title: A novel epigenetic clock for rhesus macaques unveils an association between early life adversity and epigenetic age acceleration

city: Belmont

first: Torsten

last: Klengel

state: MA

address: 115 Mill St.

institute: McLean Hospital

summary: Because DNA methylation changes reliably with age, machine learning models called epigenetic clocks can estimate an individual’s age based on their DNA methylation profile. This epigenetic measure of age can deviate from one’s true age, and the difference between the epigenetic age and true age, known as epigenetic age acceleration (EAA), has been found to directly correlate with morbidity and mortality in adults. Emerging evidence suggests that EAA is also associated with aberrant health outcomes in children, making epigenetic clocks useful tools for studying aging and development. We developed two highly accurate epigenetic clocks for the rhesus macaque, utilizing 1,008 blood samples from 690 macaques between 2 days and 23.4 years of age with diverse genetic backgrounds and exposure to environmental conditions. The first clock, which is trained on all samples, achieves a Pearson correlation between true age and predicted age of 0.983 and median absolute error of 0.210 years. To study phenotypes during development, the second clock is optimized for macaques younger than 6 years and achieves a Pearson correlation of 0.974 and a median absolute error of 0.148 years. Using the latter clock, we investigated whether epigenetic aging is affected by early life adversity in the form of infant maltreatment. Our data suggests that maltreatment and increased hair cortisol levels are associated with epigenetic age acceleration right after the period of maltreatment.

overall_design:
DNA methylation beta values from peripheral whole blood samples of rhesus macaques in captivity. The ages of the rhesus macaques and the DNA methylation of the CpGs included here were used to train epigenetic clock models.
Data processing: Samples and CpG sites were filtered as described in Bronk et al. After filtering, the data was normalized using quantile normalization followed by beta-mixture quantile normalization (BMIQ). 705 of these CpG sites are provided here as these were the sites used in the creation of our epigenetic clocks. (Current IUCAC protocols prevent us from submitting the entire set of CpGs measured). The beta values for these CpGs prior to normalization are provided in RawBetaValues.csv, and NormalizedBetaValues.csv contains the normalized beta values.
Data processing: The methylumi package (version 2.40.1) in R version 4.1.2 was used to obtain methylation beta values.
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Submitter states that Current IUCAC protocols prevent us from submitting the entire set of CpGs measured
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first: Gabriel

last: Bronk


title: Effect of depletion of Paxbp1 on gene expression of mouse epidermis

status: Public on Jul 01 2026

city: Shenzhen

first: Wen

middle: Ting

last: Li

address: No,1120,LianHua Road,FuTian District

country: China

institute: Shenzhen PKU-HKUST Medical Center

type: Expression profiling by high throughput sequencing

summary: Here, we report that the targeted deletion of Paxbp1 in epidermal keratinocytes mediated by Keratin14-Cre leads to severe disruption in skin architecture. Mice deficient in Paxbp1 exhibited a substantially reduced epidermal thickness and pronounced separation at the dermo-epidermal junction upon birth. Mechanistically, we demonstrate that the absence of Paxbp1 hinders cellular proliferation, marked by a halt in cell cycle transition, suppressed gene expression of proliferation, and a compromised DNA replication pathway in basal keratinocytes, resulting in the thinning of skin epidermis. Moreover, molecules and pathway associated with hemidesmosome assembly were impaired in Paxbp1-deficient keratinocytes, culminating in the detachment of the skin epidermal layer. Therefore, our study highlights an indispensable role of Paxbp1 in the maintenance of epidermal homeostasis.

overall_design: To investigate the regulation of Paxbp1 in epidermal homeostasis, we separated epidermis from Control and Paxbp1 Knockout mice, then subjected these tissues to RNA sequencing (RNA-seq).

first: Cong

last: Huang

first: Shenglin

last: Liu

first: Wenting

first: Shizheng

last: Zhao


title: Effect of Knockdown of PAXBP1 on gene expression of HaCaT keratinocytes

overall_design: To examine the role and possible molecular mechanisms of PAXBP1 on human HaCaT keratinocytes, we subjected si-PAXBP1 and si-CTL-transfected HaCaT cells for RNA-seq analysis.


title: Analysis of differential gene expression in a Streptococcus sanguinis SSA_0451 deletion mutant

city: Richmond

first: Ping

last: Xu

state: VA

address: 521 North 11th street

department: School of Dentistry

country: USA

institute: Virginia Commonwealth University

summary: Gene expression profile comparison of Streptococcus sanguinis SK36 wild type with SSA_0451 mutant of Streptococcus sanguinis SK36.

overall_design: SSA_0451 mutant vs. wild-type SK36. Biological replicates independently grown and prepared for each sample.

first: Vysakh

last: Anandan


title: Single Cell RNA Sequencing of Radiation-Induced Esophageal Injury in Rats

city: Chengdu

first: Wenling

last: Tu

address: No. 4 North Section 4, Second Ring Road

institute: the Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital

summary: We utilized single-cell RNA sequencing (scRNA-seq) to understand the effects of radiation on the cell type composition and transcriptional profiles of esophagus during self-repair after radiation-induced esophageal injury in rats.

overall_design: Thirty male Sprague-Dawley (SD) rats (6 weeks old)  were randomly assigned to six groups (0Gy_7d, 35Gy_7d, 5x7Gy_7d, 5x7Gy_14d, 5x7Gy_21d, 5x7Gy_28d; n=5 per group). Radiation doses of 5 × 0 Gy, 1 × 35 Gy, or 5 × 7 Gy (7 Gy administered daily for 5 days) were administered to the esophageal region at a fixed dose rate of 1.7 Gy/min using an X-ray linear accelerator (KUBTEC XCELL 320, Milford, CT). Rats were sacrificed 7, 14, 21 or 28 days after radiation and esophageal tissues were collected. Fresh rat esophageal tissues from the 0Gy_7d, 35Gy_7d, 5x7Gy_7d, and 5x7Gy_14d groups were stored in MACS tissue storage solution (Miltenyi Biotec) at 4°C and shipped to the processing lab within 48 hours for scRNA-seq. Esophageal tissues from five rats per group were pooled for processing. scRNA-seq libraries of each pooled sample were sequenced using an Illumina NovaSeq 6000 sequencer.

first: Yangfeng

first: Shuyu

last: Zhang


title: Single-cell Transcriptomic and Proteomic Analysis of Acute Myeloid Leukemia (AML) Patients with Abnormalities on Chromosome 7

city: Bethesda

first: Laura

last: Dillon

state: Maryland

address: Room 10CRC 6-5142, 10 Center Drive

department: Hematology Branch

institute: National Heart Lung and Blood Institute, NIH

summary: Chromosome 7 (chr7) abnormalities are commonly seen in patients with acute myeloid leukemia (AML) or myelodysplastic syndromes and are associated with poor prognosis. Flow cytometry (FCM) is typically used clinically to quantify residual malignancy during treatment but the relationship of cell surface immunophenotype with genetic features is incompletely defined. Single-cell RNA sequencing (scRNA-seq) with oligonucleotide-conjugated antibodies may be able to integrate cytogenetic genotypes found within leukemic clones with specific transcriptomic and immunophenotypic signatures. Bone marrow (BM) aspirate was collected from 12 AML patients with known abnormalities on chr7 according to cytogenetics studies. Among all 12 patients, 3 of them only had monosomy 7 as the sole genetic aberration, while 9 patients had abnormalities on additional chromosomes. By scRNA-seq with oligonucleotide-conjugated antibodies, we identified the correlation between cell types showed distinct features among patients, and cells in different groups had different protein expression profiles. By comparing the expression profile of AML patients with abnormalities on chr7 to HDs, this study provides evidence that leukemic immunophenotype is correlated with chromosomal structural changes. The experiments on a single-cell level were able to identify clones in higher resolution and revealed potential cell surface protein markers that could be used clinically to identify specific malignant populations in patients with myeloid malignancies.

overall_design: Bone marrow (BM) aspirate was collected from 12 AML patients with known abnormalities on chr7 according to cytogenetics studies. Cells were incubated with 1μl (0.5μg) each of the 32 TotalSeq-A oligo-tagged antibodies (Biolegend) added. The 10x Genomics 3’v2 Single Cell Profiling platform was used for scRNAseq. For the GEX library, 50ng of amplified cDNA was carried forward for library construction.

first: Gege

last: Gui

first: Christopher

middle: S

last: Hourigan

middle: W


title: Diploid embryo complementation of embryonic stem cells efficiently generates a homozygous Gjb2 mutant deaf mouse model

city: Shanghai

first: Qing

state: Shanghai

address: Xuhui Yueyang road 320, ShangHai, China

institute: Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences

summary: Our work demonstrates that generating all ESC-derived mice via diploid embryo complementation is more efficient and feasible than the tetraploid approach. The broad application of this method will significantly accelerate the construction of disease models and xenogeneic chimeras using stem cell technology. Besides, our results indicate that the cell fate plasticity of eight-cell embryos is both flexible and variable. This plasticity is influenced by material exchange, through which embryonic stem cells transmit information, similar to the transmission of information from the second polar body. The efficient generation of Gjb235delG/35delG mice via diploid complementation will accelerate the understanding of pathogenic mechanisms and the investigation of therapeutic effects for hereditary deafness. Additionally, other disease models with GJB2 pathogenic mutations (235delC, V27I, R75W, etc.) can also be efficiently produced using this method for pre-clinical research

overall_design: To elucidate the mechanism for this phenomenon, we collected the single cells from reconstructed blastocysts for RNA-seq. To isolate single cells from reconstructed embryos, we first released the blastocyst fluid using a micromanipulator, followed by three washes with HCZB as previously described. Five E7.5 reconstructed embryos by injecting Actin-RFP2-p9 ESCs into Actin-GFP eight-cell embryo were collected and digested by 0.25% Trypsin-EDTA in a 37°C water bath for 20 minutes. Cell quality was conducted on Countstar Rigel S2 to determine cell concentration, cell viability, and cell clump. These single cells were subjected to scRNA-seq. The genomic DNA of various tissues (brain, heart, liver, testis, and tail) from wild-type mice and Gjb235delG/35delG mice derived from diploid compensation, was isolated using the TIANamp Genomic DNA Kit (TIANGEN). This was followed by PCR amplification for deep sequencing. Genomic DNA was extracted from MEF-p2, Gjb235delG/35delG-p7 ESCs, and Actin-RFP2-p10 ESCs by using TIANamp Micro DNA Kit (TIANGEN, Cat#DP316) according to the manufacturer’s instructions. The DNA was fragmented into 200-400 bp using a Covaris S220 (Covaris, USA). Single-stranded DNA fragments underwent bisulfite treatment, converting unmethylated cytosine to uracil while leaving methylated cytosine unchanged. The treated DNA fragments were then ligated to methylation sequencing adapters, followed by size selection and PCR amplification, using the Accel-NGS Methyl-Seq DNA Library Kit (Swift, USA, Catalog #30096). Library quality was assessed using the Agilent 5400 system (Agilent, USA) and quantified by qPCR (1.5 nM). Paired-end sequencing was performed on an Illumina platform (Illumina, USA).

