitors and PARP inhibitors significantly blocks tumor growth in both CCA patient-derived xenograft models and the somatic CCA model induced by hydrodynamic tail vein injection. Transcriptomic profiling analysis showed that the combination treatment activated the inflammatory signaling pathway and upregulated senescence-associated secretory phenotype gene expression, resulting in genomic instability in CCA. Mechanistically, combination treatment disrupted XRCC1 function and increased PARP1 trapping, leading to persistent DNA damage and senescence. Together, our study provides a preclinical proof-of-concept for the use of DNMT inhibitors in combination with PARP inhibitors as a novel therapeutic strategy and potentially optimizes current clinical practice in the treatment of CCA.

overall_design: 1.RNA-seq for HUCCT1 cells after vehicle and decitabine treatment. 2. RNA-seq for EGI-1 after vehicle, decitabine, talazoparib or combinational treatment.

first: Peili

last: Wang

first: Jing

last: Tan


title: V. cholerae transcriptome of WT and modification deletion mutants with sub-MIC tobramycin or ciprofloxacin

city: Paris

first: Zeynep

last: Baharoglu

address: 28 Rue du Docteur Roux

department: Génomes et Génétique

institute: Institut Pasteur

summary: We study gene expression levels of V. cholerae N16961 hapR+ corrected strain in exponential phase with tobramycin or ciprofloxacin.

overall_design: Bacterial cells were grown to OD 0,25 and RNAseq was performed.

first: Manon

last: Lang


title: Epithelial Cell Membrane Perforation Induces Allergic Airway Inflammation

city: Beijing

first: Yao

last: Lv

state: Beijing

address: No. 7 Science Park Road, Zhongguancun Life Science Park, Changping District,   Beijing 102206, P.R. China

institute: National Institute of Biological Sciences,Beijing

summary: Allergens that induce allergic airway inflammation are highly diverse, yet they commonly activate type 2 immune responses1,2. Airway epithelial cells are crucial in the immune sensing of allergens3-5. However, what shared features among diverse allergens lead to their similar innate immune sensing, and how epithelial cells detect these features, remain poorly defined1,2,6-9. Here, we show that pore-forming proteins represent one of the common stimuli of allergic airway inflammation and elucidate their immune activation mechanisms. Using the prevalent mold allergen Alternaria alternata (A. alternata) as a model, we established a unique in vitro system to investigate type 2 innate immune sensing. Through a six-step biochemical fractionation, we identified its core immune-stimulatory components as Aeg-S and Aeg-L. Biochemical reconstitution and cryo-electron microscopy demonstrate that these proteins form 16-20-mer transmembrane pore complexes. Their cooperative perforation acts as a bona fide type 2 immune adjuvant to support antigen-specific TH2 and IgE responses. Genetically engineered A. alternata strains lacking such pore-forming activity fail to induce allergic responses in mice. Moreover, pore-forming proteins from various species, despite structural and membrane target differences, are sufficient to trigger respiratory allergies. Perforations in airway epithelial cells initiate allergic responses through two mechanisms: one triggers IL-33 release; another involves Ca2+ influx, which induces MAPK pathway activation and type 2 inflammatory gene expression. These findings provide insight into how type 2 immune responses detect common perturbations caused by structurally diverse stimuli. Targeting downstream signaling of epithelial cell perforation may open new avenues for treating respiratory allergies.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
To assess early airway epithelial cell responses induced by pore-forming proteins, mice were intranasally administered one of the following treatments: mock, A. alternata extract, or pore-forming proteins. Lung epithelial cells were isolated 6 hours post-treatment, with each treatment including at least two biological replicates. •  To investigate the transcriptomic response induced by pore-forming proteins in vitro, NCI-H1437 and NCI-H292 cells were treated with A. alternata extract or pore-forming proteins, with at least two biological replicates for each condition. Total RNA was extracted after 4 hours of stimulation for RNA sequencing.
Differential gene expression analysis was then performed using RNA-seq data, comparing the different treatments to the mock control.

