title: Differences in heart gene expression between aging and young mice

city: hangzhou

first: wei

last: wu

state: zhejiang

address: 2318 Yuhangtang Road, Yuhang District

department: School of Public Health

institute: Hangzhou Normal University

summary: The study of gene expression in aging heart is necessary for the study of heart disease. We raised old mice and young mice to detect gene expression differences in the heart by RNA-seq.

overall_design: Mice in the model group were fed in SPF environment until 12 months of age, and mice in the control group were fed until 8 weeks of age. Total heart RNA was extracted and RNA-seq was detected.

first: W

last: Wu

first: Ruo

middle: X

last: Lei

first: Xue

last: Fang


title: Analysis of differential gene expression in NSCLC cancer cell with or without EGFR-TKI resistance

status: Public on Mar 22 2025

city: Tainan

first: Kuan-Chung

last: Hsiao

address: 367 shengli road

country: Taiwan

institute: NHRI

type: Expression profiling by high throughput sequencing

summary: We have established a Genfitnib resistant cell line, Ire, from a NSCLC cell line, PE089, with deletion of exon 19 in EGFR. RNA-sequencing analysis was performed to analyze the diffreential gene expression between thes two cell lines

overall_design: Total RNA was extracted from PE089 or Ire cell and the differential gene expression was determined by using RNA-sequencing analysis


title: Replication stress underlies genomic instability at CTCF/cohesin-binding sites in cancer

city: Bangalore

first: Radhakrishnan

last: Sabarinathan

state: Karnataka

address: GKVK, Kodigehalli

country: India

institute: National Centre for Biological Sciences- Tata Institute of Fundamental Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: CCCTC-binding factor (CTCF) and cohesin play a significant role in the formation of chromatin loops and topologically associating domains (TADs), which influence gene expression and DNA replication. CTCF/cohesin-binding sites (CBSs) present at the loop anchors and TAD boundaries are frequently mutated in cancer; however, the molecular mechanisms underlying this remain unclear. Here, we investigate whether the binding of CTCF/cohesin on DNA imposes constraints on DNA replication, leading to replication stress and genomic instability. Our results reveal that CTCF and cohesin remain cobound to DNA during replication (S phase) in cancer cells (HeLa). Further, examination of replication stress through ChIP-seq of the DNA damage response/repair proteins (MRE11, STN1, FANCD2, γH2AX, RAD51 and ATM) showed high enrichment of these proteins at CBSs (as compared to their immediate flanking regions and control sites) and positively correlated with the binding strength of CTCF/cohesin at CBSs in the S phase. Moreover, analysis of somatic mutations from cancer genomes supports that the enrichment of mutations at CBSs is significantly higher in samples harbouring somatic copy number deletion in MRE11 and STN1 compared to wild-type samples. Together, these results demonstrate that the co-binding of CTCF/cohesin on the DNA during the S phase causes replication stress and DNA strand breaks, and this could lead to genome instability at CBSs observed in cancer.

overall_design: Chromatin Immunoprecipitation (ChIP-seq) for the ATM/ CTCF/ FANCD2/ gH2AX/ H2AX/ MRE11/ RAD21/ RAD51 were performed in Mid S synchronized HeLa cells (2mM Thymidine treatment for 16h followed by 4 h release) with or without DNA damage using 2mM HU (for 3h) or 25uM Etoposide (for 3h). Prolonged (ie, 16h) HU (2mM) treatment was performed in asynchronous HeLa cells

first: Elangoli Ebrahimkutty

last: Faseela


title: Sytemic and respiratory responses to intravenous or inhaled administration of flagellin in non-human primates

status: Public on Mar 21 2025

city: LILLE

first: Florence

last: MAURIER

address: 1 rue du Professeur Calmette BP 245

department: Plateformes Lilloises en Biologie & Santé

country: France

institute: Institut Pasteur de Lille

summary: Respiratory delivery of the Toll-like receptor 5 agonist FLAMOD, a recombinant flagellin, offers a promising approach for treating bacterial pneumonia in mouse models. This study represents the first comprehensive assessment of FLAMOD delivered by nebulization in the non-human primate Macaca fascicularis. RNA sequencing was used to establish the transcriptional response across the respiratory tract (from the nose, trachea, bronchi to the lungs) and in the blood. The findings demonstrated that innate immunity, cytokine and chemokine signaling, and chemotaxis are key biological pathways modulated by FLAMOD in the respiratory tract. Blood transcriptional response overtime after nebulization was also analyzed and compared to the response observed after intravenous injection of FLAMOD.

overall_design: Eleven female cynomolgus macaques (Macaca fascicularis, Vietnam) were administered with flagellin (FLAMOD) either by nebulization or via intravenous bolus injection (I.V.).  Nose, trachea, bronchus, and lung tissue were collected at one hour post-administration. Blood samples were sampled at varying timepoints after administration for the purpose of a kinetics analyses. All samples were  processed for RNA isolation and sequencing.

first: Jean-Claude

last: Sirard

first: Mara

last: Baldry

first: Arndt

last: Benecke


title: Interferon Tau-Dependent and -Independent Changes in the Bovine Corpus Luteum of Early Pregnancy

status: Public on Mar 24 2025

city: University Park

first: Camilla

middle: H. K.

last: Hughes

state: PA

address: 439 Shortlidge Rd

department: Animal Science

country: USA

institute: Penn State University

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

overall_design: Refer to individual Series


title: Neutrophil Extracellular Trap-borne C3-Driven Endothelial Dysfunction in Klebsiella pneumoniae Liver Abscess

city: Shenyang

first: Lulu

last: Chen

address: No. 36, Sanhao Street, Heping District

country: China

institute: Shengjing Hospital of China Medical University

summary: Klebsiella pneumoniae liver abscess (KPLA) is a severe bacterial infection complicated by intrahepatic thrombophlebitis and extrahepatic metastatic infections, leading to high mortality rates. This study investigates the role of neutrophil extracellular traps (NETs) in endothelial injury and disease progression in KPLA. Our findings demonstrate that C3 deposition on NETs significantly contributes to endothelial damage. In a KPLA mouse model, increased C3 levels were observed in the liver, with NETs carrying substantial amounts of C3, disrupting the endothelial barrier and exacerbating liver injury. Treatment with the C3 inhibitor AMY-101 reduced C3 deposition on NETs, alleviated endothelial damage, significantly improved survival, and reduced extrahepatic dissemination, inflammatory infiltration, and lung injury while also suppressing systemic inflammation. Molecular analysis revealed that the TLR4-PI3Kα-AKT signaling pathway is crucial in K. pneumoniae-induced NET formation. Our findings underscore the pivotal role of C3 in NET-mediated endothelial damage and the pathogenesis of KPLA. Thus, targeting C3 deposition on NETs may be a promising therapeutic strategy to reduce endothelial injury, thrombosis, and extrahepatic infections in KPLA without compromising neutrophil antimicrobial function.

overall_design: K. pneumoniae strains used in this study were isolated from a patient with KPLA who had intrahepatic thrombophlebitis and extrahepatic dissemination, including pulmonary abscess. For the KPLA mouse model, mice were infected with 2×10^7 CFU K. pneumoniae via the esophagus.

first: Hongguang

last: Wang

first: Chuanzhuo

first: Zhihui

last: Chang


title: Comprehensive immunophenotyping of gastric adenocarcinoma identifies an inflamed class of tumors amenable to immunotherapies

status: Public on Mar 23 2025

city: Lleida

first: Robert

last: Montal

address: Av. Alcalde Rovira Roure 80

country: Spain

institute: IRBLleida

summary: RNA from 56 gastric adenocarcinoma was analyzed on the nCounter system using the PanCancer IO 360, a curated panel including 770 genes across key immuno-oncology pathways and processes

overall_design: Frozen samples (primary gastric adenocarcinoma) from patients treated with surgical resection

first: R


title: Light induced expression of gRNA allows for optogenetic gene editing of T lymphocytes in vivo

city: Stockholm

first: Alexander

last: Espinosa

address: Visionsgatan 18

department: Dept of Medicine

country: Sweden

institute: Karolinska Institutet

summary: There is currently a lack of tools capable of perturbing genes in both a precise and spatiotemporal fashion. The flexibility of CRISPR, coupled with light's unparalleled spatiotemporal resolution deliverable from a controllable source, makes optogenetic CRISPR a well-suited solution for precise spatiotemporal gene perturbations. Here we present a new optogenetic CRISPR tool (BLU-VIPR), that diverges from prevailing split-Cas design strategies and instead focuses on optogenetic regulation of gRNA production. We engineered BLU-VIPR around a new potent blue-light activated transcription factor and ribozyme-flanked gRNA. The BLU-VIPR design is genetically encoded and ensures precise excision of multiple gRNAs from a single mRNA transcript This simplified spatiotemporal gene perturbation and allowed for several types of optogenetic CRISPR, including indels, CRISPRa and base editing. BLU-VIPR also worked in vivo with cells previously intractable to optogenetic gene editing, achieving optogenetic gene editing in T lymphocytes in vivo.

overall_design: To achieve optogenetic base editing of an endogenous gene, 4x10^4 293FT cells were seeded in black walled, optical bottom 96 well plates and transfected and transfected with 50 ng pRS0035 and 50 ng BLU-VIPR plasmids with NEAT1 targeting or non-targeting gRNA. Twenty-four hours post-transfection, cells were exposed to pulses (20 seconds ON, 60 seconds OFF) of 1 mW/cm^2 of 470 nm light for 48 hours or kept in the dark. Light-exposed cells were harvested and sorted for mCherry expression on a Sony SH800 cell sorter (Sony Biotechnology). Genomic DNA was extracted from cells exposed to light, and from cells kept in the dark, using the Monarch Genomic DNA Purification Kit following the manufacturer’s protocol (New England Biolabs). The targeted region in NEAT1 was amplified by genomic PCR. Amplicons were first sequenced by Sanger sequencing and analyzed with EditR software21. Next, to obtain precise quantification of edits, we performed Illumina sequencing. Briefly, a sequencing library was generated by equimolar pooling of indexed genomic PCR products of endogenous NEAT1. The PCR products were isolated using QIAquick Gel Extraction Kit (Qiagen) and quality control was performed with the Agilent High Sensitivity D1000 ScreenTape System (Agilent Technologies). The pooled library was sequenced using the MiSeq System with the MiSeq Micro Flow Cell (4 million reads) paired-end i7 indexed reads (150 cycles). Fastq files were demultiplexed and analyzed with CRISPResso2 for base editing.

first: Diego

last: Velaszquez Pulgarin

first: Nathalie

last: Pelo


title: Spatial transcriptome analysis for squamous cell carcinoma arising from mature teratoma

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

country: Japan

institute: Nagoya University

summary: Squamous cell carcinoma arising from mature teratoma (SCC-MT) is one of the rare ovarian malignancies. Therefore, the molecular background of SCC-MT remains largely unelucidated. In this study, we performed the spatial transcriptomics for SCC-MT.

overall_design: Archival fresh-frozen samples of SCC-MT were obtained from the National Cancer Center Biobank and Nagoya University. We prepared four slices from three patients with SCC-MT. Spatial transcriptomics was performed using the Visium Spatial Gene Expression Reagent Kits (10x Genomics) according to the manufacturer’s instructions.

