title: Assay for transposase-accessible chromatin-sequencing (ATAC-seq) of liver samples from  Ythdc1flox/flox and Ythdc1-HKO mice, respectively.

summary: The goal of this study is to determine whether hepatic deletion of Ythdc1 affects chromatin accessibility.

overall_design:
To assess chromatin accessibility in the liver casued by hepatic deletion of Ythdc1, ATAC-seq analysis of liver samples in Ythdc1flox/flox and hepatocyte-specific Ythdc1 knockout (Ythdc1-HKO) mice was performed.
Each liver sample was pooled from four Ythdc1-HKO and Ythdc1flox/flox mice, respectively. Nuclei was extracted from liver samples, and the nuclei pellet was resuspended in the Tn5 transposase reaction mix. The transposition reaction was incubated at 37°C for 30 min. Equimolar Adapter1 and Adatper 2 were added after transposition, PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufactuer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina NovaSeq 6000 platform and 150 bp paired-end reads were generated. ATAC-seq analysis was performed using a standard protocol.
The chromatin accessibility in the livers of Ythdc1flox/flox and Ythdc1-HKO mice were characterized.


title: The Regulatory Logic of Planarian Stem Cell Differentiation [scRNAseq]

status: Public on Jun 15 2025

city: Exeter

first: Jordi

last: Solana

address: Northcote House

department: Health and Life Sciences

country: United Kingdom

institute: University of Exeter

type: Expression profiling by high throughput sequencing

summary: Stem cell differentiation underlies development and regeneration in multicellular organisms. Cell type identity is determined by the expression of specific transcription factors (TFs) regulating target genes (TGs) via binding to open chromatin regions (OCRs). The regulatory logic of differentiation includes factors specific to one or multiple cell types, functioning in a combinatorial fashion. Single cell transcriptomics has emerged as a revolutionary approach to study gene expression with cell type resolution, but integrating it with single cell analysis techniques to study chromatin remains challenging. Planarians, with their pluripotent neoblast stem cells continuously giving rise to all cell types, offer an ideal model to attempt this integration. Despite extensive single cell transcriptomic studies, the transcriptional and chromatin regulation at the cell type level remains unexplored. Here, we investigate the regulatory logic of planarian stem cell differentiation by obtaining an organism-level integration of single cell transcriptomics and single cell ATAC-seq. We identify specific open chromatin profiles for major differentiated cell types and analyse their transcriptomic landscape, revealing distinct gene modules expressed in individual types and combinations of them. Integrated analysis unveils gene networks reflecting known TF interactions in each type and identifies TFs potentially driving differentiation across multiple cell types. To validate our predictions, we combined TF knockdown RNAi experiments with single cell transcriptomics. We focus on hnf4, a TF known to be expressed in gut phagocytes, and confirm its influence on other types, including parenchymal cells. Our results demonstrate high overlap between predicted targets and experimentally-validated differentially-regulated genes. Overall, our study integrates TFs, TGs and OCRs to reveal the regulatory logic of planarian stem cell differentiation, showcasing the potential of single cell methods for characterising differentiation trajectories and their regulation.

overall_design: Four SPLiT-Seq RNA-Seq libraries of ACME-dissociated whole Schmidtea mediterranea animals in unperturbed conditions and two SPLiT-Seq RNA-Seq libraries of ACME-dissociated whole S. mediterranea animals in gfpi and hnf4i knock-down conditions.

first: Alberto

middle: A

last: Perez-Posada

first: Helen

middle: H

last: Garcia-Castro

first: Elena

middle: E

last: Emili

first: Virginia

middle: V

last: Vanni

first: Cirenia

middle: C

last: Arias-Baldrich

first: Siebren

middle: S

last: Frolich

first: Simon

last: Van Heeringen

first: Nathan

middle: N

last: Kenny

middle: J


title: The Regulatory Logic of Planarian Stem Cell Differentiation

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: RNF5-DNAJA1 Axis Dictates Selinexor Sensitivity of Multiple Myeloma by Regulating Mitochondrial Function

status: Public on Jun 14 2025

city: Tianjin

first: Zhiqiang

last: Liu

address: 22 Qixiangtai Rd

department: Pathophysiology

country: China

institute: Tianjin Medical University

summary: We performed RNA-seq to analyse the different expression genes of RNF5-KD LP-1 cells and non-target control.

overall_design: Examination of differentially expressed genes in RNF5-KD LP-1 cells compared with non-target control.

first: Mengqi

last: Wang

first: Linchuang

last: Jia

first: Danchen

last: Su


title: TBK1 enhances antifungal immunity by forming a SRC-TBK1 positive feedback loop in phagosomes of macrophages

city: Jinan

first: Xiaochen

last: Cheng

state: Shandong

address: 44 Wenhua Xi Rd.

institute: Shandong University

summary: TBK1 is a serine/threonine kinase known for its role in antiviral immunity. Here, we identify TBK1 as a key amplifier of antifungal immune responses. Using a mouse model of Candida albicans infection, we show that TBK1 is recruited to phagosomes via SRC-SHP2 signaling and phosphorylates SRC to establish a positive feedback loop. This enhances downstream cytokine production, including IL-6 and TNF-α, and promotes fungal clearance. Bone marrow-derived macrophages (BMDMs) from TBK1fl/fl and TBK1fl/fl Lyz2-Cre mice were stimulated with various fungal components, and RNA-seq was performed to assess transcriptional changes. Our findings define a new role for TBK1 in antifungal host defense and suggest TBK1 as a potential therapeutic target.

overall_design: RNA-seq profiling was performed on BMDMs isolated from TBK1fl/fl and TBK1fl/fl Lyz2-Cre mice. Cells were stimulated with HKCA hyphae, HKCA yeast, Zymosan depleted particles, or left untreated (CTRL) for 30 minutes. Total RNA was extracted, and polyA+ RNA was used for library preparation with the NEBNext Ultra II RNA Library Prep Kit. Sequencing was conducted on the Illumina NovaSeq 6000 platform to obtain 150 bp paired-end reads.

