title: Transcriptomic Responses to chronic psychological stress: Insights from Mouse Liver, Brain, and Testis

first: Xiaoguo

last: Zheng

address: 145 Guangyuan Road

institute: Shanghai Jiaotong University

summary: Chronic psychological stress become synonymous with modern life. It can disrupt homeostasis and lead to numerous health risks. However, the molecular basis is still in its infancy. Here, we employed a chronic restraint stress (CRS) mouse model to investigate the effects of psychological stress on metabolism, behavior, and fertility. Subsequently, we conducted a transcriptome analysis on the liver, brain, and testes, aiming to understand the molecular basis of CRS-induced physiological and behavioral alterations. The results showed that two consecutive weeks of CRS treatment led to delayed growth in mice, abnormalities in blood glucose metabolism, anxiety-like behaviors, and a decline in semen quality. Transcriptome analysis of 18 samples obtained from liver, brain and testis of both control and CRS-treated micerevealed significant changes in gene expression in the liver, brain, and testes. Gene function enrichment analysis, protein and protein interaction analysis, and gene set enrichment analysis highlighted that differentially expressed genes (DEGs) in the liver were primarily involved in the synthesis, metabolism, and transport of fatty acids and ribose, closely associated with glucose metabolism, insulin resistance, the synthesis and secretion of growth hormones, and extensively linked to adaptive immune responses. In the brain, DEGs were not only related to hormone secretion and cognitive function alterations but also played a part in regulating insulin secretion and the development of the reproductive system, closely linked to abnormalities in blood sugar metabolism and semen parameters. In the testes, DEGs mainly concerned immune responses, DNA damage, and hormone regulation, closely associated with abnormalities in semen parameters. These observations suggested that the multitude of health risks stemming from psychological stress-induced homeostatic imbalance could be mediated through the impact on gene expression profiles across various tissues. Despite the challenges in investigating the effects of psychological stress on human tissues and organs, with a reliance on animal models for insights, the role of psychological stress as a contributing factor to male metabolism issues, emotional disturbances, and infertility issues is undeniable. Highlighting its health implications among humans is essential. The study emphasizes the need for further research to explore the broader implications of stress on human health and the potential for intergenerational effects of stress-induced disorders.

overall_design: To investigate the effects of chronic restraint stress (CRS) on the transcriptome of mouse liver, brain, and testis, aiming to understand the molecular basis of stress-induced physiological and behavioral alterations, we collected tissue samples from the liver, brain, and testis of mice in both control and CRS-treated groups, setting up three biological replicates for each type of tissue sample, totaling 18 samples, which were subsequently subjected to RNA-seq.

first: Jianbo

first: Fang

last: Yu

first: Jianhua

last: Shi

first: Zhenhua

last: Li

first: Hui


title: Effect of enhanced early life nutrition on the anterior pituitary transcriptome of bull calf

status: Public on Jul 09 2025

city: Co. Meath

first: Kate

last: Keogh

address: Dunsany

department: Animal and Bioscience Department

country: Ireland

institute: Teagasc Grange

type: Expression profiling by high throughput sequencing

summary: This study evaluated the effect of enhanced dietary intake during the early life period on the anterior pituitary transcriptome in bull calves. Between 2-12 weeks of age bull calves were offered either a high (HI; n=15) or moderate (MOD; n=15) plane of nutrition, with diets designed to evoke growth rates of 1.0 and 0.5 kg/day, respectively. At 12 wk of age,  anterior pituitary tissue samples were harvested from all calves and subsequently subjected to mRNAseq.

overall_design: 30 anterior pituitary RNA samples were analysed for this study, comprising. 15 samples were derived from bull calves fed the High plane of nutrition (HI, n=15) and 15 samples  derived from the calves fed the Moderate plane of nutrition (MOD, n=15). Calves on the High-plane of nutrition received 1.5 kg of milk replacer (10 liters) per day and ad libitum concentrates. The MOD plane of nutrition group received 0.5 kg of milk replacer (4 litres) per day and 0.5 kg of concentrates. All tissue samples were collected at the same time-point (12 weeks of age).

first: Stephen

last: Coen

first: Pat

last: Lonergan

first: Sean

last: Fair

first: David

last: Kenny


title: ATAC-seq of PBMC from dog bearing mammary gland tumor

city: Seoul

first: Jeong-Woon

last: Lee

address: Gwanak-ro 1

country: South Korea

institute: Seoul National University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Circulating immune cells that have interacted with tumor tissue exhibit distinct characteristics compared to those in healthy individuals, potentially offering critical insights into tumor presence and malignancy. However, the epigenetic mechanisms governing these blood immune cells in cancer patients remain poorly understood. In this study, we investigated chromatin accessibility and transcription factor binding in peripheral blood mononuclear cells (PBMCs) from dogs with mammary gland tumors using ATAC-seq. Our analysis revealed altered chromatin accessibility near genes associated with immune function, neuronal activity, and lipid metabolism in affected dogs. Notably, we identified CEBPD-bound peaks that were upregulated in cancer-affected PBMCs and demonstrated that the transcription of their associated genes, CD47 and MAP4K4, was also upregulated in monocytes under cancer co-culture conditions—an effect that was mitigated following CRISPR interference of these regions. These findings underscore the critical role of chromatin accessibility and transcriptional regulation in the immune response to cancer

overall_design: 42 ATAC-seq generated from 6 normal dogs, 6 dogs with benign mammary gland tumor, and 9 dogs with maliganant mammary gland tumor

first: Dabin

first: Kyung-Ju

last: Shin

first: Keun Hong

last: Son

first: Je-Yoel

last: Cho


title: CUT&RUN of the kidneys from diabetic mice with MAT2A inhibitor II

city: Chicago

first: Yalu

last: Zhou

state: IL

address: 303 E Superior St

department: Department of Medicine

country: USA

institute: Northwestern University

summary: H3K27me3 was enhanced in the gene loci related to the inflammatory pathway.

overall_design: MAT2Ai (10 mg/kg BW) was injected into intraperitoneal cavity of SGLT2 MT mice with prior exposure to HFD for eight weeks.

first: Hiroshi

last: Maekawa

first: Yuki

last: Aoi


title: Chromatin Accessibility Dynamics in the Reprogramming of Somatic Cells to Pluripotency

city: Madison

first: Rupa

last: Sridharan

state: WI

address: 330 N. Orchard Street

department: Wisconsin Institute for Discovery

institute: University of Wisconsin

summary: Pluripotent stem cells have the incredible ability to self-renew indefinitely and to differentiate into all the cell types of the body. Remarkably, somatic cells can transition back into a pluripotent state through ectopic expression of the transcription factors OCT4, SOX2, KLF4, and MYC. This shift towards a state of higher differentiation potential represents an extraordinary capability to alter cell fate. However, reprogramming studies are challenging due to the inefficient and heterogeneous nature of the process. Single-cell analysis of chromatin accessibility changes uncovered enhanced enrichment for 3D chromatin reorganization factor (KLF4, MAZ, and PATZ1) binding in high-efficient reprogramming. Cells experience more changes upon withdrawal of the ectopic reprogramming factors, including a Tcfap2c-mediated maintenance of the pluripotent state. Development of a new computational algorithm, scCISINT, allowed for prediction of long-range interactions among differentially accessible regions across reprogramming clusters. We used CRISPRi repression at candidate interacting loci to validate the essential role of the putative long-range interactions in transforming cell fate. Altogether, our work has uncovered key gene expression and chromatin-associated features that guide cells along a path towards successful pluripotency acquisition.

overall_design: Single-cell ATAC-sequencing of mouse embryonic fibroblasts (MEFs), MEFs undergoing reprogramming, mouse embryonic stem cells, and mouse induced pluripotent stem cells

first: Stefan

middle: J

last: Pietrzak


title: Batf3-dependent type 1 dendritic cells drive the accumulation of lung resident memory CD4+ T cells

city: Research Triangle Park

first: Donald

middle: Nelson

last: Cook

state: NC

address: 111 T.W. Alexander Drive

department: IIDL

institute: NIEHS

summary: Tissue resident memory cells have recently emerged as a critically important cell type for both protective and pathogenic immune responses. In particular, these cells are required for allergen-induced airway hyperresponsiveness in animal models of allergic asthma. However, relatively little is known of the cellular and molecular mechanisms underlying the accumulation of these cells in the lung. Here, using gene targeted mice and MHC class II tetramers specific to clinically relevant house dust mite allergen, we show that allergen-specific resident memory CD4+ T cells are virtually absent in mice lacking Batf3, a transcription factor required for the development of type 1 lung dendritic cells. As a result, these animals display markedly reduced airway inflammation and very weak airway hyperresponsiveness in a house dust mite model of allergic asthma. Single cell RNA sequencing revealed that Batf3-deficient mice lack a subset of lung resident CD4+ T cells characterized by expression of the chemokine receptor-encoding gene, Cxcr6. Together, these data suggest that blocking the development or function of allergen-specific resident memory CD4+ T cells might be an effective approach to treat patients with allergic asthma.

overall_design: Wild type and Batf3-deficient mice were sensitized twice with house dust mite allergens, then rested for 5 weeks. Immediately prior to harvest, the animals received intravenous injections of anti-CD45 antibodies to label circulating leukocytes. Following euthanasia, lungs were excised and digested, and CD45 positive and CD45 negative T cells from both mouse strains separately purified by flow cytometry. The cells were subjected to single cell RNA sequencing and the data analyzed.

first: Antonio

middle: M

last: Patterson

first: Hideki

last: Nakano

first: Christina

middle: L

last: Wilkinson

first: Gregory

middle: S

last: Whitehead

first: Abdull

last: Massri

middle: N


title: Diabetic mice with MAT2A inhibitor

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

overall_design: Refer to individual Series


title: Effect of early-life plane of nutrition on the transcriptional profile  of skeletal muscle tissue of Angus heifer calves

first: Kate

last: Keogh

summary: The study examined changes in the transcriptional profile of skeletal muscle tissue in heifer calves offered varying planes of nutrition during the early life period. From approximately 3 weeks of age Angus X Holstein-Friesian heifer calves  were offered either a high or moderate plane of nutrition to achieve  target growth rates of 1.2 kg/d and 0.5 kg/d, respectively. After 18 weeks of differential feeding all calves were euthanized and skeletal muscle tissue samples collexted from each calf. RNA was extracted and subsequently subjected to RNAseq analysis. 482 genes were significantly differentially expressed between calves on the High plane of nutrition and those on the Moderate plane of nutrition. Biological pathway analysis revealed an enrichement from these genes for processes and pathways related to energy production and cellular growth and proliferation.

overall_design: 20 skeletla muscle RNA samples were analysed in this study. 10 samples from each High and Moderate plane of nutrition groups. Calves on the High-plane of nutrition received 1.5 kg of milk replacer (10 liters) per day and ad libitum concentrates during the calf phase. During the subsequent post-weaning phase this group were then offered concentrates ad libitum and hay to appetite. During the calf phase, the Moderate plane of nutrition group received 0.5 kg of milk replacer (4 litres) per day and 1 kg of concentrates, subsequently receiving 1kg of concentrates and hay to appetite during the post-weaning phase. The calf phase lasted for 8 weeks and was followed by the post-weaning phase which lasted for 11 weeks. All samples were collected at the same time-point (21 weeks of age) all differentially expressed genes reported were up- or down-regulated in HP calves compared to MP calves.

