title: Long -chain unsaturated fatty acids promote trans-kingdom communication during immune responses

city: Geneva

first: Aleksander

last: Czauderna

address: Rue Michel-Servet 1

department: PATIM

institute: University of Geneva

summary: Immune responses can significantly influence the gut microbiota by altering its structure and function, leading to rapid transcriptional and metabolic shifts in commensal microbes. However, the specific host mediators involved in this process and their effects on bacteria remain poorly elucidated. Here, using a flagellin injection model, we identified unsaturated long-chain fatty acids (uLCFAs) as broad modulators of bacterial gene expression released in the gut lumen during immune responses. In Blautia, a prominent commensal in humans and mice, uLCFAs triggered the expression of ohyA, encoding oleate hydratase, which produces non-toxic hydroxy-fatty acids with immunomodulatory properties. Remarkably, oral administration of uLCFAs to mice replicated many of the bacterial transcriptional changes induced by flagellin injection, revealing an intriguing parallel between immune responses and dietary habits. This molecular loop underscores the sophisticated interactions between host and microbiota, and sheds light on how immune responses affect gut commensal functions.

sample_organism:
Mus musculus
mouse gut metagenome

platform_organism:
Mus musculus
mouse gut metagenome

overall_design: dual RNAseq (bullk) profiling of host cecal tissue and "4mix" microbial consortium within the cecum was performed 6h after i.p. flagellin administration (2.5 ug/animal) or 2h after oral administration of uLCFAs (50 ug OA + 50 ug LA). Additionally, 16S-seq data of microbial consortium from the experiment with flagellin stimulation is provided.

first: Simone

last: Becattini

first: Grishma

last: Kulkarni

first: Liqing

last: Cheng

first: Marissa

last: Sim

first: Joanna

last: Gach

first: Aurelie

last: Caillon

first: Gerard

last: Lambeau

first: Stefano

last: Serra

first: Matthew

last: Sorbara

first: Annika

last: Hausmann

first: Niccolo

last: Bianchi

first: Nicola

last: Realini


title: Targeted inhibition of Bcl-xL following radiation reduces tumourigenesis in preclinical models of H3K27M-altered diffuse midline glioma

status: Public on Jul 03 2025

city: London

first: Scott

last: Haston

address: 30 Guilford Street

department: Developmental Biology and Cancer

country: United Kingdom

institute: Institute of Child Health, University College London

type: Expression profiling by high throughput sequencing

summary: Abstract Background: Diffuse midline gliomas (DMGs) with histone H3K27M mutations represent a devastating paediatric brain cancer characterized by abysmal prognosis and limited treatment options. The only approved treatment is radiotherapy (RT), but most of the tumours relapse with fatal consequences. In this study, we sought to investigate whether irradiation leads to senescence induction and explore the efficacy of senolytics against DMG. Methods: We have characterised the senescent phenotype of five genetically heterogeneous H3K27M-altered human DMG cell lines, combining cellular and/or molecular approaches. The sensitivity of senescent cells to Bcl-xL inhibition has been demonstrated in dose/response curves in vitro and in a PDX model of DMG. Results: Here, we show that ionizing radiation induces senescence and SASP responses in both TP53 mutant and wild-type H3K27M-altered human DMG cell lines. We identify Navitoclax as a potent senolytic agent that selectively targets senescent DMG cells into apoptosis by inhibiting Bcl-xL. Related compounds, such as a proteolysis-targeting chimera (PROTAC)-mediated Bcl-xL degradation and a galacto-conjugated form of Navitoclax also show an effective senolytic activity in senescent cancer cells. Finally, we show that a combination therapy of irradiation and Navitoclax results in reduced tumor burden and increased mouse survival in an orthotopic xenograft DMG model. Conclusion: These results offer a rationale for further clinical development of senolytic therapies as part of multimodal treatment approaches for DMG patients/

overall_design:
DIPG cell lines, were irradiated, with sham (0Gy), 6 Gy and 24 Gy, following 24 hours, and 5 days RNA isolated from the cells and subsequent sequencing.
Bulk RNA-seq

first: Assley

last: Vardon

first: Juan Pedro

last: Martinez-Barbera


title: Cancer-Associated Fibroblast-derived exosomal LINC02420 drives glycolytic reprogramming via AEG-1/HIF-1α to promote Laryngeal Cancer progression

status: Public on Jul 02 2025

city: guangzhou

first: Yun

last: Li

state: Guangdong

address: 58 Zhongshan Road Ⅱ

country: China

institute: sun-yat sen university

summary: Laryngeal squamous cell carcinoma (LSCC) has an insidious onset and strong heterogeneity. The lack of effective biomarkers makes early diagnosis difficult. Liquid biopsy technology provides a new direction to break through this bottleneck. The co-culture model of CAFs and LSCC cells confirmed that CAFs can promote LSCC glycolysis through exosomes to promote its malignant progression. Further screening of differential lncRNAs that drive LSCC glucose metabolism reprogramming and promote tumor progression was performed using exosome lncRNA chips.

overall_design: The Agilent platform was used to analyze the differentially expressed lncRNAs in CAFs-derived exosomes and NFs-derived exosomes from six pairs of LSCC patients using human lncRNA array.


title: Partial removal of visceral epididymal white adipose tissue in obese Ldlr-/-.Leiden mice alters adipokine secretion and improves cerebrovascular health

city: Leiden

first: Eveline

last: Gart

state: Zuid Holland

address: Sylviusweg 71

department: MHR

country: Netherlands

institute: TNO

summary: Visceral white adipose tissue (WAT) dysfunction is thought to contribute to obesity-related brain impairments but no causal relationship has been demonstrated yet. We herein investigated the impact of visceral epididymal WAT (eWAT) lipectomy on brain health and obesity-associated comorbidities (liver steatosis, atherosclerosis, WAT dysfunction) in obese Ldlr-/-.Leiden mice. To do so, high-fat diet (HFD)-fed mice with manifest obesity underwent sham surgery or partial removal (~70%) of eWAT. A separate group of mice was kept on chow diet (control). Liver disease, atherosclerosis and three WAT depots were examined histologically, and WAT biopsies were also used for ex vivo culture experiments. Brain structure and function were monitored longitudinally using neuroimaging and cognitive tests. Brain pathology was further analyzed using histological analyses and hippocampal RNA sequencing. The portion of eWAT depot which was surgically removed appeared to secrete multiple adipokines and pro-inflammatory factors ex vivo. Histological analyses at the end of the study showed that partial eWAT lipectomy had no effect on the development of liver pathology and atherosclerosis, but it reduced the number of severely hypertrophic adipocytes in the residual-eWAT. This was consistent with reduced secretion of adipokines (e.g., leptin, adiponectin) and pro-inflammatory mediators (e.g., PAI-1, MIP-1α, IL-17) in ex vivo residual-eWAT culturing experiments. Importantly, partial eWAT lipectomy also alleviated HFD-induced adverse effects on hippocampal vasoreactivity, increased cortico-hippocampal (resting-state) functional connectivity and prevented the development of sedentary behavior. Hence, partial eWAT lipectomy in mice with manifest obesity partly prevents hippocampal cerebrovascular disturbances, demonstrating a causal involvement of visceral WAT in obesity-associated brain impairments. The beneficial effects of eWAT lipectomy may, at least partly, be mediated by the observed changes in the release of adipokines and inflammatory mediators.

overall_design: At the start of the experiment the animals (Male Ldlr-/-.Leiden, fed on standard Chow diet ) were 10-12 weeks old (corresponding to young adults). A healthy control group was (Chow) was kept for 28 weeks on Chow diet (n=15). Another group was kept for 28 weeks on obesigenic energy-dense diet (HFD = High Fat Diet, n=34). At 8 weeks half of the HFD group underwent a surgical procedure to remove 70% of eWAT tissue (HFD+WATx group, n=17), while the other half underwent sham surgery (HFD+sham, n=17). Sham surgery is a similar operation as WATx without removing the WAT tissue and serves as a control for operation effects. At 28 weeks mice were sacrified and RNAseq was performed on isolated right hemisphere hippocampi totRNA.

first: Florine

last: Seidel

first: Martine

middle: C

last: Morrison

first: Ilse

last: Arnoldussen

first: Vivienne

last: Verweij

first: Joline

last: Attema

first: Christa

last: de Ruiter

first: Wim

last: van Duyvenvoorde

first: Jessica

last: Snabel

first: Bram

last: Geenen

first: Ayla

last: Franco

first: Maximilian

last: Wiesmann

first: Robert

last: Kleemann

first: Amanda

middle: J

last: Kiliaan


title: characteristions of CRKP pneumonia at the single cell level

city: Harbin

first: jiao

middle: ya

last: sun

state: Heilongjiang province

address: No. 246 Xuefu road, Nangang district

department: Respiratory and critical care department

institute: The second affiliated Hospital of Harbin Medical University

summary: Detailed exploration was performed on the T cell and B cell transcriptional profiles when comparing moderate and severe patients to healthy donors, identifying candidate gene signatures. Furthermore, we analyzed the properties of cytotoxicity and exhaustion within T cell subgroups derived from CRKP samples.

overall_design: 5 samples derived from 3 patients with CRKP pneumonia

first: Yajiao

last: Sun

first: Fuhui

last: Chen

first: Hui

last: Ma

first: Dong

last: Wang

first: Jingwen

last: Zhang

first: Zhe

last: Jiang

first: Rongyao

last: Xia

first: Tian

last: Tian

first: Dongjie

first: Wei


title: transglutaminase 2 (TGM2) and Its Novel Targeted Activator in Diabetic Bone Regeneration: From Mechanism to Application

city: Xi’an

first: Dian

last: Gan

state: Shaanxi

address: No. 145, Changle West Road

institute: School of Stomatology, The Fourth Military Medical University

summary: To screen and identify key molecule regulating T2DM (Type 2 diabetes mellitus)-impaired bone regeneration, cellular osteogenic potential and mitochondrial function, and to elucidate the regulatory mechanisms of this molecule. Microarray analysis was performed to compare transcriptional profiles between bone marrow mesenchymal stem cells (BMMSCs) derived from normal rats (Wistar) and T2DM rats (GK). BMMSCs were transfected with overexpression plasmids targeting candidate molecule and small interfering RNA (siRNA) was used to silence candidate gene expression, then the osteogenic differentiation potential and mitochondrial function of BMMSCs were assessed. Microarray and qRT-PCR revealed significantly elevated expression of TGM2 in BMMSCs from T2DM rats compared to those from normal rats. TGM2 silencing suppressed osteogenic differentiation and mitochondrial function of BMMSCs, and TGM2 overexpression rescued osteogenic capacity. TGM2 serves as a critical regulator of osteogenic differentiation potential and mitochondrial function in BMMSCs derived from T2DM rats

overall_design: BMMSCs were isolated and purified from femurs of the normal and T2DM rats, and then cultured in osteogenic induction medium for 7 days. BMMSCs from normal rats were used as  the control group.

first: Xuan

last: Li

first: Faming


title: Roles of 3'UTR and IDR in regulating activity and chromatin localization of JMJD3 [ChIP-seq]

city: New York

first: Yang

last: Luo

state: NY

address: 408 E 69th St

department: Cancer Biology and Genetics

country: USA

institute: Sloan Kettering Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: JMJD3 cellular activity can be regulated by altered chromatin localization to genomic targets or by protein conformation changes that alter its catalytic activity. We found that the 3'UTR in the KDM6B mRNA template  is required for the JMJD3 protein to achive full demethylase activity in cells and that 3'UTR dependent regulation requires its intrinsically disordered region (IDR). In order to dissect the mechanism underlying 3'UTR- and IDR-coordinated control of JMJD3 protein activity in cells, we used ChIP-seq to identify localization and demethylase activity of full-length JMJD3 expressed from constructs with or without its 3'UTR and a IDR-deleted mutant.