first: Meng

last: Yan


title: Integrated ChIP-seq and Transcriptomic Profiling of Histone Modifications Across Breast Cancer Progression in MCF10A-Derived Cell Lines

city: Burlington

first: Seth

last: Frietze

state: VT

address: 149 Beaumont Avenue

department: Biomedical and Health Sciences

institute: University of Vermont

summary: Cancer arises from complex epigenetic mechanisms that drive tumorigenesis. Gene regulatory elements play a pivotal role in reprogramming gene expression patterns, facilitating tumor initiation, progression, and metastasis. However, a comprehensive characterization of epigenetic alterations across cancer development remains incomplete, particularly for the spectrum of post-translational histone modifications in the evolution of breast tumors. In this study, we explored the dynamic landscape of epigenetic changes using a breast cancer progression model based on the MCF10A cell line. We integrated ChIP-seq and transcriptomic profiling to investigate the epigenetic heterogeneity across four MCF10A-derived cancer cell lines: normal (MCF10A), HRAS G12V transformed, ductal carcinoma in situ (DCIS), and metastatic (CA1a). Our analysis revealed significant changes in chromatin patterns at regulatory elements, including stage-specific variability in H3K27me3 and H3K9me3-marked heterochromatin domains.  These profiles underly the epigenomic changes in each of these cell states to provide insights into human breast cancer progression.

overall_design: This study includes an analysis of bulk RNA-seq data from four MCF10A-derived cell lines representing different stages of breast cancer progression: normal (MCF10A), HRAS G12V transformed, ductal carcinoma in situ (DCIS), and metastatic (CA1a). We investigated the gene expression changes through RNA-seq profiling using biological triplicates were included to ensure robustness and reproducibility of the data.

last: Gao


title: Cancer-Associated Fibroblasts Promote Vasculogenic Mimicry of Colorectal Cancer by Epigenetic Silencing of Decorin [Methylation array]

city: guangzhong

first: yurui

last: liu

address: No. 1023-1063, Shatai South Road, Baiyun District, Guangzhou City, Guangdong Province

institute: Southern Medical University

type: Methylation profiling by genome tiling array

summary: To investigate the DNA methylation landscape differences between CAFs and NFs in colorectal cancer, we extracted primary fibroblasts from colorectal cancer tissue and para-cancerous tissue for 850K chip analysis.

overall_design: Comparison of DNA methylation profiles between CAFs and NFs 850K chip data.

first: Yin

last: Zhu

first: Yurui


title: Erianin induces GSDMD-dependent pyroptosis and synergistically enhances doxorubicin efficacy via the PI3K/AKT signaling pathway in Diffuse large B-cell lymphoma

city: Tianjin

first: Minghan

last: Qiu

state: Tianjin

address: Department of Oncology, Tianjin Union Medical Center of Nankai Univercity, 190 Jieyuan Street, Hongqiao District, Tianjin, China.

department: Department of Oncology

summary: Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphoma, characterized by high aggressiveness and rapid growth.Erianin, a natural compound derived from the Chinese herb Dendrobium, has been proven to have anti-cancer effects in some types of cancer, but its role and mechanism in DLBCL have not yet been reported. Therefore, this study aims to investigate whether Erianin can be a potential therapeutic drug for DLBCL.RNAseq was performed on SU-DHL-8 cells after treating with 100nM Erianin or DMSO for 24 h.

overall_design: SU-DHL-8 cells after treating with 100nM Erianin or DMSO for 24 h，in three replicate experiments.

first: Hanwei

last: Mei

first: Ming

first: Huaqing

last: Wang


title: Temporal Transcriptomic Profiling of MutuDC Cells Treated with Fanchinoline Reveals Mechanistic Insights

city: Guangzhou

first: Kun

address: 232 Waihuandong Road, Panyu district

institute: Guangzhou University of Chinese Medicine

summary: This study investigates the mechanistic effects of Fanchinoline on Murine dendritic cell line MutuDC by performing temporal transcriptomic analysis. We treated MutuDC cells with Fanchinoline and collected samples at 0, 2, 6, 12, and 24 hours post-treatment to examine the dynamic changes in gene expression. Our data provides comprehensive insights into the regulatory pathways and biological processes influenced by Fanchinoline, highlighting its potential impact on immune response modulation and cellular function in dendritic cells.

overall_design: We conducted a time-series experiment where MutuDC cells were treated with a defined concentration of Fanchinoline. Untreated cells served as controls. Samples were collected at five time points: 0 (baseline), 2, 6, 12, and 24 hours post-treatment. Each time point included triplicates to ensure reproducibility and statistical robustness. RNA was extracted from these samples and subjected to high-throughput RNA sequencing to assess the transcriptomic landscape. Differential gene expression analysis was performed to identify genes and pathways significantly altered by Fanchinoline treatment over time, aiming to unravel its underlying mechanisms of action.

first: Yuan

last: Liao


title: Control of bioenergetic balance in mouse spermatogonial stem cells by alanine metabolism

city: kyoto

first: takehiro

last: miyazaki

state: kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo

country: Japan

institute: Kyoto University

summary: GS cell culture medium contains glucose, lactate and pyruvate. To understand the role of pyruvate in the culture medium, we tested the effect of each of these compounds on proliferation on laminin-coated dishes and compared gene expression levels by RNA-seq.

overall_design: We performed gene expression profiling analysis using data obtain from RNA-seq of 3 different culture medium.Comparative gene expression profiling analysis of RNA-seq data for complete medium, glucose medium and 8mM pyruvate medium.

first: Takashi

last: Shinohara


title: Cetylpyridinium chloride exposure contributes to apoptosis and follicular atresia in mouse ovaries by inducing DNA damage in granulosa cells

city: Chongqing

first: Xin

last: Yin

address: 1 Yixueyuan Road, Yuzhong District

institute: Chongqing medical university

summary: Cetylpyridinium chloride (CPC), a widely used cationic surfactant, is commonly employed as an antimicrobial agent in pharmaceuticals and personal care products. Recent studies have suggested that exposure to CPC may pose potential risks to female reproductive health, yet the specific effects of CPC on the ovary remain poorly understood. In this study, we observed that CPC exposure in mice resulted in weight loss, increased follicular atresia, and apoptosis of granulosa cells within the ovary. Through RNA-Seq data analysis, we discovered that the downregulation of the FOXM1 gene played a critical regulatory role in the DNA damage pathway triggered by CPC. In summary, our findings indicate that CPC induces DNA damage, leading to apoptosis of ovarian cells and follicular atresia in mice, thereby providing novel insights into the association between female infertility and CPC exposure

overall_design: To investigate the effects of cetylpyridinium chloride (CPC) exposure on ovarian health and elucidate the underlying mechanisms in mice

first: Liyao

last: Ma

first: Junlin

last: He


title: Transcriptional Analyses of Acinar- And Ductal-Cell-Derived Pancreatic Cancer

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

country: Canada

institute: University of British Columbia

summary: Pancreatic ductal adenocarcinoma (PDAC) is the most common form of pancreatic cancer, with one of the lowest 5-year survival rates at 10%. From mouse models, PDAC arises from acinar or ductal cells, and previous transcriptomic analyses have identified specific markers of acinar- and ductal-cell-derived PDAC. Although we have developed a more comprehensive understanding of the cellular origin of PDAC from mouse models, this knowledge has not been effectively utilized to classify patient tumors. Here, we generated mouse models where acinar or ductal cells, using Ptf1aCreER or Sox9CreER, respectively, expressed oncogenic Kras in the absence of Trp53 or Pten and formed PDAC tumors. Using both in vivo and in vitro methods, we reveal that acinar- and ductal-cell-derived tumors are largely similar to one another with small differences in gene expression. We also found variability in the expression levels of previously predicted markers of cellular origin, and propose a more comprehensive set of transcriptomic markers. Moreover, our acinar-cell-derived PDAC showed gene expression profiles resembling the classical subtype, supporting previous studies, while the ductal-cell-derived PDAC had an expression of both classical and basal subtypes. Overall, our findings demonstrate that acinar and ductal tumors have similar expression profiles and further research is required to identify reliable traits of acinar- and ductal-cell-derived PDAC.

overall_design: To investigate the cellular origin of PDAC, we generated mouse models where acinar (Ptf1aCreER ) or ductal (Sox9CreER), expressed oncogenic Kras in the absence of Trp53 or Pten for a total of 4 genotypes: AC:Trp53 (Ptf1aCreER; LSL-KrasG12D; Trp53flox; R26RYFP), DU:KTrp53 (Sox9CreER; LSL-KrasG12D; Trp53flox; R26RYFP), AC:KPten (Ptf1aCreER; LSL-KrasG12D; Ptenflox; R26RYFP), and DU:KPten (Sox9CreER; LSL-KrasG12D; Ptenflox; R26RYFP). The tumors were divided into 2 parts, one for bulk sequencing and the other for in vitro cell culture using complete and dropout media formulations for 3 conditions. No bulk tumors were analyzed from AC:KPten and DU:KPten tumors. All samples were subsequently sent for RNA sequencing.

first: Janel

middle: L

last: Kopp

first: Ken

middle: H

last: Chu


title: A -catenin-related transcriptional signature predicts survival outcomes in hepatocellular carcinoma patients.

city: Rome

first: Stefano

last: Scalera

address: Via Elio Chianesi 53

country: Italy

institute: IRCCS Regina Elena National Cancer Institute

summary: Hepatocellular carcinoma (HCC) is the most common form of liver cancer and a major cause of cancer-related deaths worldwide. Nevertheless, treatment and prognosis are still dependent on clinical and pathological factors, given that molecular biomarkers predicting survival outcomes are lacking. The extensive molecular heterogeneity characterizing HCC is denoted by the large number of signaling pathways involved in tumor initiation and progression. Among these, aberrant activation of the Wnt/-catenin pathway is the most frequent alteration. Various mechanisms can contribute to signaling hyperactivation, including somatic mutations and epigenetic alterations. Here, we have identified a Wnt/-catenin-related transcriptional signature denoting hyperactivated pathway signaling regardless of the presence of pathway-related activating mutations. The WNT signature predicts survival outcomes in two independent HCC patient cohorts and is associated with distinctive immunogenomic features denoting immune exclusion.

overall_design: RNA-Sequencing library were prepared using AmpliSeq for Illumina RNA WNT panel (the panel include 169 genes involved in the regulation of WNT signaling pathway) by following the manufacturer’s. Pooled sequencing libraries were sequencing in 150-bp single-end reads on Illumina MiSeq sequencer (Illumina).


title: Molecular Dynamics of Immortalized Chicken Fibroblasts from Adherent Cultivation to Carrier-Free Suspension Culture

city: Nanjing

first: meng

middle: yu

last: Zhang

address: Xiaoling Wei street

institute: Nanjing Agricultural University (Weigang Campus)

summary: This study aimed to elucidate the internal mechanisms of biological changes in immortalized chicken embryo fibroblasts (DF-1) by transitioning them from adherent to suspension culture. Initially, we determined the optimal growth conditions necessary for suspension cell culture. The adherent DF-1 cells (2D) were then adapted to suspension culture, resulting in short-term (3D_E) and long-term (3D_L) suspension cells. Growth metrics were monitored throughout the suspension phase. Subsequently, RNA-seq analysis was conducted to identify key genes and signaling pathways that exhibited distinct changes in 2D, 3D_E and 3D_L cells. The transcriptome data guided further investigations into the transdifferentiation of 2D, 3D_E, and 3D_L cells into lipids and their collagen secretion capabilities.