first: Alan

middle: K

last: Kelly

first: David

middle: A


title: Bulk RNAseq of the kidneys from diabetic mice with MAT2A inhibitor

summary: These analysis detected the Loci of genes regulated in a SAM-dependent manner.

overall_design: SGTL2 WT and MT mice were fed with HFD for 8 weeks, then they were treated with placebo (DMSO) or (E)-4-(2-Chloro-6-fluorostyryl)-N-methylaniline (MAT2Ai, 10 mg/kg BW) through the intraperitoneal route three times per week for 8 weeks.


title: Gene expression profile at single cell level of kidney from Sglt2 WT and mutant mice fed with normal diet and high-fat diet.

summary: Analysis of scRNA seq data showed emergence of a new cluster of proximal tubular cells with a distinct molecular fingerprint, predominantly found in WT-HFD mice.

overall_design: SGLT2 MT and WT mice (10 weeks old) were fed with fed with high fat diet (60% Cal) or normal diet for 8 weeks.

first: Margaret

middle: E

last: Fain

first: Susan

last: Quaggin


title: Next generation trophoblast organoids with apical-out trophoblast polarity and central villous core-like cavity

city: Beijing

first: Shufan

last: Fan

address: A3 Datun Road

country: China

institute: Institute of Zoology

summary: Human trophoblast organoid serves as a revolutionary tool for studying trophoblast cell development and maternal-fetal interactions. However, currently reported trophoblast organoids exhibited opposite trophoblast polarity to in vivo or a solid cell spheroid lacking of central villous core-like cavity, both of which fail to model the physiological structure of in vivo placenta villi. Here, using human naïve embryonic stem cells, we constructed a trophoblast organoid with both peripheral apical-out bilaminar trophoblast cells and central villous core-like cavity, named ppTO. Besides, ppTO simulated the typical molecular and secretory features of in vivo trophoblast. Single-cell RNA sequencing (scRNA-seq) analysis demonstrated that the development of ppTO simulated in vivo trophoblast syncytialization process and pan-trophoblast transcriptome features. Using ppTO, we revealed that the syncytialization process relied on a suppressed HIPPO signaling for initiating syncytialization and followed by a reactivated HIPPO signaling for STB maturation. By comparative study with reported organoids, we revealed the important role of the expression and orientation of polarity molecule aPKC in the formation and spatial patterning of STB within trophoblast organoids. In summary, we develop a trophoblast organoid simulating the physiological structure and molecular features of placental villous trophoblast for studying the mechanisms underlying trophoblast development and function.

overall_design: The single cells from a new trophoblast organoid (ppTO) modeling the real structure of placenta villi with peripheral apical-out trophoblast cells and a central villous core-like cavity for scRNA-seq

first: Hongmei

last: Wang

first: Hao

last: Wu

first: Yan

last: Zhao


title: A novel immunosenescent CD8+ T cell subset in patients with Ankylosing Spondylitis and Psoriatic Arthritis links spontaneous motility to telomere shortening and dysfunction

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

summary: Objectives: A pathogenetic role of CD8+ T lymphocytes in ankylosing spondylitis (AS) and other spondyloarthritis (SpA) is sustained by genome-wide association studies (GWAS) as well as the expansion of public T cell clonotypes in the target tissues. This study focuses on CD8+ T cells from AS and psoriatic arthritis (PsA) patients with the aim to correlate their phenotype and function with motility. Methods: Peripheral blood CD8+ and CD4+ T cells were isolated from AS (n= 128), PsA (n= 60) and rheumatoid arthritis (RA, n= 74) patients and healthy donors (HD, n= 79). Transwell migration assay was performed in the presence of different chemokines. CD8+ T cell immunoprofiling and effector functions were assessed by multiparametric flow cytometry. Transcriptome signature was evaluated by RNA-seq analysis while telomere length and dysfunction were measured by RT-PCR and IF-fluorescence in situ hybridization (FISH), respectively. Results: A significantly higher number of CD8+ T cells migrating in the absence of chemokine stimuli was found in patients with SpA compared to HD and RA patients. This subset, producing cytotoxic (granzyme B, perforin, granulysin) and inflammatory molecules (TNFα), was significantly enriched in terminally differentiated (CCR7-CD45RA+) and senescent (CD28-CD57+) cells with a gene expression profile characterized by cytolytic signature and natural killer (NK) markers. Of note, these spontaneously migrating CD8+ T cells showed activation of DNA damage response (DDR), telomere shortening and dysfunction.  Conclusions: Our data describe a terminally differentiated CD8+ T cell subset with a senescent and cytotoxic/proinflammatory profile and an intrinsic invasive potential enriched in SpA patients that represents a possible player in disease pathogenesis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for migrated and not migrated CD8+ T lymphocytes isolated from

first: Giorgia

last: Paldino

first: Valentina

last: Tedeschi

first: Maria

middle: T

last: Fiorillo


title: Proneural-Mesenchymal hybrid glioblastoma cells are resistant to therapy and dependent on nuclear import_scRNAseq

city: Orsay

first: Giorgio

last: Seano

address: Bâtiment 110, Rue Henri Becquerel

department: INSERM U1021 - CNRS UMR3347

country: France

institute: Institut Curie

summary:
Background: Despite extensive research efforts, glioblastoma (GBM) remains a deadly disease with poor prognosis. Although previous studies have identified various cell states within GBM tumors, the molecular mechanism underlying adaptive GBM cell plasticity induced by conventional therapy remains unclear.

Methods: We used fluorescent reporters for proneural (PN) and mesenchymal (MES) subtypes to monitor GBM cell plasticity in real-time across multiple patient-derived cell lines. This approach revealed cells that concurrently expressed both proneural and mesenchymal markers. To investigate this unique hybrid population, we implemented a comprehensive methodological approach encompassing bulk and single-cell RNA sequencing, single-cell ChIP sequencing, nuclear proteomics, high-resolution imaging, orthotopic mouse models, clinical dataset analysis, and pharmacological and genetic techniques. This multifaceted strategy allowed us to gain functional and molecular insights into this distinct cellular population.

Results: We showed that these hybrid cells are increased by conventional therapies, and are resistant to these therapies. At the molecular level, hybrid cells display significant alterations in chromatin structure and nuclear protein composition, elevated transcriptional activity, Myc activation, and improved transport between the nucleus and cytoplasm. Genetic and pharmaceutical inhibition of the nuclear import/export shuttling machinery, increased in hybrid cells, effectively suppressed adaptive GBM cell plasticity and hybrid identity, thereby enhancing the sensitivity of GBM cells to therapies.

Conclusion: Our results indicate that GBM hybrid cells play a crucial role in chemoradiation resistance. The nuclear transport machinery presents a potential therapeutic target for hybrid cells, offering a way to counteract the typical resistance to treatment observed in GBM.

overall_design: Gene expression profiling by bulk RNA sequencing of MGG4 and MGG8 sorted Hybrid cells vs bulk and hybrid-low cells. Profiling of MGG4, MGG8 and P3 cells after therapies in-vitro and MGG4 in-vivo. Single-cell RNA sequencing of MGG4 and MGG8. Single-cell chromatin immunoprecipitation of histone marks in MGG8.

first: Guillaume

last: Bourmeau


title: RNA-Seq shows the effect of SLC38A2 inhibitor MeAIB on HUVEC cells

city: Dalian

first: Chunxiu

last: Du

address: Lushunkou District

institute: Dalian medical university

summary: MeAIB treated HUVEC for 12 hours, MeAIB significantly increased PI3K-Akt pathway in HUVEC

overall_design: When the HUVEC cell confluence reached 90%, the cells were treated with MeAIB for 12 h, and the experimental group was treated with ddH2O. The differences in cell pathways between the two groups were detected by RNA-Seq technology.

first: Xiaoyan

last: Zhang

first: Youfei

last: Guan


title: Cathepsin L-Dependent Positive Selection Shapes Clonal Composition and Functional Fitness of CD4 T Cells [RNA]

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

country: Germany

institute: LMU Munich

summary: The physiological significance of thymic positive selection and its reliance on a single stromal cell type, cortical thymic epithelial cells (cTECs), remain poorly understood. Cathepsin L (Ctsl) has been implicated in generating MHCII-bound peptides in cTECs for efficient CD4 T cell differentiation. Here, we addressed whether Ctsl-deficiency impacts the CD4 compartment not only numerically, but also qualitatively. When Ctsl is absent, many TCRs disappear from the repertoire due to a genuine defect in positive selection, while some allegedly ‘Ctsl-independent’ TCRs are retained. We demonstrate that these clones experience weaker positively selecting signals in absence of Ctsl, which suffice for further maturation, yet imprint aberrant responsiveness to agonist stimulation and impaired homeostatic behavior. Hence, the Ctsl-generated peptidome in cTECs engenders TCR-pMHCII interactions at the upper end of the permissible affinity spectrum to optimize both CD4 T cell diversity and functionality.

overall_design: RNA sequencing of Lm54 TCRtg mature CD4SP thymocytes selected in Ctsl-deficient (CtslΔTEC) and -sufficient (control) mice. Each sample comes from an individual mouse.

first: Elisabetta

last: Petrozziello

first: Amina

last: Sayed

first: João

last: Freitas

first: Christine

last: Federle

first: Jelena

last: Nedjic

first: Sarina

last: Ravens

first: Anna

last: Schulz

first: Dietmar

last: Zehn

first: Marc

last: Schidt-Supprian

first: Immo

last: Prinz

first: Martijn

last: Verdoes

first: Jan

last: Kisielow

first: Thomas

last: Reinheckel

first: Stephen

middle: R

last: Daley

first: Ludger

last: Klein


title: Pharmacological inhibition of BMI1 exerts antitumor effect on MYCN-amplified neuroblastoma with activation of the p53 pathway

city: Nagoya

first: Hiromasa

last: Aoki

address: 3-1 Tanabe-dori, Mizuho-ku

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Nagoya City University

summary: BMI1, a constituent of the Polycomb Repressive Complex 1 (PRC1), has been identified as overexpressed in a variety of cancers, including neuroblastoma, highlighting its potential as a viable target for cancer therapeutics. Given its pivotal role, a number of BMI1 inhibitors have been synthesized and assessed for their therapeutic efficacy across a spectrum of cancers in recent years. This investigation demonstrates that the BMI1 inhibitors PTC-028 and PTC-209 exhibit selective antitumor activities against MYCN-amplified neuroblastoma. Notably, PTC-028, which exhibits toxicity at lower concentrations, triggers apoptosis in neuroblastoma cells, promotes G1 phase accumulation, and reduces S phase cell populations, thereby inducing cell cycle arrest. A thorough examination utilizing RNA sequencing has unveiled that treatment with PTC-028 activates the p53 signaling pathway, suggesting its critical involvement in the mechanism of cell death induction. Moreover, PTC-028 treatment leads to a decrease in the protein levels of anti-apoptotic factors, including BCL2 and MCL1. Significantly, PTC-028 has also demonstrated antitumor efficacy in a mouse xenograft model of human neuroblastoma cells. Consequently, BMI1 inhibitors, especially PTC-028, emerge as promising therapeutic agents for the management of aggressive MYCN-amplified neuroblastomas.

overall_design: RNA-seq was performed to comprehensively analyze gene expression changes upon treatment of IMR-32 cells with PTC-028 (25 nM) for 24 hours.