overall_design: ChIP-seq of HA-tagged KDM6B/JMJD3 and H3K27me3 in HeLa cells transfected with HA-tagged cDNA vectors expressing full-length KDM6B coding sequence (-NU), full-length KDM6B coding sequence and its 3′UTR, or IDR-deleted KDM6B coding sequence (IDRdel-NU). Transfected cells were enriched with FACS.

first: Pierre-Jacques

last: Hamard

first: Richard

last: Koche

first: Christine

last: Mayr


title: CUT&Tag seq of Spi-B in small intestinal tuft cells

city: Beijing

first: Jiali

address: Hai Dian

institute: Tsinghua University

summary: The binding peaks of Spi-B in tuft cells were predominantly located in intergenic regions and introns, mirroring the distribution of PU.1 binding peaks in the genome.

overall_design: Small intestinal tuft cells were sorted from naïve WT and Spib-deficient mice, and subjected to CUT&Tag assay for Spi-B.


title: sequencing in co-housed group

city: Noda

first: HAIYANG

last: SUN

state: Chiba

address: Yamazaki

country: Japan

institute: Research Institute for Biomedical Sciences,  Tokyo University of Science

summary: Dendritic cell immunoreceptor (DCIR; Clec4a2), a member of the C-type lectin receptor family, plays important roles in homeostasis of the immune and bone systems. However, the intestinal role of this molecule is unclear. Here, we show that dextran sodium sulfate (DSS)–induced colitis and azoxymethane-DSS–induced intestinal tumors are reduced in Clec4a2–/– mice independent of intestinal microbiota. STAT5 phosphorylation and expression of Csf2 and tight junction genes are enhanced, while Il17a and Cxcl2 is suppressed in the Clec4a2–/– mouse colon, which exhibits reduced infiltration of neutrophils and myeloid-derived suppressor cells. GM-CSF administration ameliorates DSS colitis associated with reduced Il17a and enhanced tight junction gene expression, whereas anti–GM-CSF exacerbates symptoms. Furthermore, anti-NA2, a ligand for DCIR, ameliorates colitis and prevents colorectal tumors. These observations indicate that blocking DCIR signaling ameliorates colitis and suppresses colonic tumors, suggesting DCIR as a possible target for the treatment of these diseases

overall_design: WT and mice on 4 weeks old were co-housed 4 weeks, the take the feces from colon, extracted DNA from fecal, then analysis of the bacteria by 16S rDNA sequencing

first: Haiyang

last: Han


title: Invasive lobular carcinoma: Integrated multi-omics analysis reveals silencing of Arginosuccinate synthase and upregulation of nucleotide biosynthesis in tamoxifen resistance

city: Columbus

first: Daniel

last: Stover

state: OH

address: Biomedical Research Tower, Room 512, 460 W. 12th Avenue

institute: Ohio State University Comprehensive Cancer Center

summary: Invasive Lobular Carcinoma (ILC), a distinct subtype of breast cancer is hallmarked by E-Cadherin loss, slow proliferation, and strong hormone receptor positivity. ILC faces significant challenges in clinical management due to advanced stage at diagnosis, late recurrence, and development of resistance to endocrine therapy - a cornerstone of ILC treatment. To elucidate the mechanisms underlying endocrine resistance in ILC, ILC cell lines (MDA-MB-134-VI, SUM44PE) were generated to be resistant to tamoxifen, a selective estrogen receptor modulator.  The tamoxifen-resistant (TAMR) cells exhibit a 2-fold increase tamoxifen IC50 relative to parental cells. Metabolomics and RNA-sequencing revealed deregulation of alanine, aspartate, and glutamate metabolism, purine metabolism, and arginine and proline metabolism in TAMR cells. Among the fifteen commonly dysregulated genes in these pathways, low ASS1 expression was identified in the TAMR cells and was significantly correlated with poor outcome in ILC patients, specifically in the context of endocrine therapy. Our study reveals methylation mediated silencing of ASS1 in TAMR cells as a likely mechanism of downregulation. Demethylation restored ASS1 expression and correspondingly reduced tamoxifen IC50 toward parental levels. Nucleic acid biosynthesis is augmented in TAMR cells, evidenced by increase in nucleotide intermediates. Both TAMR cell lines demonstrated increased expression of several nucleic acid biosynthesis enzymes, including PAICS, PRPS1, ADSS2, CAD, and DHODH. Furthermore, CAD, the key multifunctional protein of de novo pyrimidine biosynthesis pathway is differentially activated in TAMR cells. Treating TAMR cell with Decitabine, a demethylating agent, or Farudodstat, a pyrimidine biosynthesis inhibitor, markedly augmented efficacy of tamoxifen. Collectively, our study unveils ASS1 downregulation as a novel mechanism underlying acquired tamoxifen resistance in ILC and establishes a metabolic link between ASS1 and nucleic acid biosynthesis. Restoring ASS1 expression or inhibiting pyrimidine biosynthesis restored tamoxifen sensitivity. ASS1 could be a potential biomarker and therapeutic target in tamoxifen resistant ILC patients, warranting further investigation.

overall_design: RNAsequencing of ILC parental and tamoxifen-resistant lobular cancer cell lines

first: Gupta

last: Annapurna

first: Stover

last: Daniel


title: scRNAseq analysis of lung treated with GLS1 inhibitor [scRNA-seq Lung_BPTES]

city: Minato City, Tokyo

first: Teh-Wei

address: 4 Chome-6-1 Shirokanedai

institute: IMSUT

summary: We employed the Chromium GEM-X single-cell RNA sequencing platform by 10x Genomics to investigate the effects of the GLS1 inhibitor, BPTES, on the lung single-cell transcriptome of 19- to 20-month-old wild-type male mice. Previous studies have identified GLS1 as a potential senolytic reagent capable of eliminating senescent cells. Our aim was to determine which cell populations are selectively removed by GLS1 inhibition in aged mice and to assess how this intervention alters intercellular interactions across different cell types.

overall_design: After administering BPTES or DMSO (vehicle control) to 19-month-old male mice for one month, we harvested the lungs and dissociated the tissue using a Liberase-based enzymatic digestion protocol. The resulting single-cell suspension was then subjected to fluorescence-activated cell sorting (FACS) for cell collection prior to library preparation.

first: Yuki

middle: T

last: Okamura

first: Makoto

last: Nakanishi


title: Deciphering the functional impact of Alzheimer’s Disease-associated variants in resting and proinflammatory immune cells [crispr]

city: Chapel Hill

first: Marielle

last: Bond

state: NC

address: 116 Manning Dr

department: Genetics

institute: UNC Chapel Hill

summary: Genome-wide association studies have identified loci associated with Alzheimer’s Disease (AD), but identifying the exact causal variants and genes at each locus is challenging due to linkage disequilibrium and their largely non-coding nature. To address this, we performed a massively parallel reporter assay of 3,576 AD-associated variants in THP-1 macrophages in both resting and proinflammatory states and identified 47 expression-modulating variants (emVars). To understand the endogenous chromatin context of emVars, we built an activity-by-contact model using epigenomic maps of macrophage inflammation and inferred condition-specific enhancer-promoter pairs. Intersection of emVars with enhancer-promoter pairs and microglia expression quantitative trait loci allowed us to connect 39 emVars to 76 putative AD risk genes enriched for AD-associated molecular signatures. CRISPR-mediated validation of emVars confirmed the predicted variant-gene relationship. Overall, systematic characterization of AD-associated variants enhances our understanding of the regulatory mechanisms underlying AD pathogenesis.

overall_design: Massively parallel reporter assay (MPRA) on Alzheimer's Disease risk variants in resting and proinflammatory THP-1 monocyte-derived macrophages and CRISPR validation in iPSC-derived microglia and CRISPRi perturbation of prioritized variants in iTF microglia

first: Yoseli

last: Quiroga-Barber

first: Brianne

last: Rogers

first: Susan

last: D'Costa

first: Yija

last: Wu

first: Jessica

last: Bell

last: McAfee

first: Quinn

last: Johnson

first: Ashlyn

last: Anderson

first: Alejandro

last: Gomez

first: Won

last: Ma

first: Nicole

last: Kramer

first: Sool

last: Lee

first: Sylvie

last: Parkus

first: Mary

last: Patrucco

first: Jeremy

last: Burgess

first: Adriana

last: Beltran

first: Nicholas

last: Cochran

first: Douglas

last: Phanstiel

first: Hyejung

last: Won


title: Extrahepatic replication and genomic signatures of the hepatitis E virus in the kidney

city: Bochum

first: André

last: Gömer

address: University Street 150

department: MMV

country: Germany

institute: Ruhr University Bochum

summary: The hepatitis E virus (HEV; species Paslahepevirus balayani) is a common human pathogenic and zoonotic virus that can cause both acute fulminant and chronic hepatitis. Despite its reputation as a hepatotropic virus, HEV infection is also associated with a number of extrahepatic diseases, including kidney disorders. However, the extent to which HEV replicates in kidney cells remains unclear. The present study aims to investigate the capacity of HEV to propagate in kidney cells in vitro and to assess whether HEV displays mutational signatures that correlate with compartmentalisation in vivo. We use HEV cell culture models to study the replication cycle and the effect of antivirals in human kidney cell lines and primary cells. In addition, we identified patients with chronic HEV infection (n = 9) from which we then sequenced viral RNA of urine, stools and plasma to analyse the viral sequence composition, to assessintra-host diversity and compartmentalisation(n = 2). A wide range of human kidney cell lines as well as primary cells supports viral entry, replication and propagation of HEV in vitro. Interestingly, the broad-spectrum antiviral ribavirin was less effective in inhibiting HEV replication in some kidney cells. Sequencing of HEV RNA-directed RNA polymerase coding region from plasma, stool and urine and subsequent phylogenetic analysis revealed diversification of HEV into tissue-specific viral subpopulations. In particular, the viruses derived from urine were found to be distinct from those derived from plasma and stool. In conclusion, kidney cells support the propagation of HEV in vitro and exhibit reduced sensitivity to antiviral treatment. Furthermore, HEV patient-derived sequences demonstrated compartmentalisation into distinct clusters that correlated with sample source. Collectively, these data indicate the potential for extrahepatic replication of HEV, which may result in clinically significant disease or serve as a reservoir for patient relapse.

overall_design: Plasma, stool and urine samples were collected from nine patients with chronic HEV-3 infection who participated in the HepNet-SofE study (NCT03282474) (24). These samples were collected from patients who previously failed or were ineligible for antiviral therapy with RBV and at a time when the patients were not being treated with antiviral drugs for at least 3 month. Subsequently, the samples were employed for the assessment of clinical parameters and viral high-throughput sequencing.