overall_design:
In order to establish the carrier free suspension system of immortalized chicken embryo fibroblasts (DF-1), the suspension culture conditions of DF-1 cells were optimized. During the suspension growth period, the cells were continuously examined to detect the growth parameters until the cells were fully adapted to suspension culture.
We performed RNA-seq on successfully suspended cells, namely 2D, 3D_E and 3D_L, and performed differential expression analysis using the acquired data.

first: Yu-meng

first: Ren-peng

last: Guo


title: Single-Cell Transcriptomics Reveals Ovarian Aging and Senescent Cell Accumulation underlying the Estropausal Transition in Mice

city: New York

first: Jiping

last: Yang

state: NY

department: OBGYN

institute: Columbia University

summary: Reproductive aging in mice leads to estropause, characterized by estrous cycle irregularity and eventual cessation, yet its underlying mechanism remains unclear. Here, we present a comprehensive single-cell atlas of mouse ovaries across precisely defined reproductive stages—from young (regular cycling) through the estropausal transition (regular versus irregular cycling) to post-estropause (acyclic)—and of ovary-specific senescent cells defined by high senescence-associated β-galactosidase activity. We mapped transcriptomic dynamics of ovarian aging and characterized the molecular features of ovarian senescent cells. Our analyses revealed that during the estropausal transition, irregularly cycling ovaries exhibited accelerated aging and cellular senescence features compared with regularly cycling counterparts, including increased transcriptional noise, altered conserved aging pathways such as oxidative phosphorylation and proteostasis, hormone dysregulation in granulosa cells, and elevated expression of the senescence marker Cdkn1a and senescence-associated secretory phenotype factors. This atlas delineates the cellular and molecular hallmarks of mouse ovarian aging and ovary-specific senescent cells, providing a resource for understanding the mechanisms underlying the estropausal transition.

overall_design: The scRNA-seq of mouse young, peri-estropausal and post-estropausal ovaries as well as Spider-bGal-high ovarian cells from post-estropausal ovaries

first: Xifan

first: Yousin

last: Suh


title: Effect of miP-PSTPIP2 overexpression on endothelial gene expression in homeostasis and inflammation. [ext501]

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

summary: Detecting microproteins (miPs) translated from small open reading frames (smORFs) by mass spectrometry poses major challenges. Here we report a high-throughput proteo-genomic pipeline that provides cumulative evidence for a large number of bona fide miPs in human and murine endothelial cells. Vascular inflammation in vitro and in vivo profoundly altered smORF expression and a large number of miPs was identified in the blood stream of patients following heart tissue damage. Human miPs presented high homology with other primates and their functional perturbation identified miPs that were essential for endothelial cell growth and viability. Moreover, combining gain/loss-of-function with multi-omic approaches demonstrated the involvement of an inflammation-regulated miP in the regulation of gene expression, proliferation and inflammation through interaction with proteins in different subcellular compartments. Thus, large numbers of uncharacterized miPs exist, play a major role in the regulation of cell function and may become biomarkers or therapeutic targets in cardiovascular disease. MiP-PSTPIP2 is upregulated in inflammatory conditions in vitro and in vivo. Therefore this study investigated global transcriptomic alterations following  overexpression of FLAG-miP-PSTPIP2 in homeostatic conditions as well as after treatment with interleukin-1beta in human endothelial cells. As the overexpression of FLAG-miP-PSTPIP2 was achieved by adenoviral infection, infection with an adenovirus to express the small protein FLAG-miRFP670nano served as control. The analysis included non infected human endothelial cells under the same experimental conditions to control for infection-dependent effects.

overall_design: To identify alterations in the gene expression profiles following overexpression of miP-PSTPIP2,  4 to 5 batches of human endothelial cells were transduced with recombinant adenoviruses to express FLAG-miP-PSTPIP2 or FLAG-miRFP670nano. Non infected human endothelial cells were also included in the analysis. Three days after infection cells were treated with solvent or Interleukin-1beta (20 ng/ml) for 16 hours. Cells were lysed and total RNA was isolated and analysed by next generation sequencing.

first: Mauro

last: Siragusa

first: Manav

last: Raheja

first: Beyza

last: Güven

first: Stefan

last: Günther


title: Early Prediction of Preeclampsia Based on Transposable Elements Deregulation in the Placenta [RNA-Seq]

city: London

first: Pradeepa

middle: M

last: Madapura

state: UK

address: 4 Newark Street, Whitechapel

country: United Kingdom

institute: Queen Mary University of London

summary: Preeclampsia (PE) is a pregnancy-associated hypertension disorder which affects 5–10% of pregnant women each year worldwide, which leads to adverse maternal and child outcomes. PE remains inadequately predicted, prevented and treated. Here we investigated the epigenetic alterations contributing to PE. We found an increase in histone acetylation levels across transposable elements (TEs) in the preeclamptic placenta. Histone hyperacetylation in PE is associated with an increased expression of endogenous retrovirus (ERV) and long interspersed nuclear element 1 (L1, LINE1) subfamilies of TEs in five independent pregnancy cohorts. A higher level of TE RNAs correlates with an elevated type I interferon (IFN-I) pathway, suggesting inflammation associated with PE could be due to the sensing of TE transcripts by the antiviral innate immune system. Furthermore, TE-focused analysis of maternal cell-free RNA (cfRNA) data revealed differential levels of TE subfamilies in PE compared to healthy controls. Training TE transcript signatures for PE prediction showed a robust performance of area under the curve (AUC) of 0.96, with validation cohort AUC of 0.88 with 81% sensitivity and 74% positive predictive value (PPV). Overall, these findings show TE deregulation is associated with PE pathology and analysis of TE levels in maternal cfRNA is an exciting approach for early diagnosis of PE, which can improve prophylaxis, obstetric and neonatal outcomes.

overall_design: RNA-sequencing (RNA-Seq) was performed for placental biopsies obtained for the normotensive controls (Control, n=6), Preeclampsia (PE, n=5) and Preeclampsia withg Intra-uterine growth retardation (PE+IUGR) individuals. RNAseq library was prepared from the RNA isolated from the two different sites for each plcanetal tissue sample.

first: Manthan

last: Patel

first: Madapura

last: Pradeepa


title: Malaria parasite manipulates erythrocyte membranes for intracellular adaptation : RNA-seq

first: chen

last: li

address: Renmin South Road

institute: Sichuan Univercity

summary: The ability to respond to stressful host environments is crucial for the survival of intracellular pathogens, during which transporters play key roles in the nutrient scavenging, such as lipid uptake. Here we discover a conserved malarial gene that orchestrates the parasitic adaption in the terminally differentiated, phospholipid scarce erythrocytes. The expression level of this gene, here named CAP, is the intensively upregulated in the erythrocyte-infecting parasites than the reticulocyte-infecting counterparts.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wild type versus CAP knockout-conditioned P. berghei trophozoite stage cells

first: Jingwen

last: Lin

first: Hancheng

last: Wei

first: Changling

last: Li

first: Qingxin


title: Endogenous expression of inactive lysine deacetylases KDAC4 (HDAC4) and KDAC7 (HDAC7)

city: New Orleans

first: Terry

middle: J

last: Watt

state: LA

address: 1 Drexel Dr.

department: Chemistry

institute: Xavier University of Louisiana

summary: To investigate the roles of KDAC4 and KDAC7, we generated cell lines containing point mutations in HT1080 cells that result in endogenous expression of mutated proteins.  For KDAC4, we introduced a mutation (H803A) to inactivate catalysis but that also contains concurrent mutations resulting in a knockout, as well as one that enhances in vitro activity of KDAC4 (H976Y, heterozygous with a knockout mutation on the second chromosal copy). For KDAC7, an inactivating mutation (H709A, homozygous) was introduced.  Expression profiling analysis was then performed on the resulting cell lines and wild-type HT1080 cells treated with the KDAC inhibitor TMP195, vs. untreated wild-type HT1080.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HT1080 cells, variants containing inactivated or enhanced KDACs, and inhibitor treatment with 3-4 replicates.  Untreated wild-type data is included in GSE228549.

first: Tasha

middle: B

last: Toro

first: Elena

middle: V

last: Skripnikova


title: AMPK regulates small RNA pathway prevalence to mediate soma-to-germ line communication and establish germline stem cell quiescence

city: Montreal

last: Jurczak

state: QC

address: 845 Sherbrooke St W

institute: McGill University

type: Non-coding RNA profiling by high throughput sequencing

summary: It is well established that cells communicate with each other via signalling molecules and pathways. Recent work has further indicated that this transfer of information can breach the soma-to-germ line barrier, thus permitting changes in germline gene expression in response to cellular decisions made in somatic lineages. We show that during periods of extended energy stress AMPK alters small RNA biogenesis in somatic cells to regulate the quiescence of germline stem cells. By combining genetic analyses and a method for miRNA imaging, we demonstrate that AMPK activity functions as a molecular switch driving the re-allocation of the endoribonuclease Dicer to the miRNA synthesis pathway during the dauer stage of C. elegans. By acting on components of the miRNA synthesis machinery, AMPK fine-tunes the production of a population of somatic miRNAs that act as a “pro-quiescence” signal to maintain germline integrity, thus bridging the gap between the soma and the germ line by altering small RNA homeostasis.

overall_design: We use the daf-2(e1370) temperature-sensitive allele to induce dauer in a controlled manner in C. elegans. We compare daf-2; aak(0) dauer larvae (AMPK mutants, lacking the catalytic subunits of AMPK aak-1 and aak-2) to wild-type daf-2 dauer larvae. We performed small RNA sequencing analysis to observe changes in the expression of endogenous small RNAs in AMPK mutant dauer larvae compared to wild-type control.

first: Christopher

last: Wong

first: Shaolin

first: Fabian

last: Braukmann

first: Eric

middle: A

last: Miska

first: Richard

last: Roy


title: The single cell transcriptomic characteristics of macrophages in liver fibrosis.

city: Philadelphia

first: Gan

last: Zhao

state: PA Pennsylvania

address: 384E Old Vet Quad 3800 spruce street

institute: University of Pennsylvania

summary: Single cell sequencing reveals macrophage transcriptomic changes in a mouse model of liver fibrosis induced by CCL4.

overall_design: FACS-sorted liver macrophages (CD45+/F4/80+) from BALB/c mice treated with or without CCl4 were used for sequencing.

first: Lulu

last: Xue

first: Andrew

middle: E

last: Vaughan

first: Michael

last: Mitchell


title: Cerebral vascular transcriptome profiling reveals intermittent fasting modulates chronic cerebral hypoperfusion-induced disease pathways.

city: Bundoora

first: Quynh Nhu

last: Dinh

state: VIC

address: Kingsbury Drive & Plenty Rd

country: Australia

institute: La Trobe University

summary: We investigated the effect of chronic cerebral hypoperfusion on transcriptomic changes in mouse cerebral arteries and whether intermittent fasting can modulate these transcriptomic changes.

overall_design: N=4 per group. 4 treatment groups and 4 timepoints

first: Quynh

middle: N

first: Thiruma

last: Arumugam


title: The transcriptomic characteristics of macrophages in liver fibrosis.

summary: High-throughput (Bulk-RNA) sequencing reveals macrophage transcriptomic changes in a mouse model of liver fibrosis induced by CCL4.

overall_design: FACS-sorted liver macrophages (CD45+/CD31-/F4/80+) from BALB/c mice treated with or without CCl4 were used for sequencing.


