title: Gene expression profile at single nucleus level of hippocampal cells from APP-TG mice treated with THC and Cel

city: San Antonio

first: Chu

last: Chen

state: Texas

address: 7703 Floyd Curl Dr

department: Cellular and Integrative Physiology

institute: UT Health San Antonio

summary: Delta-9-tetrahydrocannabinol (Δ9-THC) is reported to rescue cognitive and synaptic functions in Alzheimer's disease (AD) mice model. However, Δ9-THC treatment resulted in neuroinflammation via activating Cox2 in the brain. Our hypothesis is that inhibiting cox2 via celecoxib treatment could inhibit neuroinflammation and enhance the neuroprotective effects of Δ9-THC. Our results indicated that Cel-THC treatment inhibited spatial learning and memory impairments of APP-TG mice via water maze test. To investigate the molecular mechanisms, we performed single nucleus RNA sequence of hippocampal cells from WT-Veh, APP-TG-Veh, APP-TG-THC, APP-TG-Cel, and APP-TG-Cel-THC groups. Our results showed that Cel-THC treatment reversed changes of synaptic, inflammation-, and AD-related differentially expressed genes caused by beta amyloid accumulation.

overall_design: Single nucleus transcriptomics of hippocampus from WT and transgenic mice were analyzed by snRNA-seq.

first: Chen

last: Chu

first: Zhang

last: Jian

first: Hu

last: Mei

first: Zhu

last: Dexiao


title: KDM8 is a master regulator for hypoxia-induced metastatic heterogeneity in pancreatic cancer [Bulk RNA-Seq]

status: Public on Dec 04 2025

city: New Brunswick

first: Shin-Heng

last: Chiou

state: NJ

address: 195 Little Albany St, Room 3001

department: Medicine

country: USA

institute: Rutgers Cancer Institute of New Jersey

type: Expression profiling by high throughput sequencing

summary: This study aims to elucidate how hypoxia promotes pancreatic cancer metastasis by suppressing the JmjC-containing histone lysine demethylase KDM8. In solid tumors, hypoxia is a key factor that reprograms cancer cells into a highly metastatic state. Hypoxia is a well-established inducer of epithelial-to-mesenchymal transition, which is associated with treatment resistance and metastasis. In addition, hypoxia promotes chromosomal instability - a hallmark of cancer and a key contributor to metastasis. Despite this, the mechanisms by which cancer cells simultaneously hijack these elements of hypoxic adaptation to promote metastasis remains unknown. We found that CRISPR-mediated targeting of Kdm8 in a genetically engineered mouse model of pancreatic ductal adenocarcinoma rewires the cancer cell transcriptomic programs, leading to a profound loss of the differentiated morphology and widespread metastatic disease. Importantly, Kdm8 suppression in normoxia recapitulates major aspects of the global epigenetic changes and the transcriptomic rewiring induced by hypoxia. Further, Kdm8 deficiency leads to mitotic defects, increased micronuclei formation, Kras copy number gains, and enhanced chromosomal instability. Notably, disruption of the demethylase function of KDM8 phenocopies the effects of KDM8 loss, whereas expression of hypermorphic KDM8 variants that are resistant to hypoxic suppression reduces metastasis beyond that achieved by the wildtype Kdm8. Through the suppression of Kdm8 demethylase activity, hypoxia unleashes a potent metastatic program by simultaneously advancing cellular plasticity and chromosomal instability.

overall_design: Bulk RNA-Seq profiling of 2 Kdm8 knockout clones from the 688M pancreatic cell line (derived from a Kras-LSL-G12D;Trp53-LSL-R172H;Pdx1-Cre mouse) re-expressing the WT Kdm8 (control) or other Kdm8 variants cultured in either normoxia or hypoxia in duplicates.

first: Pradeep Moon

last: Gunasekaran


title: scRNA-seq of primary mouse and human cerebellar nestin-expressing progenitor neurosphere cultures

city: Cambridge

first: Jens

middle: Bager

last: Christensen

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

summary: Nestin-expressing progenitors (NEPs) of the developing cerebellum give rise to Bergmann glia, astrocytes and molecular layer interneurons via molecularly distinct subtypes. NEPs can be cultured in vitro as neurosphere in presence of growth factors. In order to characterise the primary neurosphere cultures generated from mouse and human developing cerebella, we performed single cell RNA-sequencing of primary NEP cultures established from 9-17 post-conception week human fetal cerebella and postnatal day 1 old mouse cerebella from two different mouse strains.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Primary NEP cultures were established from mouse and human cerebellar tissues and expanded in vitro in media containing 20 ng/mL EGF and FGF2. 12 different primary lines (2 mouse, 10 human) were dissociated into single cells and single cell RNA-sequencing was performed using CellPlex Multiplexed, 10X NextGEM 3' v3.1 chemistry.

middle: B

first: Giada

last: Vanacore

first: N. Sumru

last: Bayin


title: The role of transcription factors PES1 in Diabetic Retinopathy

city: Hefei

first: Sha

last: Liu

address: anhui hefei jingkai furong road 678

country: China

institute: Second Affiliated Hospital of Anhui Medical University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Diabetic retinopathy is the most common microvascular complication of diabetes, also as a common blinding eye disease. The transcription factor Pescadillo ribosomal biogenesis factor 1 (PES1) has been reported to be involved in many biological processes such as tumorigenesis, cellular senescence, and disorders of glucolipid metabolism.However, the role of PES1 in transcriptional regulation in DR is unclear. Here, we utilized ChIP-seq to determine the differences in gene regulation by PES1 in normal and high glucose-treated retinal microvascular cells.We found that PES1 was able to regulate a variety of angiogenic pathway-related genes, intercellular junction-related genes, and inflammation- and oxidative stress-related genes.These genes are differentially involved in the development of DR.Our results demonstrate that PES1  plays multiple roles in DR by regulating different genes.

overall_design: ChIP-seq of PES1 in HRMECs.

first: Zhengxuan

last: Jiang


title: Identification of Circulating miRNA Alterations in Diabetes Patients Excluding Periodontitis Effects: Insights into Target Gene Downregulation in Diabetic Complications

city: Yangsan

first: Haeseul

last: Lee

address: 49 Busandaehak-ro

country: South Korea

institute: Pusan National University

type: Non-coding RNA profiling by high throughput sequencing

summary: Circulating exosomal microRNAs (miRNAs) are important regulators of gene expression in diabetes mellitus (DM). In this study, we analyzed plasma exosomal miRNAs from normal individuals and patients with PD or PD combined with diabetes (PDDM). Differentially expressed miRNAs were identified using small RNA-seq, and their target genes were validated using bulk RNA-seq datasets from tissues related to diabetic complications. Analysis of target genes revealed biologically meaningful pathways that were consistently involved across affected tissues, providing insight into systemic miRNA–mRNA regulation in diabetes.

overall_design:
Venous blood was collected from participants in three groups: normal, PD, and PDDM. Plasma was isolated by centrifugation, and exosomes were extracted using the Exo2D™ kit (EXOSOMEplus, Suwon, Republic of Korea). Total RNA was extracted using the miRNeasy kit and subjected to small RNA sequencing using the SMARTer smRNA-Seq Kit. Sequencing was performed on an Illumina HiSeq 2500 platform (single-end, 51 bp).

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This submission includes only processed data and metadata. Raw FASTQ files are not included as their public release was not planned as part of the IRB-approved study design.
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first: Hae Seul

first: Yeuni

last: Yu

first: Hyun-Joo

last: Kim

first: Jung-Min

last: Oh

first: Hae Ryoun

last: Park

first: Yun Hak


title: Uracil-DNA glycosylase deficiency is associated with repressed tumor cell-intrinsic inflammatory signaling and altered sensitivity to exogenous interferons

city: Pittsburgh

first: Christopher

middle: J

last: Bakkenist

state: PA

address: 5051 Centre Avenue

department: Radiation oncology

institute: university of pittsburgh

summary: 2’-deoxyuridine (dU) is a common DNA lesion resulting from cytosine deamination and from dUMP incorporation by DNA polymerases, both of which are prevalent in cancer. The primary mechanism that repairs dU lesions in genomic DNA is base excision repair initiated by Uracil-DNA Glycosylase 1 (UNG1). We generated Ung knockout mouse B16 melanoma cells to investigate the consequences of UNG deficiency in a well-characterized, immunoproficient, syngeneic mouse cancer model. We show that UNG-deficient (ΔUNG) B16 tumors have altered growth kinetics in vivo and that their delayed growth is T-cell dependent. Immune profiling revealed reduced CD8+ T cell infiltration but augmented CD4+ Th1 responses in ΔUNG tumors. In vitro, ΔUNG tumor cells exhibit strongly suppressed cell-intrinsic type-I interferon, type-II interferon, and inflammatory signaling gene expression signatures as well as altered cytokine and chemokine secretion. In vivo, ΔUNG tumors exhibit a modified inflammatory cytokine and chemokine milieu. Furthermore, ΔUNG tumor cells have altered sensitivity to exogenous interferons in vitro, with increased sensitivity to IFN-γ but decreased sensitivity to IFN-α/β. Collectively, our data show that tumor cell-specific UNG deficiency results in an altered tumor microenvironment in vivo and provide proof-of-concept data for the use of UNG inhibitors to modulate inflammatory pathways in tumors.

overall_design: B16F10 wildtype (cas9 control) and UNG knockout clones (ΔUNG and ΔUNG_2) cells treated with DMSO or 5uM ATRi (AZD6738) for 48h.  Study was performed using two biological replicate per each condition and each cell line

first: Frank

middle: P

last: Vendetti

first: Pinakin

last: Pandya

first: Carina

middle: R

last: Sclafani

first: Reyna

middle: E

last: Jones

first: Daniel

last: Ivanov

first: Robert

middle: W

last: Sobol


title: Comparative Analysis of Species-Specific Hepatocyte Function and Drug Effects in a Liver Microphysiological System PhysioMimix® LC12 and 96-Well Plates

city: College Station

first: Ivan

last: Rusyn

state: TX

address: VIDI(Veterinary Medicine 2), 2, 402 Raymond Stotzer Pkwy

department: Interdisciplinary Faculty of Toxicology

institute: Texas A&M University

summary: Drug-induced liver injury (DILI) remains a major challenge in drug development and inter-species differences in potential liver toxicity are one area where comparative analyses may inform pre-clinical safety study design. In vitro testing for species-specific liver effects, especially in complex models such as microphysiological systems (MPS) may help predict toxicity before advancing from animal to human studies or de-risk spurious findings in pre-clinical species. This study assessed the utility of the perfusion-based PhysioMimix® LC12 MPS for evaluating species-specific DILI using primary hepatocytes from human, monkey, rat, and dog. First, functional, phenotypic, and transcriptional profiles were established over 2 weeks in cell culture. Then, cells were exposed to species-specific DILI compounds – chlorpromazine (CPZ), bosentan (BOS), and fialuridine (FIAU) – in both PhysioMimix® LC12 and traditional 2D cultures. Hepatocytes in PhysioMimix® LC12 showed more stable albumin and urea production for up to 14 days as compared to 2D cultures. Concentration-response studies with CPZ, BOS, or FIAU were performed in 2D; then, prolonged exposures (10 days) to sub-100× Cmax concentrations were tested in PhysioMimix® LC12. Species-specific differences in cellular and molecular effects of the drugs were observed in both models; data from PhysioMimix® LC12 were more reflective of the expected effects in whole animals or humans. Still, variability and low throughput are limitations of the MPS for prospective studies of species-specific responses. Overall, this study confirms the utility of liver safety studies using MPS, but also provides suggestions for experimental designs to overcome the limitations of more complex test systems.