first: Avista

last: Wahid

first: Nele

last: Meyer

first: Daniel

last: Todt

first: Eike

last: Steinmann

first: Patrick

last: Behrendt


title: Cooperativity between Ras pathway mutations in colonic tumorigenesis

city: Boston

first: Bing

last: Shui

state: MA

address: 360 Longwood Ave

department: Cancer Biology

institute: Dana-Farber Cancer Institute

summary: The Kirsten rat sarcoma (KRAS) gene is the most frequently mutated oncogene in colorectal cancer (CRC). We previously characterized two activating alleles of KRAS, A59T and A59E, that show impaired BRAF dimerization. These alleles of KRAS are enriched in CRC tumors with genetic alterations in genes that regulate MAPK signaling (e.g. EGFR, NF1). Using a new conditional mouse model of K-Ras (LSL-K-Ras A59E) we show that, despite its inability to universally activate RAF kinases, K-Ras A59E disturbs colon epithelium and decreases mouse survival in a tumor model. By combining LSL-K-Ras A59E mice with a conditional knockout of Nf1, we demonstrate cooperation between these alleles at multiple levels. Consistent with cooperation and clinical observations, we show that K-Ras A59E neither promotes EGF independence of organoid growth, nor confers intrinsic resistance to EGFR inhibition. Thus, our data provide a deeper understanding of the role of RAF isoforms in mutant KRAS driven CRC and argue for the use of anti-EGFR therapies against some Ala59 mutant alleles of KRAS.

overall_design: RNA-Seq profiling of mouse colon tumors collected from animals with the Fabp-Cre/+; Apcfl/+ alleles, the tumor samples also carry one of the following genotype: KrasWT, KrasG12D, KrasA59E, NF1-/-; KrasA159E + NF1-/-

first: Christian

middle: W

last: Johnson

first: Kevin

middle: M

last: Haigis


title: RNA-sequencing of small intestine tissues from naïve WT and Spib-deficient mice

first: Jiali

last: Wang

summary: The absence of Spib led to a notable upregulation of tuft cell-specific genes and transcripts typically associated with helminth infection characteristics

overall_design: The proximal small intestine tissues were collected from naïve WT and Spib-deficient mice,  and were sent out for RNA-seq library construction.


title: scRNAseq analysis of lung with eliminating p16h cells [scRNA-seq Lung_DTR]

first: Teh-Wei

summary: We employed the Chromium GEM-X single-cell RNA sequencing platform by 10x Genomics to investigate how the removal of p16-high-expressing cells affects the lung single-cell transcriptome of 22-month-old male mice. In this experiment, we utilized p16-CreERT2/R26-LSL-DTR mice, administering tamoxifen and diphtheria toxin at 21 months of age. Lung tissues were harvested two weeks later for analysis. Our objective was to examine how the elimination of p16-high cells influences intercellular interactions among diverse cell types in aged lungs.

overall_design: Twenty-one-month-old male p16-CreERT2/R26-LSL-DTR mice and control p16-CreERT2 mice received tamoxifen (TAM) injections for five consecutive days. Two weeks later, both groups were administered diphtheria toxin (DT) for another five consecutive days to eliminate p16-high-expressing cells. Following a two-week recovery period, lungs were harvested, and tissue dissociation was performed using a Liberase-based enzymatic digestion protocol. Single cells were then collected by fluorescence-activated cell sorting (FACS) for library preparation.

first: Xintong

last: Zheng

first: Makoto

last: Nakanishi


title: Elucidating the impact of KRAS Gly12 mutants on homeostasis and tumorigenesis in the colonic epithelium

summary: KRAS mutations constitute one of the most prevalent and therapeutically relevant oncogenic drivers in human cancers. Clinical and epidemiological data suggest association between specific KRAS alleles, therapeutic response, and patient outcomes, however, direct experimental validation of these relationships has been limited. In this study, we employed genetically engineered mouse models (GEMMs) to investigate the differential impacts of three most common KRAS Gly12 mutations (KRASG12C, KRASG12D, and KRASG12V) in the context of intestinal homeostasis and tumorigenesis. Although tumors developing from different KRAS Gly12 mutants exhibited no significant histological differences, their effects on survival outcomes of tumor bearing mice and therapeutic response displayed pronounced allele-specific differences. Our transcriptomic analyses revealed both allele-agnostic and allele specific transcriptional programs driven by KRAS Gly12 mutations in colon tumors. The allele-agnostic signature was characterized by enrichment of gene sets associated with MAPK signaling, receptor tyrosine kinase pathways, and immune-modulating pathways, compared to KRAS WT tumors. In contrast, allele-specific signature revealed unique OXPHOS pathway upregulation in KrasG12D tumors and marked enrichment of Notch and Wnt/-catenin signaling pathways in KrasG12C tumors. Inhibition of these pathways, in combination with KRASG12C inhibitor led to either addictive or synergistic reduction in tumor cell viability, in allele-specific manner. Collectively, these findings underscore the importance of understanding the distinct biological effects of KRAS Gly12 mutants on colon tumorigenesis and highlight the therapeutic relevance of allele specific signaling dependencies in colorectal cancer. These results provide key mechanistic insights and provide a foundation for the development of effective, allele-informed therapeutic strategies for KRAS mutant cancers.

overall_design: RNA-Seq profiling of mouse colonic epithelium collected from Fabp-Cre/+; KrasWT/+ or KrasG12D/+ or KrasG12V/+ or KrasG12C/+ animals; and mouse colonic tumors collected from Fabp-Cre/+; Apcfl/+ animals, the tumor samples also carry one of the following genotypes: KrasWT, KrasG12D, KrasG12C, KrasG12V.

first: Shikha

last: Sheth

first: Moon Hee

last: Yang


title: Multiplexed single-cell transcriptomics reveals diverse phenotypic outcomes for pathogenic SHP2 variants

first: Ross

last: Giglio

institute: Columbia University

summary: The protein tyrosine phosphatase SHP2, encoded by PTPN11, is an important regulator of Ras/MAPK signaling  and  a  signaling  hub downstream  of  receptor  tyrosine  kinases  and  other  transmembrane receptors.  Germline  missense  PTPN11  mutations  cause  developmental disorders  such  as  Noonan Syndrome,  whereas  somatic  mutations  drive diverse  cancers.  While  many  pathogenic  mutations enhance SHP2 catalytic activity, some are inactivating or alter protein-protein interactions, confounding our understanding of how SHP2 dysregulation causes diseases. Here, we perform multiplexed single-cell transcriptional profiling in cells expressing clinically diverse SHP2 variants, with and without receptor tyrosine kinase stimulation. We find that loss of catalytic activity does not phenocopy SHP2 knock-out at the  gene  expression  level,  and  we  show evidence  for  both  convergent  phenotypic  effects  from mechanistically distinct mutations, as well as the divergent effects from structurally similar mutations. These  findings  provide a  framework  for  understanding  how  structural  perturbations  to  SHP2  impact cellular outcomes.

overall_design: Single-cell RNA-seq libraries were generated using three-level single-cell combinatorial indexing RNA sequencing (sci-RNA-seq) of basal or EGF-stimulated HEK 293 SHP2 variant cells. Cells transfected with different SHP2 variants and exposed to varying EGF concentrations were hashed at either 24hr or 96hr and pooled prior to sci-RNA-seq using the sci-Plex nuclear barcoding strategy. This nuclear barcoding strategy relies on fixation of barcode containing well-specific oligos that are specific to a given cell type, replicate, or treatment condition. Cells represent unique timepoint, SHP2 variant, EGF concentration, and replicate.

first: Anne

middle: E

last: van Vlimmeren

first: José

middle: L

last: McFaline-Figueroa

first: Neel

middle: H

last: Shah


title: mRNA expression profile in the liver after overexpressed tsRNA-Glu-CTC oligos in C57BL/6 mice with mRNA-seq method

city: Riverside

first: Xiuchun

last: Li

address: 900 University Avenue

institute: UCR

summary: Purpose: To  reveal mRNA profiles in the liver using mRNA-seq method. Methods: 8 week old C57BL/6 male mice were injected Control Oligos and tsRNA-Glu-CTC oligos for two weeks. Liver RNA was extracted with Trizol methods. Results:mRNA-seq revealed upregulation of lipids metabolism related genes in overexpressed tsRNA-Glu-CTC oligos mice. Importantly, cholesterol synthesis key genes SREBP2 and HMGCR are significantly upregulation.

overall_design: Liver mRNA were sequenced from C57BL/6 male mice with I.P. injection of Control Oligo and tsRNA-Glu-CTC Oligo-1 for two weeks

first: Changcheng

last: Zhou

first: Tong


title: Targeting Cellular Senescence to Enhance Human Endometrial Stromal Cells’ Decidualization and Inhibit Their Migration

city: Mahasset

first: Andrew

last: Shih

address: 350 Community Dirive

institute: Feinstein Institute - Northwell Health

summary: Cellular senescence leads to stable cell cycle arrest and an inflammatory senescence-associated secretory phenotype that varies with stressor and cell type. To mitigate these effects and improve health, senotherapeutics (e.g., senolytics and senomorphics) have been developed. Senescent-like endometrial stromal cells (eSCs) lining the uterus of patients with endometriosis and infertility are proposed to impair decidualization, a differentiation process required for uterine receptivity in humans. Quercetin, a natural flavonoid senolytic, dramatically improves decidualization and reduces endometriosis in rodent models. However, little is known about the comparative effects of various senotherapeutics on eSCs. Using menstrual effluent-derived eSCs, we evaluated the effects of flavonoid and non-flavonoid compounds on eSC functions associated with endometriosis, aiming to identify optimal senotherapeutics for future clinical trials. Among flavonoids tested, all senolytics (quercetin, fisetin, and luteolin) and kaempferol, a senomorphic, significantly improved decidualization without cytotoxicity. Although non-flavonoids exhibited notable cytotoxicity, dasatinib, but neither ABT-737 nor navitoclax, enhanced decidualization. Flavonoid senotherapeutics and dasatinib significantly inhibited eSC migration. Mechanistic studies revealed that all flavonoids and dasatinib suppressed AKT phosphorylation and upregulated p53 expression. Notably, only quercetin and fisetin reduced ERK1/2 phosphorylation. Furthermore, flavonoid-senolytics and dasatinib consistently eliminated senescent eSCs. These findings support future studies to assess the therapeutic potential of in vivo supplementation with flavonoid senolytics on eSC function using menstrual effluent.

overall_design: Endometrial stromal cells derived from menstrual effluent were cultured until passage 3-4 then stimulated with either quercetin or vehicle to determine the effect of quercetin

first: Julia

last: Delenko

first: Nathaniel

last: Hyman

first: Prodyot

middle: K

last: Chatterjee

first: Polona

last: Safaric Tepes

first: Xiangying

last: Xue

first: Jane

last: Gurney

middle: G

last: Baker

first: Cheng

last: Wei

first: Daniel

last: Munoz Espin

first: Ljiljana

last: Fruk

first: Peter

last: Gregersen

first: Christine

middle: N

last: Metz


title: Deciphering the functional impact of Alzheimer’s Disease-associated variants in resting and proinflammatory immune cells

first: Marielle

last: Bond

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

overall_design: Refer to individual Series


title: CNS methylation classifiers may misclassify normal developing cerebellar cortex as medulloblastoma.

city: Los Angeles

first: Jennifer

middle: A

last: Cotter

state: CA

address: 4650 Sunset Blvd., M/S 43

department: Pathology and Laboratory Medicine

institute: Children's Hospital Los Angeles

summary: DNA methylation profiling is commonly utilized in tumor diagnosis and has shown diagnostic specificity in many contexts. We recently noted that several CNS tumor classifiers used for neuropathology clinical diagnostics fail to appropriately classify pediatric cerebellar cortex tissue as non-neoplastic. Our study illustrates a gap in classifier accuracy that is most evident with samples from very young patients (<6 months). In this setting,classifiers typically assign medulloblastoma, SHH-activated, and occasionally show high-confidence scores. Neuropathologists practicing in pediatric settings should be aware of the histologic appearance of immature cerebellar tissue, and exercise caution when performing methylation profiling of samples of uncertain neoplastic status for patients in early infancy.