first: Yiting

last: Feng

first: Tian

last: Chen

first: Chengjiang

last: Gao


title: Natural and non-natural cytokine receptors generate diverse cell states to enhance T cell therapy [scRNA-seq]

city: Stanford

first: Yang

last: Zhao

state: CA

address: Beckman B169B, 279 Campus Drive

department: MCP

country: USA

institute: Stanford University

summary: Cytokines augment T cell function, but the nature of the optimal signals are not well defined. We deployed orthogonal cytokine-receptors to diversify the JAK/STAT signaling profiles elicited by orthogonal IL-2. We designed chimeric receptors consisting of the orthogonal IL-2 receptor extracellular domain (ECD) fused to intracellular domains (ICDs) from receptors for other common gamma chain cytokines as well as ICDs from interferon receptor, IL-10 receptor and homodimeric receptor families not expressed on T cells. Such non-natural pairings with the common gamma chain expand the JAK/STAT signaling space in T cells. Natural and non-natural orthogonal chimeric receptors led to distinct T cell fates in tumors, including naturally occurring states (Tc2 differentiation driven by orthogonal chimeric IL4R) and synthetic states (myeloid-like T cells driven by orthogonal chimeric granulocyte colony stimulating factor receptor). The orthogonal chimeric IL22R (o22R) potently activated STAT-1, -3, -4, and -5, imparting T cells with stem-like and effector properties. The pronounced anti-tumor functionality mediated by o22R and oGCSFR was linked to remodeling of the exhaustion-associated epigenome. Our study broadens the cytokine receptor repertoire, providing novel solutions to overcome barriers for using engineered T cells to treat cancer.

overall_design: C57BL/6 mice were inoculated s.c. with B16F10 tumor cells (1 × 10^6), sublethally lymphodepleted by irradiation on day 7, and received i.v. adoptive transfer of 3 × 10^6 Pmel T cells (either untransduced or transduced with mo2R, mo4R, mo20R, mo22R, or moGCSFR) on day 8 post tumor followed by i.p. administration of MSA-oIL-2 (2.5 × 10^4 unit per day) or PBS control every other day until day 16. On day 17, mice were sacrificed, tumors were minced and dissociated using a mouse tumor dissociation kit (Miltenyi Biotec) and a gentleMACS Octo Dissociator (Miltenyi Biotec). Tumor-infiltrating lymphocytes (TILs) were first enriched by density gradient centrifugation against Percoll (Cytiva), and then stained with surface markers and DAPI (Thermo Fisher Scientific). Thy1.1+CD8+ or Thy1.1+CD8+ YFP+ T cells were sorted using an Aria II sorter (BD Biosciences) at the Stanford Share FACS Facility for Single cell RNA sequencing.

first: Aastha

last: Pal

first: Anusha

last: Kalbasi

first: Chris

last: Garcia


title: Heterogeneous macrophage activation in injured skeletal muscle

city: New York

first: Gregory

last: Smith

address: 1 Gustave L Levy Pl

institute: Icahn School of Medicine at Mount Sinai Hospital

summary: Macrophages are the predominant inflammatory cells during skeletal muscle injury repair. They are required for the complete repair of acutely injured skeletal muscle, but detrimentally contribute to the pathological progression of dystrophic muscle in Duchenne muscular dystrophy (DMD) patients and DMD mouse model mdx5cv mice. The cellular and molecular mechanism underlying this difference has yet to be fully elucidated. To this end, the present study compared the single-cell transcriptomes of intramuscular monocytes/macrophages from uninjured and acutely injured quadriceps of 14 weeks-old wild-typed (WT) mice, and from quadriceps and diaphragm of age-matched mdx5cv mice, using single cell-based RNA sequencing (scRNA-seq) analysis. Our results identified multiple functionally diverse monocyte/macrophage clusters co-existing in each injured muscle sample. Both Ly6Chi and Ly6Clo intramuscular monocytes/macrophages were heterogenous, containing different clusters among different injury conditions. These clusters did not conform to strict M1/M2 activation, and were involved differentially in inflammation, extracellular matrix (ECM) remodeling, and myogenesis during skeletal muscle injury repair. These findings uncovered the heterogeneity of monocyte/macrophage activation in both acutely injured and dystrophic skeletal muscle, shedding light on the molecular and cellular mechanisms underlying the differential roles of monocytes/macrophages in acute skeletal muscle injury and muscular dystrophy in DMD.

overall_design: Single cell suspensions were prepared from 14 weeks-old quadriceps of WT mice day 1 and day 3 post BaCl2-induced acute muscle injury, and were then used for single cell-based RNA sequencing.

first: Xingyu

first: Justin

last: Moy

first: Yinhang

middle: R

first: Frederique

last: Ruf-Zamojski

first: Pawel

last: Przytycki

first: Stuart

last: Sealfon

first: Lan

last: Zhou


title: Loss of Activating transcription factor 3 restricts KRASG12D’s ability to promote PanIN progression through epithelial specific transcriptional regulation

city: London

first: Christopher

middle: L

last: Pin

state: Ontario

address: 1151 Richmond St

country: Canada

institute: University of Western Ontario

summary: Pancreatic ductal adenocarcinoma (PDAC) is the 3rd leading cause of cancer-related deaths in North America with ~12% survival 5 years after diagnosis. Risk factors for PDAC, including smoking and chronic pancreatitis, trigger the unfolded protein response (UPR) and global loss of Activating Transcription Factor 3 (ATF3), a mediator of the UPR, restricts preneoplastic progression in mice expressing oncogenic KRAS (KRASG12D). Since ATF3 is expressed in multiple cell compartments during PDAC progression, the goal of this study was to determine epithelial-specific roles for ATF3 during pre-neoplastic stages of PDAC. APK and AacinarPK tissue showed restricted neoplasia progression compared to Ptf1acreERT/+KRASG12D/+ mice. Ptf1acreERT/+KRASG12D/+ and APK organoids showed differential gene expression, and morphology, with APK organoids having reduced viability over time. This study reveals an epithelial-specific role for ATF3 in restricting KRASG12D -mediated PDAC and indicates ATF3 has functions in multiple cell compartments during PDAC progression.

overall_design: Pancreatic epithelial cells from KRASG12D-inducible mice with (Ptf1acreERT/+KRASG12D/+) or without ATF3 (Atf3-/-Ptf1acreERT/+KRASG12D/+; referred to as APK) were isolated 21 days after tamoxifen induced recombination. Gene expression was examined from isolated cells. Isolated cells were also grown in 3D cultures and morphology examined.RNA-seq analysis identified reduced KRAS-signalling in the absence of ATF3, correlating with reduced ADM in APK cultures. Alternatively, we generated mice allowing acinar cell-specific Atf3 deletion at the same time as KRASG12D activation (AacinarPK mice). AacinarPK mice were compared to Ptf1acreERT/+KRASG12D/+ and APK mice two weeks after cerulein-induced pancreatic injury for tissue morphology and gene expression.

first: Martin

last: Martin

first: Fatemeh

last: Mousavi

first: Liena


title: mRNA profiles of livers during postnatal development

city: Harbin

first: Zheng

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

summary: The goal of this study is to investigate how gene expression changes in the liver during postnatal development.