sample_organism:
Macaca fascicularis
Homo sapiens
Canis lupus familiaris
Rattus norvegicus

overall_design: Primary hepatocytes from 4 different species (human, monkey, rat, and dog) were evaluated for species specific drug-induced liver injury (DILI). Species-specific differences in gene expression effects of three drugs (chlorpromazine (CPZ), bosentan (BOS), and fialuridine (FIAU)) were assessed.

first: Chander

middle: K

last: Negi

first: Courtney

last: Sakolish

first: Han-Hsuan

middle: D

last: Tsai

first: Katharina

last: Nitsche

first: Hans

last: Bouwmeester

first: Han

last: Gang

first: Piyush

last: Bajaj

first: Stephen

middle: S

last: Ferguson


title: Long non-coding RNA AFAP1-AS1 promotes alternative splicing of AXIN2 by facilitating SRSFs phase separation to induce drug resistance in lung adenocarcinoma

city: Changsha

first: Wei

last: Xiong

state: Hunan

address: 110 Xiangya Road

department: Cancer Research Institute

institute: Central South University

summary: In this study, we identified that the long non-coding RNA actin filament associated protein 1 antisense RNA 1 (AFAP1-AS1), which is highly expressed in lung adenocarcinoma, regulates RNA alternative splicing by recruiting splicing factors such as serine and arginine rich splicing factor 1 and 3 (SRSF1 and SRSF3), promoting their liquid-liquid phase separation. To investigate the effect of AFAP1-AS1 on alternative splicing, we overexpressed and knocked down AFAP1-AS1 in lung adenocarcinoma cell lines and obtained all regulated alternative splicing events through RNA seq, exploring the potential mechanism of AFAP1-AS1 promoting the occurrence and development of lung adenocarcinoma.

overall_design: In A549 cells, RNA sequencing was performed on control and experimental groups after overexpression or knockdown of AFAP1-AS1.


title: GDF10 cell-autonomously alleviates fibrotic response in HSCs

city: shanghai

first: yajie

last: peng

address: dongan road 130

institute: fudan university

summary: Liver fibrosis has emerged as the primary determinant of outcomes in metabolic dysfunction associated steatohepatitis (MASH). Quiescent hepatic stellate cells (HSCs) differentiate into activated HSCs or myofibroblasts, which drives liver fibrosis and contribute to the progressive loss of hepatic function. However, the underlying mechanisms of autocrine signals driving and reversing HSC activation and fibrotic response within the liver microenvironment remains incompletely delineated. Here, through searching for cytokines highly enriched expression in HSCs compared to other liver cell types by single-cell transcriptomic analysis, we found that Gdf10 is specifically expressed in HSCs, whereas its protein levels were elevated during fibrosis associated with MASH and CCl4-induced liver injury. The functional importance of GDF10 in alleviating the progression of liver fibrosis was demonstrated using gain and loss of GDF10 function mice and cultured HSCs treated with GDF10. Furthermore, the novel HSC-targeted delivery strategy of Gdf10 mRNA in fibrosis mice reversed their fibrotic phenotypes. These results reveal a new regulatory pathway in MASH microenvironment, suggesting a promising strategy for delivering drugs that can shift HSC functions to restore HSC balance.

overall_design: We isolated HSCs from mice livers and immortalized. The cells were treated with GDF10 recombinant protein (200 ng/ml) 24 hours and were harvested to conduct RNAseq.

first: Yajie

last: Peng

first: Bo

last: Wang

first: Xuelian


title: KAT2A-driven succinylation of SRSF11 enforces spliceosome-mediated RAD52 splicing to promote homologous recombination and radioresistance in hepatocellular carcinoma [RNA-seq]

city: Chengdu

first: Jun

last: Wu

address: Guoxue street

institute: West   32 China Hospital, Sichuan University

summary: Posttranslational modification succinylation plays a pivotal role in tumorigenesis across malignancies, yet its mechanistic contributions to hepatocellular carcinoma (HCC) pathogenesis and therapeutic resistance remain poorly characterized. In this study, we systematically demonstrated that the splicing factor SRSF11 undergoes functional consequential succinylation in HCC progression. Mechanistically, lysine acetyltransferase 2A (KAT2A) directly interacts with SRSF11 to catalyze its succinylation at lysine 419 (K419), thereby enhancing DNA damage repair capacity in both in vitro and in vivo HCC models. Structural and functional analyses revealed that K419 succinylation stabilizes SRSF11-spliceosome interactions, which promote the inclusion of exon 10 of RAD52 through enhanced pre-mRNAs binding. This exon-specific splicing event preserves the RAD51-binding domain essential for homologous recombination (HR) repair, ultimately facilitating RAD52-RAD51 dimer assembly and HR-mediated genomic stabilization. Clinically, elevated SRSF11 expression is correlated with increased HR activity, radioresistance, and reduced survival in HCC patients. Notably, genetic disruption of the KAT2A-SRSF11 axis sensitizes HCC cells to radiation-induced apoptosis. Our findings establish succinylation as a novel regulatory mechanism linking alternative splicing to DNA repair fidelity in HCC, while proposing therapeutic targeting of this pathway to overcome radioresistance in advanced HCC.

overall_design: RNA-seq for identifying the slpcing mRNA of SRSF11

first: Jingsheng

last: Yuan

first: Jiayin

last: Yang


title: PRRX1 Orchestrates Pericyte-Myofibroblast Transition in Pathological Retinal Fibrosis

first: Zhishang

last: Meng

address: No 139 Renmin Middle Road

department: Department of Ophthalmology

institute: The Second Xiangya Hospital, Central South University

summary: This study investigates the role of PRRX1 in the pericyte-myofibroblast transition and its contribution to retinal fibrosis.  Mouse retinal microvascular pericytes (Pricella Biotechnology, CP-M315) were cultured under hypoxic conditions (1% O2, 24 hours) with or without Prrx1 knockdown. Total RNA was extracted from 7 samples (3 control, 4 Prrx1 knockdown), sequenced on an Illumina NovaSeq 6000 platform with 150bp paired-end reads, and processed to quantify gene expression as raw counts.

overall_design: RNA-seq profiling of mouse retinal microvascular pericytes under hypoxic conditions (1% O2, 24 hours), comparing control (NC, 3 biological replicates) and Prrx1 knockdown (Si-Prrx1, 4 biological replicates). Paired-end sequencing (150bp) was performed. Raw data are deposited in SRA under BioProject PRJNA1184331.


title: Normal macrophage signaling and gene expression in Rosa26 Cas9-expressing mice

city: Martinsried

first: Assa

last: Yeroslaviz

state: Bavaria

address: Am Klopferspitz 18

department: computational Biology

country: Germany

institute: Max-Planck-Institute for biochemistry

summary: Cas9 expression in the Rosa26 “safe harbor” locus is widely used for gene manipulation and Crispr-based screening. Recently, experimental evidence suggested that macrophages isolated from Rosa26-Cas9 mice may have signaling differences compared to control mice in terms of TRIF signaling downstream of TLR3 and TLR4. As we frequently use the Rosa26-Cas9 mice made by Feng Zhang (Cas9-FZ, JAX stock No. 026179), arguably the strain with the widest distribution and utilization, we were motivated to test macrophage signaling in these mice under our conventional conditions. We used different macrophage polarization and signaling conditions combined with RNA sequencing and measurement of TLR signaling by immunoblotting. Our results suggest that the Cas9-FZ bears no obvious defects in any commonly used macrophage signaling pathway. We document the differences in our macrophage culture techniques compared to Raychowdhury et al., which may aid in how individual laboratories use Cas9-expressing macrophages, especially for focused or genome-wide screening.

overall_design: RNA-seq profiling of wildtype C57BL/6N and Feng Zhang Cas9 mice differentiated with SCF1 and activated for 24 hours with IL4/IL13, LPS/IFNg, or a media control.

first: Monika

last: Hermann

first: Nuria Fernandez

last: Perez

first: Peter

last: Murray


title: Transcription factor 4 regulates the interhemispheric midline remodeling through neuron–astroglia communications during corpus callosum formation

city: Shanghai

first: lanhui

last: zeng

address: Yixueyuan Road, Xuhui

department: Institutes of Brain Science

institute: Fudan University

summary: Agenesis of the corpus callosum (CC), the largest axon tract bridging the two hemispheres of the brain to support higher cognitive functions, is linked to various neurological disorders, including intellectual disability and autism spectrum disorders. Mutations of the transcription factor 4 (TCF4) cause Pitt-Hopkins Syndrome, an autism spectrum brain disorder characterized by severe intellectual disability. Through ex vivo transplantation assays and pioneering single-cell RNA sequencing of the interhemispheric midline, we found that Tcf4-mediated neuron-astroglia communication is essential for establishing the midline structure and subsequent CC formation. Conditional inactivation of Tcf4 in guidepost neurons disrupts astroglia functions and impedes interhemispheric fissure closure, thereby preventing axonal crossing of callosal projection neurons to the contralateral cortex. Moreover, we identified Sema7A as a key mediator of neuron-astroglia communications. Therefore, our study reveals a crucial, previously unappreciated role of cell-cell communication in interhemispheric midline remodeling, providing novel insights into the potential mechanisms underlying TCF4 associated neurological disorders.

overall_design: single-cell RNA sequencing profiles with mouse brain corticoseptal boundary tissue(CSB), at E16.5,from wildtype mosue and Tcf4f/f;Emx1Cre(Tcf4cKO) mouse.

first: Yunli

last: Xie

first: Lanhui

last: Zeng

first: Yandong

last: Zhang

first: Yue

last: Zhu

first: Rui

last: Zou

first: Yuxin

last: Zhao

first: Ruiqi


title: TP53 Mutation is a Prognostic Biomarker for Patients with Advanced RAS Wild-Type Colorectal Adenocarcinoma Treated with Cetuximab and Pembrolizumab [dataset 2]

city: Buffalo

first: Spencer

last: Rosario

address: Elm & Carlton Sts

institute: Roswell Park Comprehensive Cancer Center

summary: Immunotherapy with checkpoint inhibitors targeting the PD1/PD-L1 and CTLA4 pathways has limited activity in patients with microsatellite stable (MSS) colorectal adenocarcinoma (CRC). In a prior study, the combination of cetuximab and pembrolizumab failed to improve outcomes for patients with advanced RAS wild-type (RASwt) CRC. In this post hoc secondary analysis, we show that patients with TP53 mutant (p53mt) tumors had significantly higher progression-free survival (PFS) and decrease in tumor burden compared to patients with TP53 wild-type (p53wt) tumors. The gene set enrichment analysis showed uniform upregulation in several metabolic gene sets and most immune gene sets including NK-mediated immunity and IL-12 pathway while the IL6 pathway was downregulated. While there were no overlapping transcriptional alterations between the p53mt and p53wt groups with treatment that remain constant despite the therapeutic intervention, we did identify functional overlap with treatment in both groups in proliferative, immune, and metabolic pathways. In the pre-treatment tumor samples, the number of PD-L1+ tumor cells was significantly higher in p53mt tumors while the number of exhausted-1 immune cells (defined as OX40-/AE1_AE3-/PD-L1- cells, positive for 1/3 exhaustion markers, LAG3 or CTLA4 or TIM3) was significantly higher in p53wt tumors. In conclusion, TP53 status was prognostic of improved disease control with cetuximab plus pembrolizumab in RASwt CRC. Future studies evaluating immune-oncology agents in patients with MSS, RASwt CRC should include TP53 as an integrated biomarker and evaluate its performance as a positive predictive biomarker (ClinicalTrials.gov NCT02713373).