overall_design: DNA methylation array was performed using Infinium MethylationEPIC v1.0 and/or v2.0 on postmortem cerebellar cortex samples ranging from premature (28 gestational weeks) to postnatal 10 days and 4 months of age.


title: Analysis of Streptococcus dysgalactiae subspecies equisimilis gene transcripts during experimental primate necrotizing myositis

city: HOUSTON

first: Jesus

last: Eraso

state: TX

address: 6670 Bertner

department: Pathology and Genomic Medicine

institute: Methodist Hospital

summary: Streptococcus dysgalactiae subspecies equisimilis (SDSE) is a Gram-positive bacterial pathogen capable of causing various infections in humans. Recently, isolates of SDSE emm type stG62647 have emerged as a cause of severe invasive infections, including necrotizing myositis. However, the molecular processes underlying these infections remain poorly understood. To address this gap, we performed RNAseq analysis to examine SDSE gene transcript levels during experimental necrotizing myositis infection in non-human primates, an animal phylogenetically closely related to humans. We analyzed the transcriptomes of two related SDSE stG62647 human isolates (MGCS36044 and MGCS36089) during necrotizing myositis infection in six non-human primates. The transcriptome from in vitro growth in nutrient-rich media differed considerably from that of SDSE bacteria grown in vivo in experimental necrotizing myositis, with 254 genes differentially expressed, indicating extensive genetic adaptation in infected skeletal muscle. Notably, we observed marked upregulation of ihk-irr genes encoding a two-component regulatory system that promotes evasion of phagocytosis and resistance to killing by human polymorphonuclear leukocytes in Streptococcus pyogenes. Similarly, genes comprising the sag operon encoding the streptolysin S cytolytic toxin virulence factor demonstrated very high transcript abundance in vivo. Additionally, we present evidence that a 40-nt deletion in fasB alters expression of ska, encoding streptokinase. Collectively, our data provide new insights into the SDSE genes transcribed in vivo, thereby enhancing our understanding of the molecular basis of pathogen and primate host interactions. The SDSE genes identified in this study offer promising targets for future studies on molecular pathogenesis and therapeutics interventions.

overall_design: RNAseq was performed on SDSE MGCS36044 and MGCS36089 grown in vitro in THY (quadruplicates) that had been collected at mid-exponential (ME) (OD=1) and early stationary phase (ES) (OD=2). RNAseq was also performed on MGCS36044 and MGCS36089 isolated from skeletal muscle biopsies from six NHPs at 24h post-infection. Each NHP was concurrently infected with strain MGCS36044 in the right leg and strain MGCS36089 in the left leg. Muscle biopsies were obtained in five concentric layers (L1 to L5), with L1 corresponding to the inoculation site, and L5 to the outermost layer, and reads from all five biopsy layers per NHP were pooled.

first: James

last: Musser


title: Mitotic MTH1 Inhibitor Karonudib Kills Epithelial Ovarian Cancer Independent of Platinum Sensitivity

city: Rochester

first: Cristina

last: Correia

state: Minnesota

address: Kellen Bld 3 th Floor, 200 1st street SW

institute: Mayo Clinic

summary: The prognosis for women with ovarian cancer (OC) is particularly poor if resistance to platinum compounds, the mainstay of standard-of-care OC therapy, develops. Inhibitors of the Nudix hydrolase MuT homolog 1 (MTH1) have previously been shown to arrest cancer cells in mitosis, increase 8-oxo-2’-deoxyguanosine (8-oxo-dG) incorporation into DNA, and selectively kill neoplastic cells while sparing normal cells. Here we explored the cytotoxic mechanism of these agents as well as their activity against platinum-resistant OC in vitro and in vivo. Two mitotic MTH1 inhibitors (mMTH1is), TH588 and karonudib, decreased colony formation and induced cell death in both platinum-sensitive OC cell lines and their platinum-resistant counterparts in vitro but had limited effects on fallopian tube and immortalized ovarian surface epithelial cells. Treatment with karonudib stalled OC cells in mitosis and caused elevated 8-oxo-dG levels in DNA. Cytotoxicity of this agent was blunted by overexpression of the pre-mitotic checkpoint protein CHFR, which inhibits other anti-mitotics, or treatment with the antioxidant N-acetylcysteine, which diminishes nuclear 8-oxo-dG staining, suggesting a role for both mitotic stalling and increased nuclear incorporation of oxidized nucleotides in karonudib efficacy. In three orthotopic OC patient-derived xenograft models, karonudib induced growth delay in vivo. Moreover, addition of karonudib to carboplatin doubled median overall survival in two models and prolonged survival for the duration of the study (110 days) in the third. These results, which demonstrate activity of mMTH1 as monotherapy and in combination with carboplatin in OC, suggest that karonudib-based combinations warrant further investigation as potential therapies for platinum-resistant OC.

overall_design: RNAseq data of 12 samples of A2780 cell lines treated with DMSO or MTH1 (TH-588, 6 𝜇M for 48h) each in three independent experiments.

first: Scott

last: Kaufmann


title: Circular RNA Expression Profiling in Cardiac Tissue from Heart Failure Patients and Healthy Controls

city: Hannover

first: Maximilian

last: Fuchs

address: Carl-Neuberg-Str. 1

department: IMTTS

institute: Hanover Medical School

summary: Non-coding RNAs (ncRNAs) play critical regulatory roles in cardiovascular pathophysiology, with emerging therapeutic potential for cardiovascular diseases (CVDs). Circular RNAs (circRNAs), a recently characterized subclass of ncRNAs, have garnered significant interest due to their unique covalently closed-loop structures, which confer exceptional stability compared to linear RNAs. These molecules are generated through back-splicing, a non-canonical processing event of pre-mRNA transcripts. CircRNAs exhibit tissue-specific expression patterns, with notable enrichment in cardiac tissue, and demonstrate high evolutionary conservation—properties that underscore their translational relevance. Their functional versatility includes roles as microRNA sponges, protein interactors, and modulators of gene expression, positioning them as promising diagnostic biomarkers and therapeutic targets for cardiovascular conditions, particularly heart failure (HF).                                      This study provides a comparative analysis of circular RNA (circRNA) expression patterns in left ventricular myocardial tissue from patients with heart failure (HF) and healthy controls, revealing differentially expressed circRNAs with potential therapeutic implications. Furthermore, we investigate novel circRNAs that may represent promising candidates for targeted interventions in heart failure.

overall_design: Global circRNA expression profiling was performed using RNA-seq on left ventricular tissue samples obtained from healthy controls and heart failure patients.

first: Thomas

last: Thum

first: Mira

last: Jung

first: Fuchs

last: Maximillian


title: Methylation and gene expression patterns in adamantinomatous craniopharyngioma highlight a panel of genes associated with disease progression-free survival

city: Ribeirão Preto

first: Junier

middle: Marrero

last: Gutiérrez

state: São Paulo

address: Av Bandeirantes, 3900

department: Pediatric

country: Brazil

institute: Ribeirão Preto Medical School-University of São Paulo

summary: Introduction: Over the past decade, advancements in next-generation sequencing have significantly enhanced our understanding of the molecular pathogenesis of adamantinomatous craniopharyngiomas (ACP). Objective: This study integrated methylome and transcriptome analyses in ACP samples to explore the potential interplay between DNA methylation and RNA expression signatures for diagnostic and prognostic applications in ACP patients. Methods:  This cross-sectional study evaluated clinicopathological features, DNA methylation, and gene expression profiles in 15 patients with ACP (33% women, age range: 3–55 years, 53% diagnosed before 18 years) treated at Ribeirao Preto Medical School, University of São Paulo. Results: Multidimensional scaling and principal component analysis identified two distinct clusters (ACP-A: n=9, ACP- B: n=6) with consistent composition across DNA methylation and gene expression profiles. While most clinical and histopathological characteristics were similar between clusters, ACP-A exhibited a longer median progression-free survival. ACP-B showed a higher prevalence of hypomethylated probes in CGI sites, with 63% of differentially methylated positions (DMPs) located in gene body regions. Differential methylation patterns were categorized into Methyl-Set1 (hypomethylated in ACP-A and hypermethylated in ACP-B) and Methyl-Set2 (hypermethylated in ACP-A and hypomethylated in ACP-B). Clustering analyses based on the methylation levels of probes and expression levels of the stringently filtered-in 212- and 37-gene sets further confirmed these two distinct ACP subgroups. Functional enrichment analysis highlighted key roles in synaptic modulation, nervous system development, cell adhesion, as well as pathways linked to RAS signaling, GTPase activity, and membrane potential regulation. Conclusion: Although clinical characteristics were largely comparable between the clusters, ACP-B patients exhibited shorter median progression-free survival, suggesting a more aggressive phenotype. The higher prevalence of hypomethylation in ACP-B indicates increased transcriptional activation, potentially driving tumor aggressiveness. The strong concordance between methylation and transcriptomic data in the 212- and 37-gene sets underscores their potential as a clinically relevant molecular biomarker panel. These gene sets demonstrate robustness in distinguishing ACP clusters, making it a promising tool for clinical sample classification.

overall_design: In this cross-sectional study, we evaluated 15 subjects with clinically diagnosed and pathologically confirmed ACP, followed at FMRP-USP (n = 8, with data on endocrine and clinical manifestations) or at the Federal University of Rio de Janeiro (UFRJ, n = 7), both in Brazil. These subjects represent a subset of a larger cohort in which the methylation profile of ACP samples was recently analyzed (28). RNA were extracted from microdissected, fresh frozen ACP samples using Rneasy kit (QIAGEN, Hilden, Germany) according to the manufacturers’ instructions. Quantification was performed by fluorometry using Qubit RNA BR Assays (Qubit Fluorometer, Thermo Fisher Scientific,Waltham, MA). Integrity was assessed by electrophoresis using the TapeStation 4200 System (Agilent, Santa Clara, CA). We considered adequate RNA integrity number (RIN) ≥7

last: Marrero Gutiérrez

first: Ana

last: C Bueno

first: Margaret

last: de Castro


title: Single-cell RNA-seq uncovers cellular heterogeneity of granulosa cells and provides a signature for follicular development in chicken

city: Leshan

first: Shigang

last: Yu

address: No. 778, Binhe Road, shizhong distinct

institute: Leshan normal university

summary: The functional differentiation of the granulosa cell (GC) layer plays an essential role in follicular development and oocyte maturation in avian. In the current study, single-cell RNA sequencing (scRNA-seq) was employed to identify GC types, uncover heterogeneity, and construct developmental trajectories of chicken GCs in two developmental stages of hierarchical follicles (HF-GCs) and prehierarchical (PHF-GCs). The ﬁndings enhance our understanding of the cellular biology of GC layer of ovarian follicles and will assist studies of the molecular mechanisms of follicle development and selection in chicken.

overall_design: The granulosa layers were isolated from prehierarchical and hierarchical follicles. The GC layers were processed further to obtain single cell suspension for scRNA-seq.


title: Inhibition of PCSK9 Attenuates Liver Endothelial Cell Activation Induced by Colorectal Cancer Stem Cells during Liver Metastasis

city: Muenster

first: Marcos

middle: J.