title: UCHL1 Maintains Microenvironmental Homeostasis of Male Germline Stem Cells by Antagonizing HSPA8

city: xian yang

first: donghui

last: Yang

state: shaanxi

address: No. 3rd, Taicheng Road, Yangling, Shaanxi

institute: Northwest A&F University

summary:
To illustrate the mechanism of UCHL1 and HSPA8 affects SSCs in the testis, mGSCs-I-SB cells were used to study in vitro, we down-regulated UCHL1 and HSPA8 using shRNA in mGSCs-I-SB cells.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different cells

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mGSCs-I-SB cells and its KD derivatives (shControl, shUCHL1, and shHSPA8).

first: Mengfei

last: Zhang

first: Wenbo

last: Chen


title: Investigating T cell responses in the dura to systemic infection

city: Cambridge

first: Colin

middle: YC

last: Lee

address: Wellcome Genome Campus, Hinxton

institute: Molecular Immunity Unit

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

overall_design: Refer to individual Series


title: Bulk RNA-sequencing of whole dura tissue

summary: Bulk RNA-sequencing of whole dural tissue in wild-type C57BL/6 mice

overall_design: Adult C57BL/6 mice were culled by rising C02 concentration and transcardially persued with ice-cold PBS. Dural skull-cap tissue was harvested by dissection using anti-static tweezers of whole mounts under a dissecting microscope and immediately placed in RNA Later for RNA extraction

first: Aaron

last: Fleming

first: Menna

middle: R

last: Clatworthy

middle: Y


title: Bulk TCR-sequencing of various tissues in mice treated with 2% DSS or H2O control.

summary: A study to determine TCR clonotype overlap analysis between the dura and intestinal tissues of mice given a colitis-like illness.

overall_design: Adult C57BL/6 mice were given 2% (w/v) DSS in their drinking water for 7 days to induce colitis and intestinal inflammation, and then returned to normal drinking water for 14 days. Control (H20) mice did not received DSS in their drinking water. Following CO2 perufsion, mice were culled and transcardially perfused with ice-cold PBS and dural and defined segments of small and large intestine were harvested into RNA Later for RNA extraction.

first: Zewen

last: Tuong


title: G-CSF mobilized apheresis as an alternative source of CAR T-cells

city: Atlanta

first: Krishnendu

state: Georgia

address: 345 ferst drive NW, marcus nanotechnology building, room no 3102B, 3rd floor

department: IBB

institute: Georgia tech

summary: Cellular therapies such as chimeric antigen receptor-redirected T cells (CART cells) are typically manufactured from an unmanipulated apheresis product collected from the patient or from an allogeneic donor. Whether CART cells can be manufactured from recombinant human granulocyte colony stimulating factor (rhG-CSF) mobilized products, such as those that are cryopreserved for a planned hematopoietic stem cell transplant (HSCT), remains unknown. Production of CART cells from G-CSF mobilized material would be particularly beneficial in settings where CART cells are paired with a HSCT platform, including in the context of acute myeloid leukemia (AML) as we have recently shown.  We therefore compared the phenotype and function of CAR T-cells manufactured from paired samples obtained from blood before or after rhG-CSF exposure in healthy volunteer donors, to test the hypothesis that rhG-CSF mobilized CAR T-cells (mobCAR) are functionally equivalent to steady state CAR T-cells (ssCAR). The products were compared using a broad range of phenotypic and functional analytics in vitro and then tested in an in vivo xenograft model, focusing on anti-CD33 CAR T cells for the treatment of AML. CART33 products were successfully manufactured from all four donors.  We found mobCART33 equivalent to ssCART33 across all domains tested, and in fact inter-donor variability usually exceeded the intra-donor inter-condition variability. This work supports the use of G-CSF exposed T-cells as a novel starting product for CAR T-cell manufacture, paving the way to the manufacture of an adjunct cell therapy to allogeneic hematopoietic stem-cell transplant from a single apheresis, and providing a means by which previously cryopreserved mobilized units may be utilised.

overall_design: Single cell RNAseq with 10x Genomics chromium platform with 3'-5' V3.1 kit to identify differences in transcriptomics profiles for the CAR-T cells manufactured from GCSF mobilized products

first: Paramita

last: Chatterjee

first: Saar

last: Gill

first: Roy

last: Krishnendu

first: Katherine

middle: D

last: Cummins


title: scRNA-sequencing of colon and dura CD45+ cells following Salmonella infection

summary: Single cell sequencing of colon and dura tissue CD45 cells in an orally-primed, intravenously recalled  S.typhimurium-2W1S mouse infection model.

overall_design: C57BL/6 Mice were orally infected with 1 X 10^7 CFUs of S. typhimurium-2W1S (strain BRD509) (OG_IV group) or PBS control (IV group). 130 days later mice received 1 X 10^6 CFUs of S. typhimurium-2W1S (strain BRD509) in 100uL sterile PBS intravenously in the tail vein. 7 days later mice received a flourescent anti-CD45 labelling antibody intravenously 5 minutes before sacrifice. Mice were sacrificed with a rising C02 concentration and dural and colon tissues harvested and digested for cell sorting. Cells were labelled with a live/dead dye and an ex-vivo CD45 marker to discriminate circulating from tissue cells. Cells were sorted as Live CD45IVneg CD45pos cells on a BD Influx jet-in-air sorter and loaded for 10X sequencing using a 10X Chromium Controller


title: Effects of Dip2c deletion on neural differentiation of mouse embryonic stem cells

first: xiaojuan

last: teng

address: 2 Lujing Road, Yuexiu District, Guangzhou City

institute: Dermatology Hospital, Southern Medical University

summary: We sought to validate the function of Dip2c during neural differentiation of mouse embryonic stem cells.

overall_design: RNA-seq

first: Xiaoyu

last: Xing

first: Mingze

last: Yao


title: Single cell RNAseq of murine dendritic cells in presence or absence of Il13ra1

city: Chiba

first: Masato

last: Kubo

address: 2669 Yamazaki, Noda-shi

institute: Tokyo University of Science

summary: To identified a unique role of IL-13 singal in DCs to generate anaphylactic IgE responses, single cell RNAseq data of cutaneous allergen sensitized wild type or Il13ra1flox/flox Cd11c-Cre mice were generated.

overall_design: Bilateral ear skin was topically treated with MC903 (2mM in 15 µL of 100% ethanol) and with OVA (100 µg), daily for 10 times. Then, NP-OVA (100 µg) alum was injected, and after 7 days, CD11c+ MHCII+ Lin- (CD3, B220, NK1.1, Ly-6G, TER119) splenic cells were  sorted.

first: Yasuyo

last: Harada

first: Takanori

last: Sasaki

first: Shigeyuki

last: Shichino

first: Satoshi

last: Ueha

first: Wu

last: Bin


title: Expression data from never smokers, smokers, and e-cig users in human bronchial epithelium

city: Columbus

first: Daniel

middle: Yui

last: Weng

state: OH

address: 420 W. 12th Ave. Room 390

department: Comprehensive Cancer Center

institute: The Ohio State University

summary: Background: Nicotine-containing electronic cigarette (e-cig) use has become widespread. However, understanding the biological impact of e-cigs compared with smoking on the lung is needed. There are major gaps in knowledge for chronic effects and for an etiology to recent acute lung toxicity leading to death among vapers. Methods: We conducted bronchoscopies in a cross-sectional study of 73 subjects (42 never-smokers, 15 e-cig users, and 16 smokers). Using bronchoalveolar lavage and brushings, we examined lung inflammation by cell counts, cytokines, genome-wide gene expression, and DNA methylation. Results: There were statistically significant differences among never-smokers, e-cig users, and smokers for inflammatory cell counts and cytokines (FDR q < 0.1). The e-cig users had values intermediate between smokers and never-smokers, with levels for most of the biomarkers more similar to never-smokers. For differential gene expression and DNA methylation, e-cig users also more like never-smokers; many of these genes corresponded to smoking-related pathways, including those for xenobiotic metabolism, aryl hydrocarbon receptor signaling, and oxidative stress. Differentially methylated genes were correlated with changes in gene expression, providing evidence for biological effects of the methylation associations. Conclusions: These data indicate that e-cigs are associated with less toxicity than cigarettes for smoking-related pathways. What is unknown may be unique effects for e-cigs not measured herein, and a comparison of smokers completely switching to e-cigs compared with former smokers. Clinical trials for smokers switching to e-cigs who undergo serial bronchoscopy and larger cross-sectional studies of former smokers with and without e-cig use, and for e-cigs who relapse back to smoking, are needed.

overall_design: Gene expression in human bronchial epithelium from 72 patients undergoing bronchoscopy was analyzed by Affymetrix arrays

first: Min-Ae

last: Song

first: Peter

middle: G

last: Shields


title: The histone methyltransferase NSD3 enhances rDNA transcription in cancer

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

institute: OSR - San Raffaele Scientific Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The histone methyltransferase NSD3 is one of the most recurrently amplified oncogenes in several cancer types and yet how NSD3 promotes tumorigenesis remains largely unknown. Most studies have focused on the short isoform of NSD3, lacking enzymatic activity while very little is known on the long NSD3 isoform, NSD3L, which also includes the SET methyltransferase domain. We found that NSD3L is a key regulator of ribosome biogenesis in cancer. NSD3L localises in the nucleolus and interacts with several nucleolar proteins. NSD3L overexpression is associated with enhanced expression of nucleolar genes and ribosomal RNA (rRNA) transcription in several tumour types. In cancer cells, but not in immortalised fibroblasts, NSD3L knock-down abrogates rRNA transcription and the binding to the entire sequence of ribosomal DNA of Polymerase I, as well as of the PolI activator upstream binding factor UBF, both required for rRNA transcription. Cut&Tag analyses demonstrated that NSD3 localises genome-wide on promoters. Conversely, on rDNA, NSD3L binds upstream of the rRNA transcription start site to a narrow sequence bound also by the FOS/JUN transcription factors. NSD3L deposits di- and tri- methyl groups to the histone lysine 36 on histone H3 throughout the entire rDNA sequences, competing with the histone methyltransferase SUV4-H20, thus preventing the deposition of the repressive histone mark H4K20me3. We propose NSD3L as one of the first chromatin remodelers actively promoting rRNA transcription and ribosome biogenesis. These findings usher novel therapeutic opportunities to target cancers presenting with NSD3 overexpression.

overall_design: Cut&Tag of NSD3, UBF, PolI, and FOSL2 proteins in HeLa cells after shCTRL or shNSD3L. All groups in 2 to 5 replicates.

first: Federica

last: Corigliano

first: Giovanni

last: Tonon


title: Leukemia impose cell autonomous defects in long-term stem cell function.