overall_design:
Targeted DNA sequencing was performed using the Archer VariantPlex panel
Submitters state "Due to the consenting procedure for this study and NY state law, we are not allowed to release the raw FASTQ files associated with this study"

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

last: Fountzilas

first: Henry G

last: Withers

first: Spencer R.


title: Transcriptomic analysis of pancreas from Elp3 epithelial-specific knockout and wild-type mice with and without caerulein treatment

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

country: Belgium

institute: University of Liège

summary: To study the role of Elp3 in pancreatic homeostasis and pancreatitis, pancreas tissues were collected from Elp3(fl/fl); Pdx-Cre and wild-type mice either untreated or after caerulein-induced pancreatitis. RNA sequencing was performed to identify transcriptional changes associated with Elp3 loss and pancreatic injury.

overall_design: Pancreatic tissues were collected from Elp3(fl/fl); Pdx-Cre (Elp3 knockout) and Elp3 wild-type mice under two conditions: untreated and caerulein-induced pancreatitis. Mice were administered six caerulein injections over three injection days (every other day), and the pancreas was harvested the day after the final caerulein injection. Each group included four biological replicates. RNA was extracted and subjected to RNA sequencing to assess gene expression changes associated with Elp3 deletion and/or pancreatitis. The four experimental groups were: control Elp3 wild-type, control Elp3 knockout, caerulein Elp3 wild-type, and caerulein Elp3 knockout.

first: Elias

last: Aajja

first: Marine

last: Leclercq

first: Pierre

last: Close

first: Christophe

last: Pierreux


title: Elevated FTO alleviates sepsis-induced acute kidney injury by regulating macrophage inflammatory phenotypes [MeRIP-seq]

city: shenzhen

first: Xiaona

last: Chen

state: China

address: No. 113 Baohe Road, Longgang District, Shenzhen

institute: Southern University of Science and Technology

summary: Recent studies have linked the dysregulation of N6-methyladenosine (m6A) to sepsis-induced acute kidney injury (SAKI), highlighting the persistent challenge of managing excessive proinflammatory cytokine production and subsequent organ dysfunction. In this study, we analyzed the dataset GSE32707 and GSE69063, fat mass and obesity-associated protein (FTO) was identified as the sole gene exhibiting significant downregulation within the transcriptome of peripheral blood samples from sepsis patients among m6A-related proteins. We further demonstrated that septic mice subjected to cecal ligation and puncture (CLP) presented increased m6A modifications and reduced FTO expression in both renal tissues and peritoneal macrophages (PMs). Our findings revealed that increased levels of FTO correlated with reduced mortality and kidney damage during sepsis and that the upregulation of FTO in lipopolysaccharide (LPS)-stimulated macrophages led to decreased production of proinflammatory cytokines. Mechanistically, through multiomic analysis of macrophages, we identified a novel mechanism involving matrix metalloproteinase 9 (MMP-9) as a direct target of FTO, which positively affects its translation efficacy. Furthermore, both in vivo and in vitro data confirmed that reduced MMP-9 levels exerted adverse effects on mitigating inflammatory responses and alleviating renal injury. Overall, our findings underscore the critical role of the FTO/m6A/MMP-9 axis in the regulation of proinflammatory secretion and improve our understanding of the transcriptomic landscape during the progression of SAKI.

overall_design: MeRIP-seq of wildtype RAW267.4 cells with or without LPS stimulation (Ctrl, LPS).

first: Quan

last: Li

first: Zhixia


title: Retrotransposon expression analysis for mouse spermatogonia defficient in Dnmt3l and Pld6.

city: Nagoya

first: Kenji

last: Ichiyanagi

address: Furo-cho, Chikusa-ku

department: Graduate School of Bioagricultural Sciences

country: Japan

institute: Nagoya University

summary: In the male germline of mammals, the expression of retrotransposons is restricted by DNA methylation, trimethylation of histone H3 at lysin-9 (H3K9me3) and PIWI-interacting small RNAs (piRNAs). To elucidate their relative importance in regulating retrotransposons during germ-cell development as well as relationships between these mechanisms, we performed mRNA, DNA methylation, and histone methylation analyses using mouse spermatogonia from Dnmt3l and Pld6 mutants deficient in de novo DNA methylation and piRNA production, respectively. The results revealed that a loss of DNA methylation results in decreased H3K9me3 and increased H3K4me3, suggesting a pivotal role of DNA methylation in maintaining the epigenome integrity.

overall_design: RNA was extracted from wild-type, Dnmt3l KO, and Pld6 KO mouse spermatonia at postnatal day 7, which were purified by FACS (EPCAM+). mRNA-seq libraries were made using NEBNext Ultra II Directional mRNA library prep kit for illumina (New England Biolab). Sequencing was performed on HiSeq2500 (Illumina) using 50-bp single-end mode.

first: Hirotaka

last: Sugimoto

first: Masaki

last: Kawase


title: ChIP analysis of H3K9me3 and H3K4me3 for mouse spermatogonia and leptotene/zygotene spermatocytes defficient in Dnmt3l and Pld6.

summary: In the male germline of mammals, retrotransposon expression is restricted by DNA methylation, trimethylation of histone H3 at lysin-9 (H3K9me3), and PIWI-interacting small RNAs (piRNAs). To elucidate their relative importance in regulating retrotransposons during germ cell development and the relationships between these mechanisms, we performed mRNA, DNA methylation, and histone methylation analyses using mouse spermatogonia from Dnmt3l and Pld6 mutants deficient in de novo DNA methylation and piRNA production, respectively. The results revealed that loss of DNA methylation resulted in decreased H3K9me3 in young L1 subfamilies and increased H3K4me3 in many retrotransposons, suggesting a pivotal role of DNA methylation in maintaining epigenomic integrity in spermatogonia and later stages of spermatogenesis. The transcriptional upregulation of retrotransposons by a loss of DNA methylation was more evident during meiosis (spermatocytes) than before meiosis (spermatogonia). These results are aligned with a global reduction of H3K9me3 at retrotransposons in spermatocytes. The piRNA system also regulated H3K9me3 and H3K4me3 at retrotransposons in spermatogonia likely through the regulation of DNA methylation, since the loss of DNA methylation resulted in decreased H3K9me3 and increased H3K4me3 at the same retrotransposon loci even in the presence of piRNAs.

overall_design: Chromatin was prepared from wild-type, Dnmt3l KO, and Pld6 KO spermatonia at P7 (50,000 to 150,000 cells, EPCAM-positive) and spermatocytes at P21 (~200,000 cells, sorted by Hoechst fluorescence) , and fragmantaded by micrococal nuclease treatment. Chromatin immunoprecipitation was conducted against anti-H3K9me3 antibody (MABI0308, Monoclonal Research Institute) or anti-H3K4me3 antibody (07-473, Merck) for 2 hours at 4   C using Dynabeads M280 Sheep anti-mouse or rabbit IgG (ThermoFisher Scientific). Captured DNA was obtained by proteinase K digestion and ethanol precipitation. The sequence library was prepared by using NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolab) and sequenced on HiSeq Ten X (Illumina) using 150-bp paired-end mode.


title: Long-Term TIL Engraftment and Clonal Expansion After Multiple TIL and Anti-PD-1 Therapy: A Five-Year Immunogenomic Case Study

city: Solna

first: Lucas

last: Arruda

address: Nanna Svartz väg  4

country: Sweden

institute: CuraCell AB

summary: Adoptive cell therapy using tumor-infiltrating lymphocytes (TIL) can achieve durable responses in metastatic melanoma and other indications, but the long-term clonal dynamics after multiple administration and synergy with checkpoint blockade are still to be explored. We present a longitudinal case study of a prostate cancer patient treated with serial TIL infusions and delayed anti-PD-1 therapy, analyzed using high-throughput T-cell receptor (TCR) sequencing from serial blood and tumor samples over five years. TIL-derived clonotypes exhibited sustained persistence and clonal expansion in blood, with peaks corresponding to clinical response. Multiple TIL administration increased the patient exposure to the therapy, improving its pharmacokinetics profile over time. Notably, anti-PD-1 therapy administered six months post-first TIL administration further expanded both previously infused and novel TIL-derived clonotypes, coinciding with durable complete response. Serial tracking revealed stable levels of TIL-derived clonotypes up to five years post-treatment, with persistent tumor infiltration. T-cell clonotype expansion was associated with decreased TCR diversity and increased frequency of hyperexpanded clones, suggesting selective amplification of tumor-reactive populations. Our findings provide mechanistic insight into the long-term persistence and reactivation of TIL-derived immunity and illustrate the potent synergy between adoptive transfer and delayed PD-1 blockade, supporting the integration of longitudinal immunogenomic monitoring in personalized immunotherapy.

overall_design:
Peripheral blood and tumor biopsies were collected at baseline, following each TIL infusion, and periodically up to five years. TCRβ deep sequencing was performed to track TIL-derived, blood-borne, and unique clonotypes longitudinally
D= day
M= month
W= week
Y= year
TIL-1-D1: sample collected one day after first infusion,   TIL-2-D1: sample collected one day after second infusion, and so forth.


title: SF3B6 promotes the cellular proliferation by extensively interacting with and regulating transcripts expression and alternative splicing in MDA-MB-231 cells [RNA-seq]

city: Wuhan

first: Dong

state: Hubei

address: 888 Gaoxin Avenue

institute: Nissi Biotech

summary: SF3B6 functions as a splicing factor, and is closely associated with the malignant progression of multiple cancer types, including breast cancer. However, its underlying mechanism is largely unknown. In this study, we investigated the molecular mechanism of SF3B6 in MDA-MB-231 cells by transfection with siRNA of SF3B6 combined with high-throughput transcriptome sequencing (RNA-seq) and improved RNA immunoprecipitation sequencing (iRIP-seq) technology. We found siSF3B6 significantly repressed cellular proliferation level. Downstream RNA-seq analysis revealed that SF3B6 silencing resulted in widespread changes in differentially expressed genes (DEGs) and regulatory alternative splicing events (RASEs) that are involved in inflammatory response and immune regulatory pathways, such as the NF-κB signaling pathway. iRIP-seq analysis indicated that SF3B6 regulates gene expression and alternative splicing by directly interacting with target mRNA. Further analysis showed that SF3B6 potentially contributes to the malignant properties of TNBC by regulating the expression and splicing of key oncogenes including PPM1F and FASN, and tumor suppressor genes, including RLF and RECQL4. This study highlights the crucial role of SF3B6 in TNBC, providing new insights into its potential as a biomarker or therapeutic target in breast diagnosis and treatment in future.

overall_design: We investigated the molecular mechanism of SF3B6 in MDA-MB-231 cells by transfection with siRNA of SF3B6  combined with high-throughput transcriptome sequencing (RNA-seq) and improved RNA immunoprecipitation sequencing (iRIP-seq) technology. RNA-seq experiments were performed with three biological replicates for siSF3B6 and siNC. The iRIP-seq experiments were performed with two biological replicates for SF3B6 and Input.