last: Araúzo-Bravo

address: Rogentstrasse

department: Cell and Developmental Biology

institute: Max Planck Institute for Molecular Biomedicine

summary: Colorectal cancer often leads to liver metastases, a major cause of patient mortality. This study investigates the role of PCSK9, a protein traditionally known for its role in cholesterol metabolism, in the metastatic process. Researchers found that conditioned media from colorectal cancer stem cell strongly upregulates PCSK9 expression in liver sinusoidal endothelial cells (LSECs). PCSK9 activation enhances LSEC proliferation and migration, contributing to the formation of a pro-metastatic niche. Inhibiting PCSK9 with the small molecule PF-06446846 reduced endothelial activation and normalized gene expression, decreasing LSEC potential support of the metastatisis. Immunofluorescence confirmed PCSK9 expression in  Liver Endothelial Cells (LSEC)s of human colorectal cancer liver metastases. These results suggest that PCSK9 could represent a promising therapeutic target to prevent and treat liver metastases in colorectal cancer patients.

overall_design: LSECs were stimulated with conditioned media derived from differentiated colorectal cancer cells and cancer stem cells (CSCs), the latter generated by reprogramming SW620 and CT26 cell lines. RNA sequencing was used to profile gene expression in LSECs. PCSK9 mRNA and protein levels were quantified by qPCR and Western blotting, respectively. PCSK9 expression in CRC liver metastases was evaluated by immunofluorescent staining. RNA Extraction and Quantitative Real-Time PCR: To compare PCSK9 expression in LSEC and CSC markers in colon cancer cells total RNA isolation from cell cultures was performed using the NucleoSpin RNA isolation kit (740955, Macherey & Nagel). The RNA was reverse transcribed using the iScript cDNA synthesis kit (1708891, BioRad,) according to manufacturer´s guidelines and was used for real-time PCR. Real-time PCR was performed using the Power SYBR Green Master Mix (1725271, BioRad). The quantitative polymerase chain reaction (qPCR) data were acquired with the CFX96 C1000 Touch Real-Time PCR Detection System (Biorad). The expression levels were normalized to beta18S ribosomal RNA (18S rRNA). All the reactions were performed in triplicate, and the relative expression of each gene was calculated via the 2−ddCt method. RNA sequencing: After performing quality control, checking the RIN value of each sample was bigger than 6, and ensuring RNA quantity was higher than 200ng, library construction was performed following Ilumina’s recommendation. Sequencing library was prepared by random fragmentation of the cDNA sample, followed by 5' and 3' adapter ligation. The fragmentation and ligation reactions were performed in a single step that increases the efficiency of the library preparation process. Then, adapter-ligated fragments were amplified by PCR and purified in a gel. Subsequently, library was loaded into a flow cell where fragments were captured on a lawn of surface-bound oligos complementary to the library adapters. Each fragment was then amplified into distinct clonal clusters through bridge amplification. When cluster generation was completed, sequencing was performed using Illumina SBS technology. All sequencing data was converted in raw data in FASTQ format, allowing its bioinformatics analysis. RNA data analysis: RNA-sequencing (RNA-seq) transcriptomics data analysis was conducted useing HISAT2 to align the RNA-seq reads to the human reference genome hg38 and to calculate counts and Cufflinks to annotate them. We merged the transcriptomics data into a single text file and used it in the downstream analysis using in-house functions developed in MATLAB (MathWorks). We equalized the data and stabilized them through the log2 transform of the data plus one, calculated the average values for each group of replicates, selected the Differentially Expressed Genes (DEGs) whose absolute difference in mean values between the two groups was less than the selection threshold = 1 of fold change in the log2 scale, and selected the statistically significant DEGs using Student’s t test with a significance threshold = 0.05. DEG sets were subjected to Gene Ontology (GO) enrichment analysis. The functional GO enrichment of the DEGs was calculated using the hypergeometric test over the mid-p-values with a significance threshold of 0.05.

first: Ander

last: Martín

first: Daniela

last: Gerovska

first: Marcos J.

first: Maitane

last: Duarte García-Escudero

first: Helena

last: García García

first: Iratxe

last: Bañares

first: Naroa

last: Fontal

first: Geraldine

last: Siegfried

first: Serge

last: Evrad

first: Simon

last: Pernot

first: Abdel-Majid

last: Khatib

first: Iker

last: Badiola


title: Forskolin induced pluripotency of caudal fin fibroblasts of Topmouth culter.

city: Hangzhou

first: 劳

last: 霁晖

state: Zhejiang

address: 866 Yuhangtang Road, Xihu District

department: College of life sciences

institute: Zhejiang University

summary: As the passage number increases, the spontaneous aggregation phenomenon of TCCF2022 cells gradually weakens and eventually disappears, and occasional instances of post-passage cells being unable to proliferate are observed. This suggests that the characteristics of the cells may have changed during the culture process.We found that when individual factors were used to induce TCCF2022, on the third day after treatment with 5μM Forskolin, TCCF2022 cells regained the ability to form cell aggregates, and alkaline phosphatase detection was also positive. Therefore, we need to determine the possible mechanism of this state recovery through RNA-seq.

overall_design: The caudal fin fibroblasts of Topmouth culter with 5μm of Forskolin and without any treatment were cultured for seven days, and the RNA-seq data were analyzed for differential expression.

first: Xiao

last: Huang

first: Jun

last: Chen

first: Jihui

last: Lao

first: Zongyun

last: Du

first: Yuyan

last: Jiang

first: Jingyu

last: Liu


title: High-Fat Diet-Induced Liver-Gut Crosstalk Suppresses Autophagy and Exacerbates Colitis [colon]

city: Beijing

first: Tian

last: Xu

state: Beijing

address: No.1 Shuaifuyuan, Dongcheng District, Beijing,China

institute: Peking Union Medical College Hospital

summary: The goal of this project is to investigate the mechanisms through which high fat diet (HFD) exacerbates colitis via the liver-gut axis, particularly focusing on liver dysregulated lipid metabolism and intestinal autophagy. We examined colon transcriptomes of C57BL6/J mice fed a control diet (CD) or HFD with or without dextran sulfate sodium (DSS) by RNA seq analysis.

overall_design: The colon mRNA profile of DSS-induced mice that treatd with CD and HFD by RNA sequencing.


title: MiRNA networks mediate a compensatory response in heart  failure induced cognitive impairment [smallRNA-Seq]

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

institute: German Center for Neurodegenerative Diseases (DZNE)

type: Non-coding RNA profiling by high throughput sequencing

summary: Heart failure (HF) is associated with an increased risk of cognitive impairment and hippocampal dysfunction, yet the underlying molecular mechanisms remain poorly understood. In this study, we utilized CaMKIIδC transgenic (TG) mice, a model for HF, to investigate the role of microRNA (miRNA) networks in hippocampus-dependent memory recovery. While 3-month-old CaMKIIδC TG mice displayed significant memory deficits and dysregulated hippocampal gene expression, these impairments were no longer detectable at 6 months, despite persistent cardiac dysfunction. Small RNA sequencing revealed a dynamic shift in hippocampal miRNA expression between 3 and 6 months old CaMKIIδC TG mice , with 27 miRNAs, termed "compensatory miRs," targeting 73% of reinstated transcripts and mediating transcriptional homeostasis. Notably, miR-181a-5p emerged as a central hub in the compensatory miRNA network, with its downregulation aligning with restored neuronal function and memory. These findings highlight a synergistic miRNA response that compensates for early transcriptional deficits in HF. In conclusion, our results suggest that better understanding of these microRNA networks may provide novel therapeutic targets to manage heart failure related cognitive dysfunctions.

overall_design: Non coding RNA-seq profiling from CaMKIIδC transgenic mice and wildtype controls at 6 months and 3 months of age.

first: Verena

last: Gisa

first: Rezaul

last: Islam

first: Dawid

last: Lbik

first: Raoul

last: Hofmann

first: Tonatiuh

last: Pena

first: Dennis

last: Krüger

first: Susanne

last: Burkardt

first: Anna-Lena

last: Schütz

first: Farahnaz

last: Sananbenesi

first: Karl

last: Toischer

first: André


title: Proton-secreting cells modulate mucosal immune surveillance in the male reproductive tract

first: Maria

middle: Agustina

last: Battistone

state: Massachusetts

department: Program in Membrane Biology, Center for Systems Biology and Nephrology Division, Department of Medicine

institute: Massachusetts General Hospital. Harvard Medical Scholl

summary: We identify clearly distinct transcriptomic signatures between clear cells from the caput, corpus, and cauda regions after LPS intravasal epididymal injection compared to control (saline injection).

overall_design: EGFP+ clear cells were isolated by double cell sorting from the caput, corpus and cauda epididymal regions of B1 V ATPase - EGFP transgenic mice that specifically express EGFP in clear cells. Mice were subjected to in vivo intravasal epididymal injections of LPS or saline (control)

first: A

last: Da Silva

first: F

last: Barrachina

first: M

last: Avenatti

last: Elizagaray

first: I

last: Bastepe

first: E

last: Sasso-Cerri


title: The DNA-PKcs/JNK/p53 pathway underlies changes in cell fate decision toward death during DNA replication catastrophe

city: Stony Brook

first: Hyungjin

last: Kim

state: New York

address: 101 Nicolls Rd. BST 8-120

institute: SUNY Stony Brook

summary: Exacerbating the DNA replication problem of cancer cells serves as a viable therapeutic approach. Nevertheless, the cytotoxicity of cancer drugs is often hampered by therapy-induced senescence, leading to unfavorable patient outcomes. Here, we employ acute replisome dysfunction in combination with ATR inhibition as a strategy to divert senescent cells toward death by triggering DNA replication catastrophe, a form of irreversible replication fork collapse caused by excessive single-stranded DNA (ssDNA) accumulation. RNA-sequencing revealed a distinct set of p53-responsive genes responsible for death. We identify c-Jun N-terminal kinase (JNK) to be essential for augmenting p53-dependent apoptotic programs and inducing pan-nuclear distribution of H2AX, together constituting a feed-forward loop to drive cell death. Activation of DNA-PKcs initiates the signaling cascade of replication catastrophe, including CHK1-dependent JNK activation, which relies on MRE11 and PARP1 to expand and recognize ssDNA gaps, defining replication-associated gaps as an underlying basis for replication catastrophe. Our study elucidates the dynamic regulation of proximal and distal effectors along the DNA-PKcs/JNK/p53 axis that govern the cell fate decision between senescence and death. We propose that key determinants of replication catastrophe signaling are targetable vulnerabilities that can be exploited to limit senescent cell populations and increase the efficacy of anti-cancer therapies.

overall_design: RNA-seq profiling of HCT116 TIM-mAID cells treated with DMSO, 5-Ph-IAA, ATRi, or 5-Ph-IAA/ATRi combination for 40 h. Experiements were done in three biological replicates.

first: Jinal

last: Patel


title: Single-cell multiomic analysis reveals deviations following oocyte maturation in vitro

city: Caserta

first: Francesco

last: Cecere

state: Caserta

address: Via A. Vivaldi, n. 43

department: DiStABiF

country: Italy

institute: University of Campania "Luigi Vanvitelli"

type: Methylation profiling by high throughput sequencing

summary: In vitro maturation of oocytes is a routine step in assisted reproduction, however, it is associated with lower embryo development rates compared to oocyte maturation in vivo. The objective of the current study was to characterize the genomic profile of oocytes derived from the same cow, but submitted to maturation either in vivo or in vitro. To this end single-cell methylome and transcriptome sequencing of individual oocytes and transcriptome analysis of their corresponding cumulus cells was carried out. The resulting data revealed alterations in both the transcriptome and methylome of the  oocytes matured in vitro, suggesting compromised oocyte maturation. Notable changes included alterations in CpG islands associated with imprinted genes, including decreased methylation levels in MEST (PEG1), NNAT (both implicated in large offspring syndrome), and MIMT1 following in vitro maturation. Additionally, transcriptomic analysis of their cumulus cells highlighted significant alterations in gene expression linked to impaired mitochondrial function and altered responses to hypoxia and cell adhesion. Our findings highlight the extent to which the maturation environment can influence the key epigenetic regulators and mRNA profiles that affect oocyte quality and subsequent developmental outcomes. The data provides a valuable resource for optimising assisted reproduction technologies.