first: M

last: Hirayama

first: E

last: Yamada

first: H

first: K

last: Izumi

first: A

last: Amano

last: Toriuchi

last: Ogami

last: Nagasaka

first: Y

last: Inoue

last: Hayashi

first: S

last: Takeshita

last: Kakita

last: Aoyama


title: Proneural-Mesenchymal hybrid glioblastoma cells are resistant to therapy and dependent on nuclear import_scChIPseq

first: Giorgio

last: Seano

first: Guillaume

last: Bourmeau


title: Proneural-Mesenchymal hybrid glioblastoma cells are resistant to therapy and dependent on nuclear import-bulk RNAseq

summary:
Abstract
Background

Despite extensive research efforts, glioblastoma (GBM) remains a deadly disease with poor prognosis. Although previous studies have identified various cell states within GBM tumors, the molecular mechanism underlying adaptive GBM cell plasticity induced by conventional therapy remains unclear.
Methods

We used fluorescent reporters for proneural (PN) and mesenchymal (MES) subtypes to monitor GBM cell plasticity in real-time across multiple patient-derived cell lines. This approach revealed cells that concurrently expressed both proneural and mesenchymal markers. To investigate this unique hybrid population, we implemented a comprehensive methodological approach encompassing bulk and single-cell RNA sequencing, single-cell ChIP sequencing, nuclear proteomics, high-resolution imaging, orthotopic mouse models, clinical dataset analysis, and pharmacological and genetic techniques. This multifaceted strategy allowed us to gain functional and molecular insights into this distinct cellular population.
Results

We showed that these hybrid cells are increased by conventional therapies, and are resistant to these therapies. At the molecular level, hybrid cells display significant alterations in chromatin structure and nuclear protein composition, elevated transcriptional activity, Myc activation, and improved transport between the nucleus and cytoplasm. Genetic and pharmaceutical inhibition of the nuclear import/export shuttling machinery, increased in hybrid cells, effectively suppressed adaptive GBM cell plasticity and hybrid identity, thereby enhancing the sensitivity of GBM cells to therapies.
Conclusion

Our results indicate that GBM hybrid cells play a crucial role in chemoradiation resistance. The nuclear transport machinery presents a potential therapeutic target for hybrid cells, offering a way to counteract the typical resistance to treatment observed in GBM.


title: Gremlin1 repression-mediated mitochondrial hyperfunction contributes to TCE-induced zebrafish cardiac defects

first: Zhijie

last: Bai

state: 北京Beijing

address: Taiping Road, Haidian District

institute: beijing institute of radiation

summary: Trichloroethylene (TCE) is a ubiquitous pollutant with potential capacity to induce congenital heart disease (CHD). However, the mechanisms underlying TCE-induced CHD is largely unraveled. Herein, we found that early-stage exposure to TCE induced significant cardiac defects characterized by elongated SV-BV distance, thinned myocardium and attenuated contractility. Gremlin1 encoding gene, grem1a, was screened out as a putative target of TCE and was expressed in heart since its appearance. Further, grem1a knockdown in zebrafish induced phenotypes generally similar to that of TCE-treated group, accompanying with the disarrangement of myofibril structure. Single-cell RNA sequencing depicted that mitochondria respiration in grem1a-repressed cardiomyocytes were greatly enhanced, ultimately leading to an abnormal branch from normal developmental trajectory. Accordingly, the results from AC16 and human pluripotent stem cell-derived cardiomyocytes showed that GREM1 repression increased mitochondrial content, ATP production, mitochondrial reactive oxygen species and mitochondrial membrane potential, which probably disrupted the process of myofibril expansion. Altogether, these results suggested that TCE-induced gremlin1 repression could prematurely stimulate mitochondrial hyperfunction, thereby hamper cardiomyocyte development and cause cardiac defects in zebrafish embryos. This study provided a novel insight of gremlin1 in the associations between TCE exposure burden and CHD risk and a better understanding of the etiology of environmental stressor-caused CHD.

overall_design: Cells from zebrafish whole body at 12 hpf were subjected to bulk RNA-seq for detection of responding genes to TCE treatment. After screening out grem1a as candidate target genes of TCE, we collected cells from zebrafish rostral half at 48 hpf for singl-cell RNA-seq in order to illustrate the function of grem1a in cardiomyocyte dysplasia induced by TCE.


title: Proneural-Mesenchymal hybrid glioblastoma cells are resistant to therapy and dependent on nuclear import


title: Transcriptional and immunohistochemical signatures of transition dairy cows’ adipose tissue during subclinical ketosis

city: Lexington

first: Shavahn

middle: C

last: Loux

state: KY

address: 1400 Nicholasville

department: Veterinary Science

institute: University of Kentucky

summary: The objective of this experiment was to determine transcriptional differences in the visceral (VAT) and subcutaneous adipose tissue (SAT) of dairy cows with or without subclinical ketosis.

overall_design: The experiment was conducted from February to March 2022 at a commercial dairy farm located near Friona, TX. Ten multiparous Holstein dairy cows [Days in milk (DIM) 7.6 ± 1.9, parity 3.2 ± 1.4, body condition score (BCS) 3.6 ± 0.3] were enrolled in a nonrandomized trial. Fresh Holstein dairy cows with 5 to 10 DIM were evaluated for BCS and blood BHB. BCS (scale 1 = thin to 5 = obese) was assigned by two experienced individuals, while blood BHB was determined with the Precision Xtra Blood Glucose & Ketone Monitoring System (Abbott Laboratories, Chicago, IL, USA). Cows were then blocked according to parity, BCS, and blood BHB, and assigned into two groups: subclinical ketosis (SCK, n=5, BHB > 1.0 mmol/L) and non-ketotic (NK, n=5, BHB ≤ 1.0 mmol/L). Abdominal SAT and omental VAT samples were obtained through laparotomy (right paralumbar fossa). AT samples were sequenced on an Illumina Novaseq 6000 platform, and 150 bp paired-end reads were generated. Blood was sampled from the coccygeal vein before morning feeding and analyzed for biomarkers related to energy metabolism [i.e., glucose, β-hydroxybutyric acid (BHB), non-esterified fatty acids (NEFA)], muscle mass catabolism [i.e., blood urea nitrogen (BUN)], and liver function (i.e., albumin and cholesterol) by a commercial laboratory.

first: Tainara

last: Michelotti

first: Bruno

last: Menarim

first: Alexandra

middle: P

last: Tegeler

first: Jean

middle: F

last: Fiallo

first: Vinicius

last: Machado

first: Yava

last: Jones-Hall

first: Oscar

last: Benitez

first: Clarissa

last: Strieder-Barboza


title: INTESTINAL EPITHELIAL-DERIVED IL-34 REGULATES MACROPHAGE POLARIZATION AND GASTROINTESTINAL TRACT GRAFT VERSUS HOST DISEASE

city: Milwaukee

first: Anthony

middle: Elston

last: Zamora

state: Wisconsin

address: 8701 Watertown Plank Road

department: Medicine

institute: Medical College of Wisconsin

summary: Gastrointestinal (GI) tract graft versus host disease (GVHD) is a major complication after allogeneic hematopoietic stem cell transplantation (HSCT) and is attributable to dysregulation that occurs between the effector and regulatory arms of the immune system.  Whereas regulatory T cells have a primary role in counterbalancing GVHD-induced inflammation, identifying and harnessing other pathways that promote immune tolerance remains a major goal in this disease.  Herein, we have identified interleukin 34 (IL-34) as a tissue-intrinsic regulatory cytokine that is able to mitigate the severity of GVHD within the GI tract.  Specifically, we observed that absence of recipient IL-34 production exacerbated GVHD lethality, promoted intestinal epithelial cell death, and compromised barrier integrity.  Mechanistically, the absence of host IL-34 skewed donor macrophages towards a proinflammatory phenotype and augmented the accumulation of pathogenic CD4+ GM-CSF+ T cells within the colon.  Conversely, the administration of recombinant IL-34 significantly reduced GVHD mortality and inflammation in the GI tract which was dependent upon the expression of apolipoprotein E (ApoE) in donor macrophages.  Complementary genetic and imaging approaches demonstrated that intestinal epithelial cells were the biologically relevant source of IL-34.  Colonic biopsies from patients with GVHD also revealed expression of IL-34 in intestinal epithelial cells, as well as ApoE in lamina propria macrophages, validating similar cellular localization in humans.  Thus, these studies define IL-34 as an intestinal epithelial-derived cytokine that regulates macrophage polarization in an ApoE-dependent manner, positioning this cytokine as a key regulator of GVHD in the GI tract and a potential therapeutic target for amelioration of this disease.

overall_design: Cells were isolated from the colons of mice that were transplanted with Bone marrow (BM) alone or BM plus adjunctive spleen cells (GVHD). To delineate macrophage populations within colon microenvironment, scRNAseq was performed on sorted donor derived CD11b+ CD64+ macrophages from the colons of BM and GVHD mice. To define the effect of IL-34 on the regulation of macrophages, scRNAseq was performed on sorted donor CD11b+ CD64+ macrophages from the colons of WT and IL-34-/- transplant recipients. To address the question of whether IL-34 binding to CSF-1R on macrophages affects the emergenece of proinflammatory T cells in GVHD target organs, scRNAseq was performed on donor derived sorted T cells.

first: Aditya

last: Rayasam

first: Alison

last: Moe

first: Ravi

last: Shah

first: Chengyin

last: Yuan

first: James

last: Miller

first: Mary

last: Rau

first: Mollie

last: Patton

first: Marco

last: Colonna

first: William

last: Drobyski


title: Epigenetic regulation of Ucp1 by trandcription factor Etv4

city: Berkeley

first: Pengya

last: Xue

state: CA

address: Morgan hall, 220

institute: UC Berkeley

summary: We found a far regualtory element on Ucp1 genome locus at -12kb region which was drasticlly regulated by transcription factor Etv4.

overall_design: ATAC-seq and H3K27ac, H3K27me3, CTCF cut&run was performed in BAT and iWAT tissue. ATAC-seq of -12kb enhancer repression by CRISPRi and knocking down Etv4 was performed in BAT cell line. RNA-seq of Etv4 knockdown was performed


title: Single-nuclei RNA-Seq profiles from Group 3 and Group 4 medulloblastomas [scRNA-Seq]

city: Baden-Württemberg - Heidelberg

first: Piyush

last: Joshi

state: BW

address: Im Neuenheimer Feld 280

institute: DKFZ

summary: Frozen Group 3 and Group 4 medulloblastoma samples were processed using Chromium Single Cell Multiome ATAC+Gene or Chromium Single Cell 3'/ATAC to obtain single-cell gene and chromatin accessbility profile for individual tumors.

first: Konstantin

last: Okonechnikov


title: CUT&RUN of the kidneys from diabetic mice with MAT2A inhibitor I

first: Yalu

last: Zhou

summary: H3K27me3 was enhanced in the gene loci related to the inflammatory pathway.

overall_design: SGTL2 WT and MT mice were fed with HFD for 18 weeks.

first: Hiroshi

last: Maekawa

first: Yuki

last: Aoi


title: Root meristem growth factor 1 (RGF1) controls the PLETHORA 2 (PLT2) protein stability by redox-based modification in root meristem

city: Tainan

first: Masashi

last: Yamada

address: No. 100, Sec. 1, Guiren 13th Rd., Guiren Dist.,

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica

summary: The root meristem size and activity are maintained by the distributions of two reactive oxygen species (ROS) along root developmental zones and the gradient concentrations of a master regulator, PLETHORA 2 (PLT2). The ROOT MERISTEM GROWTH FACTOR 1 (RGF1) peptide modulates these two ROS distributions. The alterations of the ROS distribution by RGF1 result in the extended localizations of PLT2 and the enlarged root meristem. Therefore, deciphering the regulation mechanism of how ROS modulates the PLT2 protein stability is critical to study the root stem cell function.