overall_design:
mRNA profiles in livers during postnatal development (day 1, day 10, day 20 and day 60 after birth) were generated by deep sequencing using Illumina Novaseq 6000 platform (n=3 for each group).
Methods: Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from livers of WT mice at day 1, day 10, day 20 and day 60 after birth. Three independent biological replicates for each group were used for RNA-seq. RNA-seq was performed by deep sequencing using an Illumina Novaseq 6000 platform. Paired-end clean reads were aligned to the mouse reference genome(GRCm38/mm10) with Hisat2 v2.0.5, and the aligned reads were used to quantify mRNA expression by using featureCounts v1.5.0-p3.
Our study represents the detailed analysis of liver transcriptomes from mouse livers during postnatal development, generated by RNA-seq technology.

first: Xinzhi

last: Li


title: NOP16 is a histone mimetic that regulates Histone H3K27 methylation and gene repression

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

summary: Post-translational modifications of histone tails alter chromatin accessibility to regulate gene expression. Some viruses exploit the importance of histone modifications by expressing histone mimetic proteins that contain histone-like sequences to sequester complexes that recognize modified histones. Here we identify an evolutionarily conserved and ubiquitously expressed, endogenous mammalian protein Nucleolar protein 16 (NOP16) that functions as a H3K27 mimic. NOP16 binds to EED in the H3K27 trimethylation PRC2 complex and to the H3K27 demethylase JMJD3. NOP16 knockout selectively globally increases H3K27me3, a heterochromatin mark, without altering methylation of H3K4, H3K9, or H3K36 or acetylation of H3K27. NOP16 is overexpressed and linked to poor prognosis in breast cancer. Depletion of NOP16 in breast cancer cell lines causes cell cycle arrest, decreases cell proliferation and selectively decreases expression of E2F target genes and of genes involved in cell cycle, growth and apoptosis. Conversely, ectopic NOP16 expression in triple negative breast cancer cell lines increases cell proliferation, cell migration and invasivity in vitro and tumor growth in vivo, while NOP16 knockout or knockdown has the opposite effect. Thus, NOP16 is a histone mimic that competes with Histone H3 for H3K27 methylation and demethylation. When it is overexpressed in cancer, it derepresses genes that promote cell cycle progression to augment breast cancer growth.

overall_design: To investigate NOP16 function in macrophage cells, we tried to knockdown Nop16 genes with siRNA in Raw264.7 cells and performed RNA-seq analysis.

first: Ken

last: Takashima

first: Eric

last: Greer


title: Transcriptome sequencing of Ilex x 'Nellie R. Stevens' and its yellow leaf mutant

city: Nanjing

first: Yiping

last: Zou

address: 159 Longpan Road

institute: Nanjing Forestry University

summary: Ilex x ‘Whoa Nellie’ is a yellow leaf (YT) mutant of I. x ‘Nellie R. Stevens’ (WT), an important ornamental woody species. However, the molecular mechanism of the YT mutant remains unknown. Therefore，we compared yellow-colored mutant leaves and normal green leaves in transcriptomic terms. Our study contributed to uncovering molecular mechanisms underlying yellow leaf mutaion and provided a reference for the application of leaf color mutants.

overall_design: Total RNA was isolated from green leaves of WT and golden leaves of YT using the NEBNext® Ultra™ Plant RNA Extraction Kit (TaKaRa, Dalian, China). Three biological replicates were analyzed for each RNA sample.

first: Yajian

last: Huang

first: Donglin

last: Zhang

first: Mingzhuo

last: Hao

first: Yunlong

last: Yin

first: Youwang

last: Liang


title: The human microglia response a resource to better understand microglia states in health and disease

city: NEW YORK

first: Hyomin

last: Seo

state: NY

address: 1 Gustave L. Levy Pl

department: Neurosciences

institute: Icahn school of medicine at Mount Sinai

summary: Microglia, the immune cells of the brain, are increasingly implicated in neurodegenerative disorders through genetic studies. However, how genetic risk factors for these diseases are related to microglial gene expression, microglial function, and ultimately disease, is still largely unknown. Microglia change rapidly in response to alterations in their cellular environment, which is regulated through changes in transcriptional programs, which are as yet poorly understood. Here, we compared the effects of a set of inflammatory and restorative stimuli (lipopolysaccharide, interferon-gamma, resiquimod, tumor necrosis factor-alpha, adenosine triphosphate, dexamethasone, and interleukin-4) on human microglial cells from 67 different donors (N = 398 samples) at the gene and transcript level. We show that microglia from different anatomical brain regions show distinct responses to inflammatory stimuli. We observed a greater overlap between human stimulated microglia and human monocytes than with mouse microglia. We define specific microglial signatures across conditions which are highly relevant for a wide range of biological functions and complex human diseases. Finally, we used our stimulation signatures to interpret associations from Alzheimer's disease (AD) genetic studies and microglia by integrating our inflammatory gene expression profiles with common genetic variants to map cis -expression QTLs (eQTLs). Together, we provide the most comprehensive transcriptomic database of the human microglia responsome.

overall_design: We compared the effects of a set of inflammatory and restorative stimuli (lipopolysaccharide, interferon-gamma, resiquimod, tumor necrosis factor-alpha, adenosine triphosphate, dexamethasone, and interleukin-4) on human microglial cells from 67 different donors (N = 398 samples) at the gene and transcript level.

first: Gijsje

last: Snijders

first: Katia

last: de Paiva Lopes

first: Marjolein

middle: M

last: Sneeboer

first: Benjamin

middle: Z

last: Muller


title: Machine Learning-based Exceptional Response Prediction of Nivolumab Monotherapy with Circulating MicroRNAs in Non-Small Cell Lung Cancer

city: Tokyo

first: Yifan

last: ZHANG

address: Otemachi Bldg. 1-6-1 Otemachi, Chiyoda-ku

country: Japan

institute: Preferred Networks, Inc.

type: Non-coding RNA profiling by high throughput sequencing

summary: Detecting cancer patients with exceptional response to immune check-point inhibition therapy is necessary to improve the treatment.  This study demonstrated machine learning models that utilize both microRNA expression and clinical information achieved much higher sensitivity and accuracy in identifying Exceptional-responder to nivolumab monotherapy when comparing to conventional method only using companion PD-L1 testing.

overall_design: This case control study profiled circulating microRNA expressions of 213 non-small cell lung cancer (NSCLC) patients treated with nivolumab monotherapy to identify patients with exceptional response.