first: Chunxiu

last: Yuan

first: Sheng

last: Wang


title: SF3B6 promotes the cellular proliferation by extensively interacting with and regulating transcripts expression and alternative splicing in MDA-MB-231 cells [RIP-seq]


title: MYEOV is a novel marker of differentiated corneal epithelium

city: Seattle

first: Yuzuru

last: Sasamoto

state: WA

address: 750 Republican St

department: Ophthalmology

institute: University of Washington

summary: PURPOSE. Myeloma Overexpressed gene (MYEOV) was initially identified as a gene amplified in several malignancies, and it was found to promote cell proliferation and metastasis. Our previous comparative RNA-seq and epigenetic analyses revealed high MYEOV levels in differentiated corneal epithelial cells and showed that MYEOV expression was epigenetically regulated by TET2. In the current study, we aimed to characterize further the expression and regulation of MYEOV in the human ocular surface epithelium.  METHODS. MYEOV expression was examined by immunostaining and publicly available single-cell RNA-seq data. Gene knockdown (KD) of MYEOV and the regulators of corneal epithelial differentiation, PAX6 and KLF4, in in vitro-expanded corneal epithelial cells was performed by siRNA transfection. Protein expression levels were examined by Western blot. MYEOV KD cells were subjected to colony-forming assay and RNA-seq analysis.  RESULTS. Human cornea immunostaining revealed high MYEOV expression in the nuclei of KRT12-positive differentiated corneal epithelial cells, while KRT13-positive differentiated conjunctival epithelial cells were MYEOV-negative. MYEOV expression was not detected in the other surface ectoderm-derived epithelia: epidermis and oral mucosa. Both PAX6 KD and KLF4 KD led to the reduction of MYEOV and KRT12 protein expression. MYEOV KD decreased colony-forming efficiency while afflicting limited global gene expression change.  CONCLUSIONS. Our study revealed specific MYEOV expression in KRT12-positive corneal epithelial cells among surface ectoderm-derived epithelia. Similar to KRT12, MYEOV expression is regulated by PAX6 and KLF4. Functionally, MYEOV regulates cell proliferation of corneal epithelial cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data. We used cultured human corneal epithelial cells treated with siRNAs (Control, MYEOV knockdown #1, and MYEOV knockdown #2)

first: Yoshiko

last: Fukuda

first: Chao

last: Zhang

first: Bruce

last: Ksander

first: Vickie

last: Jo

first: Christine

last: Lian

first: George

last: Murphy

first: Markus

last: Frank

first: Natasha


title: Small RNA-seq reveals the effect of formaldehyde exposure on chicken embryo liver microRNA profile

city: Kayseri

first: Saffet

last: Teber

address: Erciyes Üniversitesi Ziraat Fakültesi Köşk Mahallesi Fuat Sezgin Caddesi No:12 Melikgazi/KAYSERİ

country: Turkey

institute: Erciyes University

summary: Formaldehyde (FA) is commonly used for hatchery disinfection, but its effects on embryonic development remain unclear. MicroRNAs (miRNAs) regulate gene expression post‑transcriptionally and may mediate FA‑induced transcriptional responses. This study investigates the impact of FA exposure on the miRNA landscape in chicken embryo liver. Small RNA‑seq libraries were constructed and sequenced using the Illumina NextSeq platform. Reads were trimmed and quantified. Differential expression analysis was performed with DESeq2. Target genes of differentially expressed miRNAs (DEMs) were predicted (miRDB), and GO/KEGG/Reactome enrichment was conducted. A total of 662 mature miRNAs were detected. Differential expression analysis identified 30 DEMs (11 up‑regulated, 19 down‑regulated).  FA exposure at the embryo stage may significantly alter miRNA expression, affecting pathways involved in epigenetic, oxidative stress, and immune regulation. These results warrant reconsidering FA use in poultry hatcheries and further functional validation of miRNA‑target interactions.

overall_design: miRNA expression profiling by high throughput sequencing between FA-treated and control samples

first: Mustafa

last: Özdemir

first: Ghulam Asghar

last: Sajid

first: Selma

last: Büyükkılıç Beyzi

first: Mehmet

last: Kızılaslan

first: Yunus

last: Arzık

first: Servet

last: Yalçın

first: Mehmet Ulas

last: Cinar


title: L-Fucose is a candidate monosaccharide neuromodulator and mitigates Alzheimer’s synaptic deficits II

city: Sacramento

first: Jacopo

last: Di Lucente

state: CA

institute: UC Davis

summary: Fucosylation, a major glycan modification, has been shown to influence neuronal and microglial mechanisms, but whether unconjugated free L-fucose can impact brain function is unknown. L-fucose can be transported into cells and metabolized by fucokinase (FCSK) via the poorly understood salvage pathway. Using mouse hippocampal slices, we showed that L-fucose enhanced excitatory neurotransmission and long-term potentiation (LTP) through regulation of pre-synaptic release. Such effects required L-fucose metabolism through the FCSK-driven salvage pathway and were not likely dependent on fucosylation, suggesting a metabolic-signaling mechanism. Human Alzheimer’s disease (AD) and 5xFAD mouse brains showed signs of fucose hypometabolism with impaired L-fucose signaling. Such abnormalities were corrected by exogenous L-fucose, exemplified by rectification of LTP deficits in 5xFAD hippocampus. Dietary L-fucose supplement, which increased cerebral free L-fucose levels and upregulated FCSK to drive the salvage pathway, mitigated synaptic and behavioral deficits of 5xFAD mice. Our data suggests an unrecognized neuromodulatory function of free L-fucose and reveals its therapeutic potential for AD.

overall_design: RNA-seq profiling of WT and 5xFAD after 1 months of Control or Fucose diet

first: Izumi

last: Maezawa

first: Lee-Way

last: Jin


title: L-Fucose is a candidate monosaccharide neuromodulator and mitigates Alzheimer’s synaptic deficits

overall_design: RNA-seq profiling of WT brain sections incubated with aCFS or aCSF+L-fucose for 5 hours


title: Spatial Transcriptomics of Patients with Kaposi Sarcoma Identifies Mechanisms of Immune Evasion

city: Bethesda

first: Joseph

middle: M

last: Ziegelbauer

state: MD

address: 10 Center Dr. 6N110

institute: NIH / National Cancer Institute

summary: We performed Visium Spatial on Seven Skin Samples with Kapiosi Sarcoma tumor. For four of the samples, we included custom probes for five KSHV genes that allowed us to measure human and KSHV expression patterns at the same time.

overall_design: Punch biopsies from (LANA-positive) Kaposi sarcoma skin lesions were fixed with FFPE. Sections were cut and placed on 10X Genomics Visium slides for spatial transcriptomics.

first: Afsari

last: Bahman

first: Knudsen-Palmer

last: Daphne


title: A Multi-Omics Landscape of Programmed Cell Death in Acetaminophen-Induced Acute Kidney Injury

city: Xiamen

first: Jianxin

last: Zheng

address: Jinhu Road No.668

department: Department of Urology

institute: Zhongshan Hospital (Xiamen), Fudan University

summary: Acetaminophen (APAP) overdose is a known cause of acute kidney injury, yet the underlying molecular mechanisms remain incompletely understood. In this study, we conducted integrated transcriptomic, proteomic, and phosphoproteomic analyses of kidney tissues from mice with early-stage APAP-induced nephrotoxicity and corresponding controls.

overall_design: In this study, we combined transcriptomic, proteomic, and phosphoproteomic profiling of kidneys from APAP-exposed mice to explore molecular mechanism and potential therapeutic strategies. Ten-week-old male C57BL/6 mice were fasted overnight for 16 hours prior to APAP treatment. Acute kidney injury was induced by intraperitoneal injection of APAP overdose (300 mg/kg body weight) for 6 hours (n = 4). Control mice received an equivalent volume of PBS via intraperitoneal injection (n = 4). Kidney tissues were subsequently collected from APAP-induced kidney injury mice and PBS-injected controls.


title: Fatty acid-binding protein 4 drives neuroinflammation after intracerebral hemorrhage

city: Shaanxi Xi'an

first: Jia qing

last: He

state: -- None selected --

address: Tangdu Hospital, Xi'an City, Shaanxi Province

institute: Air Force Medical University Tangdu Hospital Department of Neurosurgery

summary: As key immune sentinels of the central nervous system (CNS), microglia rapidly respond to acute brain injury and engage in dynamic crosstalk with infiltrating peripheral immune cells, collectively shaping the neuroinflammatory milieu—a critical factor governing mortality and long-term functional deficits after intracerebral hemorrhage (ICH). However, the underlying molecular regulatory mechanisms of microglial pathogenic activities remain elusive. Fatty acid-binding protein 4 (FABP4), a metabolic disorder-associated adipokine, have been recognized as a key modulator in inflammatory response. In our study, clinical analyses in ICH patients demonstrated a significant positive correlation between elevated serum FABP4 levels and unfavorable neurological outcomes. Moreover, microglial Fabp4 knockout resulted in attenuated neuronal loss, mitigated cerebral edema, and improved functional recovery after ICH in mice. Mechanistically, increased FABP4 not only promoted lipid droplet deposition, but also inhibited the ubiquitin-proteasome degradation of S100A9 in microglia, synergistically amplifying neuroinflammatory responses. Interestingly, microglial FABP4 also facilitated peripheral neutrophil transendothelial migration into brain parenchyma, and exacerbated brain injury through neutrophil extracellular trap release. Notably, pharmacological inhibition of FABP4 using brain-targeted nanoparticles demonstrated substantial neuroprotective effects in ICH models. These results collectively establish a novel role of FABP4 in orchestrating brain inflammation after ICH and could be targeted to improve neurological outcome.

overall_design: Forty-eight hours after ICH, experimental subjects underwent terminal anesthesia prior to cerebral tissue harvesting using established protocols. Hematoma-adjacent regions (1-2 mm radius) were cryosectioned into 1-mm thick slices using precision surgical blades under cryogenic conditions (0-4°C). Sham-operated controls underwent identical tissue procurement procedures excluding injury induction. After cooling the surrounding tissue in liquid nitrogen, we placed it in a -80°C until library preparation.

first: Jiaqing

first: Zijuan

last: Qin

first: Haixiao

last: Liu


title: The targeted genes of KIF11 of PLC8024 cell after drug treatment

first: Jun

last: Mi

address: 280 South Chongqing Rd.

department: Biochemistry & Molecular Cell Biology

institute: Shanghai Jiao Tong University

summary: We found that KIF11 played an inportant role in PLC8024 apoptosis after drug treatment

overall_design: The CUT&Tag assay was performed in PLC8024 cells using the NovoNGS® CUT&Tag® 4.0 High-Sensitivity Kit (designed for Illumina®) (Novoprotein, N259-YH01, Shanghai, China), following the manufacturer’s instructions. The experiment included four groups: an IgG negative control group, a Pol II positive control group, a PLC8024 control group, and a PLC8024 group treated with drug(10 nM for 6 hours).The key experimental steps involved ConA magnetic bead purification, cell preparation, binding of nuclei to ConA magnetic beads, overnight incubation with a primary antibody, secondary antibody binding followed by washing, transposition complex binding and washing, a one-hour fragmentation reaction, termination of fragmentation, DNA extraction, PCR amplification, purification of PCR products, library construction using index primers, and sequencing. Finally, specific primers were designed for qPCR analysis based on the sequencing results.

first: Yonggang

last: Zhang


title: RNA sequencing of kidneys of sham-operated mice and mice with unilateral ureteral obstruction (UUO) treated with istradefylline or vehicle

city: Toronto

first: Andrew

last: Advani

state: Ontario

address: 6-151 61 Queen Street East

country: Canada

institute: St. Michael's Hospital

summary: RNA-sequencing of mouse left kidneys where the left ureter was obstructed (UUO) or not obstructed (sham), isolated 14 days after the surgery in C57 mice treated with either istradefylline or vehicle.

overall_design: Whole left kidneys were collected from either sham-operated or UUO mice and RNA was isolated for sequencing

first: Advani

last: Andrew

first: Yeung

last: Emily

first: Nagarjun Batchu

last: Sri


title: The different genes expression of PLC8024 cell after drug treatment

summary: Liver cancer is a highly malignant tumor. Current treatments are not effective.  Hence, more effective treatment methods need to be sought. We aim to identify different genes after drug treatment  by RNA-seq, and subsequently explore their functions, in the hope of finding better targets for liver cancer treatment.