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

summary: To investigate the effect of B-ALL on hematopoietic stem cells

overall_design: We single-cell profile HSCs exposed to a B-ALL mouse model an a non B-ALL control

first: Christina

last: Jensen

first: Mikael

last: Sigvardsson


title: The RNA exosome complex function in non-coding RNAs processing during erythropoiesis.

city: bethesda

first: Xiang

last: Guo

state: MD

address: 50 south drive, blg50

department: NIDDK

institute: NIH

summary: To gain insight into DIS3 and EXOSC10 function during  erythropoiesis, RNA-seq was performed in CD71/Ter119 Fluorescence-Activated Cell Sorting (FACS) cells of WT and KO E14.5 fetal liver(S0-S5). Notably, depletion of DIS3 in E14.5 E4/E5 fetal liver cells significantly accumulated noncoding RNAs.

overall_design: RNA-seq were performed using WT and KO E14.5 fetal liver cells to identify the key genes and non-coding RNAs regulated by DIS3 and EXOSC10 during erythrocyte maturation.


title: Identification of the endothelial cell microproteome.

first: Carsten

last: Kuenne

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Identification of the endothelial cell microproteome. [ext305]

summary: Non-canonical small open reading frames (smORFs) that encode microproteins (miPs; <100 amino acids) are present in the genome. However, the study of smORF-encoded miPs has been hampered by technical challenges associated with the detection of small peptides by mass spectrometry. Here we combined deep RNA sequencing of ribosome-associated transcripts and optimized bioinformatic pipelines for downstream proteomic studies to identify thousands of smORF-derived miPs in endothelial cells (human 2,256, murine 7,597). Profound alterations in smORF/miP expression were detected following human endothelial cell activation by interleukin 1beta (IL-1beta) in vitro and by hypercholesterolemia and altered blood flow in vivo (in mice). Genome-wide homology analyses revealed that human smORFs are highly conserved among primates, and poorly in rodents or zebrafish. Functional characterization of selected miPs demonstrated their physical interaction with proteins in different subcellular compartments and their involvement in the regulation of proliferation, cell death, gene expression and inflammation. Moreover, it was possible to demonstrate that miPs can be released into the blood stream following cellular damage in humans. These findings demonstrate the value of this proteo-genomic pipeline for smORF and miP identification and highlight that the potential impact of miPs on cell and tissue function is much larger than previously presumed.

overall_design: Total RNA from HEK-293 cells transfected with a plasmid expressing FLAG-smORF-100 (miP30) or a control plasmid (CTRL). Three independent experiments.

first: Mauro

last: Siragusa

first: Stefan

last: Guenther


title: Identification of the endothelial cell microproteome. [ext284]

overall_design: Total RNA from HEK-293 cells transfected with a plasmid expressing FLAG-smORF-15 (miP2) or a control plasmid (Ctrl). Three independent experiments.


title: Identification of the endothelial cell microproteome. [ext234]

overall_design: Total (input) and RiboTag-associated RNA from right and left carotid arteries of endothelial cell-specific RiboTag mice 7 days after partial left carotid artery ligation.  n=5 samples with 5-7 mice/sample.


title: Identification of the endothelial cell microproteome. [ext224]

overall_design: Total (input) and RiboTag-associated RNA from thoracic aorta (aorta), aortic arch (arch), heart and lung of endothelial cell-specific RiboTag mice.  n=5-6 mice/group.


title: Identification of the endothelial cell microproteome. [ext187]

overall_design: Total (input) and RiboTag-associated RNA from human endothelial cells (HUVEC) treated with solvent or IL-1β. Four independent cell batches/group


title: Expression data of human facial skin metabolites isolated from minimally invasive microneedles

city: Seoul

first: Kwang Hoon

last: Lee

address: 50-1, Yonsei-ro, Seodaemun-gu

department: Dermatology

country: South Korea

institute: Yonsei University College of Medicine

summary:
Minimally invasive skin sampling is useful tool for skin molecular biological study.
We obtained the skin RNA using minimally invasive microneedles, and transcriptomic analysis was performed.

overall_design: Facial skin RNA samples of 33 Koreans (aged 23 to 64) were obtained using minimally invasive biodegradable microneedles and transcriptomic analysis was conducted.

first: Kwang

first: Seo

last: Kim

first: Ji


title: Macrophage Heterogeneity in Progression and Regression Phases of Cisplatin Induced AKI Mice Model - A single-cell RNA sequencing study

city: Nanjing

first: Bingquan

last: Deng

state: Jiangsu

address: Nanjing Medical University, No.109 Longmian Avenue, Jiangning District

institute: Nanjing Medical University

overall_design: Refer to individual Series


title: Single-cell RNA Sequencing of Wild Type and Cisplatin Induced AKI (3d and 7d groups) Mouse Kidney

summary:
Purpose: By using single-cell RNA sequencing to reveal the heterogeneity and dynamic variation of immune cell subsets in kidney injury and repairment phases
Methods: 10×Genomic single-cell RNA sequencing at Sham, day 3 and day 7 time points of murine model of cisplatin induced AKI were conducted to distinguish cell subsets according to transcriptomic profile and displayed dynamic changes during acute inflammation and resolution of renal injury
Results: In total, over 150.2 Gb clean reads were produced. A single-cell atlas of 36 clusters (11 cell types) of murine kidneys were generated and revealed marked changes in the proportion and gene expression of macrophage (MΦ) and proximal tubular (PT) cell subsets during injury and repair. Novel resident-MΦ cluster (Cx3cr1+Mki67+ MΦ) and PT cell cluster (repairing PT) with obvious proliferation potential were identified
Conclusions: Macrophage took the dominant proportion in immune cells, displayed significant heterogeneity and experienced dramatic subpopulation replacement during the progression and regression stages of cis-AKI

overall_design: Different AKI phases of renal single cell RNA profiles was generated by scRNA-seq, with three biological repeats, using Illumina NovaSeq 6000 sequencing system

first: Shensen

last: Li

first: Changchun

last: Cao


title: Bulk RNA Sequencing of Wild Type and Cisplatin Induced AKI (3d and 7d groups) Mouse Kidney

summary: The study of transcriptome analyses using the Illumina HiSeq 4000 platform for renal tissue from three groups (Sham, 3 and 7 days after cisplatin induced AKI, n=3). In total, over 66.2 Gb clean reads were produced; Differentially expressed gene analysis identified 3984 and 2139 genes which were expressed higher or lower in cis3d group when compared to Sham group. Among which, injury related genes, such as Havcr1, Lcn2, krt20 were significantly increased in cis3d group. On the other hand, the scale of different genes between cis7d and sham groups were greatly shrunk to 2144 (1564 up regulated and 580 down regulated). Accordingly, both the cell injury markers (krt20, lcn2 and havcr1) were markedly restored in cis7d group. In brief, the result of sham, cis3d and cis7d group shown the gene expression transition of injury pattern (progression stage) to repair pattern (regression stage) from 3 days to 7 days after acute injury of kidney tissue.

overall_design: Different AKI phases of renal mRNA profiles was generated by RNA-seq, with three biological repeats, using Illumina 4000 platform


title: LncRNA-NFYB axis drives immune suppression to promote HCC progression by a positive feedback

city: Guangzhou

first: Fang

last: Zheng

address: 107 Yanjiang West Road

institute: Sun Yat-Sen Memorial Hospital

summary: Metastases are the main cause of cancer mortality, but the mechanisms underlying aggressive progression remain poorly understood. Genome-wide characterization of chromatin accessibility reveals the opening of large numbers of distal regulatory elements across the genome during metastatic progression, which correlate with NFYB. Further, hepatocellular LINC01137 mitigates antitumour T cell responses by expanding MDSC to promote HCC metastasis via stabilizing NFYB to recruit SMYD3 to upregulate IL-1β, CXCL2 and CCL20.  Mechanistically, LINC01137 recruits SMYD3 to increase the occupancy of H3K4me3 on promoters of IL-1β, CXCL2 and CCL20 by NFYB. Importantly, LINC01137 transcription is activated by NFYB/KAT2B complex in a feed-forward loop. Clinically, Concordant overexpression of LINC01137-NFYB and MDSC markers positively correlates with poorer survival. Notably, IL-1β inhibitor enhances the blockade efficacy of PD-L1 in LINC01137-overexpressing HCC. Our results delineate an immunosuppressive mechanism of LINC01137-NFYB signalling during HCC progression and supply a proof for the concept of engineering microenvironment in HCC immunotherapy.

overall_design: The high metastatic cell line LM9 were infected by lentivirus-CTR and lentivirus-HA-3’-NFYB and lentivirus-HA-5’-NFYB for stably expressing-NFYB cell lines. Lysates of CTR-, HA-3’-NFYB-infected and HA-5’-NFYB-infected LM9 cells were immunoprecipitated using anti-HA primary antibody. RNA immunoprecipitation was performed using Magna RIP RNA-Binding Protein Immunoprecipitation Kit and all RNA were submitted for lncRNA expression array.

first: Bo-xuan

last: Zhou

first: Zi-feng

last: Wang

first: Jia-nan

last: Tan

first: Jie

last: Xu


title: Gene expression profiling of  EMT-associated breast cancer models

first: Whitney

last: Henry

state: MA

address: 500 Main St

department: Biology

institute: MIT

summary: Study identifies metabolic genes that are differentially expressed upon acquistion of an EMT in breast carcinoma cells.

overall_design: Total RNA  was derived from four murine mammary carcinoma cell lines (pB2, pB3, 687g and EpcamHi) grown in monolayer culture; two  replicates per sample. RNASeq single-end reads from Illumina 1.5 encoding were aligned using STAR (v 2.6.1a) [PMID:23104886] to the mouse genome (GRCm38/mm10) with Ensembl annotation v91 in gtf format.  Differential expression was assayed using featureCounts [PMID: 24227677], using stranded option -s 2, and DESeq2 [PMID: 25516281].

middle: S

first: Anushka

last: Dongre

first: Robert

last: Weinberg


title: Diurnal Temperature Fluctuation Impact on Transcriptomic Profile in V. vinifera L. 'Reisling' and 'Cabernet Franc'

status: Public on Jun 30 2026

city: Brookings

first: Anne

last: Fennell

state: SD

address: Raven Precision Ag Building Box 2100A

department: Agronomy, Horticulture & Plant Science

institute: South Dakota State University

summary: The influence of temperatures on dormant bud gene expression was analyzed during an eighteen-day period in January 2016 (January 14th to 31st) when daily temperatures ranged between 13 ºC and -15 ºC. This study collection period captured three different natural consecutive temperature events that fluctuated above and below 0 ºC or remained constantly below 0 ºC. Dormant buds were collected from two different wine grapevine cultivars, Cabernet Franc’ and ‘Riesling’. The buds were collected from Ravines Wine Cellar vineyards in Geneva, New York (42.843898, -77.003488. There were two 84-hour diurnal cycles (DC) that included temperatures fluctuating above and below 0 ºC (DC1: Jan 14 to Jan 17; DC2: Jan 24 to Jan 27) (Figure 1, Table 1). In DC1 and DC2, samples were collected 3 times/day, during the dark periods (6:00 and 18:00) and once in the light at warmest part of the day (14:00). The DC1 and DC2 periods bracketed four days (96 h) of constant daily temperatures below 0 ºC (Jan 18 to Jan 22). This constant below 0 ºC period was sampled in the light period only (14:00) (Figure 2, Table 1). Three replicate bud samples, each consisting of 3 buds per replicate were collected, each replicate from a separate vine for Reisling and Cabernet franc.  Bud samples were immediately plunged into liquid nitrogen and stored at -80 ºC until RNA extraction.

overall_design: There were two 84-hour diurnal cycles (DC) that included temperatures fluctuating above and below 0 ºC (DC1: Jan 14 to Jan 17; DC2: Jan 24 to Jan 27). In DC1 and DC2, samples were collected 3 times/day, during the dark periods (6:00 and 18:00) and once in the light at warmest part of the day (14:00). The DC1 and DC2 periods bracketed four days (96 h) of constant daily temperatures below 0 ºC (Jan 18 to Jan 22). This constant below 0 ºC period was sampled in the light period only (14:00). Three replicate bud samples, each consisting of 3 buds per replicate were collected, each replicate from a separate vine for Reisling and Cabernet franc.  Bud samples were immediately plunged into liquid nitrogen and stored at -80 ºC until RNA extraction.