first: Akira

last: Yokoi

first: Yusuke

last: Yamamoto


title: IRF1 activation and target gene induction drive all-trans retinoic acid efficacy in acute promyelocytic leukemia with potential as a predictive indicator for cancer treatment

city: Shanghai

first: Peng

last: Jin

address: Ruijin Rd. II

department: Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics

institute: Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: All-trans retinoic acid (ATRA) exhibits significant therapeutic potential in various cancers, most notably for its success in treating acute promyelocytic leukemia (APL) by promoting differentiation. Beyond differentiation, ATRA can also induce cell cycle arrest, growth inhibition, and immune modulation in both hematopoietic and non-hematopoietic malignancies. Despite these multifaceted effects, the mechanisms driving ATRA efficacy remain incompletely understood, which has hindered its application to other cancers. To investigate the molecular basis of the anti-tumor actions of ATRA, we performed detailed time-series transcriptome analyses to identify key regulatory factors involved in ATRA's early transcriptional responses. Furthermore, chromatin immunoprecipitation sequencing (ChIP-seq) and functional assays evaluated the role of the key regulator, IRF1, to determine how it drives ATRA efficiency.

overall_design: ChIP-seq profiling of IRF1 in NB4 cells treat with ATRA for 4 hours and control.

first: Wen

first: Kankan


title: Whole transcriptome analysis of mouse liver tissues after treatment with or without polystyrene microplastics

city: Taipei

first: Hui-Wen

last: Chiu

address: No.301, Yuantong Rd., Zhonghe Dist., New Taipei City

institute: Taipei medical university

summary: Six-week-old male C57BL/6 mice were orally dosed with 0.4 mg/day PS-MPs twice weekly for eight weeks. When the study ended, the mice were humanely euthanized. Their livers were harvested and the transcriptome analysis of these livers was evaluated.

overall_design: Six-week-old male C57BL/6 mice were orally dosed with 0.4 mg/day PS-MPs for 8 weeks. When the study ended, the mice were humanely euthanized, their livers were harvested, and the histology of their livers was analyzed.

first: Yu-Jhe

first: Yung-Li

first: Yu-Hsuan

last: Lee


title: The Differential Expression of Circulating MicroRNAs in Sickle Cell Trait and Sickle Cell Anemia compared to the Normal Hemoglobin Phenotype.

city: Dallas

first: Kabir

last: Olaniran

state: TX

address: 5939 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

type: Non-coding RNA profiling by high throughput sequencing

summary: The heterozygous inheritance of the sickle cell gene, called sickle cell trait (HbAS), was previously thought to be benign. HbAS is now associated with an increased risk for chronic kidney disease, pulmonary embolisms, and exertional rhabdomyolysis. The role of gene expression, as regulated by microRNAs, in these clinical HbAS associations has not been investigated. We explored the association between HbAS and the differential expression of circultaing (plasma) microRNAs when compared to the normal hemoglobin phenotype (HbAA). In stark contrast, the homozygous inheritance of the sickle cell gene, called sickle cell anemia (HbSS) is a severe disease that was previously associated with early mortality and severe morbidity. With appropriate care and early interventions, people with HbSS have improved life expectancy but still experience significant morbidity including cardiac, kidney, and pulmonary disease. The role of gene expression as regulated by microRNA in these clinical HbSS associations has not been investigated. We also explored whether the presence of HbSS is associated with the differential expression of circultaing (plasma) microRNAs as compared to the normal hemoglobin phenotype (HbAA).

overall_design: Circulating microRNA profiles in frozen plasma samples obtained from self-identified Black race human subjects with HbAS, HbSS, and HbAA selected from the Mass General Brigham Biobank. HbAA (controls) were matched to HbAS (1:1) and HbSS (1:3) based on age, sex, and eGFR. All subjects were healthy with no comorbidities.

first: Ronak

last: Lakhia

first: Scott

last: Krinsky

first: Sagar

last: Nigwekar

first: Susan

last: Hedayati


title: muscle transcriptional changes with rs6190 SNP genocopy in mice

city: Cincinnati

first: Mattia

last: Quattrocelli

state: OH

address: 240 Sabin Way

institute: Cincinnati Children's Hospital Medical Center

summary: this dataset encompasses the muscle transcriptomic changes elicited in quadriceps of 4months-old male mice comparing homozygous carriers of the rs6190 genocopy allele (homo) versus homozygous carriers of the reference allele (WT).

overall_design: Mice were obtained and interbred from the CCHMC Transgenic Core facility, genotypes were confirmed through sequencing during the first generations then routinely checked thwough PCR. Analyses were performed at ~16 weeks of age in male littermate mice from heterozygous parents. Tissues were harvested at ~ZT4 and immediately flash-frozen for downtream analyses.

first: Ashok

last: Prabakaran


title: FABP4-mediated lipid accumulation and lipolysis in tumor associated macrophages promote breast cancer metastasis

city: Iowa City

first: Henry

last: Keen

state: IA

department: Pharmacology

institute: University of Iowa

summary: Fatty acid binding protein 4 (FABP4) is known to play important roles in lipid metabolism in multple cell types including in macrophages.  In the present study, we used single cell RNA-sequencing in macrophages extracted from either wild-type or mice deficient in FABP4 to further explore the pathways downstream of FABP4 in splenic macrophages.

overall_design: Splenic macrophages from FABP4 knockout mice and control wild-type mice were examined using single cell RNA sequencing.

first: Matthew

last: Yorek

first: Xingshan

last: Jiang

first: Shanshan

last: Liu

first: Jiaqing

last: Hao

first: Jianyu

last: Yu

first: Anthony

last: Avellino

first: Zhanxu

first: Melissa

last: Curry

first: Anand

last: Kanagasabapathy

first: Maiying

last: Kong

first: Yiqin

last: Xiong

first: Sonia

last: Sugg

first: Bing

last: Li


title: RNA-seq on FFPE skin samples

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

summary: We evaluated the expression profiles on skin samples that are FFPE.

overall_design: Three FFPE skin samples were RNA-seq profiled

first: Johann

middle: E

last: Gudjonsson

first: Lam

middle: C

last: Tsoi


title: Molecular insights into human soleus muscle atrophy development: long-term dry immersion effects on the transcriptomic profile and post-translational signaling

city: Moscow

first: Roman

middle: O.

last: Bokov

state: Moscow

address: Khoroshevskoye shosse, 76A

country: Russia

institute: Institute of Biomedical Problems of the Russian Academy of Sciences

summary: Muscle disuse results in complex signaling alterations followed by structural and functional changes, such as atrophy, force decrease and slow-to-fast fiber-type shift. Little is known about human skeletal muscle signaling alterations under long-term muscle disuse. In this study, we describe the effects of 21-day dry immersion on human postural soleus muscle. We performed both transcriptomic analysis and Western blots to describe the states of the key signaling pathways regulating soleus muscle fiber size, fiber-type, and metabolism. 21-day dry immersion resulted in both slow-type and fast-type myofibers atrophy, downregulation of rRNA content, and mTOR signaling. 21-day dry immersion also leads to slow-to-fast fiber-type and gene expression shift, upregulation of p-eEF2, p-CaMKII, p-ACC content and downregulation of NFATc1 nuclear content. It also caused massive gene expression alterations associated with calcium signaling, cytoskeletal parameters, and downregulated mitochondrial signaling (including fusion, fission, and marker of mitochondrial density).

overall_design: Eight young healthy male volunteers participated in this study. Their characteristics were next: the average age is 29.3 ± 3.56 years, the height is 175.8 ± 0.03 cm, the body weight is 73.24 ± 10.97 kg, the body mass index (BMI) is 23.2 ± 3.24 kg/m2 (mean ± standard deviation). A ground-based hypogravity model, dry immersion (DI), was used as an unloading model (Figure 1). The duration of DI was 21 days. Under an immersion environment, the volunteer’s body is subjected to an impact of the buoyant force of water, and the support reactions are eliminated. The studies were carried out under standard conventional conditions, during which volunteers were placed one at a time in a pool measuring 200 x 100 x 100 cm, filled with water, in a horizontal position, the water temperature in the pool was maintained constant at +33 ± 0.5 °C. The daily routine in immersion was regulated by time intervals selected for examinations, preventive measures (if any), meals and sanitary and hygienic procedures, the participants of the study ate and slept inside the pool. The detailed description of the experiment, including diet and inclusion criteria, was published previously (17, 18). Briefly, the daily routine was as close as possible to the space station life, including 8 hours of sleep, 3 meals per day, a medical monitoring program and experimental studies. To carry out sanitary and hygienic measures, once a day the volunteers removed from the bath for 15–20 minutes. Periods of verticalization are excluded and all manipulations during the hygienic toilet of the volunteers are carried out in a horizontal position, if possible. All subjects gave written consent to participate in the experiment. The experimental protocol was approved by the Commission on Biomedical Ethics of the Institute of Biomedical Problems, Russian Academy of Sciences (Moscow, Russia) – Physiological Section of the Russian Committee on Bioethics under the Russian Federation Commission for UNESCO (protocol № 483, August 3rd, 2018). All procedures complied with the Declaration of Helsinki, international and Russian legislation.

middle: O

first: Kristina

middle: A

last: Sharlo

first: Natalia

last: Vilchinskaya

first: Sergey

last: Tyganov

first: Olga

middle: V

last: Turtikova

last: Rozhkov

first: Ruslan

middle: M

last: Deviatiiarov

first: Oleg

last: Gusev

first: Elena

middle: S

last: Tomilovskaya

first: Boris

last: Shenkman

middle: I

last: Orlov


title: Epigenetic Alteration of Smooth Muscle Cells Regulates Endothelin-Dependent Blood Pressure and Hypertensive Arterial Remodeling [km_human_mouse]

summary: Long-standing hypertension (HTN) affects multiple organs and leads to pathologic arterial remodeling, which is driven by smooth muscle cell (SMC) plasticity. To identify relevant genes regulating SMC function in HTN, we considered Genome Wide Association Studies (GWAS) of blood pressure, focusing on genes encoding epigenetic enzymes, which control SMC fate in cardiovascular disease. Using statistical fine mapping of the KDM6 (JMJD3) locus, we found that rs62059712 is the most likely casual variant, with each major T allele copy associated with a 0.47 mmHg increase in systolic blood pressure. We show that the T  allele decreased JMJD3 transcription in SMCs via decreased SP1 binding to the JMJD3 promoter.  Using our unique SMC-specific Jmjd3-deficient murine model (Jmjd3flox/floxMyh11CreERT), we show that loss of Jmjd3 in SMCs results in HTN due to decreased EDNRB expression and increased EDNRA expression. Importantly, the Endothelin Receptor A antagonist, BQ-123, reversed HTN after Jmjd3 deletion in vivo. Additionally, single cell RNA-sequencing (scRNA-seq) of human arteries revealed strong correlation between JMJD3 and EDNRB in SMCs. Further, JMJD3 is required for SMC-specific gene expression, and loss of JMJD3 in SMCs increased HTN-induced arterial remodeling. Our findings link a HTN-associated human DNA variant with regulation of SMC plasticity, revealing targets that may be used in personalized management of HTN.

overall_design: Femoral artery specimens were harvested during femoral endarterectomy, femoral-femoral bypass, or aorto-bi-femoral bypass operations.