first: Yasushi

last: Goto

first: Shigehiro

last: Yagishita

first: Yuki

last: Shinno

first: Kazue

last: Mizuno

first: Naoaki

last: Watanabe

first: Yusuke

last: Yamamoto

first: Nobuyuki

last: Ota

first: Takahiro

last: Ochiya

first: Yu

last: Fujita


title: The UNC5D-NuRD Repressor Complex Promotes Breast Cancer Progression by Negatively Regulating GSK3B

city: Beijing

first: Yongjia

last: Zeng

address: 10 You’anmen Outer West 1st Street

department: Biochemistry and Molecular Biology

institute: Capital Medical University

summary: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for UNC5D in MDA-MB-231 cells. UNC5D serves as a receptor for Netrin-1 and is highly expressed in breast cancer. Here, we report that UnICD, generated by caspase cleavage of UNC5D, translocates to the nucleus, interacts with the NuRD complex, and promotes tumorigenesis and development by relieving or reducing its suppression of β-catenin through inhibiting the transcription of GSK3B. In vitro experiments showed that the knockdown of UNC5D can inhibit the proliferation of breast cancer cells. Consistently, the expression level of UNC5D in breast cancer was negatively correlated with the expression level of GSK3B, and high levels of UNC5D were associated with poor prognosis in breast cancer patients. These results suggest that UNC5D is a pivotal driver in breast carcinogenesis, potentially inducing the initiation and progression of breast cancer through the UnICD/NuRD-GSK3B-β-catenin axis.

overall_design: Genome binding/occupancy profiling by high throughput sequencing

first: Shumeng

last: Liu

first: Yikai

last: Jie

first: Dong

last: Yan

first: Songfu

last: Shi

first: Linghang


title: Characterizing dynamics and lineage of bihormonal cell in mammalian pancreatic islets

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

institute: Peking University


title: Circadian clock-mediated neuronal gene expression in Aβ toxicity and excitotoxicity

city: Hong Kong

first: KIM

last: Jin Young

address: Tat Chee Avenue, Kowloon, Hong Kong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

summary: In recent decades, transcriptome analysis has been widely used to understand human disease pathogenesis and identify therapeutic targets and biomarkers. Accumulated reports in patients with neurodegenerative diseases, such as Alzheimer’s and Parkinson’s disease, have also provided evidence of dysregulated gene expression related to neuropathogenesis. However, obtaining samples from neurodegenerative patients is more challenging than other human diseases due to low accessibility. Also, brain tissues and cerebrospinal fluid are composed of multiple cell types, so they are unsuitable for obtaining neural cell-type-specific gene expression profiles. Thus, we here report gene expression profiles in primary neuronal cultures exposed to Aβ toxicity and glutamate excitotoxicity to understand pathological gene expression in neurons. By RNA-sequencing analysis, we compare transcriptomes and find that two groups of genes show similar expression patterns in Aβ toxicity excitotoxicity—they are either up- or down-regulated in both conditions. Genes in the two groups are related to synaptic function and cell signaling, which are well-known biological functions altered in Aβ toxicity and excitotoxicity. Interestingly, the analysis reveals a possibility that circadian clock (molecular oscillator generating daily rhythms)-related genes are dysregulated in both conditions. We confirm the reduced circadian transcription factor Bmal1 levels in Aβ toxicity and glutamate excitotoxicity. RNA-sequencing analysis in Bmal1-deleted neurons shows potential relationships between BMAL1 and synaptic functions. Thus, this transcriptome study provides evidence of the potential roles of the circadian clock in neuropathogenesis.

overall_design: Transcriptomes in two neuropathological conditions, Aβ toxicity and glutamate excitotoxicity, were examined. Total RNAs were extracted in primary neuronal cultures and subjected to RNA-sequencing analysis to understand neuron-specific gene expression profiles. Then, similar experiments were performed in neurons cultured from the circadian transcription factor Bmal1-deleted mice. We compared transcriptomes between the samples to understand their relationships.

first: Xuebing

last: Zhang

first: Tan

last: Wu

first: Hao

last: Huang

first: Yuchen

last: Chang

first: Geoffrey

last: Lau

first: Xin

last: WANG

first: Jin

middle: Y

last: KIM


title: Phenotypic analysis of dental pulp stem cells derived from deciduous teeth in Down syndrome.

status: Public on Jun 13 2025

city: Fukuoka

first: Itaru

last: Komine

address: 3-1-1 Maidashi Higashi-ku

institute: Kyushu University

summary: Down syndrome is a condition commonly seen in pediatric dentistry, presenting not only morphological abnormalities but also conditions such as progeria. In order to clarify the details of the phenotype of Down syndrome,we perfomed to collect dental pulp cells from deciduous teeth and investigate their gene expression.

overall_design: RNA-seq was performed using deciduous dental pulp stem cells from three healthy children and three children with Down syndrome

first: Yuta

last: Chiba

first: Hiroshi

last: Sato

first: Sae

last: Oka

first: Keigo

last: Yoshizaki

first: Aya

last: Yamada

first: Satoshi

last: Fukumoto


title: Gonadal gap junctions activate Notch signaling to suppress intestinal innate immunity via p38/PMK-1 and lysosome pathway

city: Changsha

first: Zhang

middle: xiu

last: mei

address: tian ma road

institute: Haijun Tu

summary: We showed that the innexin genes encoding gap junction subunits positively regulated GLP-1/Notch signaling to suppress the innate immunity of C. elegans via PMK-1/p38 pathway. The unc-17 acts in the dowmstream of inx-14/glp-1 to regulate innate immunity.

overall_design: Transferring synchronized larval 4-stage wild type N2 and unc-17(e245) worms to a new plate with PA14 infection or OP50 fed  and collecting worm samples after 24 hours. Then design some different assays to identify the important tips obtained from RNA-seq data analysis.

first: Haijun

last: Tu

first: Xiumei

first: Yirong

last: Wang


title: Effects of transient thermal stress on thyroid cancer cells

city: Taipei

first: Shih-Ping

last: Cheng

address: 92, Chung-Shan North Road, Section 2

department: Department of Surgery

country: Taiwan

institute: MacKay Memorial Hospital

summary: Radiofrequency ablation has been used to treat low-risk thyroid cancer; however, its oncological safety remains unclear. We applied transient sublethal thermal stress to thyroid cancer cells to simulate clinical scenarios in which incomplete radiofrequency ablation leads to residual viable thyroid cancer cells.

overall_design: Thyroid cancer cell lines TPC-1 and B-CPAP were grown in T25 flasks submerged at 37 or 40 degrees Celsius for 20 minutes. Total RNA was extracted and subjected to RNA-seq.


title: Drosophila melanogaster as a model organism to investigate sex specific differences

city: Gießen

first: Sonja

last: Dähn

address: Wilhelmstrasse 20

country: Germany

institute: Justus-Liebig-Universität Gießen

summary: Sex differences in physiology, anatomy, behavior, and genetics are well-documented throughout the animal kingdom. These differences are often neglegted in reasearch. This imbalance can have detrimental effects, as seen in cases where certain drugs have stronger side effects in females than in males. The fruit fly, Drosophila melanogaster, presents a promising model for studying these sex-specific differences because it shares many disease-related genes and is easy to use. RNA of 10-day-old and 30-day-old D. melanogaster (w1118) was isolated and sequenced. In 10-day-old flies 3969 genes are significantly higher expressed in males than in females, and 7176 genes are significantly lower expressed in males. In 30-day-old males 3735 genes are significantly higher expressed than in females, and 7101 genes are significantly lower expressed. In detail, the present study shows that male flies exhibit higher expression levels of genes involved in toll signaling, Imd signaling, insulin signaling, and lipid metabolism. These findings highlight D. melanogaster as a valuable model organism for studying sex differences in these highly conserved signaling pathways. This model may additionally help to analyze the sex-specific effects of dietary interventions or drugs, ultimately leading to a better understanding of sex-specific interconnections and improving the development of more effective, sex-specific medical treatments.