first: Mo

last: Xu

first: Kejian

last: Shi


title: Transcriptomic remodeling of myeloid cells in response to maternal obesity

city: Portland

first: Alina

last: Maloyan

state: OR

address: 3181 SW Sam Jackson Park Rd

department: Medicine

institute: Oregon Health and Science University

summary: The goal of this project is to determine the effect of maternal obesity on the offspring's bone marrow CD11b+ cells gene transcriptomic profile. CD11b+ cells were isolated from the bone marrow of newly weaned mice born to high fat diet fed mothers to assess changes in gene expression.

overall_design: CD11b+ cells isolated from mouse bone marrow via StemCell Technologies CD11b+ isolation kit (via magnet and beads)

first: Yem

last: Alharithi


title: Emergence and disruption of cooperativity in a denitrifying microbial community

city: Seattle

first: Alex

middle: V

last: Carr

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

summary: Anthropogenic perturbations to the nitrogen cycle, primarily through use of synthetic fertilizers, is driving an unprecedented increase in the emission of nitrous oxide (N2O), a potent greenhouse gas, and an ozone depleting substance, causing urgency in identifying the sources and sinks of N2O. Microbial denitrification is a primary contributor to the biotic production of N2O in anoxic regions of soil, marine systems, and wastewater treatment facilities. Here, through comprehensive genome analysis, we show that pathway partitioning is a ubiquitous mechanism of complete denitrification by microbial communities. We have further investigated the mechanisms and consequences of process partitioning through detailed physiological characterization and kinetic modeling of a synthetic community of Rhodanobacter R12 and Acidovorax 3H11. We have discovered that these two bacterial isolates from a heavily NO3- contaminated superfund site complete denitrification through the exchange of nitrite (NO2-) and nitric oxide (NO). Our findings further demonstrate that cooperativity within this denitrifying community emerges through process partitioning of denitrification and other processes, including amino acid metabolism. We demonstrate that certain contexts, such as high NO3-, cause unbalanced growth of community members, due to differences in their substrate utilization kinetics and inter-enzyme competition. The altered growth characteristics of community members drives accumulation of toxic NO2- , which disrupts denitrification causing N2O off gassing.

sample_organism:
Acidovorax sp.
Rhodanobacter sp.

platform_organism:
Acidovorax sp.
Rhodanobacter sp.

overall_design: Time series mRNA profiling of two bacterial strains and their co-culture. Three conditions were tested, strain1 (3H11), strain2 (R12), and their co-culture (SynCom). Each condition consists of measurements at various growth phases (2-5 time points) and were made in triplicate.

first: Annie

middle: E

last: Otwell

first: Kristopher

middle: A

last: Hunt


title: Single Cell Analysis Reveals The Essential Role of TGFbeta Pathway in Shaping Immune-suppressive Microenvironment and Promoting CRPC Development

first: Zhenpeng

last: Wu

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

summary: To understand the dynamic changes of different cell populations within the Pten-null prostate cancer model in response to ADT, we carried out scRNA-seq transcriptome analysis on CD45- and CD45+ FACS-sorted cells from Pten-null intact (CP), early-(CRPC-4wks) and late-(CRPC-12wks) stage castrated prostates, respectively. To systematically investigate the effects of androgen deprivation therapy (ADT) on the cellular landscapes of primary and CRPC as well as intra- and extra-tumoral immune cells and their functional status at single cell level, we conducted scRNA-seq on CD45+ cells from bone marrow, blood, spleen and thymus of intact, early- and late-stage castrated Pten-null mice.

overall_design: We carried out scRNA-seq transcriptome analysis on CD45- and CD45+ FACS-sorted cells from Pten-null intact (CP), early-(CRPC-4wks) and late-(CRPC-12wks) stage castrated prostates,  and CD45+ cells of bone marrow, blood, spleen and thymus derived from same mice.

first: Jinping

last: Li