first: Kevin

last: Mangum


title: Physiological transcriptional profiling of murine osteocytes from calvaria and long bones

city: Bethesda

first: Eva

last: Mezey

state: MD

address: 30 Convent Dr.

department: NIDCR

institute: NIH

summary: Different bones of the skeleton originate from three distinct embryonic lineages. Osteoblasts derived from bones of different embryonic origin displayed cell intrinsic difference. Osteocytes are terminally differentiated osteoblasts which displays a unique genetic makeup and a distinct morphology. It is not know if osteocytes display a cell intrinsic differences depeding on their origin. To understand the difference in the gene expression profiles of osteocytes of three different embryonic origins we examined osteocytes from three different bones neural crest origin-frontal bone, paraxial mesoderm origin-parietal bone, and lateral plate mesoderm- femur bone.

overall_design: Examine the changes in the transcriptome in frontal, parietal and femur osteocytes.

first: Vamsee

middle: D

last: Myneni

first: Martin

last: Daniel


title: Chronic morphine treatment leads to a global DNA hypomethylation via active and passive demethylation mechanisms in mESCs

city: Leioa

first: Iraia

middle: Maialen

last: Muñoa Hoyos

state: Bizkaia

address: Barriso Sarriena S/N

institute: Universidad del País Vasco

type: Methylation profiling by high throughput sequencing

summary: Epigenetic changes are essential for normal development and ageing, but there is still limited understanding of how environmental factors can cause epigenetic changes that leads to health problems or diseases. Morphine is known to pass through the placental barrier and impact normal embryo development by affecting the neural tube, frontal cortex and spinal cord development, and, as a consequence, delaying nervous system development. In fact, in-utero morphine exposure has shown alterations in anxiety-like behaviours, analgesic tolerance, synaptic plasticity and the neuronal structure of offspring. However, how morphine leads to abnormal neurogenesis and other physiological consequences during embryo development is still unknown. Considering that DNA methylation is a key epigenetic factor crucial for embryo development, our aim is to elucidate the role of methylation in response to morphine. Chronic morphine treatment (24h, 10μM) induces a global hypomethylation in mESC.  WGBSeq identifies 16,808 sensitive to morphine which are involved in embryo development, signalling pathways, metabolism and/or gene expression, suggesting that morphine might impact methylation levels at developmental genes. Integrative analyses between WGBSeq and RNASeq identified Tet1 as morphine-sensitive gene. Morphine increased the gene expression of Tet1, modifying the methylation levels at the promoter. On the other hand, RNASeq and qRT-PCR analyses revealed that Dnmt1 gene expression decreased after morphine treatment, without altering the methylation patter at its promoters. By MS/MS approaches confirms a decrease in DNA methylation after chronic morphine treatment, together with an increase in hydroxymethylation global levels in mESCs. In conclusion, morphine induces a global hypomethylation in mESC through different mechanisms that involves passive demethylation and a self-regulatory mechanism via active demethylation.

overall_design: Examination of methylation profiles using methylation sequencing data of control mESCs and morphine treated mESCs

first: Manu

last: Araolaza-Lasa

last: Muñoa-Hoyos

first: Itziar

last: Urizar-Arenaza

first: Ainize

last: Odriozola

first: Irune

last: Calzado

first: Mikel

last: Albizuri

first: Nerea

last: Subiran Ciudad


title: Biobank of genetically defined murine prostate cancer tumoroids uncovers oncogenic pathways and drug vulnerabilities driven by PTEN-loss

city: Vienna

first: Gerda

last: Egger

address: Waehringer Guertel 18-20

department: Pathology

country: Austria

institute: Medical University of Vienna

summary: Prostate cancer (PCa) is the second most common cancer in men and shows high inter- and intra-patient heterogeneity. Thus, treatment options are limited and there is a lack of representative preclinical models. Here we establish a biobank of murine organoids and tumoroids that reflect common patient mutations. The deletion of Pten alone, or in combination with Stat3, or Tp53, led to an upregulation of cancer-related pathways in organoids and in tissue-derived tumoroids. By performing a medium-throughput drug screen we identify two compounds, the PDPK1/AKT/FLT dual pathway inhibitor and tenovin-6, that effectively inhibited tumoroid growth. Additionally, these compounds inhibited the growth of several human PCa cell lines and could be used in combination with Enzalutamide. Overall, we provide evidence that murine tumoroids are versatile preclinical models for studying PCa tumorigenesis and drug sensitivities to develop novel therapeutic options for PCa patients.

overall_design: We derived prostate organoids from healthy mice with lox sites for Pten alone, or Pten/Stat3, or Pten/Tp53. These mice were bred with Cre-expressing mice to generate knock out mice for the respective genotypes. We then derived prostate cancer tumoroids from the tumours of Pten KO, Pten/Stat3 KO, or Pten/Tp53 KO mice. We transduced healthy organoids carrying lox sites for the respective genes in vitro with a Cre-lentivirus to induce the deletion. We then generated single clones from these KO tumoroids. We also transduced healthy organoids with a non-functional Cre as a control and derived single clones from those. Differential gene expression was done on biological replicates for all wildtype and KO genotypes or single clones (N=3).

first: Jessica

last: Kalla

first: Kristina

last: Draganič


title: Single cell RNA sequencing analysis of Mig-6 mutant mouse reveals progesterone susceptibility genes for uterine receptivity

city: Columbia

first: Shamsun

last: Nahar

state: MO

address: 1030 Hitt Street

department: Obstetrics, Gynecology and Women’s Health

institute: University of Missouri

summary: The majority of pregnancy losses result from implantation failure. Successful embryo implantation involves a delicate interaction between the receptive uterus and an implantation-competent blastocyst. Understanding the mechanisms regulating the endometrial receptivity during preimplantation are essential for improving pregnancy outcomes. Mitogen-inducible gene 6 (MIG-6) is a key mediator of progesterone signaling in the endometrium.MIG-6 loss results in implantation failure due to non-receptive endometrium. We applied single cell RNA sequencing to determine the composition of different cell types and functions within non-receptive endometrium from uterine specific Mig-6 knock-out (Pgrcre/+Mig-6f/f; Mig-6d/d) mice. Mig-6d/d mice revealed altered gene expression in the epithelial and stromal cells. We identified key gene expression changes in the non-receptive endometrium of Mig-6d/d mice, providing valuable insights into the role of progesterone signaling in implantation.

overall_design: At pregnancy day 3.5, the scRNA-seq was performed using Mig-6f/f and Mig-6d/d (Pgrcre/+ Mig-6f/f) mouse uterus (n=1). Immunohistochemistry was done to varify the changes between clusters Mig-6f/f and Mig-6d/d.

first: Kim

last: Tae Hoon

first: Jeong

last: Jae Wook


title: HaloPROTAC3 treatment activates the unfolded protein response of the endoplasmic reticulum in non-engineered mammalian cells

first: Aleksandra

last: Anisimova

address: Dr. Bohr Gasse 9

institute: Max Perutz Labs, Vienna BioCenter, University of Vienna, Medical University of Vienna

summary: Proteins fused to HaloTag, an engineered haloalkane dehalogenase, can be depleted by a heterobifunctional degrader compound HaloPROTAC3. The binding of HaloPROTAC3 to both the HaloTag and the E3 ligase von Hippel-Lindau (VHL) brings them into proximity and mediates the degradation of the HaloTag fusion proteins. Here, we generated a colon cancer cell line HCT116 expressing HaloTag fused to the RNA-binding protein IGF2BP3 to study its function. HaloPROTAC3 treatment depleted 75% of HaloTag-IGF2BP3 in 5 hours. Transcriptomics revealed that HaloPROTAC3 treatment resulted in the destabilization of IGF2BP3 target mRNAs and activated the unfolded protein response (UPR). Surprisingly, we found that HaloPROTAC3 treatment results in UPR activation in non-engineered mammalian cells. Our data demonstrate that HaloPROTAC3 causes mild endoplasmic reticulum stress independent of IGF2BP3 function and shall guide future studies using the HaloPROTAC3 protein depletion strategy.

overall_design: SLAMSeq of HCT116 cells expressing endogenously tagged HaloTag-IGF2BP3 upon HaloPROTAC3 treatment

first: G

last: Karagöz


title: Activation of T-regulatory cells during allograft tolerance-induction requires mitochondrial-induced TGFB1 in type 1 conventional dendritic cells

city: Chicago

first: Samantha

middle: L

last: Schroth

state: IL

address: 320 E Superior St

institute: Northwestern University Feinberg School of Medicine

summary: The role of type 1 conventional dendritic cells (cDC1) in tolerance-induction to solid organ allografts is unknown and important for strategies that seek to prolong allograft viability. Utilizing a murine model deficient in cDC1s, we report cDC1s to be required for donor antigen and costimulation blockade (DST + CoB) tolerance-induction and survival of cardiac allografts. Single-cell RNA sequencing and metabolic analysis revealed upregulation of cDC1 mitochondrial metabolic signatures after in vivo exposure to DST + CoB. Genetic inactivation of cDC1 mitochondrial metabolism reduced both expression of cDC1 TGF-β1 and induction of antigen specific CD4+CD25+FoxP3+ T cells.

overall_design: Splenic cells magnetically enriched for DCs and CD45+ cells from mice infused with allogenic BALB/c splenocytes and 500μg anti-CD40L (LACoB) antigen 48 hours prior and subjected to single cell RNA sequencing.

first: Schroth

last: Samantha

first: Thorp

last: Edward


title: Asparagine availability controls B cell homeostasis

city: Oxford

first: Alexander

last: Clarke

address: Roosevelt Drive

department: Kennedy Institute of Rheumatology

country: United Kingdom

institute: University of Oxford

summary: Study of the effects of asparagine deprivation on germinal centre B cells.

overall_design: B-WT or B-Asns mice were assigned to either an Asn-free or control diet (Asn-replete) for 12 days, before immunisation with 100μg NP-CGG precipitated in Alum hydrogel (1:1) intraperitoneally and sacrificed on day 14 for scRNAseq analysis of splenic GC B cells. GC B cells were sorted by flow cytometry (CD19+CD38-GL-7+). Each batch contains cells from 4 mice (one from each experimental condition), labelled with Biolegend TotalSeq C Cell Hashing antibodies.

middle: J


title: Myeloid Fatty Acid Metabolism Activates Neighboring Hematopoietic Stem Cells to Fuel Heart Failure with Preserved Ejection Fraction

status: Public on Mar 20 2025

first: Edward

last: Thorp

address: 303 E Chicago Ave

institute: Northwestern University

summary: Background: Despite the high morbidity and mortality of heart failure with preserved ejection fraction (HFpEF), treatment options remain limited. The HFpEF syndrome is associated with a high comorbidity burden, including high prevalence of obesity and hypertension. While inflammation is implicated to play a key role in HFpEF pathophysiology, underlying causal mechanisms remain unclear. Methods: Comparing patient samples and animal models, we defined the innate immune response during HFpEF in situ and through flow cytometry, and single cell RNA sequencing. After identification of transcriptional and cell signatures, we implemented a high fat diet and hypertensive model of HFpEF and tested roles for myeloid and hematopoietic stem cells (HSCs) during HFpEF. Contributions of macrophage metabolism were also evaluated, including via mass spectrometry and carbon labelling. Primary macrophages were studied ex vivo to gain insight into complementary cell- intrinsic mechanisms. Results: Here we report evidence that patients with cardiometabolic HFpEF exhibit elevated peripheral blood hematopoietic stem cells (HSCs). This phenotype was conserved across species in a murine mode of high fat diet and hypertension. HSC proliferation was coupled to striking remodeling of the peripheral HSC niche, and expression of the macrophage adhesion molecule Vcam1. This could be partially inhibited by SGLT2 inhibitors and explained by elevated fatty acid metabolism in macrophage mitochondria, which in turn remodeled the Vcam1 promoter to enhance its expression. Conclusion: These findings identify a significant new stem cell signature of cardiometabolic HFpEF and support a role for myeloid maladaptive fatty acid metabolism in the promotion of systemic inflammation and cardiac diastolic dysfunction.