overall_design: mRNA-Seq of male and female, 10-and 30-day old w1118 Drosophila melanogaster

first: Anika

last: Wagner


title: PUS10-induced tRNA fragmentation impacts retrotransposon-driven inflammation [RNA-seq PUS10KO tdR-5-GlyGCC]

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

country: Sweden

institute: Lund University

summary: Pseudouridine (Y) is the most widespread RNA modification type on cellular RNAs and is dynamically catalyzed by a family of Y synthases (PUSes) in response to pathophysiological cues. PUS10 has been previously shown to regulate miRNA biogenesis in addition to modifying tRNAs, however its role in adapting gene expression to stress remains elusive. Here, we establish a novel role for PUS10 as a regulator of LTR retrotransposon-driven inflammatory response. Using Pus10 KO mice,  we demonstrate that Pus10 depletion leads to upregulation of interferon-stimulated genes (ISGs) and increased resistance to viral infection in vitro and in vivo. Mechanistically, PUS10 regulates a subset of 5’-derived tRNA (tdR) fragment, 5’ tdR Gly-GCC, that via targeting specific LTR retroelements modulates RNA-DNA hybrids accumulation and cGAS/STING/IRF3 pathway. Importantly, reduced PUS10 activity correlate with chronic autoimmune conditions, pinpointing PUS10 as a potential contributor to human immune regulation.

overall_design: 2 sets of samples including control (PUS10KO MEFs tdR-SCR) and PUS10KO MEFs tdR-5-GlyGCC were included in the study.

first: Magdalena

last: Madej

first: Cristian

last: Bellodi


title: The differentially expressed genes after overexpression of RNF128 in neonatal rat cardiomyocytes

city: Shanghai

first: Kai

last: Huang

address: 168 Changhai Road, Yangpu District, Shanghai, China

department: Department of Cardiovascualr Surgery

institute: Changhai Hospital

summary: This study aimed to explore the underlying molecular mechanism of RNF128 in Heart Failure with preserved ejection fraction (HFpEF). RNF128 acts as mitochondrial function suppressor by inactivation of PPARγ/VCP axis.

overall_design: Neonatal rat cardiomyocytes were seeded into 6-well plates and treated with 500 μM palmitic acid for 24h. The differentally expressed genes by RNF128 overexpression were screened by RNA sequencing. The transcriptome sequencing studies were performed by deep sequencing, using Illumina NovaSeq 6000.

first: Lin

last: Han


title: PUS10-induced tRNA fragmentation impacts retrotransposon-driven inflammation [CUT&RUN]

overall_design: CUT&RUN was performed on  WT and Pus10KO MEFs cells with goat anti-rabbit IgG (Abcam, CAT#ab97047), rabbit anti-H3K4me3 (Active motif CAT#39159)


title: Modulation of striatal cAMP levels: a paradigm shift in the treatment of hyperkinetic movement disorders

city: Paris

first: Mohamed

last: Doulazmi

state: Paris

address: 9 quai St Bernard

department: Neurocsiences

country: France

institute: Sorbonne Unversity

summary: Study of the striatal transcriptome consequences of a mutation of the ADCY5 gene, encoding the adenylyl cyclase 5 protein, an enzyme producing cAMP in the striatum. The Adcy5R419W mouse line was generated on a C57BL/6N background using CRISPR/Cas9-mediated genome editing. Mutations were introduced into exon 2 of the Adcy5 gene, located on chromosome 16. The c.1255C>T (p.R419W) substitution recapitulates the human p.R418W variant, accounting for the one-residue offset between mouse and human proteins.

overall_design: RNA profiling of striatal homogenates from adult animals of the Adcy5R419W (Adcy5 KI) mouse line mice and their Wild-type littermates (WT)

first: Ruiyi

last: Yuan

first: Yuki

last: Nakamura

first: Louise-Laure

last: Mariani

first: Jean-Antoine

last: Girault


title: Single cell RNA sequencing of mouse bone marrow stroma during aging

city: Dallas

first: Zhiyu

last: Zhao

state: Texas

address: 5323 Harry Hines Blvd.

department: Children's Medical Center Research Institute

institute: University of Texas Southwestern Medical Center

summary: To better understand the changes in bone marrow stromal cells during aging, we performed single cell RNA sequencing of Lineage-CD45-CD71- bone marrow stromal cells from 2, 12, and 24 month-old mice.

overall_design: Single cell RNA sequencing of bone marrow stromal cells from 2-month, 12-month, and 24-month mice.


title: H3K27me3 and SUZ12 CUT&Tag in K562 cells depleted of CRAMP1 or SUZ12

city: Cambridge

first: Iva

last: Tchasovnikarova

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

summary: The essential role of the core histones (H2A, H2B, H3 and H4) in DNA packaging has been well understood for decades, but the function of the linker histone (H1) remains enigmatic. H1 compacts nucleosome arrays in vitro, but the multiple H1 subtypes and variants encoded in mammalian genomes (11 in both mice and humans) hamper genetic studies to determine H1 function in vivo. Challenging the prevailing view that linker histones are a general feature of heterochromatin, here we show a critical requirement for linker histones in the function of Polycomb Repressive complex 2 (PRC2). Through a CRISPR/Cas9 genetic screen in a fluorescent reporter cell line responsive to PRC2 perturbation, we identified an essential requirement for the poorly characterised gene CRAMP1 in PRC2-mediated repression. CRAMP1 localises to the promoters of all expressed H1 genes where it acts as a positive transcriptional regulator. Ablation of CRAMP1 provides a unique tool to simultaneously deplete all linker histones, which results in selective decompaction of H3K27me3-marked loci and derepression of PRC2 target genes without concomitant loss of PRC2 occupancy or enzymatic activity. Strikingly, in contrast to the broad genomic distribution previously ascribed to H1, we find that linker histones selectively localise to genomic loci marked by H3K27me3 across diverse cell types and organisms. Altogether, our data demonstrate a prominent role for linker histones in epigenetic repression by PRC2.

overall_design: CUT&Tag for H3K27me3 or SUZ12 was performed in K562 cells transduced with a non-targeting shRNA or shRNAs targeting CRAMP1 or SUZ12. IgG was used as a negative control.