overall_design: RNA-seq for different genes after drug treatment


title: Metformin inhibits mitochondrial complex I in intestinal epithelium to promote glycemic control

city: Chicago

first: Zachary

middle: Lee

last: Sebo

address: 303 E Superior St

institute: Northwestern University

summary: Metformin is a therapeutically versatile biguanide drug primarily prescribed for type II diabetes. Despite its extensive use, the mechanisms underlying many of its clinical effects, including attenuated postprandial glucose excursions, elevated intestinal glucose uptake, and increased production of lactate, Lac-Phe and GDF15, remain unclear. Here, we map these and other clinical effects of metformin to intestine-specific mitochondrial complex I inhibition. Using human metabolomic data and an orthogonal genetics approach in male mice, we demonstrate that metformin suppresses citrulline synthesis, a metabolite generated exclusively by small intestine mitochondria, and increases GDF15 by inhibiting the mitochondrial respiratory chain at complex I. This inhibition co-opts the intestines to function as a glucose sink, driving uptake of excess glucose and converting it to lactate and Lac-Phe. Notably, the glucose-lowering effect of another biguanide, phenformin, and berberine, a structurally unrelated nutraceutical, similarly depends on intestine-specific mitochondrial complex I inhibition, underscoring a shared therapeutic mechanism.

overall_design: RNA-seq profiling of mouse jejunum from Vil-Cre and Vil-Cre:NDI1 animals (i.e., cre controls and mice that express Saccharomyces cerevisiae NDI1 in jejunum) to determine if NDI1 expression effects the transcriptome.


title: Beclin1 Deficiency Unlocks Cardiac Lineage Commitment through Convergent Wnt and BMP Signaling Activation

city: wuhan

first: yu

middle: zhang

last: yi

state: hubei

address: donghu street

department: wuhan

institute: wuhan university

summary: Beclin1 plays significant roles in cardiac organogenesis. Beclin1 can regulate the fate conversion of fibroblasts into cardiomyocytes. However, the function and mechanism of Beclin1 in regulating early cardiac lineage commitment and differentiation remain unclear. To explore its potential role in cardiac lineage development, we utilized model of cardiomyocyte differentiation from mouse embryonic stem cells (mESCs) to simulate early cardiogenesis and investigated the function of Beclin1. We show that the knockdown of Beclin1 facilitates cardiomyocyte differentiation. Through bulk RNA-sequencing analysis, we found that knocking down Beclin1 activated the Wnt signaling pathway at the embryoid body stage but inhibited its activity at the cardiomyocyte stage. Moreover, the Bone morphogenetic protein (Bmp) signaling pathway was continuously activated throughout cardiomyocyte differentiation process. Our findings demonstrate a novel function of Beclin1 during cardiac differentiation. The activation of Wnt-mediated Bmp signaling pathway represents a major mechanism by which the deficiency of Beclin1 promotes mESCs differentiation into cardiomyocytes.

overall_design: To determine the molecular basis by which knockdown Beclin1 enhances cardiomyocyte differentiation, we conducted bulk RNA-sequencing (RNA-seq) with shNT- and shBcelin1-treated mESCs (d0) and their differentiated cells towards cardiac lineage on day 4 and day 10.

first: Li

last: Wang

first: LiLin

last: Xiang


title: The effect of CPXM2-aligned collagen on gene expresssion and the intracellular signaling pathway in PaTu 8988t cells.

summary: Changes in the structure and composition of the extracellular matrix can influence intracellular signal transduction. We have observed that CPXM2 in the extracellular matrix is capable of aligning collagen. Then, does the alignment of collagen by CPXM2 affect gene expression and signaling pathway transduction in cancer cells? For this purpose, we treated cancer cells with an extracellular matrix containing CPXM2WT  or CPXM2R213A for 24 hours and then subjected the cancer cells to RNA-seq.

overall_design: RNA-seq for  cancer cells treated with an extracellular matrix containing CPXM2WT  or CPXM2R213A


title: The different genes expression in clinical para-tumor and pancreatic ductal adenocarcinoma samples

summary: Pancreatic cancer is a highly malignant tumor. Current treatments are not effective.  Hence, more effective treatment methods need to be sought. We aim to identify genes that differ between clinical para-tumor and pancreatic ductal adenocarcinoma samples by RNA-seq, and subsequently explore their functions, in the hope of finding better targets for pancreatic cancer treatment.

overall_design: RNA-seq for clinical para-tumor and pancreatic ductal adenocarcinoma samples


title: DNA methylation analysis for mouse spermatogonia defficient in Pld6.

first: Kenji

last: Ichiyanagi

type: Methylation profiling by high throughput sequencing

summary: In the male germline of mammals, the expression of retrotransposons is restricted by DNA methylation, trimethylation of histone H3 at lysin-9 (H3K9me3) and PIWI-interacting small RNAs (piRNAs). To elucidate their relative importance in regulating retrotransposons during germ-cell development as well as relationships between these mechanisms, we performed mRNA, DNA methylation, and histone methylation analyses using mouse spermatogonia from Dnmt3l and Pld6 mutants deficient in de novo DNA methylation and piRNA production, respectively. The results revealed that a loss of DNA methylation results in decreased H3K9me3 and increased H3K4me3, suggesting a pivotal role of DNA methylation in maintaining the epigenome integrity.

overall_design: DNA was extracted by phenol chloroform extraction from wild-type and Pld6 KO mouse spermatonia at postnatal day 7, which were purified by FACS (EPCAM+). DNA was then fragmented by sonication on Bioruptor for 15 cycles of high output for 30 seconds. After purification by AMPure, DNA was treated with high concentration of bisulfite at 70 degree for an hour, then purified using EZ methylation kit. BS-seq libraries were made using ACCEL-NGS methyl-seq library Kit (Swift Biosciences) and sequenced on HiSeq Ten X with a 150-bp paired-end mode.

first: Hirotaka

last: Sugimoto

first: Masaki

last: Kawase


title: Elevated FTO alleviates sepsis-induced acute kidney injury by regulating macrophage inflammatory phenotypes [RNA-Seq]

first: Xiaona

last: Chen

summary: Recent studies have linked the dysregulation of N6-methyladenosine (m6A) to sepsis-induced acute kidney injury (SAKI), highlighting the persistent challenge of managing excessive proinflammatory cytokine production and subsequent organ dysfunction. In this study, we analyzed the dataset GSE32707 and GSE69063, fat mass and obesity-associated protein (FTO) was identified as the sole gene exhibiting significant downregulation within the transcriptome of peripheral blood samples from sepsis patients among m6A-related proteins. We further demonstrated that septic mice subjected to cecal ligation and puncture (CLP) presented increased m6A modifications and reduced FTO expression in both renal tissues and peritoneal macrophages (PMs). Our findings revealed that increased levels of FTO correlated with reduced mortality and kidney damage during sepsis and that the upregulation of FTO in lipopolysaccharide (LPS)-stimulated macrophages led to decreased production of proinflammatory cytokines. Mechanistically, through multiomic analysis of macrophages, we identified a novel mechanism involving matrix metalloproteinase 9 (MMP-9) as a direct target of FTO, which positively affects its translation efficacy. Furthermore, both in vivo and in vitro data confirmed that reduced MMP-9 levels exerted adverse effects on mitigating inflammatory responses and alleviating renal injury. Overall, our findings underscore the critical role of the FTO/m6A/MMP-9 axis in the regulation of proinflammatory secretion and improve our understanding of the transcriptomic landscape during the progression of SAKI.

overall_design: RNA-seq of wildtype RAW267.4 cells and their overexpressed FTO with or without LPS stimulation (Ctrl, LPS and FTO+LPS).

first: Quan

last: Li

first: Zhixia


title: Phloem-Specific Translational Regulation of Soybean Nodulation

city: Columbia

first: Gary

last: Stacey

state: Missouri

address: 271E Christopher S. Bond Life Sciences Center

institute: University of Missouri at Columbia

summary: Soybean (Glycine max) root nodulation is a symbiotic process that requires complex molecular and cellular coordination. The phloem plays a crucial role not only in nutrient transport but also in long-distance signaling that regulates nodulation. However, the molecular mechanisms underlying phloem-specific regulation during nodulation remain poorly characterized. Here, we developed a phloem-specific Translating Ribosome Affinity Purification sequencing (TRAP-seq) system to investigate the translational dynamics of phloem-associated genes during nodulation. Using a phloem-specific promoter (Glyma.01G040700) combined with the GAL4-UAS amplification system, we successfully captured the translatome of soybean root phloem at early (72 hours post-inoculation, hpi) and late (21 days post-inoculation, dpi) nodulation stages. Differential expression analysis revealed dynamic translational reprogramming, with 2,628 differentially expressed genes (DEGs) at 72 hpi and 8,422 DEGs at 21 dpi. Gene ontology and pathway enrichment analyses showed stage-specific regulatory shifts, including early activation of ethylene and defense pathways and late-stage enhancement of nutrient transport and vascular development. Transcription factor analysis identified GmbHLH121 as a key phloem-specific regulator of nodulation. Functional validation using RNAi knockdown and overexpression experiments demonstrated that GmbHLH121 negatively regulates nodule formation, likely acting downstream of or independently from early nodulation signaling pathways. Additionally, we uncovered dynamic regulation of cell wall-modifying enzymes (PME and PMEI) in the phloem, implicating their role in modulating plasmodesmata permeability and facilitating symplastic connectivity during nodulation. Our findings highlight the critical role of phloem-mediated translational regulation in coordinating root nodulation, emphasizing the phloem as an active regulatory hub for long-distance signaling and symbiotic efficiency. This study provides a foundational framework for future research on phloem-specific gene regulation and its impact on legume symbiosis.

overall_design: Examination of 2 different time point (72hpi and 21dpi) samples with or without B.Japonicum treatment using translating ribosome affinity purification (TRAP) followed by RNA sequencing technology

first: Jaehyo

last: Song

first: Shin-ichiro

last: Agake

first: Sayuri

last: Tanabata

first: Yaya

last: Cui

last: Su

first: Dong

last: Xu


title: Effect of a 1-week mind-body intervention retreat on exosome-derived miRNA for 21 healthy human participants

city: La Jolla

first: Andrei

last: Chernov

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

summary: We employed  exosome-specific small RNA transcriptomics to analyze extracellular RNA (exRNA) profiles in human plasma-derived exosomes isolated via differential ultracentrifugation. Total exRNAs were extracted, quantified, and used to generate small RNA libraries, targeting transcripts between 16-120 nucleotides for sequencing on an Illumina NovaSeq X Plus platform. Sequencing reads were processed using Cutadapt, STAR aligner, and MultiQC, and differential expression analysis was conducted using EdgeR, applying TMM normalization and a paired negative binomial generalized linear model to assess intervention effects. Functional annotation of differentially expressed exRNAs was performed using ClusterProfiler and Reactome Pathways. The analysis accounted for participant-specific factors such as experience level, sex, and age. This is the first study to analyze human exosomal RNA changes following an intensive mind-body (meditation, reconceptualization, open label placebo healing ritual) intervention.

overall_design: Exosomes were isolated from whole plasma from 21 human participants (15 females; mean age=46 yrs.) before ("pre") and after ("post") a 6-day intensive mind-body retreat, and miRNAseq was performed on an Illumina NovaSeq X Plus platform.