overall_design: scRNA-seq and scBS-seq were perfomed on bovine MII oocytes after in vivo or in vitro maturation. scRNA-seq was also performed on MII oocytes after in vivo + in vivo maturation. We sequenced 88 MII oocytes and 2 Negative control.

first: Camilla

last: Benedetti

first: Carlo

last: Giaccari

first: Yannick

last: Gansemans

first: Gavin

last: Kelsey

first: Antonio

last: Galvao

first: Simon

last: Andrews

first: Nima

last: Azari-Dolatabad

first: Andrea

middle: F

last: Montoro

first: Osvaldo

middle: B

last: Pascottini

first: Tine

last: De Coster

first: Filip

last: Van Nieuwerburgh

first: Trudee

last: Fair

first: Erik

last: Mullaart

first: Krishna

last: Pavani

first: Katrien

last: Smits

first: Ann

last: Van Soom


title: Role of OCT4 as a transcription factor in pluripotent stem cells [ChIP-seq]

first: Wenpeng

last: Song

address: Department of Stomatology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China

department: Department of Stomatology

institute: Capital Medical University

summary: Pluripotent stem cells (PSCs), known for their unlimited ability to self-renew and differentiate into all three germ layers, have emerged as a promising cell source for regenerative therapies aimed at treating various diseases and injuries.OCT4 is a key pluripotent marker and transcription factor in PSCs, which regulates numerous biological processes of PSCs. This data demonstrates the potential role of OCT4 as a transcription factor.

overall_design: In this study, the biological role of OCT4 as a transcription factor was investigated using OCT4 antibody and ChIP-Seq.


title: Sequencing results of several pluripotent stem cells

summary: Pluripotent stem cells (PSCs), known for their unlimited ability to self-renew and differentiate into all three germ layers, have emerged as a promising cell source for regenerative therapies aimed at treating various diseases and injuries.

overall_design:
In this study, several pluripotent stem cells were analyzed using RNA-seq.
These five sequencing files represent results from three cell types across five sequencing runs: one for EPSC-001-5, two for iPSC-001-5, and two for iPSC-006-1.
EPSCs are a new type of pluripotent stem cell, known as Extended Pluripotent Stem Cells. Compared to iPSCs, EPSCs exhibit greater stemness and lower epigenetic memory.


title: A systematic evaluation of isolation techniques and freeze-thaw effects on plasma extracellular vesicle heterogeneity and subpopulation profiling

city: Guangzhou

first: Xueqi

last: Li

state: Guangdong

address: No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island

institute: Guangzhou National Laboratory

summary: A Proximity-dependent Barcoding Assay (PBA) was applied to evaluate three distinct EV isolation methods—asymmetrical flow field-flow fractionation (AF4), automated centrifugal microfluidic disc system combined with functionalized membranes (Exo‑CMDS), and size-exclusion chromatography (SEC)—comparing their efficiency in isolating EVs from both freshly frozen and freeze-thawed plasma samples by detecting 262 EV membrane proteins and analyzing them at both bulk and single-EV levels.

overall_design: In this study, plasma was isolated from peripheral blood of a healthy subject through sequential centrifugation and storage at –80 °C, with a subset undergoing freeze-thaw cycles every 3 to 7 days. Subsequently, extracellular vesicles (EVs) were extracted using three distinct isolation methods, and 262 EV membrane proteins were profiled using Proximity Barcoding Assay (PBA) technology at both bulk and single-EV levels.

first: Wen

last: Zhong


title: Vemurafenib response and resistance analysis of metastatic melanomas with mutant and wild type BRAF

city: Detroit

first: Malathy

middle: P

last: Shekhar

state: MI

address: 421 East Canfield Avenue

department: Oncology

institute: Wayne State University

summary: Vemurafenib response and resistance effects on gene expression in metastatic melanomas with mutant and wild type BRAF

overall_design: Parental M14 or A2058 cells, and their isogenic VemR counterparts were cultured in DMEM/F12 media containing 5% FBS. The VemR M14 and A2058 cells maintained in 100 nM or 4 mM vemurafenib, respectively, were rinsed three times to remove drug and incubated in drug free media prior to RNA isolation. Mel-14-108 and Mel-14-089 cells were treated overnight with 10 nM or 4 mM vemurafenib, respectively.


title: The impact of high-cholesterol diet feeding on hepatic mRNA and small non-coding RNA profiles in mice

first: Xiuchun

address: 900 University Avenue

institute: UCR

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

overall_design: Refer to individual Series


title: Xenoline-polarized macrophages as a physiologically relevant in vitro model of tumor-associated macrophages in glioblastoma

city: Birmingham

first: Christopher

middle: D

last: Willey

state: AL

address: 1700 6th Avenue South

department: Radiation Oncology

institute: University of Alabama at Birmingham

summary: Tumor-associated macrophages (TAMs) are the most abundant non-cancerous cell type in glioblastoma (GBM) and heavily influence GBM biology, contributing to tumor progression, therapeutic resistance, immune evasion, and neovascularization. Current in vitro models that utilize IL-4/IL-13 stimulation fail to capture the transcriptional and functional heterogeneity of TAMs observed in vivo. In this study, we utilize a serum-free indirect co-culture model with patient-derived xenolines to polarize primary human macrophages and characterize their molecular and functional phenotypes. We demonstrate that xenoline-polarized macrophages diverge from classical M1/M2 states and instead adopt transcriptional signatures reflective of TAM subsets identified from patients. Notably, macrophages polarized with the radiation-therapy selected xenoline, JX14P-RT, exhibited gene expression patterns enriched for interferon response and hypoxia, mirroring recurrent GBM samples. In contrast, JX14P TAMs showed enrichment in phagocytic gene sets. Functional validation of these phenotypes revealed discrepancies between the transcriptionally predicted and observed phenotypes, emphasizing the importance of integrating phenotypic validation in sequencing studies. Altogether, our findings establish xenoline-polarized macrophages as a more physiologically relevant alternative to traditional models, offering a useful model for studying tumor-immune interaction in vitro.

first: Hasan

last: Alrefai

first: Benjamin

last: Lin

first: Elkohly

last: Amr

first: Manoj

last: Kumar

first: Taylor

last: Schanel

first: Kevin

middle: J

last: Lee

first: Patricia

last: Hicks

first: Joshua

middle: C

last: Anderson

first: Gao

last: Guo

first: Eun-Young

last: Ahn

first: C

middle: R

last: Miller


title: Role of ACK1 condensates in STAT5 activation in LUSC cells

city: Wuhan

first: Wei

last: Wang

state: Hubei

address: 13 Hangkong Road

institute: Huazhong University of Science and Technology Tongji Medical College

summary: ACK1 is a non-receptor tyrosine kinase that phosphorylates multiple substrates involved in cancer progression. Additional regulatory mechanisms governing ACK1 activity remain to be elucidated. We demonstrate that ACK1 is frequently amplified and overexpressed in lung squamous cell carcinoma (LUSC). We found that ACK1 undergoes liquid-liquid phase separation (LLPS), a process dependent on the intrinsically disordered region (IDR, 96-156aa), but independent of its kinase activity.  Our data also reveal that ACK1 phosphorylates STAT5 and promote STAT5 nuclear localization and transcriptional activity.

overall_design: To examine the gene regulation mediated by ACK1 condensates, we performed RNA-seq profiling of H2170 cells expressing GFP, ACK1 (WT)-GFP, or ACK1 (IDRmut)-GFP.

first: Xia

last: Lu


title: MiRNA networks mediate a compensatory response in heart  failure induced cognitive impairment [RNA-Seq]

first: Andre

last: Fischer

overall_design: RNA-seq profiling from CaMKIIδC transgenic mice and wildtype controls at 6 months of age.

first: Verena

last: Gisa

first: Rezaul

middle: M

last: Islam

first: Dawid

last: Lbik

first: Raoul

last: Hofmann

first: Tonatiuh

last: Pena

first: Dennis

last: Krüger

first: Susanne

last: Burkardt

first: Anna-Lena

last: Schütz

first: Farahnaz

last: Sananbenesi

first: Karl

last: Toischer

first: André


title: Ptprz Signaling, Tubule and Macrophage-Mediated Renal Injury and Subsequent Chronic Kidney Disease [macrophages]

city: Mainz

first: Federico

last: Marini

address: Obere Zahlbacher Strasse 69

department: Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI)

institute: University Medical Center - Mainz

summary:
Background: Macrophages and tubular epithelial cell interactions are integral in kidney ischemia-incited interstitial inflammation leading to acute kidney injury (AKI). Ischemia/reperfusion injury (I/R) triggers tubular epithelial cells to express IL-34, a  macrophage growth factor, that promotes AKI and subsequent CKD. IL-34 engages the cognate receptor, c-FMS, expressed by macrophages, and the recently discovered Protein-Tyrosine Phosphatase Z (Ptprz). Ptprz, binds to multiple ligands other than IL-34 that progressively increase their expression in kidneys after I/R.
Methods: We tested the hypothesis that signaling through Ptprz promotes macrophage-mediated AKI and subsequent CKD, by comparing Ptprz knockout (KO) with wild-type (WT) mice after I/R.
Results: Ptprz was expressed by leukocytes and in tubular epithelial cells after I/R in mice. Using Ptprz KO mice we determined that during AKI and CKD renal pathology, and loss of renal function were ameliorated. Ptprz-dependent mechanisms mediated: (i) tubular epithelial cell expression of chemokines that fostered macrophage and T cell rich renal inflammation, and (ii) tubule injury and apoptosis, that resulted in the loss of tubules and interstitial fibrosis during CKD. As macrophages release mediators that induce tubular epithelial cell apoptosis, thus Ptprz-dependent mechanisms promote tubule damage. These findings are translational, as after I/R in human kidney transplants, PTPRZ and PTPRZ ligands were upregulated and expressed by the same cell populations as in mice. Moreover, PTPRZ levels in sera were elevated in kidney transplant patients.
Conclusion: Intra-renal Ptprz-dependent macrophage and tubular epithelial cell mediated mechanisms promote AKI and subsequent CKD.

overall_design: RNA-sequencing of Ptprz KO and Ptprz WT Bone marrow derived macrophages (BMDM), differntiated to M1 macrophages (LPS/IFNy) or M2  macrophages (IL-4) or control.