first: Rachael

last: Matthews


title: ATAC-seq in K562 cells depleted of CRAMP1 or SUZ12

overall_design: K562 cells were transduced in duplicate with shRNAs targeting CRAMP1 or SUZ12. A non-targeting shRNA served as a control. ATAC-seq was performed seven days later.


title: Time-course transcriptome analysis of podocyte injury in Pod-TRECK mice

city: Towada

first: Masaki

last: Watanabe

department: School of Veterinary Medicine

institute: Kitasato University

summary: Podocytes are critical components of the glomerular filtration barrier, and their injury leads to chronic kidney disease (CKD). To elucidate the temporal molecular responses following podocyte depletion, we performed bulk RNA-seq on whole kidneys from Pod-TRECK mice. These mice express the human diphtheria toxin receptor under the control of the podocin promoter, allowing for selective ablation of podocytes upon diphtheria toxin (DT) administration. Samples were collected at 0 (control), 5, 14, and 21 days after DT injection.

overall_design: Pod-TRECK mice were administered 100 ng of diphtheria toxin intraperitoneally to induce podocyte-specific injury. Total RNA was extracted from whole kidneys at four time points: control (no DT), and days 5, 14, and 21 post-injection. Three biological replicates were prepared per group (n=3). RNA libraries were constructed and sequenced on an Illumina NovaSeq 6000 platform using paired-end reads. The resulting data were used to analyze dynamic transcriptomic changes associated with podocyte depletion and kidney injury progression.

first: Kenta

last: Nakano

first: Tadashi

last: Okamura

first: Nobuya

last: Sasaki


title: H1 ChIP-seq in C. elegans L3 larvae

overall_design: ChIP-seq for HIS-24 was performed in wild-type C. elegans L3 larvae.


title: Illumina sequencing of Upf1-TAP immunoprecipitated transcripts in yeast

first: Gwenael

last: Badis

address: 46 rue d'Ulm

department: Genomique fonctionnelle (Section 2)

institute: IBENS

summary: Nonsense-mediated mRNA decay (NMD) is a conserved eukaryotic surveillance pathway known to degrade mRNAs containing premature termination codons (PTCs). A distance long enough between the stop codon and the poly(A)-binding protein (Pab1) is required for mRNA recognition by the NMD factors Upf1, Upf2 and Upf3. Using Nanopore direct RNA sequencing, we show that PTC-containing NMD targets account for only 6% of Upf1-associated RNA and have long poly(A) tails, indicating that Upf1-binding occurs prior to RNA deadenylation. Conversely, most Upf1-associated mRNAs have short poly(A) tails, lack a PTC and correspond to highly expressed genes. A short poly(A) tail is thus an important feature of NMD targets, redefining the scope of this RNA degradation pathway. We propose a model in which loss of Pab1-binding to short poly(A)-tailed mRNAs impairs translation termination and dictates the recruitment of the NMD machinery, uncovering a hitherto unknown role of NMD in the degradation of these transcripts.

overall_design: Truseq mRNA stranded sequencing of 3 replicates of each type :  total RNA from WT (LMA 2194), upf1_delta (LMA1667) and RNA Immunoprecipitated (RIP) from Upf1-TAP (LMA2194)

first: Toni

last: Gouhier

first: Cosmin

last: Saveanu


title: CUT&Tag in K562, HCT116, RPE1 and Jurkat cells

overall_design: CUT&Tag for H1 subtypes and H3K27me3 was performed in wild-type K562, HCT116, hTERT RPE-1 and Jurkat cells; H1 knockouts and IgG were used as negative controls. CUT&Tag for H3K9me3 was performed in wild-type K562 cells; IgG served as a negative control. CUT&Tag for exogenously expressed H1 subtypes was performed in K562 cells transduced with FLAG-tagged H1 subtypes; CUT&Tag for FLAG in wild-type K562 cells served as a negative control.


title: RNA-seq in K562 cells depleted of CRAMP1 or SUZ12

overall_design: K562 cells were transduced in triplicate with shRNAs targeting CRAMP1 or SUZ12. A non-targeting shRNA served as a control. Total RNA was harvested seven days after transduction.


title: Nanopore sequencing of Upf1-TAP immunoprecipitated transcripts in yeast

overall_design: Nanopore Direct RNA sequencing (SKQ_RNA002) of 3 replicates of each type :  total RNA from WT (LMA 2194), upf1delta (LMA1667), Upf1-TAP upf2delta (LMA3739), Upf1-TAP upf3delta (LMA3735) and RNA Immunoprecipitated (RIP) from Upf1-TAP (LMA2194), eIF4G2-TAP(LMA3314), Upf1-TAPupf2delta (LMA3739), UPF1-TAPupf3delta (LMA3735) strains


title: CRAMP1 drives linker histone expression to enable Polycomb repression

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

sample_organism:
Caenorhabditis elegans
Homo sapiens

platform_organism:
Caenorhabditis elegans
Homo sapiens

overall_design: Refer to individual Series


title: PUS10-induced tRNA fragmentation impacts retrotransposon-driven inflammation [Polysome profiling]

first: Phuong

last: Cao Thi Ngoc

overall_design: 3 sets of samples including control (CTRL) or PUS10KO were included in the study.

first: Magdalena

last: Madej

first: Cristian

last: Bellodi


title: Blood transcriptome of ICU pateints with blood stream infections on admission

city: Amsterdam

first: Joe

last: Butler

address: Meibergdreef 9

department: Infectious diseases

country: Netherlands

institute: Amsterdam UMC

summary: Knowledge of the contribution of the pathogen to the heterogeneity of the host response to severe infection is limited. We aimed to compare the host response in critically ill patients with a blood stream infection (BSI).

overall_design: Patients with a blood-stream infection (BSI) were selected if they had a positive blood culture taken (day of draw) within +/-1 day of the PAXtube draw, which was measured using RNAseq. The five main BSI groups were coagulase-negative staphylococci (CoNS), Escherichia coli (EC), Enterococcus species (ENT), Staphylococcus aureus (SA), and Streptococcus species (STR). Two further patient groups are included: those with other bacterial and fungal BSIs (OTH), and those with BCs positive for multiple pathogens (MIX). We also include a non-infectious group (NI), patients who had a blood culture taken which was negative.

first: Hessel

last: Peters-Sengers

first: Tom

last: van der Poll


title: RNA-seq in CRAMP1 and SUZ12 knockout KBM-7 cells

overall_design: Total RNA was extracted from wild-type, CRAMP1 knockout or SUZ12 knockout KBM-7 cells. Three independent CRAMP1 knockout clones and two independent SUZ12 knockout clones were used as biological replicates.