first: Alex

last: Jinich-Diamant

first: Sierra

last: Simpson

first: Juan

last: Zuniga-Hertz

first: Ramamurthy

last: Chitteti

first: Jan

last: Schilling

first: Jacqueline

middle: A

last: Bonds

first: Laura

last: Case

middle: V

first: Joe

last: Dispenza

last: Maree

first: Natalia Esther

last: Amkie Stahl

first: Michael

last: Licamele

first: Narin

last: Fazlalipour

first: Swetha

last: Devulapalli

first: Leonardo

last: Christov-Moore

first: Nicco

last: Reggente

first: Michelle

last: Poirier

first: Tobias

last: Moeller-Bertram

first: Hemal

middle: H

last: Patel


title: DNA methylation dynamics associated with visual system remodeling during flatfish metamorphosis

city: Vigo

middle: Guerrero

last: Peña

state: Pontevedra

address: Eduardo Cabello, 8

department: Aquaculture and Biotecnology

country: Spain

institute: CSIC

summary: Flatfish metamorphosis is characterized by extensive tissue remodeling, associated with a transition from pelagic to benthic lifestyle, being the migration of one eye the most dramatic change. Epigenetic mechanisms exert a pivotal role in developmental programs. This study investigates the DNA methylation profiles of migrating and non-migrating eyes using reduced-representation bisulfite sequencing (RRBS) during three developmental stages of turbot: pre-metamorphosis, climax and post-metamorphosis. Over 31% of all identified regions were hypermethylated during climax stage in both eyes, coinciding with elevated expression of the dnmt3a gene, responsible for de novo methylation. Additionally, transcription factors crucial for retinal ganglion cells (RGCs) development, including the eomesa and tbr1b, exhibited differential methylation and expression between the migrating and non-migrating eye during the climax phase. These findings underscore the significance of DNA methylation in the intricate remodeling of the visual system during turbot metamorphosis, particularly regarding RGC-mediated ocular migration and the transmission of visual signals.

overall_design: Methylation profiling (RRBS-seq) of migrating and non-migrating turbot eye samples from the pre-metamorphic, climax metamorphic and post-metamorphic stages.

last: Guerrero-Peña

first: Paula

last: Suarez-Bregua

first: Núria

last: Sánchez-Baizán

first: Francesc

last: Piferrer

last: Tena

first: Josep

last: Rotllant


title: Testing the effects of two different exposure paradigms on transcriptomic-based chemical risk assessment using the flame retardant Triphenyl Phosphate.

city: Saskatoon

first: Morgan

last: Kirzinger

state: Saskatchewan

address: 110 Gymnasium Place

institute: National Research Council Canada

summary: We use a larval zebrafish model to assess the transcriptomic alterations caused by sub-phenotypic concentrations triphenyl phosphate using two different exposure paradigms.

overall_design: We use two approaches to evaluate potential toxicological mechanisms; using two exposure paradigms, we determine differentially expressed genes, and compare serial dilutions of triphenyl phosphate to the vehicle control and we determine the Point of Departure (POD) for each drug by modelling gene expression changes as continuous systems.

middle: G

last: Morash

first: Lee

last: Ellis


title: Fibrinogen triggers intial perivascular fibroblast activation in a mouse model of cortical ischemic stroke

city: Miami

first: Jae

last: Lee

state: FL

address: 1095 NW 14th Terrace #48

institute: University of Miami

summary: Perivacular fibroblasts (PVFs) in the perivascular space delaminate from blood vessels, expand, express and deposit an excess of collagen I (Col I) and become an integral component of the fibrotic scar after central nervous system (CNS) disease. Here, we show that blood-derived fibrinogen deposition in the perivascular space initially induces PVF activation after photothrombosis, a mouse model of ischemic stroke. Pharmacological fibrinogen depletion reduces PVF activation and their delamination from blood vessels to build up the fibrotic scar. Fibrinogen induces beta1 integrin signaling in PVF to induce Col I expression and secretion. Single-cell RNA sequencing (scRNA-Seq) and genetic approches revealed a contribution of fibrinogen-induced perivascular macrophages to PVF activation. Finally, fibrinogen depletion abrogates PVF-astrocyte signaling and astrocyte lesion border formation, promoting neuronal survival and plasticity. Therefore, we propose that fibrinogen is a critical trigger for PVF activation and fibrotic scar formation, inhibiting neuronal regeneration after stroke.

overall_design: C57Bl/6J mice were implanted with subcutaneous pumps filled with saline or Ancrod (2.4 U) 2 days before receiving photothrombotic stroke using rose bengal and a cold light illuminator over 4-mm diameter of the right sensorimotor cortex. After 6 days, the lesion and 1-mm of surrounding spared tissue (not including the corpus callosum) was microdissected and dissociated. No FACS or beads were  used to filter the cells or to enrich for a specific cell type.

first: Jose

middle: C

last: Martínez Santamaría

first: Corey

last: Fehlberg

first: Pasquale

last: Conforti

first: Jan

middle: N

last: Ness

first: Francesca

last: Justiniano

first: Felicitas

last: Bucher

first: Christian

last: Schachtrup


title: Epigenetically controlled ZEB2 expression promotes the cytotoxic potential of CMV-specific CD8+ T cells

city: Braunschweig

first: Stefan

last: Floess

address: Inhoffenstr. 7

department: Experimental Immunology

institute: Helmholtz-Centre for Infection Research

summary: Zinc finger E-box binding protein 2 (ZEB2) is a key factor in the differentiation of naive CD8+ T cells into effector and memory T cells. However, the precise regulatory role of ZEB2 in cytotoxic CD8+ T cells remains unknown. Our recent DNA methylation analysis of cytomegalovirus (CMV)-specific human CD8+ T cells revealed two differentially methylated regions (DMRs) within the ZEB2 locus. We showed that these ZEB2 DMRs undergo pronounced demethylation during T cell differentiation. In particular, terminally differentiated CD8+ T cells and cytotoxic CD4+ T cells show almost complete demethylation. A ZEB2 knockout approach in CD8+ effector T cells followed by RNA-seq analysis revealed an altered gene expression profile, affecting genes related to cell-cell adhesion and impairing cytotoxicity in CMV-specific killing assays. Our data show that ZEB2 expression contributes to the differentiation of naive CD8+ T cells into effector and memory T cells and regulates the functional properties of virus-specific cytotoxic CD8+ T cells.

overall_design: RNA-seq profiling of ZEB2-deficient and control human CD8+ effector T cells

first: Jochen

last: Huehn

first: Varun

first: Zheng

last: Yu


title: The role of Inmt knockout in renal proximal tubules.

city: Tokushima

first: Kazuhiro

last: Hasegawa

address: 3-18-15 Kuramoto-cho

department: Department of Nephrology

institute: Tokushima University Graduate School of Biomedical Sciences

summary: Indolethylamine N-methyltransferase (Inmt), an enzyme responsible for detoxifying local uremic toxins, including indole. This study used genetically engineered mice to explore the role of Inmt in kidneys. Using conditional knockout (Conditional KO) mouse models, renal proximal tubule–specific Inmt function was assessed. Gene expression changes, apoptotic cell percentages, and mitochondrial DNA copy numbers were examined by RNA sequencing, histopathology, and various molecular assays. Those analyses were further complemented by immunofluorescence and electron microscopy to investigate cellular and structural alterations.Results: Inmt downregulation induced AKI associated with increased production of reactive oxygen species, and increased tubular apoptosis.

overall_design: Bulk RNAseq using the whole kidneys of Inmt conditional KO mice and Control mice.


title: Short-term starvation boosts anti-PD-L1 therapy by reshaping tumor-associated macrophages in hepatocellular carcinoma

city: Hu Bei

first: Kun

last: Cheng

state: --- Select One ---

address: No. 1037 Luoyu Road, Hongshan District, Wuhan

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.

summary: STS was found to attenuate tumor progression by inducing tumor-associated macrophages (TAMs) to switch to an antitumoral phenotype, enhancing phagocytosis of tumor cells, and stimulating subsequent antitumor immunity of CD8+ T cells as demonstrated in 3 HCC mouse models, NCG mice, and Rag2-KO mice. Furthermore, STS combined with anti-PD1/L1 suppressed tumor progression, while the efficacy of anti-programmed cell death 1 ligand 1 (PD-L1) was improved when combined with STS. Our data therefore provide information on gene expression changes in liver tumor tissue in mice after starvation.

overall_design:
RNA-seq profiling in liver tumors of mice undergoing short-term starvation and normal diet at the experimental endpoint.

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title: Self-Reported Race as a Determinant of Differential Methylation in Peripheral Artery Disease

city: Nashville

first: Lindsey

middle: "Joey"

last: Stolze

state: TN

address: 1211 Medical Center Dr

institute: Vanderbilt University Medical Center

summary: Peripheral Artery Disease (PAD) is a manifestation of atherosclerosis within the lower extremities that affects approximately 10 million people in the United States. Despite the rising prevalence of PAD, Black Americans are disproportionately affected and experience worse outcomes, including higher rates of limb loss compared to White counterparts. To dissect mechanisms within PAD, we performed DNA methylation analysis utilizing methyl-binding domain-capture sequencing. Within the DNA methylation profiles, we observe a large driver of variation is self-reported race. Specifically, samples separate into White and Black groups. Interestingly, when comparing PAD to Control samples within each self-reported racial group, there are different differentially methylated CpGs between the two groups. This suggests that the methylation landscape both at baseline and in disease is different based on self-reported racial background and could begin to explain some of the differences we see in downstream outcomes between White and Black Americans.

overall_design: prospective cohort

first: Joshua

last: Beckman

first: Alexander

last: Sullivan


title: An mRNA cap-binding complex in giant viruses controls protein synthesis

city: Boston

first: Amy

middle: Si-Ying

state: MA

address: 450 Brookline Ave SM520

department: Cancer Immunology and Virology

institute: DFCI

summary: In contrast to living organisms, viruses lack the machinery necessary for protein synthesis, instead co-opting host factors to translate viral transcripts. Giant DNA viruses, which encode putative orthologs of translation factors, challenge this dogma and blur the line between cellular and acellular biology. Here, we discover a complete mRNA cap-binding complex in mimivirus that we name viral IF4F. This complex associates with host ribosomes to orchestrate the temporally regulated synthesis of structural proteins critical for assembly of viral progeny. The m7G cap-binding subunit of viral IF4F has evolved specificity for viral cap structures through additional interactions with methylated adenosines in mRNAs. Viral IF4F further facilitates dynamic gene expression required to evade host abiotic stresses that normally restrict viral replication. Our study thereby extends a paradigm of eukaryotic translation regulation to include viruses and illuminates a series of evolutionary innovations to a core process of life.

overall_design: Ribosome profiling (RNA-seq and RIBO-seq) of Acanthamoeba castellanii infected with APMV WT and mutant viruses lacking viral translation factors (APMV Δ4A, Δ4E, Δ4G). Samples were collected at early (4 h) and late (8 h) times of infection.

first: J Maximilian

last: Fels

first: Aidan

middle: B

last: Hill

first: Richard

last: Han

first: Chantal

last: Abergel

first: Philip

middle: J

last: Kranzusch


title: EZHIP boosts neuronal-like synaptic gene programs and depresses polyamine metabolism in human neural models

city: Houston

first: Marco

last: Gallo

state: Texas

address: 1102 Bates Avenue

institute: Baylor College of Medicine

summary: EZHIP (Enhancer of Zeste Inhibitory Protein) is an enigmatic protein with no discernible domains, primarily known for its role in inhibiting PRC2-mediated H3K27 methylation. It is highly expressed in posterior fossa type A (PFA) ependymoma, where it drives global chromatin reorganization. Using human neural models, we show that EZHIP activates neuronal-like transcriptional programs while repressing genes involved in metabolic regulation. Metabolomic analyses indicate that EZHIP suppresses methionine and polyamine metabolism, potentially contributing to the histone and DNA methylation alterations observed in PFA. These findings highlight a metabolic dimension to EZHIP’s function and suggest that targeting polyamine metabolism may represent a therapeutic avenue for PFA.