overall_design:
To investigate the PLT2 protein stability in the regulation of root development, we created three Arabidopsis lines with the genotypes plt2, plt2/gPLT2-GFP, and plt2/gPLT2C212S-GFP.
We then conducted gene expression profiling analysis using RNA-seq data from three different lines under three distinct RGF1 treatment conditions.

first: Yu-Chun

last: Hsiao

first: Hiao-Yu

last: Hsiue

first: Yi-Han

last: Weng

first: Ming-Ren

last: Yen


title: Co-STARs: Combining the advantages of chimeric antigen and T cell receptors for cancer targeting

city: Baltimore

first: Brian

last: Mog

state: MD

address: 1650 Orleans street, CRB1 room 520

institute: Ludwig Center at Johns Hopkins

summary: Two types of engineered T cells have been successfully used to treat cancer patients, one with an antigen recognition domain derived from antibodies (chimeric antigen receptors, CARs) and the other derived from T-cell receptors (TCRs). CARs employ high-affinity antigen binding domains and co-stimulatory domains to augment T-cell activation but can only react against target cells with relatively high amounts of antigen. TCRs have a much lower affinity for their antigens but can react against target cells displaying only a few antigen molecules. Here we describe a new type of receptor, called a Co-STAR (for Co-stimulatory Synthetic T-cell receptor and Antigen Receptor), that combines aspects of both CARs and TCRs. In Co-STARs, the antigen-recognizing components of TCRs are replaced by high-affinity antibody fragments and co-stimulation is provided by two modules that drive NFκB signaling (MyD88 and CD40). We demonstrate that Co-STARs produce robust T-cell expansion and induce long-term regressions of mouse tumors bearing very low densities of antigen.

overall_design: Unedited, STAR-3, or Co-STAR-1 T cells were co-cultured with KMS26-MUT, KMS26-NULL, or no target cells for 18 hours in cytokine-free media. After co-culture, CD4+ and CD8+ subsets of each T cell condition were flow sorted into RNAstable buffer. RNA was isolated for bulk RNA sequencing. Differentially expressed genes were identified between specified conditions.

first: Nikita

last: Marcou

first: Bert

last: Vogelstein

first: Shibin


title: Thyrotropin aggravates insulin resistance by promoting macrophage inflammation in subclinical hypothyroidism.

city: Xi 'an

first: Zhang

last: Haihong

state: Shaanxi Province

address: Xiaozhai West Road

institute: Xi'an Jiaotong university

summary: In subclinical hypothyroidism (SH), serum thyroid-stimulating hormone (TSH) correlated positively with insulin resistance; however, the precise mechanism is now unclear. Except for thyroid follicular epithelial cells, macrophages exhibit the highest level of TSHR expression. Thus, we wondered if TSH leads to insulin resistance by macrophages. We established thyroid-stimulating hormone receptor (Tshr) myeloid-specific knockout (TshrMKO) C57BL6 mice, and observed that TshrMKO mice showed improvement on high-fat diet (HFD) induced obesity and insulin resistance, compared to WT mice. TshrMKO animals showed decreased macrophages infiltration and M1 polarization in liver, adipose, and skeletal muscles. Co-culture experiments proved that Tshr deficient macrophages decreased gluconeogenesis in primary hepatocytes but increased glucose uptake in 3T3L1 adipocytes and L6 skeletal muscle cells through improving insulin signaling, versus WT. TSH promoted the release of Il6, Il1a and Il1b cytokines, which upregulated Egr1, Lcn2 and Socs3, reversed by the inhibitors Il6st and Il1ra. Lastly, EGR1 transcriptionally activated LCN2 and SOCS3. In conclusion, TSH promotes the secretion of IL6, IL1A, and IL1B via activating macrophage M1 polarization, which leads to that the upregulation of EGR1, transcriptionally activating LCN2 and SOCS3 and inducing insulin resistance in liver, adipose, and skeletal muscle in SH.

overall_design: 1.To investigate how TSH regulates macrophage activation,primary mouse bone marrow derived macrophages(BMDMs) were isolated from TshrMKO mice and age-matched Tshrf/f littermates(male, 6 weeks old),cultured and differentiated for 7 days in DMEM containing 10% FBS and 1% penicillin/streptomycin supplemented with murine recombinant M-CSF (10ng/mL) at 37 °C with 5% CO2.Then BMDMs were stimulated by 1ng/mL Tsh for 24 hours, used to perform RNAseq.2.To gain mechanistic insight into the protective action of myeloid Tshr deficiency against HFD-induced insulin resistance,TshrMKO mice and age-matched Tshrf/f littermates (male, 6 weeks old) were fed a HFD for 9 weeks. Mice were sacrificed after insulin administration (1.5 U/kg) for 5 minutes in vivo after 8-hour fasting, whose liver were used to perform RNAseq.

first: Haihong

last: Zhang


title: Single-nuclei ATAC-Seq profiles from Group 3 and Group 4 medulloblastomas [scATAC-Seq]

summary: Frozen Group 3 and Group 4 medulloblastoma samples were processed using Chromium Single Cell Multiome ATAC+Gene or Chromium Single Cell ATAC to obtain single-cell chromatin accessbility profile for individual tumors.

overall_design:
Single-cell  chromatin accessbility profiling by high throughput sequencing.

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Submitter states that missing raw files are due to patient privacy concerns.
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title: The protective effect of LCN2 knockout on the imiquimod-induced psoriatic mouse model

city: Xi'an

first: Kaixuan

last: Ren

address: Huangcheng West Road

institute: Xi'an jiaotong University

summary: LCN2 demonstrates heightened expression levels in psoriasis, providing insight into its potential implication in the development of this inflammatory cutaneous condition. We here report the discovery that LCN2 is an essential molecule involved in the pathogenesis of psoriasis. Deletion of LCN2 in mice resulted in reduced levels of epidermal hyperplasia and inflammatory infiltration in psoriatic skin lesions, as compared to wild-type mice. Hence, our findings suggest that LCN2 may hold promise as a potential therapeutic target for the treatment of psoriasis.

overall_design: To investigate the pathogenic role of LCN2 in a mouse model of psoriasis, we employed LCN2 gene knockout mice for our study.

first: Yumin

last: Xia


title: Extensive reprogramming of lipid metabolism in the liver during West Nile virus infection in mice highlights novel aspects of disease pathophysiology [liver]

city: Madrid

first: Miguel A.

last: Martín-Acebes

state: Madrid

address: Ctra. de La Coruña, km 7, 5

country: Spain

institute: INIA-CSIC

summary:
To investigate the in vivo metabolic changes during WNV infection in a mouse model, we infected mice with WNV NY99 to compare to uninfected (mock) mice.
We then performed gene expression profiling analysis using data obtained from RNA-seq from infected vs uninfected mice and treated mice.

overall_design: Comparative gene expression profiling analysis of liver RNA-seq data for mice infected with WNV vs uninfected mice

first: Patricia

last: Mingo-Casas

first: Ana-Belén

last: Blázquez

first: Juan-Carlos

last: Saiz

first: Miguel


title: Extensive reprogramming of lipid metabolism in the liver during West Nile virus infection in mice highlights novel aspects of disease pathophysiology [brain]

summary:
To investigate the in vivo lipid metabolism changes during WNV infection in a mouse model, we infected mice with WNV NY99 to compare to uninfected (mock) mice.
We then performed gene expression profiling analysis using data obtained from RNA-seq from infected vs uninfected mice and treated mice.

overall_design: Comparative gene expression profiling analysis of brain RNA-seq data for mice infected with WNV vs uninfected mice


title: Effect of EGR1 on gene expression during SFTSV-infeced HUVECs

city: Nanjing

last: Jiang

address: Hankou Road

institute: Nanjing University

summary: During viral infections, EGR1 expression can facilitate either an anti-viral or pro-viral cellular state, depending on the virus and the transcriptional events regulated by EGR1. We here report that SFTSV infection could promote the EGR1 expression. Our observations revealed similar results to other studies, underscoring the biological relevance and general importance of EGR1 in viral infections.

overall_design: To determine the mechanism underlying the inducible expression of sVEGFR1，we performed a transcriptome analysis in SFTSV-infected or mock-infected HUVECs.

first: Zhiwei

last: Wu


title: Extensive reprogramming of lipid metabolism in the liver during West Nile virus infection in mice highlights novel aspects of disease pathophysiology.

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

overall_design: Refer to individual Series


title: Effect of TFAP4 overexpression on CF function

city: Wuhan

first: jie

last: liu

state: Hubei

address: Fruit Lake Street

institute: Wuhan university

summary: Cardiac fibrosis, is a common pathophysiologic process in nearly all heart diseases, leading to cardiac dysfunction and heart failure subsequently. The transition of cardiac fibroblasts (CFs) to a myofibroblast state underlies the cardiac fibrotic response, and this process is accompanied by changes in the cardiac mechanical environment. Mechanical forces play a central role in the initiation and propagation of fibrosis, resulting in further ECM deposition, crosslinking and reorganization, leading to adverse ventricular remodeling. However, the key factors regulating mechanotransduction during cardiac fibrosis remain unknown. Here we discovered that transcription factor activating enhancer-binding protein 4 (Tfap4) regulates CF migration and proliferation. Further investigation revealed that Tfap4 correlates with heart disease and is significantly upregulated in the fibrotic hearts. We demonstrated that Tfap4 overexpression stimulated CF activation, whereas Tfap4 knockdown resulted in the opposite effect. In addition, we also knocked down Tfap4 in primary human CF (HCFs) with consistent results. Silence of Tfap4 by lentivirus carrying Tfap4 shRNA markedly enhanced functional improvement and scar size reduction in myocardial infarction (MI) mice. Mechanistically, we found that Tfap4 exerts pro-fibrotic function by regulating mechanical stress. Unexpectedly, we found that Tfap4 is a regulator of mechanosensors, Itga11 and Piezo2, thereby involved in mechanotransduction that acts as a bistable switch for the CF phenotypic transition associated with cardiac fibrosis. Taken together, our study revealed that Tfap4 plays an important role in cardiac fibrosis.