title: H3K27me3 and SUZ12 CUT&RUN in K562 cells depleted of CRAMP1 or SUZ12

overall_design: CUT&RUN for H3K27me3 or SUZ12 was performed in K562 cells transduced with a non-targeting shRNA or shRNAs targeting CRAMP1 or SUZ12. IgG was used as a negative control.


title: PUS10 driven tRNA fragmentation mediates transposon induced inflamation [HSC RNA-seq]

overall_design: 2 sets of samples including control (Murine hematopoietic stem cells) or PUS10KO were included in the study.

last: Ngoc


title: Mechanism of OGT-mediated FASN glycosylation regulating JNK/ICAM1 pathway in Liver cancer stem cell metastasis [ICAM1]

city: Guangzhou

first: changgui

last: zhong

state: Guangdong

address: Guangzhou University Town, Panyu District, Guangzhou

institute: South China University of Technology

summary: We performed transcriptome sequencing analysis on LCSCs with different metastatic abilities.  KEGG enrichment showed that genes upregulated during LCSC3 metastasis were related to cell membrane pathways. qPCR and flow cytometry confirmed that FASN expression was significantly upregulated during LCSCs metastasis. ICAM1 affects EMT, invadopodia formation, migration and invasion ability of LCSCs. ICAM1 plays a key role in the process of liver metastasis and the development of hepatocellular carcinoma in mice. FASN is also highly expressed during LCSC metastasis. Silencing FASN reduces the expression level of stemness genes, migration and invasion ability, and self-renewal ability of LCSCs. GSEA analysis indicated that transcriptome sequencing results after FASN knockdown were mainly enriched in the EMT process. FASN affects the expression of ICAM1 through the JNK/c-Jun axis in the MAPK pathway, and OGT is involved in the glycosylation process of ICAM1 regulating FASN, thereby affecting the migration ability of LCSCs.

overall_design: Liver cancer stem cells were isolated from clinical tissues and stably subcultured in mouse embryonic fibroblasts. After 2-5 generations, the liver cancer stem cells were knocked down with shICAM1 for 48 hours and then collected 48 hours after the treatment.

first: Changgui

last: Zhong


title: PUS10-induced tRNA fragmentation impacts retrotransposon-driven inflammation [small RNA-seq]

overall_design: 4 sets of samples including control (CTRL) or PUS10KO were included in the study.


title: Effect of anti-CD3 antibody treatment on islet transcriptomes in the nonobese diabetic (NOD) mouse model

city: Winnipeg

first: Peter

last: Thompson

state: MB

address: 715 McDermot ave

department: Physiology & Pathophysiology

institute: University of Manitoba

summary: Type 1 Diabetes (T1D) is a chronic autoimmune disease resulting from T cell-mediated destruction of pancreatic beta cells. Although T cells are known to destroy beta cells, how they may impact non-lethal forms of beta cell stress that also contribute to T1D development is not known. Here, we established an intermittent treatment regimen using a validated monoclonal anti-CD3 antibody on the female nonobese diabetic (NOD) mouse model for T1D at late prediabetic stages that leads to depletion of antigen-specific T cells and improvement of glucose tolerance. We used  mRNA-seq to explore transcriptomic changes in isolated pancreatic islets from mice treated with anti-CD3 antibody or IgG as a control.

overall_design: Nine week old euglycemic female NOD mice were treated once per week for 4 weeks with IgG or anti-CD3 (2.5 mg/kg). Two or three days following the last dose of antibody, pancreatic islets were isolated from the mice and total RNA extracted using a Trizol-based kit approach. The total RNA was then submitted to a service provider for paired-end mRNA-seq on the Illumina platform.

first: Jasmine

last: Pipella


title: Sensory Flicker Stimulation of 5xFAD Mice Activates Immune Pathways in a Frequency and Time Dependent Manner

city: Atlanta

first: Levi

middle: B.

last: Wood

state: GA

address: 315 Ferst Dr NW Rm 3303

institute: Georgia Institute of Technology

summary: We previously showed that exposing wild-type mice to 40Hz, but not 20Hz, visual flickering stimulation led to activation of MAPK and NFκB pathway signaling in the visual cortex within 15mins of stimulation and up-regulation of cytokines/chemokines that modulate microglia activity after 1hr. These observed frequency-dependent effects suggest that targeted frequencies, as well as durations of stimulation, hold the potential to fine-tune the effects of sensory stimulation on immune pathways, as well as possibly other pathways with the potential to correct the molecular changes associated with Alzheimer’s disease. To test this, we exposed 5xFAD mice and wild-type littermates to different frequencies of audio/visual flicker stimulation (ambient light, 10Hz, 20Hz, 40Hz) for durations of 0.5hr, 1hr, or 4hr, then used bulk RNAseq to profile transcriptional changes within the visual cortex and hippocampus. Within 5xFAD mice, we found that 1hr of stimulation yielded up-regulation immune-related pathways, but that these were no longer observed after 4hr of stimulation. In contrast, all three frequencies yielded consistent up-regulation of neurotransmission pathways at 1hr and 4hr. Importantly, a subset of genes sets were co-regulated between the visual cortex and hippocampus, suggesting that combined visual/audio flicker can target deep brain regions affected by Alzheimer’s disease. Collectively, our data indicate that specific durations and frequencies of audio/visual stimulation can be used to elicit particular changes in brain immunity and neuronal functions, supporting the importance of this non-invasive methodology to tune the brain for treatment of diverse neurological diseases

overall_design: Wild-type and 5xFAD mice, visual cortex and hippocampus tissues.  26 experimental groups,  3 time points. 4 different frequencies ( Light (60Hz), 10Hz, 20Hz, and 40Hz) , N>=3


title: miRNA sequencing of NSC-released exosomes treated with metformin or not

city: Tianjin

first: Han

last: Ding

address: No.154 Anshan Road

institute: Tianjin Medical University

summary: To determine how metformin treatment changed the expression of miRNA in NSCDEs, RNA samples were subjected to miRNA sequencing (miRNA-seq).