first: Jason

middle: P

last: Londo

first: Prakriti

last: Sharma


title: Expression data from human macrophages

city: Lille

first: Jérôme

last: Eeckhoute

address: Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc

country: France

institute: CNRS

summary: Gene expression was monitored in resting non-polarized (RM) and alternatively polarized (M2) human macrophages

overall_design: Human monocyte-derived macrophages from 3 independent donors were used to compare gene expression levels between RM and M2

first: Jerome


title: Marquette and Brianna Grapevine Bud Chilling Fulfillment

summary: Grapevine chilling fulfillment influences bud break timing in the spring. Chilling fulfillment is controlled by cultivar genetics and their interaction with local temperature.  This study was undertaken to develop an understanding of the regulation of chilling fulfillment in two cold climate cultivars: V. hybrid 'Marquette' and 'Brianna'. The chilling fulfillment profiles were monitored in Marquette and Brianna in controlled (4C chilling) and Natural (field conditions in SD). There were significant differences in chilling fulfillment transcriptome profiles between the cultivars during the endodormant and ecodormant periods of winter.  Chilling fulfillment under natural conditions and constant 4 ̊C showed significant cultivar, condition (chilling treatment), and time point interactions, indicating the cultivars differed in chilling fulfillment responses.

overall_design: Samples of the grape cultivars Marquette and Brianna were collected from bearing vines trained with bilateral low cordons and vertical shoot positioning at Tucker’s Walk commercial vineyard in Garretson, SD (lat. 43°43’2.901” N, long. 96°30’10.155” W). Canes were collected bi-weekly from November 7, 2018, to April 3, 2019 for natural field chilling condictions.  On November 7, 2018, 45 additional canes (one per vine, containing nodes 5-10 from cane origin/base) were collected randomly from vines distributed across each cultivar block. Controlled chilling canes were cut into single nodes and nodes from each cane were placed in Ziplock bags at 4 ̊C to fulfill the chilling requirements.  Chilling hours were calculated as hours of exposure to temperatures between 0 and 7 ̊C in the field or controlled conditions. Chilling hour accumulation for the field condition was calculated from October 1 to the sample time by using hourly temperature data from the Garretson station of South Dakota Mesonet. Chilling accumulation for the controlled chilling treatment was calculated by adding the field chilling hours from October 1 to November 7 to the hours accumulated in a 4 ̊C controlled refrigeration cooler (24 chilling hours/day) for each sample time point.  The resulting experimental design was a three-way factorial with two chilling treatments (natural and controlled), two cultivars (Marquette and Brianna) and four chilling periods.

first: Turhan

last: Yilmaz

first: Kopila

last: Bhattarai


title: Near telomere to telomere genome assembly of Fujian Longyan Shan-ma duck (Anas platyrhynchos)

city: Fuzhou

first: Xuequn

last: Chen

state: Fujian

address: No.1 Qiuyang Road, Shangjie Town, Minhou County,

institute: FJTCM

summary: The domestic duck (Anas platyrhynchos) is an economically important poultry species and a valuable model for studying avian domestication and trait diversification. High-quality reference genomes have been generated for meat-type ducks, including Pekin duck. By contrast, genomic resources for laying-type breeds remain limited, constraining comparative analyses across divergent production types. Here, we present a near telomere-to-telomere (T2T) genome assembly of the female Fujian Longyan Shan-ma duck (A. platyrhynchos-FJLY), a representative laying-type breed.

overall_design: An adult female A. platyrhynchos-FJLY was obtained from the National Poultry Laboratory Animal Resource Center (Harbin, Heilongjiang, China). Blood, stomach, intestine, liver, pancreas, lung, heart, spleen, kidney, ovary, brain, eye, skin, and muscle tissues were collected separately for RNA extraction. To improve transcriptome representation, an adult male A. platyrhynchos-FJLY was also sampled from the same source. The same set of tissues was collected from the male individual, except that testis was collected instead of ovary. Total RNA was extracted independently from each tissue sample. Equal amounts of high-quality RNA from all collected tissues were pooled and used for transcriptome sequencing.

first: Zhen

last: Huang


title: Advancing probabilistic risk assessment of perfluorooctanoic acid through integration of in vitro data and physiologically based toxicokinetic modeling coupled with population-specific analysis

city: Novi Sad

first: Katarina

middle: Dragiša

last: Borković

address: Trg Dositeja Obradovića 3

department: Department for biology and ecology

country: Serbia

institute: University of Novi Sad, Faculty of Sciences

summary: Current human health risk assessment for perfluorooctanoic acid (PFOA) has proven inadequate due to a lack of innovative approaches. Here, we applied benchmark dose-response modeling to derive benchmark concentrations (BMCs) for apical and transcriptomic changes in human endothelial cells EA.hy926 following both high-concentration short-term (48 h) and human-relevant long-term (6 and 12 weeks) PFOA exposures. BMCs were translated into human equivalent doses (HEDs) using a physiologically based toxicokinetic model. Long-term exposure produced sensitive biological responses: 10th percentile HEDs for apical and transcriptomic data were 0.59 and 3.84 ng/kg bw/week, respectively, both below the estimated U.S. general population exposure level (9.91 ng/kg bw/week). Predicted 10th percentile HED thresholds in individuals with certain conditions were: end-stage renal disease 0.50 ng/kg bw/week, moderate to severe reductions in glomerular filtration rate 0.18–1.00 ng/kg bw/week, cirrhosis class A 0.18 ng/kg bw/week, NAFLD 0.79 ng/kg bw/week, and class 1 obesity 0.43 ng/kg bw/week, compared to healthy individuals (1.18 ng/kg bw/week), suggesting that PFOA can elicit adverse effects in endothelial cells at exposure levels below those currently experienced by the general population. Given the global prevalence of health conditions investigated in this study, a substantial portion of the population may face increased vulnerability to PFOA-induced health effects.

overall_design: Human endothelial EA.hy926 cells were exposed to PFOA under short-term (48 h, micromolar concentrations:1, 10 and 100 µM PFOA; control:0.05% DMSO) and long-term (6 and 12 weeks, nanomolar concentrations: 1, 10 and 100 nM PFOA; control:0.05% DMSO) exposure conditions. Total RNA was isolated and subjected to RNA sequencing to characterize concentration-dependent transcriptomic responses. Experiment was done in biological triplicates. Transcriptomic data were used for benchmark dose-response modeling and derivation of transcriptomic benchmark concentrations (BMCs), which were subsequently converted to human equivalent doses (HEDs) through physiologically based toxicokinetic (PBTK) modeling for human health risk assessment.

first: Marija

last: Opacic

first: Nemanja

last: Todorovic

first: Mladena

last: Lalic-Popovic

first: Bojana

last: Stanic

first: Nebojsa

last: Andric


title: Comprehensive Transcriptomic Profiling of Oral Squamous Cell Carcinoma in Indian Patients by RNA Sequencing

city: Pune

first: Subhayan

last: Sur

state: Maharashtra

address: Survey No 87/88, Mumbai Bangalore Express Highway, Tathawade

department: Biotechnology

country: India

institute: Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Pune

summary: Oral squamous cell carcinoma (OSCC) is the most common malignancy of the oral cavity, characterized by extensive molecular alterations that contribute to tumor progression and therapeutic resistance. To investigate the transcriptomic changes associated with OSCC, RNA sequencing was performed on primary OSCC tissues and matched adjacent non-tumor tissues. Differential gene expression and pathway enrichment analyses identified significant dysregulation of the MAPK signaling pathway, with EGFR and HRAS emerging as key altered genes. This dataset provides a transcriptomic resource for identifying molecular biomarkers and therapeutic targets in OSCC of Indian patients and supports further investigations into the molecular mechanisms underlying oral carcinogenesis.

overall_design:
RNA sequencing was performed to compare the global transcriptomic profiles of three primary oral squamous cell carcinoma (OSCC) tissues and three matched adjacent non-tumor tissues obtained from male tobacco users with histologically confirmed well-differentiated OSCC. Differential gene expression analysis was conducted to identify molecular alterations associated with OSCC.

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first: Shubha

last: Behara

first: Uday

last: Yadav

first: Vishal Kumar

last: Sahu

first: Shuchi

last: Nagar

first: Soumya

last: Basu

first: Samir

last: Gupta

first: B

middle: M

last: Rudagi

first: Supriya

last: Kheur

first: Dimple

last: Davray


title: Fibroblast-driven transcriptional reprogramming in response to doxorubicin in heterotypic melanoma spheroids

city: Cluj Napoca

first: Ovidiu

middle: Ilie

last: Pavel

state: Cluj

address: Clinicilor 5-7

department: Doctoral School of Integrative Biology

country: Romania

institute: Babes-Bolyai University

summary: Bulk RNA-sequencing was used to compare the transcriptional response to doxorubicin (DOX) between two multicellular melanoma spheroid models: a baseline model composed of B16.F10 melanoma cells, 2H11 endothelial cells, and bone marrow-derived macrophages (BEM), and a fibroblast-containing counterpart (BEMF) additionally incorporating primary murine dermal fibroblasts. Spheroids of each model were exposed for 48 h to their respective IC30 concentration of doxorubicin (0.56 microM for BEM; 0.79 microM for BEMF) or left untreated as controls, in two independent biological replicates per model/treatment combination. RNA-seq was performed to identify differentially expressed genes associated with fibroblast-dependent modulation of the doxorubicin response in melanoma spheroids.

overall_design: 2x2 factorial design (cell composition: BEM vs BEMF; treatment: untreated control vs doxorubicin at the model-specific IC30 concentration for 48 h), with 2 independent biological replicates per condition (8 samples total). Differential expression was modelled using DESeq2 with cell composition, treatment, and their interaction as factors.

first: Ilie-Ovidiu

first: Giorgiana-Gabriela

last: Negrea

first: Szilvia

last: Meszaros

first: Valentin-Florian

last: Rauca

first: Bogdan-Razvan

last: Dume

first: Emilia

last: Licarete

first: Laura

last: Patras

first: Vlad-Alexandru

last: Toma

first: Alina

last: Sesarman

first: Manuela

last: Banciu


title: Endocardial Tie2 orchestrates cardiac trabeculation via sequestering FOXO1 within the cytoplasm and stimulating versican cleavage

city: Nashville

first: Qi

last: Liu

state: Tennessee

address: 2525 WEST END AVE

institute: Vanderbilt University Medical Center

summary: Abnormal cardiac trabeculation often leads to congenital heart disease (CHD). TIE2-ANG1 signaling is a key regulator of endocardial growth during trabeculation. However, little is known about the underlying mechanisms. Here we demonstrate that loss of endocardial Tie2 via Nfatc1Cre resulted in increased nuclear localization of Forkhead box O1 (FOXO1), reduced phosphorylation of AKT (the direct regulator of FOXO1) and reduced expression of several proliferation promoting genes in endocardial cells (EdCs). The cardiac defects seen in endocardial Tie2-deficient hearts were phenocopied by forced activation of FOXO1 within the endocardium and partially rescued by loss of FoxO1. Conversely, excessive PI3K signaling (the direct regulator of phosphorylation of AKT) in EdCs caused cardiac hypotrabeculation. Further, we identify that endocardial loss of Tie2 resulted in impaired cleavage of versican, which was associated with enhanced expression of ADAMTS endogenous inhibitor TIMP3 in Tie2-cko EdCs. Thus, our results suggest that TIE2 signaling in the early embryonic endocardium promotes endocardial growth via sequestering FOXO1 within the cytoplasm and modulates cardiomyocyte proliferation via stimulating versican cleavage to orchestrate myocardial trabeculation, providing insights into the pathogenesis of CHD.