overall_design: To elucidate the underlying mechanisms by which Tfap4 promotes cardiac fibroblast activation, we performed bulk RNA-sequencing analyses of the CFs treated with Tfap4 overexpression after 3 days infection. Compared with Control, Tfap4 overexpression-treated cells showed 534 commonly upregulated genes and 476 commonly downregulated genes (FC＞1.5, pvalue＜0.05)

first: Li

last: Wang

first: Jie

last: Liu


title: Heterogeneity of foam cell biogenesis across diseases

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

summary: Foam cells are dysfunctional, lipid-laden macrophages associated with chronic inflammation of infectious and non-infectious origin. To test the hypothesis that foam cell biogenesis is disease-specific, we compared bulk transcriptomics data obtained by RNA seq in human monocyte derived macrophages (MDM) subjected to two types of infections in vitro. One was with Mycobacterium tuberculosis and the other with Cryptococcus neoformans.  We also exposed MDM to cell-free conditioned medium from cultures of the ACHN cell line, which is derived from a human renal cell carcinoma, to study foam cell formation in the context of papillary renal cell carcinoma (pRCC). We found that, with both infections, the accumulation of TAG results from decreased oxidative phosphorylation, increased glycolysis, increased lipid biosynthesis, and decreased lipid catabolism. However, the molecular modalities of

overall_design: The differential expression between sample classes (treated vs non treated for each condition) was tested with coincident extreme ranks in numerical observations (CERNO) for metabolism-related Gene Ontology gene sets. The Benjamini–Hochberg method was used to calculate the false discovery rate (FDR). Gene sets (pathways) were identified at a cutoff false discovery rate of 0.05. To identify pathways underlying neutral lipid accumulation, we analyzed the Gene Ontology (GO) annotations related to metabolic processes. In addition, to conduct gene-level analyses, genes in differentially expressed metabolism-related Gene Ontology gene sets having FDR < 0.05 were selected based on individual p value (p << 0.05) and ranked by log2 fold change (treated vs non-treated in each condition) and number of occurrences in the differentially expressed gene sets.

first: Maria

last: Gennaro

first: Valentina

last: Guerrini


title: Ketolysis is a metabolic driver of CD8+ T cell effector function through histone acetylation.

city: Grand Rapids

first: Russell

last: Jones

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute


title: Prospective isolation according to melanin pigment content of melanoma cells with heterogeneous potentials for disease propagation

city: Melbourne

first: Pacman

last: Szeto

state: VIC

address: 89 Commercial Road

country: Australia

institute: Monash University

summary: To investigate the effect of RNA pol I inhibition on B16-F10 cell pigment heterogeneity

overall_design: Comparative gene expression profiling analysis of RNA-seq data for B16-F10 cells treated with DMSO or 1 uM CX5461 or 3 days.

first: Gamze

last: Abali

first: Peinan

last: Zhao

first: Mark

last: Shackleton


title: Astrocytic ZBTB7A promotes orbitofrontal cortex dysfunction associated with Major Depressive Disorder

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Overall risk for Major Depressive Disorder (MDD) is determined by complex interactions between genetic and environmental factors that influence epigenetic regulation of neuroplasticity and stress pathways. These mechanisms are specific to the distinct regulatory context within regionally-defined brain cell-types. Here, we employed genome-wide chromatin accessibility profiling of neuronal vs. non-neuronal cells in orbitofrontal cortex (OFC) to capture regulatory signatures of MDD. We mapped genetic risk for MDD to active promoters of non-neuronal cell-types in OFC and identified MDD-specific open chromatin regions, which were differentially accessible exclusively in non-neuronal cells. Characterization of these loci revealed a key role for astrocyte dysfunction, and implicated the chromatin remodeling protein ZBTB7A, which coordinates wide-ranging cellular activation programs, including NF-kB inflammatory transcription. In mice, astrocyte-specific knockdown of Zbtb7a reversed chromatin remodeling, reactive astrocyte transcription, and behavioral deficits associated with chronic stress. Conversely, ZBTB7A overexpression in OFC astrocytes induced stress-related behavioral deficits, promoted widespread inflammatory gene expression, and drove pathophysiological OFC neuronal hyperactivity in response to a mild subthreshold stressor. Our data highlight a critical role for OFC astrocytes in the bidirectional regulation of stress vulnerability and pinpoint ZBTB7A as a key factor mediating maladaptive astrocyte plasticity and OFC neuronal hyperexcitability in MDD.

overall_design: For Zbtb7a knockdown experiments: following bilateral intra-OFC injection of either the AAV6-GFAP-Zbtb7a-KD-mir virus or the AAV6-GFAP-mirNeg control virus to knockdown Zbtb7a expression specifically in OFC astrocytes, mice were randomly assigned to either the control group, or chronic stress group (10 days of chronic social defeat stress). For ZBTB7A-OE experiments: following bilateral intra-OFC injection of either the AAV6-GFAP-ZBTB7A OE virus or the AAV6-GFAP-GFP empty vector control virus to overexpress ZBTB7A specifically in OFC astrocytes, mice were randomly assigned to either the control group, or acute stress group (1 day of social defeat stress).

first: Sasha

last: Fulton

first: Jaroslav

last: Bendl

first: Panos

last: Roussos

first: Ian

last: Maze


title: Ketolysis is a metabolic driver of CD8+ T cell effector function through histone acetylation

summary: Investigating the effect of reducing ketolytic capacity on the transcriptional profile of CD8 T cells responding to listeria infection in vivo

overall_design: Control (wt) or ketolysis-deficient (DKO) OT-I CD8+ T cells were adoptively transferred into C57BL/6 mice and infected with LmOVA. LmOVA-specific T cells were isolated from spleens of infected mice 7 days later and used for RNA extraction.

first: Susan

last: Goosen

first: Eric

last: Ma

first: Lisa

last: DeCamp


title: Comparative Evaluation of miRNA Detection in Plasma, Urine, and Liquid-Based Cytology (LBC) for High-Grade Cervical Intraepithelial Neoplasia

status: Public on Jul 08 2025

city: Barretos

first: Stéphanie

last: Calfa

state: São Paulo

address: Antenor Duarte Viléla, 1331 - Dr. Paulo Prata

country: Brazil

institute: Barretos Cancer Hospital

summary: We profiled 798 miRNAs using NanoString technology in plasma, urine, and liquid-based cytology (LBC) from 24 women with and without high-grade cervical lesions (CIN2/3). LBC showed the highest detection efficiency and consistency, with the lowest proportion of low-count miRNAs and the highest expression levels, supporting its utility as the most effective specimen type for miRNA-based screening.

overall_design: In the study presented here, matched plasma, urine, and liquid-based cytology (LBC) samples were collected from 24 women—12 with high-grade cervical intraepithelial neoplasia (CIN2/3) and 12 controls. Expression profiling of 798 miRNAs was performed using the NanoString nCounter Human v3 miRNA panel to compare detection performance across specimen types.

first: Ana Julia

last: Freitas

first: Welinton

last: Hirai

first: Rhafaela

last: Causin

first: Júlio César

last: Possati-Resende

first: Ricardo

last: Reis

first: Rui

first: Márcia Maria

last: Marques


title: Single-nucleus transcriptome sequencing reveals the identity of neurons that respond to the panic attack.

city: Beijing

first: Zhenhua

last: Chen

state: China

address: West Beichen Road, Olympic Village, Beijing

department: State Key Laboratory of Molecular Development Biology

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

summary: In nature, moderate innate defensive behaviors (e.g. escaping and freezing) are commonly triggered by imminent threats in human and animal, accompanied with series of physiological responses related with activation of autonomic nervous system (e.g. tachycardia，increased blood pressure, tachypnea). According to many prior researches, posterior hypothalamic nucleus (PHN) with highly cell diversity is recognized to be connected tightly with panic attack. However, the neural substrate of sub-clusters of this important hypothalamic nucleus in panic attack-related defensive behavior has not yet elucidated. In order to justify the hypothesis, we adopted snDNA-seq to screen out a main population, Cbln2+ neurons, manipulating panic attack behaviors in PHN. Subsequently, we illustrated the neural coding mechanism of Cbln2+ PHN neurons for threats stimulus, and indicated the neurobiological functions of neural network of PHN neurons in defensive behaviors. In conclusion, our data suggested that Cbln2+ PHN neurons is sufficient and necessary to regulate panic attack related defensive behaviors in mice.

overall_design: FosTRAP2+/-::Ai9 system was used to label the neurons responded to panic attack specifically. The mice were hit by ‘battle robot’ 30 min continuously, providing controlled, quantitative and multisensory threat stimuli, to induce panic attack related defensive behaviors right after intraperitoneal injection of 50 mg/kg 4-OH Tamoxifen. snRNA-Seq was performed 2 weeks later.

first: Zhen-Hua

first: Huating

last: Gu


title: The novel RNA polymerase I transcription inhibitor PMR-116 exploits a critical therapeutic vulnerability in a broad-spectrum of high MYC malignancies [ChIP-Seq]

city: Canberra

first: Zaka

last: Yuen

address: Australian National University, Canberra ACT 2601

institute: Australian National University

summary: Ribosome biogenesis (RiBi) is a key determinant of cell growth and proliferation and is highly elevated in cancer due to the activation by oncogenes such as MYC. First-generation RiBi inhibitor CX-5461, while demonstrating clinical potential for cancer treatment, also induces DNA damage through off-target inhibition of TOP2⍺ and potentially other mechanisms, bringing into question RiBi as a target for cancer therapy. In this study, we test second-generation RiBi inhibitor, PMR-116. PMR-116 exhibits improved drug-like properties compared to first-generation RiBi inhibitors and has robust anti-tumour activity in the absence of global DNA damage signalling in a broad range of pre-clinical models of haematologic and solid cancers, particularly in malignancies where MYC is either the driver of disease or is elevated. Thus, our work demonstrates that RiBi is a genuine target for cancer therapy and highlights the potential to exploit a critical therapeutic vulnerability in high-MYC human cancers with dismal therapeutic outcomes.

overall_design: ChIP-seq of Pol I and UBF in Mv4;11 and KG-1 acute myeloid leukemia (AML) cells which were treated with PMR-116 or vehicle control for 30 minutes.


title: GATA3 Promotes Ferroptosis Resistance by Repressing Integrin β1 Signaling

city: Worcester

first: Emmet

middle: Rue

last: Karner

state: MA

address: 364 Plantation St

department: MCCB

institute: University of Massachusetts Chan

summary: Understanding mechanisms that determine the response of cells to ferroptotic stress is a timely issue that has significant ramifications for biology and pathology. We investigated these mechanisms in the context of breast cancer where tumors are comprised of diverse populations of cancer cells that differ in their ferroptosis sensitivity. Using single-cell RNA-sequencing, we determined that cancer cell populations with luminal differentiation are more resistant to ferroptosis than other cells within a heterogeneous tumor. Subsequent bioinformatic analysis and experimentation revealed that GATA3, a transcription factor that promotes luminal differentiation, has a causal role in ferroptosis resistance in luminal breast cancer cells. In pursuit of the mechanism involved, we found that GATA3 represses the expression of integrin β1 and its downstream signaling cascade. This observation led us to demonstrate that integrin β1 signaling is necessary for sensitivity to ferroptosis in basal breast cancer cells because it regulates a FAK/ROCK pathway that sustains the expression of ACSL4, a lipid-modifying enzyme that is essential for ferroptosis. The repression of integrin β1 by GATA3 inhibits this signaling pathway rendering cells ferroptosis resistant. Together, these data provide insight into mechanisms of ferroptosis sensitivity and resistance that are linked to the cell biology and signaling pathways of the diverse types of cells present in breast tumors.

overall_design: patient derived organoids were incubated with for either 3 or 12 hours with either DMSO (1:1000) or IKE (10 μM) prior to dissociation and sample collection. Specifically, the culture medium was aspirated and Matrigel was digested with trypsin at 370C for 10 minutes. The samples were then washed 3X with cold PBS and dissociated for 45 minutes with Accumax (StemCell cat. 07921) at room temperature to generate a single cell suspension, which was passed through a 0.45μm filter to prevent cell clumping. Samples were frozen at -800C in cryopreservation medium (30% organoid media with 10% DMSO and 60% FBS). Samples were then processed by GeneWiz where they underwent MACS dead cell removal and quality control prior to being processed through the 10X Genomics Chromium 3' gene expression RNA-seq protocol and Illumina sequencing. Cells were sequenced at a depth of 6000 cells per sample and 100,000 genes per cell. Raw sequencing data were converted to FASTQ and aligned to a human reference transcript using Cell Ranger(48).