overall_design: Adult male mice were treated with control diet, HFD only, L-NAME only, or HFD + LNAME for 5 weeks. Immune cells were then collected from the heart or spleens and analyzed via scRNAseq

first: Mallory

last: Filipp

first: Zhi-Dong

last: Ge

first: Matthew

last: DeBerge

first: Connor

last: Lantz

first: Kristofor

last: Glinton

first: Peng

last: Gao

first: Sandra

last: Smolgovsky

first: Jingbo

last: Dai

first: You-Yang

last: Zhao

first: Laurent

last: Yvan-Charvet

first: Pilar

last: Alcaide

first: Sam

last: Weinberg

first: Gabriele

last: Schiattarella

first: Joseph

last: Hill

last: Feinstein

first: Sanjiv

last: Shah


title: Revealing RNA poly(A) tail dynamics during spermiogenesis and its function to support male fertility [dRNA-seq_mutants]

city: Durham

first: Marcos

last: Morgan

address: 111 TW Alexander Dr

institute: NIEHS

summary: TENT5C is a terminal nucleotidyltransferase with mRNA polyadenylation activity, required for the fastening of the flagella and the head of the sperm. However, TENT5C’s role in shaping the poly(A) tail of the elongating spermatid transcriptome remains limited. Here we show that the poly(A) polymerase activity of TENT5C is required for fertility and spermiogenesis: male mice expressing catalytically inactive TENT5C (Tent5cdCat/dCat) are sterile and produce headless spermatozoa phenocopying TENT5C-deficient animals. We found that the transcript encoding for the structural proteins SMCP and ODF1 are directly targeted by TENT5C. We propose a model in which TENT5C secures the fastening of the flagella to the head of the sperm by targeting ODF1 in elongating spermatids.

overall_design:
Round (RS) and elongated (ES) spermatids were isolated from adult mice testis using Hoescht/PI staining and FACS sorting.
Cells were isolated from wt/wt male mice or mice expressing a catalytically inactive TENT5C (Tent5cdcat/dcat). Each replicate is representative of a pool of 3 individual mice - 3 replicates per condition were considered for analysis.
Nanopore technologies were used to sequence the transcriptome of round and elongated spermatids. Data were processed to measure the poly(A) tail length and the presence of 3'-end addition to mRNAs.

first: Marine

last: Baptissart

first: Ankit

last: Gupta

first: Brian

middle: N

last: Papas


title: muscle GR epigenomic changes with rs6190 SNP genocopy [ChIP-seq]

first: Mattia

last: Quattrocelli

summary: this dataset encompasses the muscle GR epigenomic changes elicited in 4-month-old mice by the rs6190 genocopy allele

overall_design: We compared 4 months-old mice (C57BL/6J background) homozygous for the rs6190 SNP genocopy allele (R24K-homo) vs homozygous for the reference allele (R24K-WT). Quadriceps muscles were collected at ~ZT4 and immediately flash frozen for further processing.

first: Ashok

last: Prabakaran


title: Gene expression profiling of LNCaP, LNCap-abl and 22Rv1 cells following transfection with toxic siRNAs (siGUGUGUA, siUGUUUGC), siAR or non-target control as indicated

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

institute: OMRF

summary: Analysis of RNA expression in LNCaP and 22Rv1 cells following transfection with siUGUUUGC or siGUGUGUA siRNAs. 22Rv1 cells were also transfected with siRNA targeting AR as a positive control for reduced AR transcriptional activity. We report global changes in AR regulated gene expression  expression.

overall_design: 22Rv1 cells were grown in RPMI supplemented with 10% charcoal-stripped FBS (CSS) in the presence  (+ ) or absence of  dyhidrotestosterone (DHT) for six days prior to siRNA transfectios. LNCaP cells were maintained in RPMI supplemented with 10% FBS. LNCaP-abl were grown in RPMI suplemented with 10% CSS. RNA was extracted 40 hrs, 48 hrs and 64 hrs after siRNA transfections in LNCaP, LNCap-abl  and 22Rv1 cells, respectively . Each sample was run in tiplicate.

first: Joshua

last: Corbin

first: M

last: Ruiz Echevarria


title: Elevated brain manganese induces motor disease by up-regulating the kynurenine pathway of tryptophan metabolism

city: Austin

first: Anna

last: Warden

address: 2500 Speedway

institute: University of Texas at Austin

summary: Elevated brain levels of the essential metals manganese (Mn), copper, or iron induce motor disease. However, mechanisms of metal-induced motor disease are unclear and treatments are lacking. Elucidating the mechanisms of Mn-induced motor disease is particularly important because occupational and environmental Mn overexposure is a global public health problem. To address this, here we combined unbiased transcriptomics and metabolomics with functional studies in a mouse model of human environmental Mn exposure. Transcriptomics unexpectedly revealed that Mn exposure up-regulated expression of metabolic pathways in the brain and liver. Notably, genes in the kynurenine pathway of tryptophan metabolism, which produces neuroactive metabolites that impact neurological function, were up-regulated by Mn. Subsequent unbiased metabolomics revealed that Mn treatment altered kynurenine pathway metabolites in the brain and liver. Functional experiments then demonstrated that pharmacological inhibition of the first and rate-limiting step of the kynurenine pathway fully rescued Mn-induced motor deficits. Finally, elevated Mn directly activates hypoxia-inducible factor (HIF) transcription factors, and additional mechanistic assays identified a role for HIF1, but not HIF2, in regulating expression of hepatic kynurenine pathway genes under physiological or Mn exposure conditions, suggesting that Mn-induced HIF1 activation may contribute to the dysregulation of the kynurenine pathway in Mn toxicity. These findings (1) identify the upregulation of the kynurenine pathway by elevated Mn as a fundamental mechanism of Mn-induced motor deficits; (2) provide a pharmacological approach to treat Mn-induced motor disease; and (3) should broadly advance understanding of the general principles underlying neuromotor deficits caused by metal toxicity.

overall_design: To analyze manganese (Mn) exposure-induced gene expression changes that may influence motor function in an unbiased manner, we performed 3’Tag-seq analyses in brain, liver and small intestine tissue collected from ~2-month old vehicle or Mn-treated (~50mg MnCl2.4H20/kg body weight daily) C57BL/6J mice.

first: Nishant

last: Sharma

first: Steven

last: Hutchens

first: Chunyi

last: Liu

first: Noah

middle: R

last: Haggerty

first: Kerem

last: Gurol

first: Thomas

last: Jursa

first: Donald

last: Smith

first: Dayne

last: Mayfield

first: Somshuvra

last: Mukhopadhyay


title: Transcriptional profiles of mouse melanocytes 27 days after neonatal BRAF activation and UVB radiation or LKB1 loss

city: Barcelona

first: Juan

middle: Ángel

last: Recio

state: Cataluña

address: Passeig Vall d'Hebron 119-129

department: Oncology

institute: Vall d'Hebron Research Institute (VHIR)

summary: BRAFV600E-induced cell growth arrest in melanocytic nevus is on debate where only one third of melanomas arise directly from nevi. We showed that simultaneous neonatal oncogene (BRAFV600E) activation and UVB irradiation prevent BRafV600E-induced growth arrest in melanocytes, allowing melanoma development. A meta-analysis of gene expression profiles of melanocytes isolated from different mouse models and numerous studies revealed multiple common genes and processes involved in preventing BRafV600E-induced growth arrest. In humans, many of these genes are associated with poor survival and are upregulated during melanoma progression and in many RAS pathway activation-driven tumors. Single-cell profiling confirmed that BRAFV600E and the identified genes cooperate in melanocyte transformation, including the acquisition of multidrug resistance features. Depletion of these genes in vitro and in vivo revealed the utility of the encoded proteins as therapeutic targets. These results support the existence of BRAFV600E-mutated melanomas unassociated with nevus progression and identify targets for melanoma treatment.

overall_design:
There are a total of 14 samples, 11 of them were obtained from mouse melanocytes derived from Tyr::CreERT2,BRafCA  mouse model, untreated (3 replicates), treated with 4-Hydroxytamoxifen (4OHT) (1µM; 48 hours) (4 replicates) and 4OHT-treated, also irradiated with UVB (30J/m2) (4 replicates). The rest of the samples (3 samples) were obtained from melanocytes derived from the Tyr::CreERT2; BRafCA/CA;Lkb1F/F mouse model, treated with 4OHT (3 replicates).
Please note that different combination of samples has been used in two different analyses and the re-analyzed samples represent the common samples in both analyses.

first: Kimberley

last: McGrail


title: Remodeling of tissue-resident macrophages by MEF2D-expressing cancer precursors primes for liver tumorigenesis [scRNA-Seq]

city: chongqing

first: li

last: ni

state: State...

address: chongqing univeristy

department: Oncology laboratory

institute: chongqing univeristy

summary: To investigate the role of MEF2D in liver tumorgenesis, we established the MEF2D WT and MEF2D KO DEN-induced mice

overall_design: Comparative gene expression profiling analysis of scRNA-seq data for Mef2d KO and Mef2d WT eHCC  cells


title: Transcript abundance in C. necator grown with piezo-stimulated ZnO

city: Wuhan

first: Pier-Luc

last: Tremblay

state: Hubei

address: 122 Luoshi Road

department: School of Chemistry, Chemical Engineering and Life Science

institute: Wuhan University of Technology

summary: The transcriptome of C. necator H16 grown autotrophically with H2:CO2:O2 in the presence of piezocatalytic ZnO nanosheets under intense tilting agitation at 200 rpm

overall_design: Illumina RNA-seq of total RNA extracted from C. necator H16 grown for 36 hours with H2:CO2:O2 (74:13:13) and 0.8 g/L ZnO nanosheets in nitrogen-limited minimal medium at 30 ℃ under intense tilting agitation at 200 rpm

first: Ziqiu

last: Li

first: Mengying

last: Xu

first: Chun

last: He

first: Yujie

last: Wang

first: Tian

last: Zhang


title: Single cell landscape of transdifferentiation using chemical components

city: Hanzhou

first: Guoji

last: Guo

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

institute: Center for Stem Cell and Regenerative Medicine

summary: We construct a  time-series atlas of in vitro mouse cell transdifferentiating atlas (MCTA) using chemical components, to reveal the gene regulatory networks which govern lineage development.

overall_design: We generated time-series RNA and ATAC sequencing data during trans-differentiation using chemical components 6TCF (E616452,Tranylcypromine, CHIR99021, FSK)).