overall_design: E10.5 hearts of embryos with Nfatcre:Tie2fl/fl(tie2 deleted) or Tie2fl/fl were used to isolated single cell samples. The dissected e10.5 hearts were dissociated in TrpLe for 5minutes, Titurated with a 1ml tip, and allow to incubate  5 more miinutes. Samples were then quinched with PBS with 5%FBS and filtered through a 70um cell strainer. Cells were centrifuged at 300g for 5 minutes and resuspended in PBS with1%FBS. Samples with viability >90% were submitted for library preparation

first: Xianghu

last: Qu

first: Kevin

last: Tompkins

first: Yan

last: Gong

first: Bryan

last: Helm

first: Scott

middle: H

last: Baldwin


title: Supporting-like cells are an alternative gonadal steroidogenic lineage that is conserved in amniotes

city: Dos Hermanas

first: Iván

last: Barberá Aura

address: Avenida Rectora Rosario Valpuesta 1

country: Spain

institute: Centro Andaluz de Biología del Desarrollo (CABD)

summary: In mammals, the production of sex hormones is widely considered to depend on the interstitial lineage of the gonad, which differentiates into Leydig cells in males or theca cells in females. However, certain mammalian species evidence gonadal steroidogenic activity prior to the specialization of these interstitial lineages, suggesting that alternative cell types may assume this function. Here, using single-cell RNA-seq of rabbits developing gonads, we reveal a previously unrecognized role for supporting-like cells (SLCs), which can act as a major steroidogenic lineage during mammalian embryonic development.

overall_design: We performed 10x single-cell RNA seq experiments on dissected Oryctolagus cuniculus gonads of seven different developmental stages of XX embryos (13, 15, 17, 19, 21, 24 and 28 days post coitum) and 5 different developmental stages of XY embryos (13, 15, 17, 19 and 21 days post coitum,)

first: Wai-Yee

last: Chung

first: Emilie

last: Dujardin

first: Alicia

last: Hurtado

first: Mathieu

last: Galmiche

first: Chloé

last: Mayère

first: Maëva

last: Guy

first: Béatrice

last: Mandon-Pépin

first: Vedran

last: Franke

last: Jaszczyszyn

first: Rafael

last: D. Acemel

first: Serge

last: Rudaz

first: Jennifer

last: Mckey

last: Nef

first: Eric

last: Pailhoux

first: Dario

last: G. Lupiáñez


title: A Patient-Derived Xenograft Model Identifies AK1 as a Key Regulator of Metastatic Potential in Primary Triple-Negative Breast Cancer

city: seoul

first: Dakyung

last: Lee

address: 101 Daehakro

institute: University

summary: Metastasis remains the major cause of mortality in triple-negative breast cancer (TNBC), yet the metastatic potential of primary tumors is difficult to predict at diagnosis. Here, we leveraged patient-derived xenograft (PDX) models as a functional readout of primary tumor metastatic propensity. We first performed integrated genomic and transcriptomic profiling of primary breast tumors and their matched PDX models and found that key driver mutations, recurrent copy number alterations, and molecular subtype features were largely conserved between patient tumors and xenografts. These findings support the utility of matched PDX models as clinically relevant platforms for studying tumor-intrinsic features associated with breast cancer progression. We next focused on TNBC PDX models with reproducible metastatic phenotypes across biological replicates and classified primary tumors into metastatic and non-metastatic groups based on their matched PDX behavior. Single-cell transcriptomic profiling of these tumors revealed that metastatic samples were characterized by hypoxia-associated metabolic reprogramming, with coordinated activation of hypoxia and glycolysis pathways. This metabolic phenotype was associated with poor clinical outcome in independent breast cancer cohorts. Network-based prioritization identified adenylate kinase 1 (AK1) as a candidate regulator of this metastatic program. Functionally, AK1 promoted metastatic potential in primary tumor by supporting glycolytic ATP production, resistance to hypoxic and oxidative stress, and promoting trans-endothelial migration. Together, our findings establish primary tumor–matched PDX models as a clinically relevant discovery platform for metastatic potential, overcoming the challenge that future metastatic events are not readily predictable from primary tumors at diagnosis. Using reproducible PDX metastasis as a functional readout, we identify AK1-mediated metabolic stress adaptation as a key mechanism underlying metastatic potential in primary TNBC.

overall_design:
RNA-seq profiling of wildtype and AK1 knockdown MDA-MB-231 cells
RNA-seq profiling of matched patient normal, patient tumor and PDX tissue samples.


title: Ferritin-mediated iron homeostasis regulates fibroblast activation and shapes post-infarction cardiac remodeling

city: sichuan

first: Mantang

last: Jiang

address: west china hospital

institute: Sichuan University

summary: Myocardial infarction (MI) triggers dynamic tissue remodeling in which fibroblast activation critically determines scar formation and long-term cardiac function. Although iron dysregulation has been implicated in acute myocardial injury, its role in non-cardiomyocyte remodeling remains incompletely understood. Here, we integrated cross-species transcriptomics, spatial transcriptomics, single-cell RNA sequencing, and functional studies to investigate iron metabolic remodeling after MI. We found that ferritin heavy chain (Fth1) was robustly induced in the infarct region during the proliferative phase after MI and was predominantly localized to macrophages and fibroblasts. Single-cell trajectory analysis revealed that high Fth1 expression characterized early or inflammatory fibroblast states, whereas progressive Fth1 downregulation accompanied differentiation into extracellular matrix–producing myofibroblasts. Functionally, ferritin depletion promoted fibroblast activation in both neonatal rat and adult mouse cardiac fibroblasts, accompanied by expansion of the intracellular labile iron pool and enhanced profibrotic gene expression. Mechanistically, intracellular iron chelation suppressed fibroblast activation and attenuated FoxO1 signaling–associated transcriptional programs. Notably, temporally targeted treatment with the cell-permeable iron chelator 2,2′-bipyridyl (BPD) during the proliferative phase (days 3–14), but not the acute inflammatory phase (days 0-3), effectively attenuated pathological fibrosis and improved cardiac function after MI. Transcriptomic profiling further showed that iron chelation modulated both fibroblast activation–associated and inflammatory gene programs within the infarcted myocardium. Collectively, these findings identify ferritin-regulated iron homeostasis as a key determinant of fibroblast plasticity and highlight phase-specific intracellular iron modulation as a potential therapeutic strategy for limiting adverse cardiac remodeling after MI.

overall_design: To further determine whether the cardioprotective effects of proliferative phase–targeted BPD treatment are associated with suppression of fibroblast activation, we performed bulk RNA-seq analysis of left ventricular tissue at day 14 post-MI.

first: Tao

last: Wang


title: HTZ-1/H2A.Z expression sustains transcriptional programs that regulate Caenorhabditis elegans lifespan (II)

city: Bonn

first: Daniele

last: Bano

state: NRW

address: Venusberg Campus 1/99

institute: DZNE, German Center for Neurodegenerative Diseases

summary: The goal of this study was to compare the transcriptional impacts of the newly generated htz-1(bon101) allele with those of the previously characterized htz-1(ok3099) and htz-1(tm2469) alleles.

overall_design: RNAseq analysis of C. elegans adult htz-1(bon101), htz-1(ok3099) and htz-1(tm2469) to assess whether distinct htz-1 mutations result in similar genome-wide gene expression changes.

first: Beijia

last: Xie

first: Enzo

last: Scifo

first: Ioanna-Maria

last: Menegatou

first: Rossella Erminia

last: Ciliberti

first: Mrityunjoy

last: Mondal

first: Elena

last: De-Domenico

first: Stefan

last: Paulusch

first: Marc

last: Beyer


title: Active repression of muscle fate preserves neural lineage identity during cerebellum development

city: Memphis

first: Xinwei

last: Cao

state: TN

address: 62 Danny Thomas Pl

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

summary: Cell fate commitment is commonly thought to entail progressive restriction of developmental potential, enforced by passive, heterochromatin-based silencing of alternative lineage programs. Here we show that maintenance of neural identity during cerebellum development instead requires active repression of a starkly divergent fate by the TEAD–INSM1 transcriptional complex. Loss of TEAD1/2 or INSM1 activates the myogenic master regulator Myod1, resulting in neural cells acquiring transcriptional, structural, and metabolic features of skeletal muscle cells. Deletion of Myod1 fully suppresses neural-to-muscle conversion while partially rescuing neural developmental defects. Our results uncover a latent alternative lineage during neurodevelopment and a surprising role for sequence-specific transcription factors in enforcing lineage boundaries, including those previously thought essentially unbreachable, with implications for understanding aberrant differentiation in disease contexts and cell-type evolution.

overall_design: The series comprises four complementary genome-wide assays: Bulk RNA-seq was performed on P2 cerebella from Tead1;2cKO, Insm1cKO, and matched littermate controls (3–4 biological replicates per genotype, one cerebellum per animal) to capture early transcriptomic changes before overt morphological defects emerged; total RNA was isolated using the Direct-zol RNA MiniPrep kit. Single-cell RNA-seq was performed on P7 cerebella using the Parse Biosciences Evercode WT v3 split-pool combinatorial barcoding platform. Ten samples were profiled across four genotypes — Tead1fl/fl;Tead2fl/fl (n = 2), Tead1;2cKO (n = 3), Insm1fl/fl (n = 2), and Insm1cKO (n = 3) — each derived from a single cerebellum without pooling, dissociated with a papain-based kit, and fixed using the Evercode Fixation v3 kit. ATAC-seq was performed on P2 cerebella from Tead1;2cKO and Insm1cKO mice and their matched controls (3–4 biological replicates per genotype) to map chromatin accessibility changes. CUT&RUN was performed on P2 cerebella to profile genome-wide binding of TEAD1 (wild-type tissue), INSM1 (Insm1^HA/HA^ tissue, anti-HA antibody), and KDM1A (wild-type tissue), and the histone marks H3K4me3, H3K27me3, and H3K27ac across wild-type/control, Tead1;2cKO, and Insm1cKO cerebella; IgG served as the negative control, with 2–4 biological replicates per condition. All libraries were sequenced on a NovaSeq X Plus.