first: Mengdie

last: Wang

first: Hira

last: Goel

first: Arthur

last: Mercurio


title: RNAseq of low-pigmented and high-pigmented cells from mouse B16 melanoma cell lines (experiment 1)

first: Pacman

last: Szeto

summary: Functional variation due to underlying genetic and phenotypic heterogeneity poses a major challenge to long-term melanoma management. Melanin pigment production is the hallmark of normal melanocytic differentiation but varies significantly between and within melanoma tumours. Detailed assessment of the functional consequences of pigment heterogeneity in viable melanoma samples has been experimentally challenging.   Here, we developed a novel method to prospectively separate melanoma cell populations based on the presence of intracellular melanin using fluorescence-activated cell sorting (FACS). We find that nearly all pigmented patient melanomas and melanoma cell lines comprise mixtures of cells ranging from very high to low or undetectable pigment content. Using viable sorted cells, we interrogated the functional characteristics of low pigmented cells (LPC) and high pigmented cells (HPC) in the B16-F10 mouse melanoma cell line.

overall_design: The B16 mouse melanoma cell lines were cultured and separated into low pigmented cells (LPC) and high pigmented cells (HPC) based on their melanin pigment content by fluorescence-activated cell sorting (FACS), exploiting the light scattering properties of intracellular melanin. RNA sequencing was performed on sorted cells with 3x replicates for each group.

first: Mark

last: Shackleton

first: Clare

last: Fedele

first: Gamze

last: Abali

first: Peinan

last: Zhao


title: Targeting Ewing sarcoma cells via small molecule YK-4-279 treatment and downregulation of DHX9 helicase

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology


title: Ketolysis is a metabolic driver of CD8+ T cell effector function through histone acetylation [ChIP-seq]

first: Russell

last: Jones

summary: Investigating the effects of Bdh1 deletion on acetylation of lysine 27 on histone 3 (H3K27ac) in CD8+ T cells 24 h post-activation with anti-CD3 and anti-CD28 antibodies

overall_design: Control (wt) or Bdh1-knockout (Bdh1KO) CD8+ T cells were activated for 24 h with anti-CD3 and anti-CD28 antibodies. Nuclei were isolated from activated T cells for chromatin immunoprecipitation sequencing (ChIP-seq).

first: Susan

last: Goosen

first: Eric

last: Ma

first: Lisa

last: DeCamp

first: Bradley

last: Dickson

first: Scott

last: Rothbart


title: Developing a T>A Base Editor via Protein Universe Mining and optimizing translesion polymerase

city: Xihu District, Hangzhou

first: Xing

last: Chang

state: Zhejiang

address: No.18 Shilongshan Road Cloud Town

department: School of Life Sciences

institute: Westlake University

summary: A engineering Pol η variants offers the exciting prospect of further tailoring its activity for base editing. Improving its processivity could ensure that Pol η completes the bypass of the AP site and perhaps extends a few more bases before dissociating, thus preventing the recruitment of other, potentially less desirable, cellular polymerases or repair factors. Base on this hypothesis, We decide to develop a novel T-to-A base editor.

overall_design: Seventy-two hours after transfection, HeLa cells were washed with PBS and digested with TRIzol (Takara). Around 5x106 cells for mRNA prepared. A total of 1.5 mg of RNA per sample was adopted as input material to get preparations for the sample. Sequencing libraries were generated by AZENTA SZ NGS LABORATORY with the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturerʼs instructions. The sequence library was puriﬁed (Agencourt AMPure XP Beads), and the quality was evaluated on a Bioanalyzer (Agilent High Sensitivity Chip). According to the manufacturerʼs instructions, index-coded samples were clustered by a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina), then the library was sequenced on an Illumina NovaSeq 6000 platform, and 125–150-bp paired-end reads were obtained.

first: Yan

last: He

first: Geng

last: Li

first: Pengfei

last: Zhang


title: Targeting VRK2 Enhances the Efficacy of Anti-PD-1 Therapy in Hepatocellular Carcinoma by Reducing Direct Phosphorylation and Stability of MYC，CUT-TAG sequencing for MYC in hepatocellular carcinoma cells [CUT&Tag]

first: chen

last: su

address: No. 1095, Jiefang Avenue

institute: Huazhong University of Science and Technology

summary: VRK2–MYC axis, a transcription-dependent regulatory axis, could be a prognostic indicator and potential therapeutic target in liver cancer.

overall_design: Cleavage Under Targets and Tagmentation (CUT&TAG) sequencing was then performed on MYC in cells from different treatment groups,

first: Chen

last: Su

first: Zhibin

last: Liao

first: Jie

last: Mo

first: Furong

last: Liu

first: Zhanguo

first: Peng

last: Zhu

first: Bixiang


title: Modelling HNSCC in mice with hyperactivated NRF2 pathway

city: Houston

first: Mitchell

last: Frederick

state: Texas

address: One Baylor Plaza

department: Otolaryngology

institute: Baylor College of Medicine

summary: Purpose: Alterations in the KEAP1/NFE2L2 (NRF2)/CUL3 pathway occur in ~20% of human head and neck squamous cell carcinomas (HNSCC) and are associated with resistance to standard-of-care therapy. However, this pathway's role in radiotherapy resistance in HNSCC has not been well-studied. Experimental Design: We generated genetically engineered mouse models and developed primary murine cancer cell lines harboring mutations commonly observed in human HNSCC, including inducible activation of PIK3CA and deletion of Trp53, with or without Keap1 loss. Primary tumors were initiated via 4-hydroxytamoxifen injection ± the tobacco carcinogen benzo[a]pyrene (BAP) into the oral buccal mucosa. Tumors were analyzed using Western blotting, immunohistochemistry, RNA sequencing (RNA-seq), and subjected to fractionated radiation therapy to investigate the role of the KEAP1/NRF2 pathway in radioresistance and modulation of the tumor immune microenvironment. Results: BAP exposure accelerated primary tumor formation within one month, with histological analysis confirming invasive squamous cell carcinoma, validated by cytokeratin and differentiation marker expression. Primary cell lines derived from Keap1-haploinsufficient tumors exhibited upregulation of NRF2 target genes and a radioresistant phenotype, which was reversed post-Nrf2 knockdown in vitro. Bulk RNA-seq revealed that Keap1 haploinsufficiency correlated with NRF2 pathway activation, increased myeloid infiltration, and enhanced angiogenic signatures. In vivo, Keap1 haploinsufficiency promoted accelerated tumor growth and decreased survival. Finally, using fractionated radiotherapy, we showed that Keap1 haploinsufficient primary tumors were significantly more radioresistant than Keap1-proficient tumors, regardless of BAP exposure. Conclusion: These data demonstrate that Keap1 haploinsufficiency in HNSCC is linked to unfavorable tumor immune microenvironment, aggressive growth, and a radioresistant phenotype.


title: The novel RNA polymerase I transcription inhibitor PMR-116 exploits a critical therapeutic vulnerability in a broad-spectrum of high MYC malignancies

first: Zaka

last: Yuen

overall_design: Differential gene expression analysis of Mv4;11 and KG-1 cells treated with PMR-116 or vehicle control.


title: Identification of differentially expressed genes involved in the enhancement of thermosensitivity by HIKESHI knockout in human oral squamous cell carcinoma HSC-3 cells

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

summary:
HIKESHI has been reported to function as a nuclear carrier protein for Hsp70 under heat-stress conditions. Functional suppression of this protein has also been shown to increase the sensitivity of cancer cells to heat. However, the molecular mechanisms underlying the enhancement of thermosensitivity in HIKESHI-suppressed cells remain unclear.
In this study, we identified differentially expressed genes associated with the enhancement of thermosensitivity resulting from HIKESHI knockout in human oral squamous cell carcinoma HSC-3 cells, using GeneChip® oligonucleotide microarrays.

overall_design: Human oral squamous cell carcinoma HSC-3 cells and HSC-3 HIKESHI-knockout (HIKO) cells (Thermal Med. 2024; 40: 17–29. https://doi.org/10.3191/thermalmed.40.17) were treated with hyperthermia (HT) at 42°C for 90 min, followed by incubation at 37°C for 3 h. As a control, each cell type was cultured at 37°C for 90 min and then incubated at 37°C for 3 h. Total RNA was extracted from the cells, and RNA quality was assessed using the Agilent 4150 TapeStation system. Gene expression analysis was performed using the Affymetrix GeneChip® system with the GeneChip® Human Genome U133 Plus 2.0 Array. Sample preparation for array hybridization was conducted according to the manufacturer’s instructions.


title: Viral Insulin/IGF-like Peptides Inhibit IGF-1 Receptor Signaling to Enhance Viral Replication

city: Chestnut Hill

first: Aurelien

last: CHUARD

address: 140 Commonwealth Ave, Higgins Hall, Altindis Lab

department: Biology

institute: Boston College

summary: The insulin/IGF system plays a central role in regulating metabolism and growth. We identified viral insulin/IGF1-like peptides (VILPs) in Iridoviridae and investigated their role in host-virus interactions. Using Grouper Iridovirus (GIV) on grouper and zebrafish cells, we show that VILPs are early viral genes and are secreted during infection. VILPs activate insulin receptor (IR) and IGF-1 receptor (IGF1R) phosphorylation and stimulate the PI3K pathway. Supernatants from infected cells trigger dose and time-dependent signaling with GIV-VILP selectively interacts with IGF1R. Functionally, IR inhibition suppresses GIV replication, whereas IGF1R inhibition enhances it, and IGF-1 stimulation reduces replication. During infection, GIV-VILP competes with IGF-1, attenuating IGF1R signaling and reducing proliferation. Transcriptome analysis confirms negative regulation of cell cycle pathways. Using a zebrafish infection model, we demonstrate VILP expression and IGF-1 signaling inhibition. Our findings reveal a viral mimicry mechanism that modulates host IGF-1 signaling to promote viral replication.

overall_design: Total RNA were extracted using the RNeasy Plus Mini Kit (Qiagen #74134) from GK cells that were serum-starved for 12 hours, followed by 6 hours of stimulation with respective ligands (100 nM) or infection with GIV (MOI 1) for 18 hours. The RNA samples were submitted to the YCGA (Yale Center for Genome Analysis) for quality testing. Subsequently, cDNA libraries were prepared using the KAPA mRNA HyperPrep Kit (Roche) and sequenced on the NovaSeq X (Illumina) with a read depth of 20 million reads. Transcriptomic datasets generated from the sequencing were trimmed for low quality reads and adaptor contamination was removed using TrimGalore 58. Trimmed reads were assembled using Trinity de novo assembly tool (version v2.15.1)59. Coding regions for the assembly were identified using TransDecoder60.The identified 65,169 contigs were annotated to identify known genes using Blast2Go61. Counts of reads mapping to the assembled cds in each sample were estimated using the Trinity tool (align_and_estimate_abundance.pl.) These read counts were used to estimate the differential transcript expression using DESeq262.All differentially expressed transcripts included in the following analysis were subject to a false discovery rate (FDR) of ≤ 0.01 and a fold change (FC) of ≥ 1.5.