first: Xiaoping

last: Han

first: Lijiang

last: Fei

first: Weigao

last: E


title: Remodeling of tissue-resident macrophages by MEF2D-expressing cancer precursors primes for liver tumorigenesis [RNA-Seq]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Mef2d KO and Mef2d WT eHCC  cells;Comparative gene expression profiling analysis of RNA-seq data for KC1 and KC2


title: Cancer hotspot mutations rewire ERK2 specificity by selective exclusion of docking interactions

city: New Haven

first: Jaylissa

middle: Marie

last: Torres Robles

state: CT

address: 333 Cedar St. Department of Pharmacology, Yale School of Medicine

department: Chemistry and Pharmacology

institute: Yale University

summary: The protein kinase ERK2 is recurrently mutated in human squamous cell carcinomas and other tumors. ERK2 mutations cluster in an essential docking recruitment site that interacts with short linear motifs found within intrinsically disordered regions of ERK substrates and regulators. Cancer-associated mutations do not disrupt ERK2 docking interactions altogether but selectively inhibit some interactions while sparing others. However, the full scope of disrupted or maintained interactions remains unknown, limiting our understanding of how these mutations contribute to cancer. We recently defined the docking interactome of wild-type ERK2 by screening a yeast two-hybrid library of proteomic short linear motifs.  Here, we apply this approach to the two most recurrent cancer-associated mutants. We find that most sequences binding to WT ERK2 also interact with both mutant forms. Analysis of differentially interacting sequences revealed that ERK2 mutants selectively lose the ability to bind sequences conforming to a specific motif. We solved the co-crystal structure of ERK2 in complex with a peptide fragment of ISG20, a screening hit that binds exclusively to the WT kinase. This co-crystal structure demonstrates the mechanism by which cancer hotspot mutations at Glu81, Arg135, Asp321, and Glu322 selectively impact peptide binding. Finally, we found that cancer-associated ERK2 mutations had a decreased ability to phosphorylate GEF-H1/ARHGEF2, a known ERK substrate harboring a WT-selective docking motif. Collectively, our studies provide a structural rationale for how a broad set of interactions are disrupted by ERK2 hotspot mutations, suggesting mechanisms for pathway rewiring in cancers harboring these mutations.

overall_design: High throughput yeast two hybrid Illumina sequencing to determine the docking site interactions between ERK2 cancer-asociated hotspot mutants D319N and E320K (rat numbering) and a library of  ELK1 variants. In the library the native MAPK docking interacting sequence in ELK1 is replaced by short linear motifs found in human proteins. Library representation is evaluated after two cycles of competitive selection.  DNA is  extracted from same size aliquots after each cycle  and the D-site coding sequence was PCR-amplified with Illumina  barcoding primers to determine sequence representation per cycle. Samples were pooled and sequenced on an Illumina HiSeq 4000 instrument with 100-bp paired end reads. Screens with ERK2 D319N and E320K mutants were performed three times independently.

first: Benjamin

last: Turk


title: Genomic crosstalk between carbachol, a muscarinic receptor agonist, and indacaterol, a long-acting, β2-adrenoceptor agonist, in human airway epithelial cells

city: Calgary

first: Mark

last: Giembycz

state: Alberta

address: 3280 Hospital Drive NW

department: Physiology & Pharmacology

country: Canada

institute: University of Calgary

summary: Many patients with chronic obstructive pulmonary disease (COPD) are susceptible to recurrent exacerbations. Long-acting, muscarinic receptor antagonists protect against exacerbations suggesting that endogenous acetylcholine (ACh) could be a pro-inflammatory mediator. This idea was explored by determining if carbachol (CCh), a stable ACh analog, was a genomic stimulus in BEAS-2B bronchial epithelial cells. The ability of CCh to interact with indacaterol (Ind), a long-acting, β2-adrenoceptor agonists (LABA), was also assessed because sympathomimetic bronchodilators can promote the expression of adverse-effect genes in airway structural cells that are often regulated by the same transcription factors. Checkerboard assays using BEAS-2B cells expressing a cAMP response element luciferase reporter determined that CCh was a weak stimulus but interacted with Ind in a supra-additive manner. Likewise, mRNA-seq revealed that CCh regulated only 20 genes in BEAS-2B cells whereas Ind and Ind+CCh were powerful genomic stimuli affecting 869 and 1027 unique mRNAs, respectively. Of those, 39 genes were induced by Ind+CCh in a supra-additive manner; for the remainder, the interaction was either additive or infra-additive. Functional annotation of the Ind-regulated transcriptome identified transcription and signaling as dominant themes with gene ontology (GO) terms associated with inflammation and immune processes being highly represented. A comparable GO signature was obtained in the presence of CCh; however, the number, magnitude and duration of gene expression changes were markedly enhanced. If genomic interactions occur between a LABA and ACh in vivo, then this may lead to the expression of adverse-effect genes that, paradoxically, could maintain features of lung pathology in COPD.

overall_design: Confluent BEAS-2B cells were treated for one, two, six and eighteen hours with either vehicle (NS), indacaterol (100 nM), carbachol (10 µM), mometasone (100 nM), or the combination of mometasone and indacaterol, mometasone and carbachol, indacaterol and carbachol, or all three in combination. Total RNA was extracted, quantified, processed into mRNA libraries, and sequenced across two high-throughput sequencing kits on a NextSeq 500 instrument (Illumina). Samples from 5 replicates were submitted for sequencing.

first: Varuna

last: Jayasinghe

first: Taruna

last: Joshi

first: Radhika

first: Mahmoud

last: Mostafa

first: Oleg

last: Iartchouk

first: Ashley

last: Mallet

first: Melody

last: Morris

first: Vera

last: Ruda

first: Yanqun


title: A novel Induced-recurrence PDX model recapitulates epi-genomic features of Glioblastoma recurrence [RNA-seq]

city: London

first: James

last: Nicholson

address: 4 Newark St

department: Blizard Institute

institute: Queen Mary University of London

summary: Glioblastoma remains incurable and, due to its infiltrative growth, high levels of treatment resistance and population of glioma initiating/stem cells (GICs), recurs in all patients. Here we design and characterize a novel induced-recurrence model in which mice xenografted with primary patient-derived GICs are treated with a therapeutic regimen closely recapitulating patient standard of care, followed by monitoring until tumours recur (IR-PDX). By tracking in vivo tumour growth, we confirm the patient specificity and initial efficacy of treatment prior to recurrence. Availability of longitudinally matched pairs of primary and recurrent GICs enabled patient-specific evaluation of the faithfulness with which the model recapitulated phenotypes associated with the true recurrence. Through comprehensive multi-omic analyses, we showed that the IR-PDX model recapitulated genomic, epigenetic, and transcriptional state heterogeneity changes upon recurrence in a patient-specific manner. The accuracy of the IR-PDX enabled both novel biological insights, including the positive association between glioblastoma recurrence and levels of ciliated neural stem cell-like tumour cells, and the identification of druggable patient-specific therapeutic vulnerabilities. This proof-of-concept study opens the possibility for prospective precision medicine approaches, in which the IR-PDX model is developed between first diagnosis and disease progression to identify target-drug candidates for use as second line of treatment at recurrence.

overall_design:
RNAseq of 2 paired  primary and recurrent Gliobalstoma tumor samples, alongside patient derived glioma initiating cells (GIC) extracted from human tumors and murine xenograft models
Silvia Marino

first: Sara

last: Luchinni


title: A novel Induced-recurrence PDX model recapitulates epi-genomic features of Glioblastoma recurrence [scRNA-seq]

overall_design: scRNAseq of murine PDX models of primary and recurrent Glioblastoma.

first: Silvia

last: Marino


title: Control of Inflammatory Response by Tissue Microenvironment [ChIP-Seq]

first: Scott

middle: Dean

last: Pope

state: Connecticut

address: 300 Cedar St

department: Immunobiology

institute: Yale School of Medicine

summary: Inflammation is an essential defense response but operates at the cost of normal functions. Whether and how the negative impact of inflammation is monitored remains largely unknown. Acidification of the tissue microenvironment is associated with inflammation. Here we investigated whether macrophages sense tissue acidification to adjust inflammatory responses. We found that acidic pH restructured the inflammatory response of macrophages in a gene-specific manner. We identified mammalian BRD4 as a novel intracellular pH sensor. Acidic pH disrupts the transcription condensates containing BRD4 and MED1, via histidine-enriched intrinsically disordered regions. Crucially, decrease in macrophage intracellular pH is necessary and sufficient to regulate transcriptional condensates in vitro and in vivo, acting as negative feedback to regulate the inflammatory response. Collectively, these findings uncovered a pH-dependent switch in transcriptional condensates that enables environmental sensing to directly control inflammation, with a broader implication for calibrating the magnitude and quality of inflammation by the inflammatory cost.

overall_design: Chip-seq of murine bone-marrow derived macrophages (BMDMs) unstimulated at pH 7.4,  LPS stimulated at pH 7.4, unstimulated at pH 6.5, and LPS stimulated at pH 6.5 with histone modifications, IRF3 and NF-kB p65

first: Xu

last: Zhou


title: MEG3 Upregulation in Myotonic Dystrophy and Its Correction by Antisense Conjugates Targeting Disease-Causing Mutations [mRNA-seq]

first: David

last: Seoane Miraz

address: IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Drive, Headington

department: Paediatrics

summary: MEG3 upregulation has been confirmed to independently promote apoptosis in cancer, cardiovascular disease, and Alzheimer’s Disease. In this study, we unveiled that MEG3 is highly upregulated in Myotonic Dystrophy 1 (DM1) human muscle cells when compared with wild type cells. It is also increased in the muscle of DM1 mouse models, 15-fold in HSA-LR, and 6-fold in LC15. We also observed an increase of MEG3 in SMA mice (5-fold) indicating that MEG3 levels could play a role in the neuromuscular pathology leading to cell loss. Additionally in DM1, RNA sequencing revealed transcript retention of miRNAs and LncRNAs in the nucleus versus the cytoplasm, a phenomenon not observed with mRNAs. This nuclear retention could exacerbate pathological mechanisms involving non-coding RNA, such as MEG3-led apoptosis. In DM1 mice (HSA-LR), the correction of DM1 pathology with a peptide antisense oligonucleotide conjugate targeting the repeat expansion, a family of compounds currently being tested in a DM1 clinical trial, was able to also reduce the levels of MEG3. When direct interventions for the root cause of a disease are unavailable, the downregulation of MEG3 and its effect on apoptosis may serve as an alternative therapeutic approach, notably in conditions that arise from complex interactions of genetic and environmental factors.

overall_design: To detect misregulated lncRNAs in sub-cellular compartments from healthy and DM1 affected human myotubes, we used PARIS kit to fraction human myotubes into nucleus and cytoplasm fractions. Then RNA-Seq was performed and expression levels of lncRNAs were determined.

last: Seoane-Miraz

first: Miguel

last: Varela

first: Matthew

last: Wood


title: Control of Inflammatory Response by Tissue Microenvironment

overall_design: ATAC-seq of murine bone-marrow derived macrophages (BMDMs) unstimulated at pH 7.4,  LPS stimulated at pH 7.4, unstimulated at pH 6.5, and LPS stimulated at pH 6.5.