overall_design: RNA-seq analysis of human neural progenitor cell (hNPC) models and their derivatives with EZHIP overexpression.

first: Elham

last: Hasheminasabgorji

first: Huey-Miin

last: Chen

first: Taylor A

last: Gatesman

first: Subhi Talal

last: Younes

first: Sameer

last: Agnihotri


title: Uncovering genetic dependencies in the DNA repair network after ionizing radiation

city: Boulder

first: Nausica

last: Arnoult

state: CO

address: 1945 Colorado ave

department: MCDB

institute: University of Colorado Boulder

summary: We constructed a combinatorial CRISPR guide library to target ~200,000 pairwise combinations of 461 genes associated with DNA Repair.

overall_design: eHAP-iCas9 cells harboring this library were grown under standard growth conditions as well as an LD30 dose of ionizing radiation to induce global DNA damage. Each condition grew for 14-15 days before being collected and sequenced.

first: Benjamin

last: Nebenfuehr

first: Lynn

last: Sanford

first: Robin

last: Dowell


title: Unraveling the role of ATOH8 in trophoblast lineage differentiation

city: Rensselaer

first: Bum-Kyu

last: Lee

state: New York

address: One Discovery Drive, Cancer Research Center, RM332

institute: University of Albany-SUNY

summary: Extravillous trophoblasts (EVTs) play a vital role in placental development by anchoring the placenta to the uterine wall, invading the maternal decidua, and remodeling maternal spiral arteries. ATOH8, a basic helix-loop-helix (bHLH) transcription factor, is central to regulating trophoblast dynamics at the maternal-fetal interface, where it orchestrates their invasive potential, proliferative capacity, and differentiation in mice. By coordinating these processes, ATOH8 ensures the formation of a functional placental structure critical for sustaining pregnancy. Although ATOH8 has been implicated in decidualization—a key preparatory event in human endometrial stromal fibroblasts essential for placental development, its precise mechanisms and contributions to human trophoblast function remain unresolved. To understand the role of ATOH8 in EVT differentiation, we performed RNA sequencing of ATOH8-depleted EVT and control EVT.

overall_design: To investigate the role of ATOH8 in trophoblast stem cell (TSC) differentiation into extravillous trophoblasts (EVTs), we depleted ATOH8 via shRNA-mediated knockdown during EVT differentiation. After 8 days of differentiation, total RNA was isolated from ATOH8-KD EVTs and control EVTs and subjected to RNA sequencing to assess genome-wide transcriptional alterations.


title: The role of Lnc9101 and Lnc8475 in innate immunity against influenza virus

city: Fuzhou

first: Song

last: Wang

state: Fujian

address: Cangshan District

institute: Fujian Agriculture and Forestry University

summary: Recent studies have shown that host long-chain non-coding RNAs (LncRNAs) is a key regulator of host-virus interactions during viral infections, however, many LncRNAs have unknown functions in host-virus interactions, especially influenza A virus (IAV). Here, we demonstrate that expression of lncRNA 9101 and lncRNA8475 can be induced by IAV infection. Expression of lncRNA 9101 and lncRNA8475 was significantly stimulated by viral genomic RNA, poly (I:C), or LPS treatment. Furthermore, inhibition of lnc9101 expression in DF-1 cells enhanced IAV replication, whereas overexpression of lnc9101 suppressed virus production. Interestingly, the role lnc8475 in viral replication was the opposite of its role; inhibition of lnc8475 expression in DF-1 cells attenuated IAV replication, whereas overexpression of lnc8475 promoted viral replication. Further studies concluded that lnc9101 and lnc8475 affected the expression of type I and type III IFNs, multiple ISGs, and the activation of STAT1 triggered by IAV infection. In addition, lnc9101 deficiency impaired the expression of TLR7 and MDA5 and decreased the phosphorylation level of IRF7, whereas lnc8475 deficiency promoted the expression of TLR3 and TLR7. The outcomes suggest that lnc9101 inhibits IAV replication by positively regulating the innate immune response and lnc8475 subject promotes IAV replication by regulating the innate immune response.

overall_design: To identify lncRNAs that play important roles in  influenza virus infection, we infected 5-day-old chicks with or without H9N2 influenza virus for 48h, and performed RNA-seq to find differently expressed lncRNA .

first: Yanmei

last: Ma

first: Ji-Long


title: Intra and Inter Tumoral Heterogeneity In Von Hippel-Lindau related Renal Cancer

city: Milano

first: Francesca

last: Genova

address: via Olgettina 60

department: COSR, Center for Omics Sciences

country: Italy

institute: IRCCS, Ospedale San Raffaele

summary: Von Hippel-Lindau (VHL) disease is a rare hereditary cancer syndrome caused by germline pathogenic variants in the VHL gene. Affected individuals develop multiple primary tumours in several organs, but the determinant of their life expectancy is clear cell renal cell carcinoma (ccRCC). The current standard of care is based on arbitrary decisions. Due to the lack of biological or molecular markers assisting clinical decision-making, patients undergo multiple surgical interventions with an incremental risk of complications and morbidity. The most important clinical need in those individuals is to overcome intra/intertumoral heterogeneity in VHL-associated ccRCC to allow tailored decisions and treatments. Therefore, we set up a methodology aiming at creating the first integrated map of intra- and inter-tumour heterogeneity in VHL-associated ccRCC by overlaying imaging, histology, multiplex immunohistochemistry, and multi-omics data from multi-region tumour biopsies. This, combined with the establishment of patient derived organoids cultures, can provide innovative tools to guide clinical management.

overall_design: Three tumors from the same VHL patient were used for the analysis: two lesions retrieved from the left kidney (L1 and L3) and one lesion from the right kidney (R1). Each tumor was divided into four distinct areas (labeled as "black," "blue," "brown," and "green"). RNA was extracted from biopsies taken from each area, and the four areas were considered replicates of the same tumor.

first: Isaline

last: Rowe

first: Alberto

last: Colombo

last: Corea

first: Francesco

last: Pisu

first: Martina

last: Uggè

first: Chiara

last: Ciaparrone

first: Antonino

last: Giangrasso

first: Giovanni Battista

last: Pipitone

first: Maria Giulia

last: Scotti

first: Alessandro

last: Larcher

first: Giorgia

last: Colciago

first: Marco Jacopo

last: Morelli

first: Roberta

last: Lucianò

first: Paola

last: Carrera

first: Pio

last: Zeppa

last: Caputo

first: Roberto

last: Bertini

last: Montorsi

first: Andrea

last: Salonia

first: Paolo

last: Verze

first: Anna

last: Palmisano

first: Antonio

last: Esposito

first: Rosa

last: Bernardi

first: Umberto

last: Capitanio


title: Fibroblast orchestration of inflammaging via NF-kB activation (Aged vs Young Lung Fibroblasts and Epithelium)

city: San Francisco

first: Nancy

last: Allen

address: 513 Parnassus Ave.

department: Medicine

institute: UCSF

summary: In this study we used scRNA sequencing to compare lung fibroblast and epithelial populations from young and aged mice. We identified enrichment of a NF-kB activation signature in aged relative to young fibroblasts, particularly in the adventitial population.

overall_design: Cells were sorted from one 2 month and one 22 month old wildtype (C57BL/6) mouse.  Fibroblasts were identified as lineage negative (CD45-Epcam-CD31-) cells. Epithelial cells were identified as CD45-CD31-Epcam+. After sorting these two cell populations were mixed to generate a 70% fibroblast/30% epithelial cell sample for sequencing.

first: Tien

last: Peng


title: Fibroblast orchestration of inflammaging via NF-kB activation (CD3+ T cell, CD8+ T cell)

summary: Aging is associated with the accumulation of Gzmk+CD8+ T cells in the blood and multiple tissues that have features of exhaustion. We have found that by genetically activating NF-kB in fibroblasts (though the deletion of the NF-kB inhibitor Tnfaip3 with the pan-fibroblast Dermo1-cre, Tnfaip3 CKO) we are able to recapitulate this age-related accumulation of Gzmk+CD8+ T cells in the lungs of young mice. We additionally generated a Gzmk reporter mouse (GATOR) that allows the identification and isolation of these cells via tdTomato expression. In the first study associated with this record, we used scRNA and TCR sequencing to compare lung resident CD3+ T cells from young Tnfaip3 CKO mice with those from young control and aged wild-type mice. As a follow-up to this initial study we utilized scRNAseq to compare the transcriptome and TCRs of lung resident Gzmk+ CD8+ T cells from aged WT mice, young Tnfaip3 CKO;GATOR mice, and young GATOR mice chronically infected with LCMV clone 13 (as a "gold standard" for T cell exhaustion).

overall_design:
Lung resident CD3+ T cells were sorted from 1) 3 month old mice in which Tnfaip3 had been deleted from fibroblasts (Young_D1cA20), 2) 3 month old controls (Young_A20) and 3) 23 month old wild-type C57BL/6 (Aged) mice. All mice were male and on a C57BL/6 background. To identify resident vs circulating immune cells mice were injected with a fluorescently-labeled anti-CD45 antibody 3 minutes prior to sacrifice. Resident CD3+ T cells were identified as ivCD45-CD45+CD11b-CD3+. For each condition cells from 3 independent mice were combined. Prior to submission for 10x library preparation cells from each condition were labeled with Biolegend Totalseq C Antibodies for multiplexing. Barcodes for samples are as follows: Young_A20 (TotalSeq-C0301 anti-mouse Hashtag 1 Antibody), Young_D1cA20 (TotalSeq-C0302 anti-mouse Hashtag 2 Antibody) and Aged (TotalSeq-C0303 anti-mouse Hashtag 3 Antibody). Samples were then submitted in one well for 5' gene expression and TCR sequencing.

For the study of lung resident Gzmk+ CD8+ T cells we performed scRNAseq on the following populations: 1) Total CD8+ T cells from 22-month (2 males, 1 female) C57BL/6 (Aged WT) mice, 2) CD8+tdTomato+ T cells from 4-month (2 males, 2 females) Dermo1-cre/+;Tnfaip3f/f;GATOR/+ (Young Tnfaip3 CKO) mice, and 3) CD8+tdTomato+ T cells from 3-month GATOR (2 males, 2 females) mice 4 weeks post-infection with LCMV clone 13 (Young LCMV). For each of the 3 conditions cells were pooled from the indicated animals. To identify resident vs circulating immune cells mice were injected with a fluorescently labeled anti-CD45 antibody 3 minutes prior to sacrifice. Resident CD8+ T cells were identified as ivCD45-CD45+CD3+CD4-CD8+. For the young Tnfaip3 CKO mice and Young LCMV mice Gzmk+(tdTomato+) cells were specifically selected from within the CD8+ population. Prior to submission for 10x library preparation cells from each condition were labeled with Biolegend Totalseq C Antibodies for multiplexing. Barcodes for samples are as follows: Young Tnfaip3 CKO (TotalSeq-C0301 anti-mouse Hashtag 1 Antibody), Aged WT (TotalSeq-C0302 anti-mouse Hashtag 2 Antibody) and Young LCMV (TotalSeq-C0303 anti-mouse Hashtag 3 Antibody). Samples were then submitted in one well for 5' gene expression and TCR sequencing.