last: Chuard

first: Emrah

last: Altindis


title: Injectable Multifunctional Hydrogel with Sustained Release of procyanidin C1 for Selective Senolysis to Remodel Ocular Fundus Neovascularization

city: Shanghai

first: Yali

last: Zhou

state: Shanghai

address: No. 100 Haining Road

department: Shanghai General Hospital, School of Medicine

institute: Shanghai Jiao Tong University

summary: The abnormal vascular growth in ocular fundus neovascularization is driven by senescent cells that evade apoptosis. These cells trigger chronic inflammation by overproducing senescence-associated secretory phenotype (SASP) factors. To address this, we developed PCC1/PHCF-Gel, a novel dual-mode hydrogel platform for long-term procyanidin C1 (PCC1) release. Its high-dose localized delivery targets p16INK4a+ senescent cells for ablation (senolysis), while low-dose sustained release inhibits SASP-mediated inflammation. To investigate the alterations in senescent features of oxygen-induced retinopathy (OIR) when treated with PCC1/PHCF-Gel, we carried out bulk RNA sequencing. Subsequently, utilizing senescence-related gene sets, namely SASP_Literature Curated UP, Fridman_Senescence_UP, and Global_Senescence_2020, we conducted a Set Gene Enrichment Analysis (GSEA). The analysis results served to reconfirm the accumulation of senescence in the OIR model. However, in the case of the PCC1/PHCF-Gel group, a significant negative correlation with senescence-related genes was observed.

overall_design: At postnatal day 17 (P17), bulk RNA-seq was performed on the retinas of normoxic mice and OIR mice that had received intravitreal injections of PBS and PCC1/PHCF hydrogel at P15 to conduct a systemic transcriptomic characterization.


title: RNA Sequencing-Based Profiling of Differentially Expressed MicroRNAs in Endothelial Cells from Offspring of Hypertensive Pregnancies

city: Cheras

first: Adila A

last: Hamid

state: Kuala Lumpur

address: Jalan Yaacob Latif, Bandar Tun Razak

department: Physiology

country: Malaysia

institute: National University of Malaysia

type: Non-coding RNA profiling by high throughput sequencing

summary: Offspring of mothers with hypertensive disorders of pregnancy (HDP) are at increased risk of developing endothelial dysfunction and cardiovascular disease (CVD) in adulthood. MicroRNAs (miRNAs), as key regulators of endothelial cells, may contribute to the early onset of endothelial dysfunction. However, there are limited studies characterizing the miRNA profile of endothelial cells in offspring of HDP. Therefore, this study aims to determine the miRNA expression profile of human umbilical vein endothelial cells (HUVECs) isolated from the offspring of HDP.

overall_design: RNA-seq profiling of HUVECs which were isolated from the umbilical cords of normal and hypertensive pregnancies.

first: Nurul Iffah

last: Mohd Isa

first: Aslah Nabilah

last: Abdull Sukor

first: Saiful Effendi

last: Syafruddin

first: Mohd Faizal

last: Ahmad

first: Shahidee

last: Zainal Abidin

first: Azizah

last: Ugusman

first: Mohd Helmy

last: Mokhtar


title: Long-range Deployment of Tumor-antigen Specific Cytotoxic T Lymphocytes Inhibits Lung Metastasis of Breast Cancer

city: Guang Zhou

first: Zhou

last: Yan

state: Please select -

address: 135 Xingang West Road Guangzhou, Guangdong China

institute: Sun Yat-Sen University

summary: Immune checkpoint blockade (ICB) has imported tremendous success in cancer therapy by reactivating effector immune cells. Patients exhibiting immune-hot or “inflamed” phenotype, characterized by extensive infiltration of effector immune cells, are usually beneficial from ICB. However, primary tumors could collaborate with the infiltrated inflammatory cells to profoundly dampen local infiltration of effector T cells, leading to an immune-cold phenotype that does not respond to ICB. Recently, we proposed that systemic deployment of effector T cells (Effector Immune Cell Deployment, EICD) is crucial in immunosurveillance, while defective EICD may result an immune-cold phenotype in cancer patients causing cancer immune evasion(Zhang et al., 2022a). It has been noted that changes in the inflammatory microenvironment of distant organs may have significant impacts on pre-metastatic immune remodeling, leading to infiltration of pro-tumoral (Kaplan et al., 2005) or anti-tumoral innate immune cells in the pre-metastatic niche(Hanna et al., 2015). These contradictory evidences presented double-edged effects of innate immune response towards metastatic protection. On the other hand, the contribution of adaptive immunity in response to primary tumors that may impact distant organ metastasis remains unclear, especially the long-range deployment of adaptive immune cells has rarely been studied.

overall_design: To identify the components of immune microenvironment of pre-metastatic lungs, 20,000 CD45+ leukocytes were isolated by magnetic-activated cell sorting (MACS) from paired murine lung samples at day 28 post-inoculation.

first: Yue

last: Xing

first: Huang

last: Di


title: MAVS signaling of long-lived brain-resident myeloid cells is needed during viral encephalitis to adjust the transcriptome of CNS-infiltrating CD8+ T cells II

city: Hannover

first: Ulrich

last: Kalinke

state: Lower Saxony

address: Feodor-Lynen-Str. 7

department: Institute for Experimental Infection Research

institute: Twincore, Centre for Experimental and Clinical Infection Research

summary: Neurotropic viruses like vesicular stomatitis virus (VSV) can infect the central nervous system (CNS) through the olfactory route. Following intranasal instillation, VSV moves along the axons of olfactory sensory neurons to the olfactory bulb. While within the olfactory bulb the spread of the virus is controlled by microglia activation and the recruitment of peripheral leukocytes, some of the underlying mechanisms remain unknown. To investigate these mechanisms, we used mice with conditional deletions of the mitochondrial antiviral-signaling protein (MAVS), an adaptor for RIG-I-like receptor (RLR)-signaling. By selectively deleting MAVS in neurons, astrocytes, or long-lived myeloid cells, we discovered that RLR-signaling specifically within brain-resident myeloid cells is crucial for protection against the virus. Mice with a MAVS deletion in these myeloid cells showed normal myeloid cell and leukocyte infiltration into the brain. However, the P2RY12+ microglia showed aberrant expression of genes involved in antigen cross-presentation.Furthermore, flow cytometry experiments revealed diminished MHC class I expression on MAVS deficient microglia. Moreover, CNS-infiltrating CD8+T cells had dysfunctional transcriptional profiles. Therefore, our findings indicate that during viral CNS infection, MAVS signaling in brain-resident myeloid cells, presumably microglia, is essential for antigen cross-presentation and the relicensing of protective, infiltrating CD8+ T cells.

overall_design: C57BL/6 (WT), CX3CR1-CreER−/−MAVSfl/fl and CX3CR1-CreER±MAVSfl/fl mice were intranasally instilled with 10^3 PFU of VSV and on 6 days post treatment the OB and the cervical lymph nodes were prepared, immune cells were isolated and CD8β+ T cells were directly sorted into 350 μl of β-mercaptoethanol RA1 buffer for RNA extraction and subsequent bulk sequencing.

first: Andreas

last: Pavlou

first: Felix

last: Mulenge


title: Transcriptome sequencing data analysis of Bacillus subtilis NCIB 3610 treated with DMSO and AQCA

city: Shenzhen

first: Shanshan

last: Xu

address: Xueyuan Avenue, No. 1066

institute: Shenzhen University

summary: In our study, we discovered that AQCA (Anthraquinone-2-carboxylic acid) effectively degrades Bacillus subtilis NCIB 3610 biofilms, a finding of significant research importance. To investigate the underlying mechanisms, we performed transcriptome sequencing of wild-type biofilms treated with either DMSO (control) or AQCA. Statistical analysis of gene expression (P < 0.05) revealed that AQCA treatment led to significant changes: 184 genes were upregulated, while 503 genes were downregulated by at least twofold compared to the DMSO control group.

overall_design: mRNA profiles of Bacillus subtilis NCIB 3610 wild type biofilms treated with DMSO and AQCA

first: Junpeng

last: Chen

first: Ying


title: Defined human tri-lineage brain microtissues

city: Seoul

first: Yongjin

last: Yoo

state: Seoul

address: 73, Goryeodae-ro, Seongbuk-gu

department: Department of Neuroscience

institute: Korea University

overall_design:
Single-cell and single-nucleus RNA seq profiling for 5 weeks tri-culture containing human iPSC-derived neuron, astrocytes and microglia.
Microglia are the immune cells of the central nervous system and are thought to be key players in both physiological and disease conditions. Several microglial features are poorly conserved between mice and human, such as the function of the neurodegeneration-associated immune receptor Trem2. Induced pluripotent stem cell (iPSC)-derived microglia offer a powerful opportunity to generate and study human microglia. However, human iPSC-derived microglia often exhibit activated phenotypes in vitro, and assessing their impact on other brain cell types remains challenging due to limitations in current co-culture systems. Here, we developed fully defined brain microtissues, composed of human iPSC-derived neurons, astrocytes, and microglia, co-cultured in 2D or 3D formats. Our microtissues are stable and self-sufficient over time, requiring no exogenous cytokines or growth factors. All three cell types exhibit morphologies characteristic of their in vivo environment and show functional properties. Co-cultured microglia develop more homeostatic phenotypes compared to microglia exposed to exogenous cytokines. Hence, these tri-cultures provide a unique approach to investigate cell-cell interactions between brain cell types. We found that astrocytes and not neurons are sufficient for microglial survival and maturation and astrocyte-derived M-CSF is essential for microglial survival. Single-cell and single-nucleus RNA sequencing analyses nominated a network of reciprocal communication between cell types. Brain microtissues faithfully recapitulated pathogenic α-synuclein seeding and aggregation suggesting their usefulness as human cell models to study not only normal but also pathological cell biological processes.

first: Ishan

last: Kumar

first: Sascha

last: Jung

first: Takeshi

last: Uenaka

first: Antonio

last: Del Sol Mesa

first: Marius

last: Wernig


title: Bioinformatic analysis identifies RGS10 as a modulator of BV-2 cell migration

city: Irvine

first: Benita

last: Sjogren

state: California

address: 847 Health Sciences Quad

department: Pharmaceutical Sciences

institute: University of California, Irvine

summary: Regulator of G protein signaling 10 (RGS10) is a GTPase activating protein, selective for Gαi, that has been proposed to play a role in suppressing microglial-driven neuroinflammation. RGS10 expression in microglia is suppressed by inflammatory stimuli and aging, and loss of RGS10 is associated with increased cytokine expression and neurodegeneration. Conversely, RGS10 overexpression provides protection against inflammatory stimuli in rodent models, however the mechanisms by which RGS10 exerts this protective effect are unknown. To understand the neuroprotective functions of RGS10 in microglia, we completed RNA-Seq analysis in the murine microglial cell line BV-2 with intact (BV-2WT) and absent (RGS10-/-) RGS10 expression under basal and IFNγ-treated conditions. RGS10 loss altered expression of 1,579 genes in unstimulated cells and 2,142 genes under IFNγ-stimulated conditions. In addition to changes in GPCR signaling, altered processes in RGS10-/- cells, under basal and stimulated conditions, included cell migration, adhesion, cytokine production and cell development. Key cell adhesion genes such as Mmp9 and Thbs1 were downregulated in RGS10-/- cells regardless of stimuli. Other genes such as Icam1 and Il1b displayed significantly lower expression only in IFNγ-stimulated RGS10-/- cells compared to their WT counterpart. Loss of RGS10 increased BV-2 cell migration, and IFNγ stimulation led to a reduction in migration of both BV-2WT and RGS10-/- cells. The effect of RGS10 on migration could only partially be blocked by the Gαi inhibitor Pertussis toxin (PTX), suggesting involvement of both G protein-dependent and -independent mechanisms. Altogether, these results suggest a novel role for RGS10 in reducing microglial migration through regulation of cell adhesion genes.