title: Single cell transcriptomic studies of an Antigen-Specific Dual Microparticle Treatment of a Mouse Model of Multiple Sclerosis

city: Tampa

first: Dorina

last: Avram

state: Fl

address: 12902 Magnolia Drive, MRC4

department: Department of Immunology

institute: Moffitt Cancer Center

summary: A microparticle system using GMCSF, TGF-b, and VD3 along with disease specific antigen (Myelin Oligodendrocyte Protein) shows effiacy in treating a mouse model of multiple sclerosis, while GMCSF, TGF-b, and VD3 and irrelevant OVA antigen did not reduce scores. Here we show that pro-inflammatory and cell cycle genes are downregulated in multiple populations. scRNA-seq further revealed a reduction in antigen-presentation gene signature.

overall_design: One pair of mice was from the spinal cord and two mice from the ingunial lymph nodes. Mice treated with an antigen-specific microparticle system were compared to mice treated with an irrelevant antigen. Results compared OVA and MOG in the CNS and OVA vs. MOG in the lymph node separately.

first: Alex

last: Kwiatkowski

first: Eric

last: Helm

first: Benjamin

last: Keselowsky


title: A novel Induced-recurrence PDX model recapitulates epi-genomic features of Glioblastoma recurrence [DNA methylation EPIC]

type: Methylation profiling by genome tiling array

summary: Glioblastoma remains incurable and, due to its infiltrative growth, high levels of treatment resistance and population of glioma initiating/stem cells (GICs), recurs in all patients. Here we design and characterize a novel induced-recurrence model in which mice xenografted with primary patient-derived GICs are treated with a therapeutic  regimen closely recapitulating patient standard of care, followed by monitoring until tumours recur (IR-PDX). By tracking in vivo tumour growth, we confirm the patient specificity and initial efficacy of treatment prior to recurrence.  Availability of longitudinally matched pairs of primary and recurrent GICs enabled patient-specific evaluation of the faithfulness with which the model recapitulated phenotypes associated with the true recurrence. Through comprehensive multi-omic analyses, we showed that the IR-PDX model recapitulated genomic, epigenetic, and transcriptional state heterogeneity changes upon recurrence in a patient-specific manner. The accuracy of the IR-PDX enabled both novel biological insights, including the positive association between glioblastoma recurrence and levels of ciliated neural stem cell-like tumour cells, and the identification of druggable patient-specific therapeutic vulnerabilities. This proof-of-concept study opens the possibility for prospective precision medicine approaches, in which the IR-PDX model is developed between first diagnosis and disease progression to identify target-drug candidates for use as second line of treatment at recurrence.

overall_design: DNAme of 2 longitudinally-paired  primary and recurrent Gliobalstoma tumor samples, alongside patient derived glioma initiating cells (GIC) extracted from human tumors and murine xenograft models seeded with primary or recurrent GICs.


title: HDAC7 promotes renal cancer metastasis by reprogramming branched-chain amino acid metabolism

city: Birmingham

first: Sunil

last: Sudarshan

state: Alabama

address: 1824 6th Avenue South

department: Urology

institute: UAB

summary: Clear cell renal cell carcinoma (ccRCC), the most common subtype of kidney cancer, exhibits significant metabolic reprogramming. We previously reported elevated HDAC7, a class II histone deacetylase, in ccRCC. Here, we demonstrate that HDAC7 promotes aggressive phenotypes and in vivo tumor progression in RCC. HDAC7 suppresses the expression of genes mediating branched-chain amino acid (BCAA) catabolism. Notably, lower expression of BCAA catabolism genes is strongly associated with worsened survival in ccRCC.  Suppression of BCAA catabolism promotes expression of SNAIL1, a central mediator of aggressive phenotypes including migration and invasion. HDAC7-mediated suppression of the BCAA catabolic program promotes SNAI1 mRNA transcription via NOTCH signaling activation. Collectively, our findings provide new insights into the role of metabolic remodeling in ccRCC tumor progression.

overall_design: RCC cell lines were obtained from ATCC. 769-P cells were cultured in RPMI 1640 medium (Corning Life Science) supplemented with 10% FBS (R&D systems) with 100 U/mL penicillin-streptomycin. CAKI-1 cells were maintained in MEM medium supplemented with 10% FBS and antibiotics. RCC cells (769-P and CAKI-1) were treated without or with BCAA (0.38 mM isoleucine, 0.38 mM leucine, and 0.17 mM valine) for 16 hours. Total RNA from these cultured cells was extracted using the RNeasy Mini Kit (Qiagen).

first: Hyeyoung

last: Nam

first: Darshan

last: Chandrashekar


title: CD163 macrophages suppress CD8 and NK cells through CD163 mediated HLA-E (H2-T23)

city: Tianjin

first: Yunhuan

last: Gao

address: No. 94, Weijin Road, Nankai District, Tianjin, China

institute: Nankai University

summary: CD163 macrophages, which can be identified in different tissues of individuals such as the colon and tumor tissues, possessed markedly immunosuppressive functions on immune cells, especially effective cells such as CD8 cells. However, the mechanism(s) by which CD163 macrophages inhibit immune responses remains to be illusive. Using single cell-sequence techniques, we identified CD163+ macrophage subset in the colon tissues. Meanwhile, we also characterized CD163+ macrophage associated immune cell populations and subpopulations in mouse colon tissues. Deletion of CD163+ macrophage subset could markedly increase the proportions of CD8 and NK cells. Mechanistically, CD163+ macrophage subpopulations can inhibit the proliferation of CD8 and NK cells through inhibitory molecules CD94/NKG2a (KLRD1/KLRC1 in mice) and their ligand HLA-E /H2-T23 (Human/mice) on the surface of CD163+ macrophages. Importantly, CD163 in macrophages could promote the expression of HLA-E/H2-T23 expression through inducing the expression of signal peptide peptidase (SPP), offering a target for immunotherapy in CD8 and NK cells associated immunosuppressive diseases such as tumor. Taken together, we demonstrate that CD163+macrophage subpopulation plays a critical role in suppressing CD8 and NK cells through CD163 mediated HLA-E/H2-T23.

overall_design: Peripheral blood monocytes were infected with CD163 shRNA lentivirus and shNC control lentivirus, and cultured for 5 days in the presence of M-CSF. Total RNA was then extracted for high-throughput sequencing.

first: yunhuan

last: gao

first: Yi

last: Shi


title: Chemical Probes Reveal Interferon-Driven Biomarkers of PRMT5 Inhibitor Sensitivity and Guide Synergistic Therapy in Triple-Negative Breast Cancer

city: Hangzhou

first: Sheyu

last: Zhang

address: Dongfang Road 150

institute: Hangzhou Institute of Medicine Chinese Academy of Sciences

summary: This study employed 10x Genomics single-cell RNA sequencing (scRNA-seq) technology to investigate the effects of the combination of the PRMT5 inhibitor LLY283 and the PARP inhibitor Olaparib, as well as the triple combination with PD-1 blockade, on the tumor microenvironment in a mouse model of triple-negative breast cancer (TNBC). Our research uncovers the regulatory effects of these drugs and their combinations on the tumor microenvironment, providing new strategies and insights for future clinical therapy.

overall_design: To establish a tumor-bearing mouse model, EMT6 cells (2×10^5) were subcutaneously injected into immunocompetent BALB/c mice. Once tumors became palpable, mice were randomized into groups and treated with LLY-283 (50 mg/kg, 3 days on/4 days off, purchased from MedChemExpress), anti-PD-1 antibody (200 μg every three days, purchased from BioCell), or Olaparib (50 mg/kg daily via intraperitoneal injection, purchased from MedChemExpress), as well as dual and triple combinations of these agents. After the treatment period, tumors were collected from the mice. Tumors free of necrosis and ulcers in the area from three mice were pooled together as one sample. Tumors were dissociated into single-cell suspensions for subsequent sequencing analysis.

first: Ziwen

first: Lu

last: Guo

first: Yishuai

last: Ji

first: Jiaqi

last: Tao


title: Revealing RNA poly(A) tail dynamics during spermiogenesis and its function to support male fertility [dRNA-seq_wildtype]

first: Marcos

last: Morgan

summary: Poly(A) tail processing of mRNAs have been shown to dictate mRNAs metabolism of a few transcripts critical for fertility, but the extent of poly(A) tail-mediated regulation at the transcriptome level remains poorly characterized. Here, we performed whole transcriptome poly(A) tail profiling of purified late spermatocytes and round spermatids using direct RNA sequencing. As the germ cells enter spermiogenesis, we show a global increase in poly(A) tail length up to ~150-nts associated with transcript stabilization.

overall_design:
Pachytene spermatocytes and round spermatids were isolated from adult mice testis using Hoescht/PI staining and FACS sorting.
Cells were isolated from C57BL/6J/B6 male mice. Each replicate is representative of a pool of 3 individual mice - 3 replicates per condition were considered for analysis.
Nanopore technologies were used to sequence the testicular transcriptome and determine mRNA poly(A) tail length.

first: Marine

last: Baptissart

first: Ankit

last: Gupta

first: Brian

last: Papas


title: Whole transcriptome analysis of purified microglia

city: Rehovot

first: Amir

last: Szitenberg

address: 234 Herzl St

department: INCPM

country: Israel

institute: Weizmann Institute

overall_design: Expression was compared among male and female,CHD8 KO and WT mouse microgila, with   4-5 replicates per combination.

first: Evan

last: Elliott

first: Orly

last: Weissberg


title: Fibroblast-Immune Cell Crosstalk and Collagen Dynamics in Lactating Sheep Mammary Gland Revealed by Single-Cell Sequencing

city: Yangling

first: Yuxuan

last: Song

state: Shaanxi

address: No. 22 Xinong Road

institute: Northwest A&F University

summary: The mammary gland is essential for milk production in sheep, and postpartum mammary health is critical for ensuring the successful transition of multiparous ewes into subsequent reproductive cycles. As lactation declines, the mammary gland undergoes substantial tissue remodeling, characterized by the dynamic reorganization of the extracellular matrix (ECM), particularly collagen. This remodeling is crucial for maintaining the structural integrity and function of the gland. Notably, during lactation, the mammary gland is prone to sagging and collagen loss, which are significant factors affecting mammary health and milk quality. In this study, we employed single-cell RNA sequencing (scRNA-seq) to characterize the cellular and molecular interactions that regulate ECM remodeling in the lactating sheep mammary microenvironment, with a focus on the crosstalk between fibroblasts and immune cells. Our comparative analysis of the peak and late lactation phases revealed significant shifts in the proportion of immune cells, including a decrease proportion in NK cells and macrophages and an increase proportion in neutrophils, T cells, and B cells, reflecting a dynamically evolving immune landscape. We identified key ligand-receptor interactions between fibroblasts and immune cells, emphasizing the central role of fibroblasts in collagen synthesis. Notably, the fibroblast-specific upregulation of the branched-chain amino acid (BCAA) degradation pathway supports their contribution to collagen production. A cross-species analysis of fibroblasts from sheep and human mammary glands revealed a conserved expression profile of ECM-related genes, suggesting a translational relevance to mammary structure and function. These findings provide new insights into mammary remodeling, with broad implications for understanding fibroblast-immune cell interactions in the context of postpartum mammary health and improving milk quality.

overall_design: Mammary gland tissues were obtained from four lactating ewes, comprising two biological replicates each from peak lactation (PL) and late lactation (LL) stages.