first: Julia

last: Weinmann-Menke

first: Hilda

last: Gonzalez-Sanchez

first: Yasunori

last: Iwata

first: Myriam

last: Meineck

first: Najla

last: Abassi

first: Francisco

last: Granados-Contreras

first: Ayumi

last: Takakura

first: Masaharu

last: Noda

first: Vicki

last: Kelley


title: Ptprz Signaling, Tubule and Macrophage-Mediated Renal Injury and Subsequent Chronic Kidney Disease [TECs]

overall_design: RNA-sequencing of Ptprz KO tubular epithelial cells (TEC) under inflammatory conditions and unstimulated, compared to Ptprz expressing TEC (Ptprz Het)


title: Gene expression data of non-mucinous colorectal cancers to support to identify molecular characteristics of mucinous colorectal cancer

city: Daejeon

first: Jeewoo

last: Seo

address: 125, Gwahak-ro

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology, KRIBB

summary: Mucinous adenocarcinoma (MuC), a subtype of colorectal cancer (CRC), exhibits distinct molecular features and a poorer prognosis compared to non-mucinous CRC (NMuC). Standard CRC treatments often fail to address MuC's unique characteristics, especially in stage II, where the benefit of adjuvant chemotherapy is unclear. Biomarkers that improve risk assessment and guide personalized treatment are needed. Based on RNA-seq data and Cox regression models, we developed a signature reflecting the characteristics of MuC which showed a strong prediction ability and clinical utility in both MuC and NMuC. Our signature represents a valuable tool for predicting recurrence and guiding personalized treatment in CRC.

overall_design: RNA-seq data of 119 fresh frozen tissues of non-mucinous colorectal cancer tissues (n = 140) were generated. Total RNA was isolated by RNeasy Plus Mini Kit (Qiagen, CA, USA), following the manufacturer’s protocol. The quality and integrity of the RNA were confirmed by RNA Integrity Number (RIN) measurements, with only samples achieving RIN value > 8 were selected for further analysis. Sequencing library was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina, CA, USA) according to the provided protocol. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented and converted into cDNA. Then adapters were ligated and the fragments were amplified on a PCR. Sequencing was performed in paired end reads (100PE) using HiSeq 2500 platform (Illumina, CA, USA).

first: Jeong-Hwan

last: Kim

first: Ye-Jin

last: Ha

first: Jee-Woo

first: Seon-Kyu

first: Jong-Lyul

last: Lee

first: Seon-Young


title: Spatial Transcriptomics Uncovers Brain Region-Specific Transcriptional Changes Associated with Development and Aging

city: Blacksburg

first: Hehuang

last: Xie

state: VA

address: BIOMEDICAL SCIENCE  MC0477,STEGER HALL

department: Biomedical Science

institute: Virginia Tech

summary: This study design encompasses sample diversity across developmental and aging stages, capturing the effects of age-related changes as a central experimental variable under investigation.

overall_design: Six C57BL/6J mice were analyzed using spatial transcriptomics at three distinct time points: postnatal day 21 (P21), 12–15 weeks (adult), and 28 months (aged), with two biological replicates for each age group.

first: Ben

last: Conacher

first: Amanda

last: Moore

first: Yu

last: Lin

first: Liduo

last: Yin


title: Divergently evolved FOXA1 mutations drive prostate tumorigenesis or therapy-resistant intra-luminal plasticity

city: Ann Arbor

first: Arul

last: Chinnaiyan

address: 1500 East Medical Center Dr

department: MCTP

institute: University of Michigan


title: Mesenchymal stem cells derived from pluripotent stem cells

first: Wenpeng

last: Song

summary: Pluripotent stem cells (PSCs), known for their unlimited ability to self-renew and differentiate into all three germ layers, have emerged as a promising cell source for regenerative therapies aimed at treating various diseases and injuries. However, the direct application of pluripotent stem cells brings many problems, including malignant teratoma formation and undirected differentiation. Pluripotent stem cell-derived mesenchymal stem cells may solve these problems. At the same time, pluripotent stem cell-derived mesenchymal stem cells can also solve the problems of adult mesenchymal stem cells, such as limited source, donor site trauma and strong heterogeneity. In this study, pluripotent stem cells were used as the starting point for differentiation into mesenchymal stem cells. Bulk RNA-seq was performed on differentiated cells.

overall_design: In this study, a variety of small molecules were used to differentiate pluripotent stem cells into mesenchymal stem cells. Bulk RNA-seq was performed on differentiated cells.

first: Shixin

last: Gong


title: Divergently evolved FOXA1 mutations drive prostate tumorigenesis or therapy-resistant intra-luminal plasticity [scRNA-Seq]

summary: FOXA1 is recurrently altered in hormone-driven malignancies, with activating hotspot mutations detected in 10-40% of primary prostate cancers based on ethnicity. Yet, the tumorigenic potential and pathobiology of FOXA1 remain unexplored in vivo. Here, we generated and characterized knock-in mouse models harboring FOXA1 mutant transgenes that represent distinct classes of activating mutations. Our findings reveal that FOXA1 class 1 mutations (i.e., wing 2 alterations) in a Trp53-null background, drive high-grade, invasive luminal adenocarcinoma with full penetrance by 40 weeks of age. These hyperproliferative lesions retain luminal characteristics, gain expression of NSD2, and regress upon androgen withdrawal—mirroring features of primary human prostate adenocarcinomas. Mechanistically, class 1 mutants aberrantly activate mTORC1/2 signaling and reprogram androgen receptor (AR) activity by expanding the enhancer landscape at non-canonical chimeric AR-half elements enriched in patient tumors. In contrast, FOXA1 class 2 mutations (i.e., C-terminal truncations) do not drive transformation but induce intra-luminal plasticity in androgen-intact normal tissues, which is otherwise triggered in response to castration. Class 2 mutants lead to a 10- to 20-fold expansion of Ar+/Ck8+ luminal epithelia expressing stem/progenitor markers such as Trop2, Ck4, and Psca. Mechanistically, class 2 mutants maintain AR activity while de-compacting over 40,000 new cis-regulatory elements bound by Klf5 and AP-1 transcription factors to activate stemness and WNT gene programs. Class 2-mutant-expressing prostate epithelial cells resist castration-induced atrophy, remain proliferative in androgen-deprived conditions, and form organoids and allografts at higher frequencies. Additionally, metastatic prostate tumors from patients harboring class 2 mutations show elevated KLF5 expression and stemness signatures. Collectively, our data establish FOXA1 as a critical oncogene in both primary and advanced AR-dependent prostate cancers, revealing its functional versatility in driving either tumor initiation or therapy resistance depending on the mutation class.

overall_design: Comparative RNA profiles of the anterior and dorsal lobes of the mouse prostate tissues upon overexpression of the FOXA1 R265-71del mutation in conjunction with Trp53 loss. These tissues were obtained from 100 week-old male mice.

first: Sanjana

last: Eyunni

first: Eleanor

last: Young

first: Yuping

last: Zhang

first: Abhijit

last: Parolia


title: Divergently evolved FOXA1 mutations drive prostate tumorigenesis or therapy-resistant intra-luminal plasticity [ChIP-seq]

overall_design: Comparative DNA binding profiles of noted proteins in FOXA1 Class 1 and class 2 mouse prostate organoids.


title: Ptprz Signaling, Tubule and Macrophage-Mediated Renal Injury and Subsequent Chronic Kidney Disease

first: Federico

last: Marini


title: XMU-MP-1, an inhibitor of the STE20-like MST1/2 kinases of the Hippo signaling pathway, induces hematopoietic tumor cells death

city: Moscow

first: Elizaveta

last: Pankratova

address: Vavilov str., 32

department: Transcription factors

country: Russia

institute: Engelhardt Instittute of Molecular Biology^ Russian Academy of Sciense

summary: In this study we have shown that treatment of hematopoietic cells with XMU-MP-1, the inhibitor of MST1/2, the key components of the Hippo signaling pathway, causes inhibition of cell population growth and increased levels of caspase 3/7 activity. RNA-Seq analysis has demonstrated that XMU-MP-1 suppresses the expression of the key cell cycle regulators in the Namalwa cells: E2F family transcription factors, cell division cycle genes (CDC6; CDC7; CDC20; CDC25A,В,С, and CDC45), cyclins CCNА2, CCNB1, CCNB2; MCM2-7, ORC1 and ORC6. At the same time, XMU-MP-1 triggers the activation of the genes regulating apoptosis, necroptosis, and autophagy. XMU-MP-1 increases the expression of the apoptosis activator genes APAF1, caspases 6 and 7, FAS; BBC3, BCL2A1, MOAP1; XAF1. Some Namalwa cells may undergo necroptosis: XMU-MP-1 causes an increase in the expression of the necroptosis activator genes RIPK1, TNFSF10, TRADD, and PEA15, the inhibitor of caspase 8. The expression of the key genes activating autophagy is significantly increased (beclin 1; DEPP1; DAP; VPS18; VPS39, and autophagy regulator AMBRA1). The activation of these three processes in the B-cell tumor population indicates a profound effect of XMU-MP-1 on cell death in hematopoietic tumor cells. The treatment of Namalwa cells with XMU-MP-1 decreases their resistance to doxorubicin. The use of MST1/2 kinase inhibitors in the treatment of hematologic tumors may be extremely promising.

overall_design: To investigate the anticancer effect of MST1/2 kinase inhibitor XMU-MP-1on hematopoietic tumor cells we performed gene expression proffiling analysis using data obtained from RNA-Seq of 3 different cell populations. Comparative gene expression proffiling analysis of RNA-Seq data for Namalwa cells and Namalwa treated with XMU-MP-1 2.5 µM or 0.3 µM (Namalwa-XMU-2.5; Namalwa-XMU-0.3).

first: Alexander

last: Stepchenko


title: Enhanced relevance of hypoxia-induced in vitro models in mimicking liver fibrosis pathways

city: Leiden

first: Robert

last: Kleemann

address: Sylviusweg 71

institute: The Netherlands Organisation for Applied Scientific Research

summary: Introduction: Preclinical models that are currently used for fibrosis research only partially mimic human disease processes. Particularly, traditional transforming growth factor beta 1 (TGFβ1) induced stellate cell models are lacking in activation of hypoxia-induced pathways, which is a relevant process in patients with liver disease. Here we investigated the synergic effect of two hypoxia-mimicking compounds (DMOG and IOX2) and TGFβ1, on fibrotic phenotype and in vivo disease recapitulation in primary human hepatic stellate cells (HSCs). Methods: Human primary HSCs were cultured, stimulated (TGFβ1 and hypoxia-mimicking compounds combinations) and harvested to identify optimal stimulation conditions for fibrotic phenotype, cell viability and toxicity levels. To assess the fibrotic phenotype, protein levels was assayed for fibrosis markers (collagen, TIMP-1, Fibronectin) were evaluated. RNA was isolated and sequenced through next generation sequencing (NGS). Bioinformatic tools using differential expression analysis (Deseq2) and Ingenuity Pathway Analysis (IPA) were used to identify differentially expressed genes (DEGs) and map these to biological functionality, respectively. Results: Our HSC model showed that stimulation with IOX2 (0.3 and 1 µM) in the presence of TGFβ1 significantly increased fibrotic markers levels (total collagen, TIMP-1, and fibronectin). DMOG showed no effect using low, non-toxic concentrations. Biological functionality from DEGs highlighted various fibrosis-related pathways, hypoxia-related genes and relevant crosslinking markers when IOX2 was added in a concentration-dependent manner. Furthermore, comparative analysis with human DEGs (Fibrotic vs non-fibrotic) showed improved disease representation in our HSC model with IOX2 addition. Conclusion: These findings suggest that IOX2 may aggravate fibrotic disease  and improve  in vivo disease recapitulation in vitro. Hypoxia-mimicking compounds like IOX2 hold promise for enhancing fibrosis in in vitro models, providing valuable insights into fibrosis pathogenesis, hypoxia-related genes and potential therapeutic strategies.