overall_design: RNA-Seq profiling of BV-2 wildtype cells and its RGS10 knockout under vehicle and IFNγ treatment for 48 hours.

first: Shwetal

last: Talele

first: Menbere

last: Wendimu

first: Shelley

middle: B

last: Hooks


title: Multi-region spatial transcriptome analysis reveals cellular networks and pathways associated with hepatocellular carcinoma recurrence after surgical resection

city: Singapore

first: Pierce

middle: Kah Hoe

last: Chow

address: 11 Hospital Cres

country: Singapore

institute: National Cancer Center Singapore

summary: Hepatocellular carcinoma (HCC) exhibits diverse aetiologies and molecular heterogeneities, with a median 5-year overall survival (OS) of less than 70% due to late diagnosis and high recurrence rates post-curative ablation or surgery. This study investigated the complex tumor microenvironment (TME) in HCC, emphasizing the interactions between various cell types and their role in disease recurrence. Using samples from the PLANet 1.0 cohort (NCT03267641), spatial transcriptomics were performed on 17 tissue samples from 4 patients, and bulk RNA-seq on multi-region tumour sectors from 91 patients. Analysis revealed extensive intra- and inter-tumour  gene expression heterogeneity, identifying a specific subset of endothelial cells (ECs), INTS6+ ECs, enriched and spatially co-localized with tumour cells in primary tumours of recurrent cases. A significant ANGPTL4-SDC1 ligand-receptor interaction was found between INTS6+ ECs and tumour cells. Interestingly, INTS6+ ECs were enriched in histologically annotated microvascular invasion (MVI). These findings suggest novel therapeutic targets focusing on endothelial cell interactions within TME.

overall_design: we conducted a spatial transcriptomic analysis using visium technology from 10x genomics, on multiple sectors per primary tumour from patients with HCC treated with curative intent surgical resection who were without recurrence at 60 months after surgery (A009) and who had early tumour recurrences between 3.6 to 14.0 months (C008, B013, C004) .These patients were part of the PLANet 1.0 longitudinal cohort study and included both chronic viral hepatitis B-positive and-negative individuals. Where possible, as reference, we profiled adjacent non-tumour tissue (‘normal’).  Each Primary tumour was sampled from 2-5 distinct regions, and at least one section per region was obtained for spatial transcriptomic analysis. In patient C004, we examined both primary and recurrent tumour sectors.

first: Pierce K.H.

first: Vinay

last: Tergaonkar

first: Veerabrahma

last: Seshachalam

first: Aziz

last: Aiderus

first: Ita

last: Sari

first: Wu

last: Lele

first: Khaireen

last: Idzham

first: Li

middle: Y

last: Chong

first: Matias

last: Caldez

first: Raghuvaran

last: Shanmugam

first: Dorcas H.H.

last: Ying

first: Jia Y. J.

last: Lee

first: Guorui

last: Zhong

first: Shay

first: Karthik

last: Sekar

first: Sin

last: Chew

first: Gao

first: Lingyan

last: Wu

first: Alexander Y. F.

last: Chung

first: Peng

last: Cheow

first: Juinn

middle: H

last: Kam

first: Alfred W.C.

last: Kow

first: Iyer

last: Ganpathi

first: Shihleone

last: Loong

first: Leow

middle: W

last: Qiang

first: Nagalakshmi

last: Jegannathan

first: Chen

last: Kaina

first: Chairat

last: Bunchaliew

first: Vanessa H. De

last: Villa

last: Koh

first: Gleen

last: Bonney

first: Brian K.P.

last: Goh

first: Wai

last: Tam

first: Lit

last: Loo

first: Joe

last: Yong


title: Integrative analysis of pooled CRISPR screens provide functional insights into AD GWAS risk genes

city: South San Francisco

first: Rebecca

middle: Yi-Shuan

last: Wang

state: CA

address: 131 Oyster Point Blvd

institute: Alector Inc

summary: Emerging research has implicated Alzheimer’s disease (AD) pathology with dysregulation of many key pathways in microglia, including lipid transport and metabolism, phagocytosis of plaques, and lysosomal function. However, the exact mechanisms underlying these pathways remain poorly understood. Leveraging high-throughput CRISPR screens to understand the interplay between these pathways may enable novel therapeutic strategies for AD and other neurological diseases. Here, we constructed activation and interference CRISPRa/i libraries targeting 203 genes, 71 of which were identified through neurodegenerative GWAS, and 132 additional genes linked to microglial functions. We used this library to conduct pooled CRISPRa/i screens across a range of functional assays relating to lipid metabolism and lysosomal function using a monocytic cell line, THP-1. We identified a core set of lipid and lysosome mediators and validated a subset in primary macrophages. To gain insights into transcriptional states modulated by these genes we also applied the CRISPRa/i libraries to Perturb-seq, enabling us to capture transcriptomic changes. Through non-negative matrix factorization, we identified five gene programs altered by our perturbation library. We then used an integrative analysis of functional screen data with Perturb-seq data that enabled us to uncover novel functions and genetic relationships between perturbations. This multidimensional resource links genetic perturbations to phenotypes and transcriptional programs, establishing a scalable framework for systematic gene discovery in neurodegeneration and beyond.

overall_design: Primary human macrophages transfected with either a custom CRISPRi or CRISPRa sgRNA library and FACS sorted based on a live cell dye, RFP+ and GFP+. Sorted cells were resuspended and used for Perturbseq analysis

first: Glenn

last: Wozniak

first: Xiaoting

first: Meer

last: Mustafa

first: Malak

last: El Khatib

first: Elias

last: Kahn

first: Peter

last: Heutink

first: Hua

last: Long

first: Sara

last: Kenkare-Mitra

first: Arnon

last: Rosenthal

first: Zia

last: Khan

first: Julia

last: Kuhn

first: Daniel

last: Gulbranson


title: RelA influence on antimicrobial action of t-cinnamaldehyde on Escherichia coli MG1655

city: Gdansk

first: Dariusz

last: Nowicki

state: pomorskie

address: Wita Stwosza 59

department: Bacterial Molecular Genetics

country: Poland

institute: University of Gdansk

summary: Antimicrobial resistance poses a global threat. Natural-origin compounds represent a valuable source of antimicrobial agents used in both human and veterinary medicine. However, understanding their mechanisms of action at the molecular level is essential to support their safe and effective application. In this study, we evaluated the antimicrobial potential of trans-cinnamaldehyde (CNMA), a major constituent of cinnamon bark oil, which can account for up to 80% of the oil content in species such as Cinnamomum zeylanicum and cassia. Although CNMA exhibits broad-spectrum antimicrobial activity against Gram-positive and Gram-negative bacteria, its precise mode of action remains incompletely understood. To elucidate CNMA's molecular effects, we performed transcriptomic profiling of Escherichia coli MG1655 wild-type (GSE252441) and its ∆relA mutant upon treatment with a sub-inhibitory concentration (0.25×MIC) of CNMA. Total RNA was isolated and assessed using the Agilent Bioanalyzer 2100, and high-throughput sequencing was conducted on the Illumina NovaSeq6000 platform, generating ~30 million paired-end 101 bp reads per sample. The reference genome and annotations of E. coli MG1655 were obtained from GenBank. RNA-seq data were analyzed to identify differentially expressed genes (DEGs) compared to untreated controls at 30 and 60 min post-treatment, using thresholds of p ≤ 0.05 and |log₂FC| ≥ 2. Transcriptomic analysis revealed profound transcriptional remodeling. The most significantly enriched functional categories included genes involved in the tricarboxylic acid (TCA) cycle, flagellar biosynthesis, amino acid transport, and oxidoreductase activity. These findings indicate that CNMA-treated E. coli undergoes a marked metabolic downshift and initiates stress responses. These transcriptomic results were supported by complementary assays showing reduced growth kinetics, cytoplasmic shrinkage, NAD/NADH imbalance, and induction of the stringent response via elevated (p)ppGpp levels. Together, our findings suggest that CNMA disrupts bacterial fitness by impairing core metabolic and regulatory pathways, ultimately leading to loss of viability. Funding: This research was funded by the National Science Center, Poland (grant SONATA UMO-2018/31/D/NZ7/02258 to D.N.)

overall_design:
To assess the impact of trans-cinnamaldehyde (CNMA) on bacterial fitness, E. coli MG1655 WT and ∆relA strains were treated with 0.25×MIC of CNMA. Total RNA was extracted at 30 and 60 minutes post-treatment in three biological replicates. Untreated cultures served as controls. High-quality RNA samples were subjected to paired-end sequencing (101 bp) using the Illumina NovaSeq6000 platform. Data were analyzed for differential expression using standard pipelines and R-based DESeq2.

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The table below lists GEO accessions reused/reanalyzed for this study.
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first: Monika

last: Karczewska


title: Uncover the molecular mechanisms underlying HNRNPF functions in ESCs [RIP-seq]

city: tianjin

first: Duan

middle: Xiao

last: wei

address: China

institute: Nankai

summary: The ERK (extracellular signal-regulated kinase) signaling pathway plays a crucial role in maintaining the self-renewal and regulating the differentiation of mouse embryonic stem cells (ESCs). However, the underlying mechanisms by which ERK exerts these effects remain incompletely understood. In this study, we identified heterogenous nuclear ribonucleoprotein F (HNRNPF) as a novel ERK2-interacting protein and phosphorylation substrate. We demonstrated that ERK2 phosphorylates HNRNPF on Ser346 and Tyr356. Hnrnpf knockout (KO) ESCs manifested impaired self-renewal, due to downregulation of CDK1 and CCNB1. Notably, phosphorylation of HNRNPF rescued CDK1 and CCNB1 expression, leading to restoring self-renewal capacity of Hnrnpf KO ESCs. Additionally, loss of HNRNPF promoted ESC differentiation toward mesoderm and trophectoderm lineages, a phenotype attributed to reduced EED expression and diminished H3K27me3 levels. Phosphorylation of HNRNPF restored EED expression and H3K27me3 levels, thereby mitigating differentiation bias in Hnrnpf KO ESCs. Collectively, our findings uncover a critical role for HNRNPF as a downstream effector of ERK2 signaling in regulating ESC self-renewal and differentiation.

overall_design: To uncovered the molecular mechanisms underlying HNRNPF functions in ESCs, we conducted RNA immunoprecipitation (RIP) experiments followed by sequencing in the FLAG-tagged HNRNPF overexpressed (OE) cell line.

first: Xiaowei

last: Duan

first: Lingyi

last: Chen


title: Comparing gene expression effects of Hnrnpf knockout in mESCs while they are pluripotent vs. after they have been differentiating for 4 days due to LIF removal [RNA-seq]

overall_design: To evaluate the differentiation potential of Hnrnpf KO ESCs, we performed RNA sequencing (RNA-seq) to profile global transcriptional changes in both differentiated and undifferentiated ESCs following HNRNPF deletion.