first: Shujuan

last: Liu

first: Zhanhang

last: Wang

first: Junru

last: Zhu

first: Heran

last: Cao

first: JiuZeng

last: Cui

first: Yonglong

last: He

first: Yan

last: Li

first: Xiaopeng

last: An

first: Lei


title: Revealing RNA poly(A) tail dynamics during spermiogenesis and its function to support male fertility [dRNA-seq_busulfan]

first: Marcos

address: 111 TW Alexander Dr

institute: NIEHS

summary: To investigate the poly(A) polymerase activity of TENT5C in testicular somatic cells, we enriched the testis of wild-type and TENT5cdcat/dcat mice with interstitial cells by depleting germ cells with busulfan. Sequencing of busulfan treated testis revealed Insl3 transcripts with poly(A) tails almost exclusively accumulating at ~180-nts in wild-type samples. In Tent5c mutants, Insl3 transcript show gradual deadenylation down to ~60-nt with a significant depletion of the ~180-nt long tails. A significant decrease in Insl3 transcripts was also observed in TENT5cdcat/dcat busulfan treated testis compared to wild-type. These results indicate that TENT5C poly(A) polymerase is required to maintain or readenylate Insl3 poly(A) tails up to ~180-nts in interstitial cells. The shortening of the poly(A) tail may lead to transcripts decay.

overall_design:
Tent5c wt/wt or Tent5c dcat/dcat adult male mice were injected with a single dose of busulfan 20mg/kg or the corresponding vehicle. Testis were harvested 4-weeks after injection to allow for an adequate depletion of germ cells.
RNA was isolated from total testis. Each sample is representative of individual mice - 2 replicates per condition were considered for analysis.
Nanopore technologies were used to sequence the testicular transcriptome and determine mRNA poly(A) tail length.


title: Insulin-like growth factor 2 (IGF2) as a driving force of exponential expansion in neonatal thymus

city: Nashville

first: Seung Woo

last: Kang

state: TN

address: MRBIV 10475, 2215 Garland Avenue

department: Department of Cell and Developmental Biology

institute: Vanderbilt University

summary: Like all organs, the thymus grows in size and function rapidly during development, which comes to a halt after birth. However, the molecular mechanisms behind such a transition in the thymus remain obscure. Using single-cell RNA sequencing (scRNA-seq) of the murine thymic stroma, we identified that major transcriptomic changes occur in the endothelium and mesenchyme across the transition to homeostasis. Differentially expressed gene and intercellular network analyses of temporally resolved scRNA-seq data revealed fibroblast-derived insulin-like growth factor 2 (IGF2) as a candidate driving neonatal thymic expansion. We demonstrated IGF2 activity promotes a cortical TEC-specific proliferation and is tightly regulated at the thymic growth transition. Bulk RNA-seq of human thymi across the transition also revealed IGF2 to drive thymic expansion, suggesting an evolutionarily conserved role. Our study highlights the role of a fibroblast-derived IGF2 in promoting cTEC proliferation, resulting in early thymic expansion that is followed by down-regulation to establish homeostasis.

overall_design: For our time-series single-cell RNA sequencing, we used 3 thymi per library. Our merged scRNAseq dataset contains 3-day-old (3 Foxn1+/+ males, 3 Foxn1lacZ/lacZ males, 2 Foxn1+/+ females, 2 Foxn1lacZ/lacZ females), 7-day-old (2 Foxn1+/+ males, 3 Foxn1lacZ/lacZ males), 14-day-old (2 Foxn1+/+ males, 2 Foxn1lacZ/lacZ males, 2 Foxn1+/+ females, 2 Foxn1lacZ/lacZ females). 30-day-old (2 Foxn1+/+ males, 3 Foxn1lacZ/lacZ males) datasets are available in a separate manuscript, Xiao*, Kang* et al. (2025). GSE264402.


title: Exploring changes in miRNA expression levels in bone marrow mesenchymal stem cells under dexamethasone  treatment using miRNA sequencing

city: shanghai

first: Rongtai

last: Zuo

address: No.600, Yishan Road, Xuhui District, Shanghai

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: In the progression of glucocorticoids (GCs) induced osteonecrosis of the femoral head (ONFH), miRNAs have important regulatory role and is involved in many biological processes. In this current study, we detected the expression levels of miRNA in bone marrow mesenchymal stem cells (BMSCs) after 48 hours of dexamethasone intervention and further explored the role of key miRNA in a GCs induced ONFH rat model.

overall_design: High-throughput sequencing of BMSCs after 48h of intervention with dexamethasone (10μM).


title: Use of synthetic circular RNA spike-ins (SynCRS) for normalization of circular RNA sequencing data.

city: Bedford Park

first: Simon

last: Conn

state: SA

address: Flinders Drive

country: Australia

institute: Flinders University

summary: High-throughput RNA sequencing is employed to quantify transcript abundance and for the de novo identification of novel transcripts, including a family of alternatively spliced RNA molecules called circular RNAs (circRNAs). However, quantification of circRNAs between sequencing libraries remains challenging because of RNA complexity in addition to confounding errors introduced during exonuclease digestion, library preparation and sequencing itself. We have developed a set of synthetic circular RNA spike-ins - termed ‘SynCRS’ - that are directly added to RNA samples before exonuclease digestion and library preparation. These SynCRS are of varying sizes and can be integrated into all NGS workflows and, critically, facilitate the quantitative calibration of circular RNA transcript abundance between samples, tissue types, species and laboratories.

overall_design: RNA was harvested from Glioblastoma cell line (U87) and two technical replicates were spiked with 6 SynCRS at varying levels prior to RNase R digestion and RNA sequencing

first: Vanessa

first: Ryan

first: Marta

last: Gabryelska


title: Remodeling of tissue-resident macrophages by MEF2D-expressing cancer precursors primes for liver tumorigenesis [CUT&Tag]

first: li

last: ni

address: chongqing univeristy

institute: chongqing univeristy

summary: To investigate the role of MEF2D in liver tumorgenesis, we established the MEF2D WT and MEF2D KO DEN-induced mice

overall_design: cut&tag-seq data were from eHCC cells from DEN-induced mice with hepatocyte-specific depletion of Mef2d or not


title: Two distinct durable human switched memory B cell populations are induced by vaccination and infection

city: Cambridge

first: Cory

middle: Adam

last: Perugino

state: MA

address: 600 Main Street

institute: Ragon Institute of MGH, MIT and Harvard

summary: The traditional definition of memory lymphocytes encompasses antigen-experienced, durable subsets that persist in the absence of antigen and are capable of responding to the antigen on subsequent encounters. We examined the relative durability of eight different non-overlapping class-switched human B cell sub-populations (excluding plasmablasts) that together encompass 100% of all human class switched B cells and identified only two long-lived B cell populations that persist after vaccination in the relative absence of their cognate antigen.  In addition to canonical switched memory B cells (SWM) with an IgD- CD27+ CXCR5+ phenotype, a second, non-canonical but distinct memory population of IgD- CD27- CXCR5+ (double negative 1, DN1) B cells is also durable. Beyond surface phenotyping, DN1 memory B cells intriguingly exhibit lower levels of replacement mutations in complementarity determining as well as framework regions of their B cell receptors and have longer CDRH3 sequences relative to canonical SWM B cells. This non-canonical, human memory B cell subset is distinguished by a distinct TP63 driven transcriptional signature that has been linked to extended cell survival and these B cells persist in the circulation at least as long as canonical SWM B cells. Non-canonical human DN1 memory B cells therefore represent a second, distinct, durable, less somatically hypermutated, class-switched human memory B cell subset defined by a unique transcriptomic signature, that likely arises outside germinal centers and may have evolved to preserve immunological breadth.

overall_design: RNA-seq data of 18 samples, comprised of three groups, N, S, and D, representing three types of cells, i.e., "Naive B", "Switched Memory B", and "DN1 B" cells. Each group has 6 biological replicates.

first: Cory A.

first: Hang

first: Jared

last: Feldman

first: Jess

last: Marbourg

first: Thomas V.

last: Guy

first: Anson

last: Hui

first: Nicole

last: Ingram

first: Neha

last: Chaudhary

first: Weiyang

last: Tao

first: Catherine

last: Jacob-Dolan

first: Blake M.

last: Hauser

first: Zayd

last: Mian

first: Anusha

last: Nathan

first: Zezhou

last: Zhou

first: Clarety

last: Kaseke

first: Rhoda

last: Tano-Menka

first: Matthew A.

last: Getz

first: Fernando

last: Senjobe

first: Cristhian

last: Berrios

first: Onosereme

last: Ofoman

first: Zachary

last: Manickas-Hill

first: Duane R.

last: Wesemann

first: Jacob E.

last: Lemieux

first: Marcia B.

last: Goldberg

first: Kerstin

last: Nundel

first: Ann

last: Moormann

last: Marshak-Rothstein

first: John A.

last: Iafrate

first: Gaurav

last: Gaiha

first: Richelle

last: Charles

first: Alejandro B.

last: Balazs

first: Aridaman

last: Pandit

first: Vivek

last: Naranbhai

first: Aaron G.

last: Schmidt

first: Shiv

last: Pillai


title: Remodeling of tissue-resident macrophages by MEF2D-expressing cancer precursors primes for liver tumorigenesis [ATAC-Seq]

first: li

last: ni

overall_design: ATAC-seq were from eHCC cells from DEN-induced mice with hepatocyte-specific depletion of Mef2d or not


title: Growth of the maternal intestine during pregnancy and lactation [gut sections]

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

summary: The organs of female animals can be dramatically enlarged and metabolically remodelled by reproduction. The cellular changes and genetic programmes that initiate and sustain these transformations remain largely uncharacterised. It is also unclear whether the mechanisms that drive reproductive growth are shared between organs, or with other environmental triggers of adult organ growth. We have tackled these questions in mouse mothers, whose intestines provide a striking and genetically tractable example of reproductive organ resizing. We find that intestinal remodelling during reproduction is anticipatory of reproductive needs and distinct from diet-induced intestinal resizing.

overall_design: Comparison of tissue samples from 3 gut sections: Ileum, jejunum and duodenum.

first: Amourda

last: Christopher

first: Miguel-Aliaga

last: Irene


title: Growth of the maternal intestine during pregnancy and lactation [gut epithelium]

overall_design: FACS-sorted epithelial cells from the Ileums of lactating female, virgin female and virgin male mice

first: Ameku

last: Tomotsune


title: Growth of the maternal intestine during pregnancy and lactation [gut pregnancy]

overall_design: FACS-sorted epithelial cells from the Ileums of female mice with varying pregnancy statuses


title: Single cell mapping of large and small arteries during hypertensive aging

city: Luzhou

first: Yan

last: Yang

address: Xianglin Road

institute: South-West Medical University

summary: Vascular aging is directly related to several major diseases including hypertension and atherosclerosis, in which endothelial dysfunction and smooth muscle phenotype changes are crucial. However, cell types within the vessel wall and their dynamic cellular communication status have not been characterized in different arteries during hypertensive aging. To depict the interconnectedness of complex mechanism between hypertension and aging, we performed single cell RNA sequencing of aorta, femoral and mesentery artery, respectively from Wistar Kyoto rats (WKY) and spontaneously hypertensive rats (SHR) aging 16-72 weeks. We found that aging and hypertension alone have a significant impact on the alteration of cellular composition and artery remodeling both on conductive and resistant arteries, even greater when superimposed. Consistently, smooth muscle cells (SMCs) underwent phenotypic switching from contractile towards synthetic, apoptotic and senescent SMCs with aging/hypertension. We identified three sub-clusters of Spp1high synthetic SMCs, Spp1high matrix activated fibroblasts and Spp1high scar-associated macrophage involved in hypertensive aging, highlighting that Spp1, encoding protein osteopontin (OPN), could be a potential regulator participating in hypertensive aging. Spp1high scar-associated macrophage enriched for ROS metabolic process, supramolecular fiber organization and actin filament organization. Cell-cell communication analysis also revealed SPP1-Cd44 receptor pairing was markedly aggravated on hypertensive aging condition. Importantly, the concentration of OPN in human serum significantly potentiated in hypertension patient compared with normal group. Thus, we provide a comprehensive cell atlas to systematically resolve the cellular diversity and dynamic cellular communication changes of the vessel wall during hypertensive aging, highlight the mechanisms of vascular vasodilation through cGMP-PKG signaling pathway and identified a protein marker osteopontin as a potential regulator of vascular remodeling during hypertensive aging.