first: Shaikh

last: Mirja Nurunnabi

first: Venkata

last: Thulabandu

first: Akira

last: Inoue

first: Joshua

last: Paré

first: Qiong

last: Zhang

first: Beisi

last: Xu

first: Jackie

last: Norrie


title: Spatial Transcriptomics Reveals Molecular Differences Associated with Malignant Transformation in Oral Epithelial Dysplasia

city: Kansas City

first: Harsh

last: Pathak

state: KS

address: 3901 Rainbow Blvd

institute: KUMC

summary:
Background
Oral epithelial dysplasia (OED) is a precancerous oral lesion with an increased risk of progression to oral squamous cell carcinoma (OSCC). The molecular mechanisms driving OED progression are still poorly understood. To address this gap, we applied spatial transcriptomics to benign, OED and OSCC samples to uncover molecular drivers of oral carcinogenesis, with a focus on OED transformation.
Methods
We performed spatial transcriptomics on 13 benign, 15 OED (8 with transformation, 7 without), and 14 OSCC biopsies using the NanoString GeoMx Digital Spatial Profiler. Regions of interest were segmented into epithelial and stromal compartments with morphological markers. Gene expression was profiled using the GeoMx cancer transcriptome atlas assay for ~1,800 tumor related genes. Differentially expressed genes (DEGs) from next-generation sequencing were subject to bioinformatic analyses.
Results
Differentially gene expression analysis between OED with and without transformation revealed eight upregulated and three downregulated genes in epithelial cells, with no significant changes in immune cells. Protein-protein interaction network analysis identified B2M, STAT1, and CD74 as central hub genes. Pathway enrichment analysis suggested interferon and cytokine-mediated immune pathways, along with myeloid and amyloid formation-related pathways, as important contributors to OED transformation. Transcription factor analysis highlighted RELA and RFX as key upstream regulators.
Conclusions
Malignant transformation of OED appears to be primarily driven by epithelial-intrinsic activation of interferon and inflammatory signaling pathways rather than overt transcriptional reprogramming of immune cells. These findings suggest that early immune-related alterations in oral carcinogenesis are tumor cell centered and may precede significant changes in immune cell composition.

first: Naren

last: Raja

middle: B

first: Amrita

last: Mitra

first: Sufi Mary

last: Thomas

first: Yong

last: Wang

first: Tanya

last: Gibson

first: Rong


title: Single-Cell RNA sequencing of hematopoietic and non-hematopoietic cells defines a distinct signature in atopic and NRG1 mouse lung

city: Columbus

first: Mitchell

middle: H.

last: Grayson

address: 700 Children's Dr

institute: Nationwide Children's Hospital

summary: Respiratory viral infections cause significant mortality. Pre-existing atopy has demonstrated protection from virus-induced death. Mice made atopic with house dust mite (HDM) extract survive normally lethal parainfluenza (Sendai virus, SeV) and influenza A (IAV) viral infection. Neuregulin-1 (NRG1) is markedly elevated in the airways of atopic mice and has been shown to significantly attenuate mortality to SeV and IAV in naïve (non-atopic) mice. Hypothesizing that atopy and NRG1 mediate protection from death through similar mechanisms, we utilized single-cell RNA sequencing data from CD45+ (hematopoietic) and CD45- (structural) lung cell populations to compare atopic versus NRG1-treated mice in an unbiased manner to determine the enrichment of cellular populations and pathways prior to viral infection. Both treatments reduced alveolar macrophages, lymphatic endothelial cells, airway smooth muscle cells, and pericytes, while increasing alveolar type 2 cells. However, atopy led to increased fibroblasts and megakaryocytes with reduced club cells compared to NRG1 treatment. Further, in the hematopoietic cell compartment, atopy drove an increase in more inflammatory cells than NRG1 and associated with significant upregulation of immune cell signaling pathways, something not seen with NRG1 administration. Moreover, NRG1 knockdown did not reverse the protection from virus-induced death in mice with pre-existing atopy. Taken together, these data strongly suggest that atopy and NRG1 mediate increased survival from a respiratory viral infection through disparate mechanisms.

overall_design: Mice were either made atopic giving intranasally (i.n), 1 µg HDM extract  and one week later challenged i.n. for five days with 10 µg HDM extract, or administered NRG1 for five days i.n. Control mice were given phosphate-buffered saline (PBS) i.n.   Lungs were harvested 72 hours after last HDM challenge or immediately after last NRG1 administration. CD45+ and CD45- cells were isolated by Fluorescence-activated cell sorting (FACS) for downstream scRNA-seq and analyses.

first: Hussain

last: Syed-Rehan A.

first: Grayson

last: Mitchell H

first: Ma

last: Qin


title: Splicing dependency between EIF4G2 introns is mediated by exon definition and relies on a downstream splicing event

city: Sherbrooke

first: Karine

last: Choquet

state: Québec

address: 3201 rue Jean-Mignault

department: Biochemistry and Functional Genomics

institute: Université de Sherbrooke

summary: In mammalian cells, pre-mRNA splicing requires the excision of multiple introns within the same nascent transcript through the coordinated action of the spliceosome and accessory factors. We and others recently demonstrated that multi-intron splicing follows a predetermined order, and that removal of proximal introns is coordinated. Notably, specific introns that are removed later within a transcript depend on their neighboring introns for efficient excision, but the underlying mechanisms remain unknown. Here, we investigated the determinants of splicing order and coordination using a multi-intron minigene splicing reporter based on the human gene EIF4G2. We found that dependency between a later-excised intron and its neighbor is partially mediated through the downstream 5' splice site, consistent with the exon definition model, but is independent from intron length. Importantly, splicing coordination also relies on a prior downstream act of splicing, but not on specific cis regulatory elements in neighboring introns. Together, these findings improve our understanding of how distinct splicing reactions are connected and coordinated to produce mature RNA molecules.

overall_design: Transfected of EIF4G2 minigenes in HEK293T cells and direct RNA or amplicon nanopore sequencing

first: Pelletier

last: Marie-Lee

first: Vincent

last: Joëlle

first: Malo

last: Téa

first: Séguin

last: Camille

first: Tsybulskyi

last: Volodymyr

first: Semenchenko

last: Egor

first: Soumana Adamou

last: Ibrahim

first: Meyer

last: Irmtraud M

first: Choquet

last: Karine


title: Single-Cell Fixed RNA Profiling of Osteosarcoma Evolution Reveals a Coordinated Multi-cellular Network Driving Metastasis

city: Osaka

first: Thuy

middle: Thi Thanh

last: Le

state: Osaka

address: 1-4-3 Asahimachi, Abeno-ku

department: Department of Global Education and Medical Sciences

institute: Osaka Metropolitan University Graduate School of Medicine

summary: Osteosarcoma remains a profound clinical challenge, particularly for patients with metastatic or recurrent disease where survival rates have stagnated for decades. In this study, we present the first systematic application of Single-cell Fixed RNA Profiling (FLEX) to the osteosarcoma clinical spectrum. We profiled over 40,000 cells across treatment-naïve, post-chemotherapy, recurrent, and lung metastatic stages. By identifying the ADAMTS12/RNASE1/S100A4/PLVAP multi-cellular network, we move beyond simple cell-type identification toward an integrated understanding of how malignant cells and their microenvironment co-evolve. These findings offer a translational framework for improved risk stratification and the development of next-generation therapies designed to disrupt the interactive networks supporting metastatic osteosarcoma.

overall_design: Frozen tumor specimens from eight patients (age 11–35 years) representing four distinct clinical stages: treatment-naïve (n=2), post-chemotherapy treated (n=2), recurrent (n=2), and lung metastatic (n=2) were fixed to stabilize cytoplasmic RNA, followed by mechanical and enzymatic dissociation. High-quality single-cell suspensions were used for single-cell fixed RNA profiling (FLEX) by the 10x Genomics Chromium platform.

first: Khanh

middle: V

last: Nguyen

first: Thanh Thuy

middle: T


title: Single-cell analysis of the progeric vascular wall reveals progressive cell-type specific dysfunction and accumulation of somatic mutations

city: Solna

first: Lara

last: Garcia Merino

state: Stockholm

address: Armégatan 32C

institute: Karolinska Institutet

summary: Background: The premature aging disorder Hutchinson-Gilford Progeria Syndrome (HGPS) is caused by de novo LMNA mutations producing the aberrant Lamin A isoform progerin. HGPS patients die from cardiovascular disease, with their arteries showing extensive cellular and structural remodeling, but the mechanisms driving vascular dysfunction are not fully understood.  Methods: To characterize the molecular processes underlying vascular degeneration in HGPS, we used LmnaG609G/G609G mice, which carry the mouse equivalent of the HGPS-causing mutation and recapitulate the vascular phenotype without atheroprone stimuli. We performed single-cell RNA-sequencing on aortic arch cells from wild-type and LmnaG609G/G609G at different ages to capture time-dependent transcriptional changes. The Smart-seq2 protocol was used for sequencing, as it has high sensitivity and provides full-length transcript coverage.  Results: We identified transcriptionally distinct VSMC and fibroblast populations that evolved over time. Disease-enriched VSMCs displayed high levels of endoplasmic reticulum (ER) stress and underwent phenotypic switching towards a fibroblast-like state, potentially expanding through intercellular communication. ER stress inhibition with TUDCA showed the ER stress and phenotypic switch develop independently. In addition, we observed increased DNA damage and somatic mutation accumulation in progeria VSMCs, correlating with high ER stress, a ROS response, and eventually increased expression of p53-related genes. Lastly, VSMC apoptosis occurred by 12 weeks of age. Progeria-enriched fibroblasts either became activated or increased cartilage production and accumulated somatic mutations, but to a lesser extent than VSMCs, suggesting cell-type somatic mutation susceptibility.  Conclusions: We provide a detailed cellular and molecular atlas of VSMCs and fibroblasts with HGPS progression. We have developed a user-friendly searchable database for the research community to access the expression data, which will be of high relevance in preclinical research to ameliorate vascular aging.

last: Merino

first: Gwladys

last: Revêchon

first: Santhilal

last: Subhash

first: Fabiana

last: Stefani

first: Daniel

last: Whisenant

first: Marianna

last: Skipitari

first: Quentin

last: Giraud

first: Lars

last: Muhl

first: Giuseppe

last: Mocci

first: Johan

last: Björkegren

first: Piotr

last: Machtel

first: Liqun

last: He

first: Christer

last: Betsholtz

first: Maria

last: Eriksson


title: Peristaltic forces drive tumor cell invasion in colorectal cancer [scRNA-seq]

city: Los Angeles

first: Shannon

last: Mumenthaler

state: California

address: 12414 Exposition Blvd

department: Translational Research

institute: Ellison Medical Institute

summary: Mechanical forces are known to influence the progression of cancer, however, the impact of naturally occurring physical forces remains less well understood. With the advent of organ-on-chip (OOC) technology, preclinical models can now incorporate human-relevant physiological forces and allow for more precise investigation of their effects.  In this study, we explore how the peristaltic motions of the gut influence the early metastatic spread of colorectal cancer (CRC).  Specifically, we use a CRC OOC model consisting of tumor epithelial and endothelial channels separated by a porous membrane to investigate, through live cell imaging and ‘omics-based approaches, how peristaltic compressions enhance the invasiveness of colorectal cancer cells. scRNA-seq analysis revealed that invaded tumor cells exhibited significantly higher expression of mechanosensitive genes compared to non-invaded cells. Among the enriched genes was the mechanosensitive calcium ion channel, PIEZO1.  Knockdown of PIEZO1 disrupted YAP1-mediated mechanotransduction and reduced invasive capability. In contrast, exposure to peristaltic contractions enhanced invasiveness.  Analysis of publicly available datasets confirmed that elevated tumor mechanosensitive gene expression is associated with poorer clinical outcomes.  These findings reveal how physiological mechanical forces drive the invasive behavior of mechanosensitive CRC tumors.

overall_design: Following a six day period of exposure to peristaltic stretch on our organ-on-chip model, fluorescently labeled tumor epithelial cells were harvested from the models and sorted by GFP+ signal using fluorescently activated cell sorting (FACS) and analyzed using scRNA-seq

first: Curran A.

last: Shah

first: Carly

last: Strelez

first: Rachel

last: Perez

first: Christopher

last: Cherry

first: Heinz-Josef

last: Lenz

first: Shannon M.