overall_design: Human primary HSCs (Hepatic Stellate Cells) were cultured -/+ stimulation with compound combinations (in total 8 treatments): Control without additions (C), 4 ng/ml TGFβ1 (T), 4 ng/ml TGFβ1 + 5 μM Alk5 (TA), 4 ng/ml TGFβ1 + 0.3 μM IOX2 + 5 μM Alk5 (TI.3A), 0.3 μM IOX2 (I.3), 1 μM IOX2 (I1), 4 ng/ml TGFβ1 + 0.3 μM IOX2 (TI.3), 4 ng/ml TGFβ1 + 1 μM IOX2(TI1). TGFβ1 = Transforming growth factor beta 1. Alk5 = ALK5 kinase inhibitor (ALK5 = TGFβ type I receptor kinase). IOX2 = a selective Inhibitor of the Hypoxia Inducible Factor (HIF) Prolyl-Hydroxylases.

first: Manuel

last: González Hernández

first: Lars

last: Verschuren

first: Martien

last: Caspers

first: Martine

last: Morrison

first: Jennifer

last: Venhorst

first: Gerard

last: van Westen

first: Beatrice

last: Coornaert

first: Roeland

last: Hanemaaijer


title: Divergently evolved FOXA1 mutations drive prostate tumorigenesis or therapy-resistant intra-luminal plasticity [Single-cell Multiome]

first: Arul

last: Chinnaiyan


title: The biological consequences of knockout of genes involved in the synthesis and metabolism of H2S in Drosophila melanogaster

middle: Petrovich

last: Rezvykh

address: Obninsk, Zvyozdnaya st. 15 - 130

institute: EIMB

summary: Here, we describe the effect of knockout (KO) of two key genes (cbs, cse) responsible for H2S synthesis in the transsulfuration pathway as well as the inactivation of sulfurtransferase gene (dtst1) encoding single domain rhodanese on Drosophila melanogaster genome expression and several life-history traits. The analysis of H2S production in the KO flies showed its minimal level in the strain with double KO (CBS-/-; CSE-/-) while flies with triple KO (CBS-/-; CSE-/-; dTST1-/-) exhibited higher H2S level and improvements in lifespan. The transcriptomic analysis of fly bodies from the double KO strain with maximum disturbances of fitness components revealed a profound increase in the expression of genes involved in the functioning of the excretory system. Besides, double and triple KO flies exhibited drastic changes in Malpighian tubules' appearance. Inactivation of genes related to H2S metabolism resulted in altered expression of numerous loci involved in mitochondrial function. While KO of the dtst1 gene did not affect the genome expression, the triple KO flies exhibited more changes in the whole-body transcriptome than double KO flies. Reduced fecundity in double knockouts correlates with pronounced changes in ovarian transcriptome data. Surprisingly, the knockout of the dtst1 gene affected the flies' memory.

overall_design: Poly-A RNA-seq of ovaries and whole bodies of Drosophila melanogaster flies lacking crucial genes involved in sulfur metabolism


title: RNA-seq profiles of HepG2 control cells and HepG2-HBx cells

city: Shenzhen

first: jianhua

last: zhong

address: 3025 Shennan Road Central, Futian District, Shenzhen

institute: The Eighth Affiliated Hospital, Sun Yat-sen University

summary: Hepatocellular carcinoma (HCC) is mainly associated with chronic hepatitis B virus infection. Hepatitis B virus X protein (HBx) is closely related to the occurrence of liver cancer. To explore the molecular mechanism by which HBx affects the occurrence of hepatocellular carcinoma, we established a stable HCC cell line HepG2-HBx expressing HBx and analyzed the transcriptome profile by RNA-seq.

overall_design: Six samples of HepG2 cells were analyzed. Three replicate samples of HepG2 cells transfected with HBx plasmid and three replicate samples of HepG2 cells transfected with pmCherry-N1 (control) plasmid.

first: Jianhua

last: Zhong

first: Yuetong

last: Li

first: Changlong

last: Bi

first: Aixia

last: Zhai


title: Effect of an AAV1 containing an sh-RNA targeting Angptl2 on the hypocampus of male and female atherosclerotic mice

city: Montréal

first: Pauline

last: Mury

state: QC

address: 5000 rue Bélanger

country: Canada

institute: Montreal Heart Institute

summary: Cerebral accumulation of inflammatory senescent cells (SnC) may compromise the continuum between endothelial (EC) and neuronal function, leading to vascular cognitive impairment (VCI). We hypothesized that targeted elimination of vascular SnC will preserve cerebrovascular and neuronal functions in atherosclerotic mice of both sexes, demonstrating the causal contribution of SnC in cognitive decline. Male and female atherosclerotic mice (ATX; LDLR-/-;hApoB+/+, n=12 per group) of 6-month of age were treated twice over 3 months with an adeno-associated virus-1 delivering a shRNA targeting vascular Angptl2, a strong inflammatory factor of SnEC; a sh-scramble was used as a control. The Morris water maze test assessed cognition. In males, targeting vascular SnC had no effect on short-term memory but improved long-term memory (p<0.05 vs. sh-scramble); in contrast, in females, the treatment reduced short-term memory (p<0.05), and had no effect on long-term memory. Endothelium-dependent flow-mediated dilations in pressurized cerebral arteries were improved (p<0.05) by the treatment in both males and females. Single-nuclei RNA-sequencing (hippocampal region) revealed a strong sexual dimorphism in transcriptomics profile, with the overexpression of senescence pathways only in male vascular cells. The analysis also revealed that male sex predicted the response to the sh-Angptl2 in oligodendrocytes progenitor cells and neurons (AUC>0.8). Accordingly, the sh-Angptl2 reduced the number of EC expressing angptl2 in males (-75%), but not in females (-10%). In conclusion, these data demonstrate a sexual dimorphism in the causal contribution of vascular senescence in cerebrovascular dysfunction and cognitive impairment: only in male atherosclerotic mice, vascular senescence contributes to VCI.

overall_design: Nuclei were isolated from the hypocampus of 12 mice randomly treated with an AAV1 containing an sh-RNA control (SCR) or targeting Angptl2. Mice were treated with the virus at 6 months old and 7 and a half months old before sacrifice at 9 months old. Our dataset include 3 males SCR, 3 males Angptl2, 3 females SCR and 3 females Angptl2.

first: Melanie

last: Lambert

first: Geraldine

last: Miquel

first: Gael

last: Cagnone

first: Louis

last: Villeneuve

first: Frédéric

last: Lesage

first: Nathalie

last: Thorin-Trescases

first: Eric

last: Thorin


title: Senolytic and anti-inflammatory efficacy of quercetin in men and women undergoing coronary artery by-pass surgery

summary: Recent studies suggest that vascular senescence and its associated inflammation could fuel the so-called inflammaging to favor atherogenesis; whether these pathways can be inactivated in CAD patients (male and female) is unknown. We performed a randomized, double-blind trial involving patients undergoing an elective coronary artery by-pass graft surgery. The patients were randomly assigned to receive either quercetin (500 mg twice daily) or placebo starting two days before surgery. The primary efficacy end point was a reduction in post-operative systemic inflammation. The secondary efficacy end-point was an improved endothelial function ex vivo of discarded segments of internal thoracic artery (ITA). The exploratory end-point was to acquire a vascular transcriptomic signature per treatment and sex by single nucleus RNA sequencing. A total of 97 patients (78 men) were recruited, 50 were assigned to the placebo group and 47 to the quercetin group. In the intent-to-treat population (ITT), quercetin tended to reduce C-reactive protein at hospital discharge (F value 3.39; p=0.073); this tendency was confirmed by a plasma proteomic analysis revealing a significant shift of differentially expressed inflammatory proteins between sexes (-48 in men and +12 in women). Quercetin increased endothelial sensitivity to acetylcholine-dependent relaxation (F value 4.01; p=0.0487). In a sub-group analysis, this effect of quercetin remained significant in men (F value 3.92; p=0.0513) but not in women (F value 0.17; p=0.678). The transcriptomic signature of the ITA revealed overexpression of classic cellular senescence pathways of both replicative- and stress-induced senescence, together with an inflammatory signature typical of inflammaging and oxidative stress; quercetin reversed this signature towards reduced senescence, stress and inflammation. In female ITA, the response to quercetin was heterogeneous and limited in efficacy, with a “cooling” of the endothelium, but a promotion of the inflammaging signature in fibroblasts. No adverse events were reported. Quercetin reduced global post-operative inflammation and improved endothelial dysfunction in the ITT population; men benefited from quercetin but not women. This study suggests that a hit-and-run senolytic strategy to reduce the vascular inflammaging may benefit men more than women with CAD.

overall_design: Nuclei were isolated from internal thoracic arteries from 12 patients with coronary artery disease (CAD) undergoing an in-patient CABG. In this clinical study, patients randomly received quercetin or placebo pills (500mg BID). Our dataset include 3 men quercetin, 3 men placebo, 3 women quercetin and 3 women placebo.

first: Olina

last: Dagher

first: Annik

last: Fortier

first: Ariel

last: Diaz

first: Yoan

last: Lamarche

first: Pierre-Emmanuel

last: Noly

first: Marina

last: Ibrahim

first: Pierre

last: Pagé

first: Philippe

last: Demers

first: Denis

last: Bouchard

first: Pierre-Luc

last: Bernier

first: Nancy

last: Poirier

first: Emmanuel

last: Moss

first: Nicolas

last: Durrlemann

first: Hughes

last: Jeanmart

first: Michel

last: Pellerin

first: Guillaume

last: Lettre

last: Carrier


title: Gestational Autoantibody Exposure Alters Early Brain Development in a Rat Model of MAR Autism

city: Davis

first: Karol

last: Cichewicz

address: 1544 Newton Ct

department: Center for Neuroscience

institute: UC Davis

summary: Maternal autoantibody related autism (MARA), in which mothers produce specific patterns of autoantibodies during pregnancy, resulting in an autism diagnosis in their offspring, has been observed clinically. Multiple patterns of MARA autoantibodies have been identified clinically, and differences in the severity of the autism phenotype based on the autoantibody pattern have been described. In this study we utilized our preclinical rat model to further elucidate the differential effects of MARA autoantibody exposure based on the known clinical patterns, including the originally identified pattern of lactate dehydrogenase A and B (LDHA/B) + collapsin response mediator protein 1 (CRMP1) + stress-induced phosphoprotein 1 (STIP1) as well as the newly described patterns of CRMP1+CRMP2, CRMP1 + guanine deaminase (GDA), and STIP1+ neuron-specific enolase (NSE). We found that, at postnatal day 2, the levels of brain-specific and serum cytokines/chemokines were altered based on the pattern of MARA autoantibody exposure. Further, we observed changes in the brain transcriptomic profiles that suggest cellular proliferation and differentiation changes due to MARA exposure.

overall_design: Seventy-one rat brains were collected at PND 2 and regions containing frontal cortex and hypothalamus were dissected for RNA isolation. Our experiment included 24 control, 12 male and 12 female samples, and 47 MARA samples stratified across 4 autoantibody combinations: 1) CRMP1+CRMP2, 8 samples, 5 males and 3 females; 2) STIP1+NSE, 8 samples, 4 males and 4 females; 3) CRMP1+GDA, 6 samples, 2 males and 4 females; 4) LDHA/B+CRMP1+STIP1, 25 samples, 12 males and 13 females.

first: Janna

last: McLellan

first: Ana-Maria

last: Iosif

last: Cichwicz

first: Cesar

last: Canales

first: Alexander

last: Nord

first: Judy

last: Van de Water