overall_design: This entry contains 10x Single-cell RNA-seq data of FACS sorted nucleated living cells from aorta, femoral and mesentery artery of Wistar Kyoto rats (WKY) and spontaneously hypertensive rats (SHR) aging 16-72 weeks.

first: Jun

last: Cheng

first: Hong

last: Wu

first: Qingbo

last: Xu


title: Fu Huang ointment promotes wound healing via the LPAR1/ EDN1 axis based on transcriptome analysis

city: xianyang

first: keshen

last: qu

address: shiji road

institute: shaanxi university of Chinese medicine

summary: Clinically, topical Fu Huang ointment  has achieved good results in the treatment of diabetic ulcers, but its specific mechanisms of action are unclear.

overall_design: Firstly, diabetic ulcers animal model was established by using db/db mice combined with surgical resection. Secondly, after 7 days of administration, the exact therapeutic effect of  Fu Huang ointment on diabetic ulcers was evaluated by observing the wound healing rate and detected the angiogenesis, granulation tissue formation, and inflammatory response in local wound tissue. Then, total RNA Sequencing was performed on the tissue samples of diabetic ulcers to screen core target genes to determine the regulatory mechanism by which  Fu Huang ointment  exerts its therapeutic effect. Finally, further verification was based on animal experiments.

first: Keshen

last: Qu

first: Meng

last: Xing


title: Astrocyte  transcriptome from mouse visual cortex after different plasticity paradigms

city: La Jolla

first: Laura

last: Sancho

state: CA

address: 10010 N Torrey Pines

institute: Salk Institute for Biological Studies

summary: Analysis of astrocyte gene expression after induction of plasticty in the mouse visual cortex, spanning the time of synapse maturation to adulthood.

overall_design: Profile of astrocyte-enriched mRNA from the mosue visual cortex after different paradigms (dark rearing, monocular deprivation, dark exposure)  from GFAP-Ribotag mice (ribosomal pulldown), with 3-5 biological replicates and 1 input (non-pulldown) sample per time point

first: Matthew

last: Boisvert

first: Jillybeth

last: Burgado

first: Nicola

last: Allen


title: Growth of the maternal intestine during pregnancy and lactation

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

overall_design: Refer to individual Series


title: Glutamine deprivation enhances metabolic reprogramming during kidney organoid directed differentiation

city: Ann Arbor

first: Rajasree

last: Menon

state: Michigan

address: 4544E, MSRB2, Catherine Street, University of Michigan

department: Department of Computational  Medicine and Bioinformatics

institute: University of Michigan

summary: In this study, we systematically performed comprehensive metabolite and transcriptome profiling of human pluripotent stem cells (hPSCs) during differentiation into NPCs and later into multicellular organoids. We found activation of distinct metabolic pathways during early stage progression from hPSCs to NPCs; however, NPCs, organoids, and the intervening developmental stages between them shared similar metabolic profiles across this later stage of maturation. Importantly, the Alanine-aspartate-glutamate and glutamine pathways were significantly altered during the first stages of differentiation. Moreover, hPSCs survived glutamine deprivation during in vitro differentiation, and NPCs were successfully generated both in the absence and presence of glutamine and glutamate. Surprisingly, metabolic deprivation resulted in enhanced maturation, specifically in podocytes, as evidenced through single cell RNA-Seq analysis. These findings highlight the critical regulatory role of glutamine metabolism in the derivation of nephron progenitor cells and kidney organoids.

overall_design: We have used 10x Genomics to perform single cell sequencing on organoid cells with and without glutamine deprivation

first: Jason

last: Wertheim

first: Iman

last: Sarami

first: Katherine

middle: E

last: Hekman

first: Edgar

last: Otto


title: PAX5-Inherited susceptibility causes leukemia by conferring sensitivity to DNA damage in preleukemic B cells

status: Public on Mar 19 2025

city: Salamanca

first: Isidro

last: Sánchez García

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

summary:
We used microarrays to analyze gene expression changes in leukemic bone marrow cells from Pax5+/- and WT mice, comparing them with preleukemic bone marrow precursor B cells from both genotypes. All mice were exposed to a single low-dose irradiation (2 Gy).
PAX5 is a master regulator of B-cell development, and germline mutations in PAX5 predispose individuals to B-cell acute lymphoblastic leukemia (B-ALL). While PAX5 alterations are a hallmark of B-ALL, the mechanisms linking inherited susceptibility to leukemic transformation remain poorly understood. Here, we provide in vivo genetic evidence demonstrating that reduced Pax5 dosage increases sensitivity to DNA damage, acting as a key factor in B-ALL initiation. Using a mouse model of Pax5 heterozygosity, we show that exposure to a single low-dose irradiation (2 Gy) significantly accelerates leukemia onset, establishing a direct link between genetic predisposition and environmental stress. Notably, the resulting murine B-ALLs closely resemble the human disease, exhibiting complete Pax5 loss, CD19 downregulation, and a high incidence of DNA double-strand breaks. Mechanistically, we identify Pax5 as a regulator of p53-mediated DNA damage responses in preleukemic B cells, highlighting its role beyond lineage specification. These findings provide a mechanistic framework for the interplay between PAX5 deficiency, genomic instability, and environmental factors in early B-ALL development, uncovering new potential vulnerabilities for therapeutic intervention.

overall_design: Leukemic bone marrow cells from 10 Pax5+/- mice irradiated with 2 Gy. Preleukemic proB and preB cells after 3 weeks of irradiation (2 Gy) from 7 Pax5+/- mice. Leukemic bone marrow cells from 4 wild-type mice irradiated with 2 Gy. Preleukemic proB and preB cells after 3 weeks of irradiation (2 Gy) from 3 wild-type mice.

first: Ana

last: Casado-García

first: Jorge

last: Martínez-Cano

first: Belén

last: Ruiz-Corzo

first: Ninad

last: Oak

first: Paula

last: Somoza-Cotillas

first: Andrea

last: Lopez-Alvarez de Neyra

first: Adrián

last: Blanco-Gómez

first: Oscar

last: Blanco

first: Diego

last: Alonso-López

first: Javier

last: De Las Rivas

first: Susana

last: Riesco

first: Pablo

last: Prieto-Matos

first: Francisco

last: García Criado

first: María

middle: B

last: García Cenador

first: Jesús

last: Pérez-Losada

first: Manuel

last: Ramírez-Orellana

first: Carolina

last: Vicente-Dueñas

first: Kim

last: Nichols

first: César

last: Cobaleda

last: Sánchez-García


title: Suppression of APAP-induced hepatotoxicity using Slit2

city: Suwon

first: younghwa

last: Kim

address: youngtonggu

country: South Korea

institute: Ajou university

summary: APAP-induced hepatotoxicity can be suppressed by treating Slit2

overall_design: Mice were divided into four groups: Control (PBS only), SLIT2 (SLIT2 only, 2 μg/mouse, intraperitoneally for 3 days), APAP (PBS + APAP, 400 mg/kg), and Double (SLIT2 + APAP). Mice were sacrificed 24 hours post-APAP administration.

first: Young Hwa

first: Yongwon

last: Choi

first: TaeJun

last: Park

first: Jaeho


title: Latilactobacillus sakei Wikim0185 alleviates allergic asthma by inducing tolerogenic dendritic cells through epigenetic rewriting

city: Gwangju

first: Sang-Pil

address: 86, Kimchi-ro, Nam-gu

institute: World Institution of Kimchi

summary: Kimchi is a traditional Korean food widely recognized for its probiotic properties and potential health benefits. Several lactic acid bacteria (LAB) from Kimchi exhibit immunomodulatory properties, and their efficacy has been evaluated for various immune-related diseases. However, the mechanisms underlying the immunomodulatory effects of LAB are not yet fully understood. In this study, we demonstrated the immunomodulatory effects of Latilactobacillus sakei Wikim0185, isolated from sweet potato Kimchi, in an ovalbumin (OVA)-induced allergic asthma mouse model by inducing tolerogenic dendritic cells (DCs) and regulatory T cells (Tregs). Bone marrow-derived dendritic cells (BMDCs) and OVA-peptide-stimulated splenocytes isolated from OT-II mice co-cultured with Wikim0185 exhibited increased secretion of the anti-inflammatory cytokine IL-10. Oral administration of Wikim0185 in allergic asthma experimental mice alleviated symptoms, including airway hyperresponsiveness (AHR), leukocyte infiltration, and reduced Th2-type cytokine levels in bronchoalveolar lavage (BAL) fluid. Notably, Wikim0185-treated mice displayed an increased proportion of Foxp3+ Tregs in mediastinal lymph nodes. Additionally, mediastinal lymph node cells restimulated with OVA exhibited decreased secretion of Th2-type cytokines while showing increased IL-10 production. Interestingly, RNA sequencing and chromatin immunoprecipitation (ChIP)-qPCR analysis revealed that Wikim0185 induced tolerogenic DCs through epigenetic histone modifications, increasing active chromatin marks (H3K4me3, H3K9ac, and H3K27ac) on the promoter regions of tolerogenic marker genes (Pdl1, Il10, Socs1, and Socs3). These findings suggest that Wikim0185 modulates immune responses by epigenetically reprogramming DCs, thereby promoting Treg differentiation and suppressing excessive Th2 immune responses in an allergic asthma mouse model.

overall_design: RNA-seq profiling of bone marrow derived dendritic cells and co-cultured with PBS or Latilactobacillus sakei Wikim0185 for 6 hours.

first: Sulhee

last: Lee

first: Min-Sung

last: Kwon

first: Ga hee

first: Young Joon

last: Oh

first: Seul Ki

last: Lim

first: Namhee

first: Misun

last: Yun

first: Hak-Jong


title: Growth of the maternal intestine during pregnancy and lactation [scRNA gut]

city: London

first: LMS

last: Bioinformatics Core

overall_design: scRNA-seq comparison of Ileum samples from virgin and lactating WT mice and lactating SGLT3a KO mice

first: Ameku

last: Tomotsune

first: Miguel-Aliaga

last: Irene


title: Human forebrain expansion is regulated by a human accelerated region controlling early Foxg1 expression

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

summary: We report the use of H3K27ac to pooled active enhancer elements during E7.5 mouse embryos. Our study is the first generated database derived from mouse E7.5 embryos, during late gastrula stages

overall_design: Examination of active enhancers during E7.5 mouse embryos

first: Sandra

last: Acosta