title: BRAF inhibition increases TGFb2 production and stimulates metastasis in mice with endogenous BRAFV600E-induced hepatocellular carcinoma

city: Stockholm

first: Martin

last: Bergö

address: Hälsovägen 7C (Neo building)

department: Department of Biosciences and Nutrition

institute: Karolinska Institute

summary: Background & Aims: The MEK-ERK pathway plays a crucial role in hepatocellular carcinoma (HCC) pathogenesis, and BRAF mutations can contribute to its activation. While BRAF mutations, particularly BRAFV600E, are rare in human HCC, their effects when expressed physiologically in liver cells, especially in combination with high-incidence co-mutations in tumor suppressor genes, remain poorly understood in immunocompetent mouse models. Moreover, the impact of BRAF inhibitors on HCC progression, especially metastasis, is not well-defined. Here, we study the role of endogenous BRAFV600E expression in liver tumorigenesis and the effect of RAF inhibition on progression and metastasis.

overall_design: Methods: We developed mouse models with hepatocyte-specific BRAFV600E expression and Trp53 or Cdkn2a deletion to assess tumor development, subtypes, and metastatic patterns. BRAF inhibitor PLX4720 effects on tumor growth and metastasis were evaluated, and cell lines were established to explore underlying mechanisms.

first: Jaroslaw

last: Cisowski

first: Ahmed

middle: E

last: Zowalaty

first: Sama

middle: I

last: Sayin

first: Piotr

last: Czarnota

first: Tomasz

last: Gromowski

first: Ella

last: Eklund

first: Muhammad

last: Kashif

first: Angana

last: Patel

last: Molinaro

first: Per

last: Lindahl

first: Clotilde

last: Wiel

first: Volkan

middle: O

last: Bergo


title: Fibroblast orchestration of inflammaging via NF-kB activation (Xenium Analysis)

summary: With age mice develop bronchus-associated lymphoid tissue (BALT) and the accumulation of Gzmk+Cd8+ T cells in the lung. We generated a mouse model in which deleting Tnfaip3 (a negative regulator of NF-kB) from fibroblasts in young mice recapitulates many of these age-related changes. Using spatial transcriptomics we identified similarity in the BALT structure formed in normal aging and that which develops in response to fibroblast deletion of Tnfaip3.

overall_design: We used the Xenium spatial transcriptomics platform to investigate the spatial relationship between immune and stromal cells in lung BALT tissue from 1) a 3 month old female mouse in which Tnfaip3 was deleted from fibroblasts (Dermo1-cre/+;Tnfaip3f/f) and 2) a 24 month old female p16-reporter mouse (INKBRITE)


title: Methionine Restriction Alleviates Kidney Fibrosis through Epigenetic Repression of the TGF-β/Smad3/Hoxc8/P-TEFb Axis

city: Tianjin

first: Zhiheng

last: Liu

state: Tianjin

address: No.22 Qixiangtai Road

department: Tianjin Research Center for Basic Medical Science

institute: Tianjin Medical University

summary: Renal fibrosis is a hallmark of chronic kidney diseases (CKDs) and a key driver of disease progression. While low-protein diets have been shown to alleviate fibrosis and slow CKD progression, the specific amino acids responsible for these effects remain unclear, and such diets often lead to malnutrition due to the restriction of essential amino acids. In this study, we evaluated 15 amino acid-restricted diets in a unilateral ureteral obstruction (UUO) mouse model and found that methionine restriction (MetR) most effectively reduced renal fibrosis. We further confirmed the efficacy of MetR in alleviating renal fibrosis in the folic acid nephropathy (FAN) mouse model. Mechanistically, we identified Hoxc8 as a key transcription factor responsive to MetR, mediating TGF-β-induced fibrotic gene expression. Our findings suggest that TGF-β-Smad3 signaling activates Hoxc8 during myofibroblast activation, initiating a self-reinforcing feedback loop through Hoxc8 self-activation. Using affinity purification-mass spectrometry, we discovered that Hoxc8 interacts with P-TEFb transcription elongation complex to enhance the expression of fibrotic genes. MetR suppresses Hoxc8 expression by reducing histone modifications, specifically H3K4me3 and H3K36me3, thereby inhibiting the TGF-β/Smad3/Hoxc8/P-TEFb axis and downregulating fibrosis-related gene expression. Notably, elevated HOXC8 expression was observed in CKD patients with kidney fibrosis, while fibroblast-specific Hoxc8 knockout mice demonstrated significantly reduced fibrosis following UUO surgery. These findings establish the TGF-β/Smad3/Hoxc8/P-TEFb axis as a crucial regulator of fibrosis and highlight MetR as a promising therapeutic strategy for the treatment of renal fibrosis.

overall_design: NRK-49F cellls were treated with TGF-β  and/or methionine restriction, siHoxc8.

first: Yunjing

first: Lirong

last: Zhang


title: Global alternative RNA splicing  analysis of Epstein-Barr Virus EBNA1-regulated cells

city: Changsha

first: Jian

last: Ma

state: Hunan

address: 110 Xiangya Road

department: Cancer Research Institute

institute: Central South University

summary: Purpose: To identify the effect of EBV EBNA1 on cellular mRNA alternative splicings Methods: HEK293 cells were transfected with either Flag-EBNA1 vector or empty vector (NC)  for 48 hours. Then the cell RNA was sequenced by a PromethION platform (P48-seq, the third generation sequencing). Results: Log-fold changes of up- or down-regulated mRNAs between the control and experiment group were selected with a significance threshold of p<0.05. Conclusions: Our study describes the mRNA alternative splicing changes  induced by EBV-EBNA1 in HEK293 cells

overall_design: HEK293 cells were transfected with either Flag-EBNA1 vector or empty vector (NC)  for 48 hours, and cellular RNA was used to sequence by Nanopore PromethION 48 (the third generation sequencing) to show the mRNA splicing profile changes induced by EBV-EBNA1 transfection.

first: Xiaoyue


title: Liver molecular networks associated with drinking behavior in nonhuman primates

city: Winston-Salem

first: Jeannie

last: Chan

state: NC

address: Medical Center Boulevard

department: Internal Medicine

institute: Wake Forest School of Medicine

summary: To test the hypothesis that molecular changes in the induction phase when rhesus macaques consume the same escalating doses of alcohol in a 3-month period are predictive of drinking behavior as light drinkers (LD) or very heavy drinkers (VHD) when they have free access to alcohol. The sirtuin signaling pathway and a molecular network regulated by the estrogen receptor were enriched with differentially expressed genes and proteins in liver biopsy samples of VHD vs. LD  when animals were alcohol naïve. After consuming the same amount of alcohol for 3 months by LD and VHD, the sirtuin signaling pathway and MYC regulatory network were most significantly enriched with differentially expressed genes and proteins in both groups in response to alcohol. However, majority of the differentially abundant genes and proteins in this pathway and network differed between LD and VHD. Moreover, the epigenetic mechanisms regulating the response to alcohol are primarily through microRNAs in LD and primarily through DNA methylation in VHD.

overall_design: Rhesus monkeys (~4.6 years old, males) were used for the study. Before and after the induction phase, liver biopsies were performed. During the induction phase, monkeys consumed the same amount of alcohol. After the induction phase, monkeys had free access to alcohol for 12 months, and they were classifiied as LD or VHD based on daily alcohol consumption. Liver samples from three LD that consumed 1.5 g ethanol/kg/day and three VHD that consumed 4.0 g ethanol/kg/day at the end of the free access period were used for mRNA and microRNA (miRNA) sequencing. Gene and protein expression in VHD livers was compared to that in LD livers before the induction phase. Also, gene and protein expression after induction was compared to that before induction to determine the molecular response to alcohol in LD and VHD livers. Differential DNA methylation sites associated with differentially expressed genes were also analyzed.

first: Laura

last: Cox

first: James

last: Daunais

first: Timothy

last: Howard

first: Ge

last: Li

first: Sobha

last: Puppala

first: Betsy

last: Ferguson

first: Kathleen

last: Grant

first: Michael

last: Olivier


title: Targeting of the CD161 Inhibitory Receptor Enhances Bone Marrow-Resident Memory CD8+ T Cell-mediated Immunity Against Multiple Myeloma [CART RNA-seq]

first: Liwen

last: Wang

address: 138 Tongzipo road

department: Department of Hematology

institute: Third Xiangya Hospital, Central South University

summary: Immune checkpoint inhibitors (ICIs) have transformed the treatment of many solid tumors. Still, their effectiveness in multiple myeloma (MM) remains underwhelming, highlighting the need to explore alternative approaches beyond conventional ICIs. Here, we identify CD161 as a novel inhibitory receptor on bone marrow resident memory CD8+ T cells (BM CD8+ TRMs), known for their sustained presence and vital role in local immune surveillance in MM BM tumor microenvironment. The CD161-CLEC2D axis, where CD161 interacts with CLEC2D on MM cells, mediates immune suppression and TRMs dysfunction. Blocking CD161 enhances TRMs function, including tissue residency, proliferation, and antitumor activity. Combining CD161 blockade with CAR-T therapy significantly alleviates CAR-T exhaustion, improving its therapeutic efficacy. Additionally, a similar CD161-driven exhaustion program is observed in other hematologic malignancies. These findings suggest that targeting the CD161-CLEC2D axis could offer a promising strategy to enhance MM treatment outcomes and CAR-T efficacy.

overall_design: CAR-T cells were cultured in 96-well plates in the presence of 5 µg/ml anti-CD161 mAb or mouse IgGκ isotype control antibody. Stimulation was achieved using 2.5 µg/ml anti-CD3 and anti-CD28 mAbs. After 24 hours, cells were collected, and total RNA was extracted using the RNA rapid extraction kit  for RNA sequencing.

first: Linzhi

last: Xie

first: Xin


title: Fibroblast orchestration of inflammaging via NF-kB activation (Lung Resident CD45+ cell and fibroblast analysis)

first: Nancy

last: Allen

state: CA

summary: In this study we used scRNA-sequencing to compare lung resident CD45+ cells and bulk RNA-sequencing to compare lung PDGFRa+ fibroblasts from 2-month-old mice in which the NF-kB inhibitor Tnfaip3 has been deleted from fibroblasts (D1cA20) with control mice (A20control). We identified enrichment of Gzmk+CD8+ T cells in the D1cA20 relative to control mice. As a follow-up to this initial study we used bulk RNA sequencing to compare the transcriptomes of lung adventitial fibroblasts from 4-month C57BL/6 (Young B6), 21-month C57BL/6 (Aged B6), 4-month Tnfaip3 f/f (Tnfaip3 Control) and 4-month Dermo1-cre;Tnfaip3f/f (Tnfaip3 CKO/D1cA20) mice. We identified that aged B6 adventitial fibroblasts share transcriptional similarity with those from young Tnfaip3 CKO mice. Pathway analysis revealed NF-kB to be significantly upregulated in both Aged B6 and Tnfaip3 CKO relative to Young B6 or Tnfaip3 control.

overall_design: Cells were sorted from 1) 2-month-old mice in which Tnfaip3 had been deleted from fibroblasts (D1cA20) and 2) 2-month-old controls (A20control). All mice were female and on a C57BL/6 background. To identify resident vs circulating immune cells mice were injected with a fluorescently-labeled anti-CD45 antibody 3 minutes prior to sacrifice. Resident CD45+ T cells were identified as ivCD45-CD45+. For each sample cells from 3 independent mice were combined. Fibroblasts for bulk RNA sequencing were sorted from the same samples and identified as CD45-Epcam-CD31-PDGFRa+. For bulk sequencing each mouse was submitted as a separate sample. For the subsequent lung adventitial fibroblast analysis, adventitial fibroblasts were isolated and sorted from Young B6, Aged B6, Tnfaip3 Control, and Tnfaip3 CKO mice and submitted for bulk RNA-sequencing. All mice were female and on a C57BL/6 background. 4 biological replicates were submitted per group. Adventitial fibroblasts were sorted as Lin- (CD45-Epcam-PECAM-Mcam-)Sca1+.

first: Tien

last: Peng