overall_design: Control group (4 replicates) were the exosomal miRNA sequencing of NSCs in normal condition; Met group  (4 replicates) were the exosomal miRNA sequencing of NSCs pretreated with metformin

first: Ping

last: Wu


title: RNAseq data from mouse MEFs with Pten C-tail phosphorylation sites mutation

city: Rochester

first: Hu

last: Li

address: 200 1st St SW

institute: Mayo Clinic

summary: NOT PROVIDED; REQUESTED

overall_design: NOT PROVIDED; REQUESTED

first: Jan

last: van Deursen

first: Janine

last: van Ree


title: Metastatic site influences driver gene function in pancreatic cancer [[InVitro ATAC-Seq]]

status: Public on Jun 12 2025

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

summary: Driver gene mutations can increase the metastatic potential of the primary tumor, but their role in sustaining tumor growth at metastatic sites is poorly understood. A paradigm of such mutations is inactivation of SMAD4 – a transcriptional effector of TGFβ signaling – which is a hallmark of multiple gastrointestinal malignancies. SMAD4 inactivation mediates TGFβ’s remarkable anti- to pro-tumorigenic switch during cancer progression and can thus influence both tumor initiation and metastasis. To determine whether metastatic tumors remain dependent on SMAD4 inactivation, we developed a mouse model of pancreatic ductal adenocarcinoma (PDAC) that enables Smad4 depletion in the pre-malignant pancreas and subsequent Smad4 reactivation in established metastases. As expected, Smad4 inactivation facilitated the formation of primary tumors that eventually colonized the liver and lungs. By contrast, Smad4 reactivation in metastatic disease had opposite effects depending on the tumor’s organ of residence: suppression of liver metastases and promotion of lung metastases. Integrative multiomic analysis revealed organ-specific differences in the tumor cells’ epigenomic state, whereby the liver and lungs harbored chromatin programs respectively dominated by the KLF and RUNX developmental transcription factors, with Klf4 depletion being sufficient to reverse Smad4’s tumor-suppressive activity in liver metastases. Our results show how epigenetic states favored by the organ of residence can influence the function of driver genes in metastatic tumors. This organ-specific gene–chromatin interplay invites consideration of anatomical site in the interpretation of tumor genetics, with implications for the therapeutic targeting of metastatic disease.

overall_design: To determine whether organ-biased differences in chromatin accessibility were maintained in vitro, we performed ATAC-seq on the Smad4-OFF primary tumor-derived cell lines used to generate liver and lung metastases, as well as on matched cell lines derived from the respective metastatic sites.

first: Kaloyan

last: Tsanov

first: Scott

middle: W

last: Lowe


title: Metastatic site influences driver gene function in pancreatic cancer [InVitro RNA-Seq]

overall_design: SMAD4 acts as a transcription factor (TF) by forming a complex with the SMAD2/3 TFs to activate gene expression programs downstream of TGFβ receptors. Hence, we performed RNA-seq of the input cells in vitro after Smad4 restoration and TGFb treatment (see Methods), and compared the resulting pathway enrichment to our in vivo data from the pancreas, liver and lungs.


title: PUS10-induced tRNA fragmentation impacts retrotransposon-driven inflammation [iCLIP]

first: Phuong

last: Cao Thi Ngoc

overall_design: iCLIP seq was performed on MEFs iPUS10 to map the genome-wide PUS10-RNA associations. FLAG antibody was used to immunoprecipitate PUS10-RNA complexes. MEF PUS10 KO cells were used as a control for non-specific binding.

first: Magdalena

last: Madej

first: Cristian

last: Bellodi


title: EPITHELIAL REMODELING AND MICROBIAL DYSBIOSIS IN THE LOWER RESPIRATORY TRACT OF VITAMIN A-DEFICIENT MOUSE LUNGS

city: Newark

first: Kiloni

last: Quiles

state: NJ

address: 205 South Orange Avenue

department: Medicine

institute: Rutgers New Jersey Medical School

summary: The World Health Organization identified vitamin A deficiency (VAD) as a major public health issue in low-income communities and developing countries, while additional studies have shown dietary VAD leads to various lung pathologies. Once believed to be sterile, research now shows that transient microbial communities exist within healthy lungs and are often dysregulated in patients suffering from malnourishment, respiratory infections, and disease. The inability to parse vitamin A-mediated mechanisms from other metabolic mechanisms in humans with pathogenic endotypes, as well as the lack of data investigating how VAD affects the lung microbiome, remains a significant gap in the field. To address this unmet need, we compared molecular, metatranscriptomic, and morphometric data to identify how dietary VAD affects the lung as well as the lung microbiome. Our research shows structural and functional alterations in host-microbe-diet interactions in VAD lungs compared to vitamin A-sufficient (VAS) lungs; these changes are associated with epithelial remodeling, a breakdown in mucociliary clearance, microbial imbalance, and altered microbial colonization patterns after 8 weeks of vitamin A deficient diet. These findings confirm vitamin A is critical for lung homeostasis and provide mechanistic insights that could be valuable for the prevention of respiratory infections and disease.

sample_organism:
Mus musculus
lung metagenome

platform_organism:
Mus musculus
lung metagenome

overall_design: RNAseq (metatranscriptomic) profiling of WT C57B/J6 adult mice maintained on VAS and VAD diets for 3 weeks and 8 weeks. Both host and microbial RNA-seq data was analyzed for epigenetic changes to host and microbial pathways.

first: Feng-Zhi

last: Shao

first: W. Evan

last: Johnson

first: Felicia

last: Chen


title: PUS10-induced tRNA fragmentation impacts retrotransposon-driven inflammation [RNA-seq]

summary: Pseudouridine synthases (PUSs) catalyze the isomerization of uridine (U)-to-pseudouridine (Ψ) and have emerging roles in development and disease. How PUSs adapt gene expression under stress remains mostly unexplored. We identify an unconventional role for the Ψ “writer” PUS10 impacting intracellular innate immunity. Using Pus10 knockout mice, we uncover cell-intrinsic upregulation of interferon (IFN) signaling, conferring resistance to inflammation in vivo. Pus10 loss alters tRNA-derived small RNAs (tdRs) abundance, perturbing translation and endogenous retroelements expression. These alterations promote proinflammatory RNA-DNA hybrids accumulation, potentially activating cyclic GMP-AMP synthase (cGAS)-stimulator of interferon gene (STING). Supplementation with selected tdR pools partly rescues these effects through interactions with RNA processing factors that modulate immune responses, revealing a regulatory circuit that counteracts cell-intrinsic inflammation. By extension, we define a PUS10-specific molecular fingerprint linking its dysregulation to human autoimmune disorders, including inflammatory bowel diseases. Collectively, these findings establish PUS10 as a viral mimicry modulator, with broad implications for innate immune homeostasis and autoimmunity.

first: Sowndarya

last: Muthukumar

first: Anna

last: Konturek-Cieśla

first: Silvia

last: Tucciarone

first: Alexandre

last: Germanos

first: Christian

last: Ashworth

first: Knut

last: Kotarsky

first: Sudip

last: Ghosh

first: Zhimeng

last: Fan

first: Helena

last: Fritz

first: Izei

last: Pascual-Gonzalez

first: Alain

last: Huerta

first: Nicola

last: Guzzi

first: Anita

last: Colazzo

first: Giulia

last: Beneventi

first: Hang-Mao

last: Lee

first: Maciej

last: Cieśla

first: Christopher

last: Douse

first: Hiroki

last: Kato

first: Vinay

last: Swaminathan

first: William

last: Agace

first: Ainara

last: Castellanos-Rubio

first: Paolo

last: Salomoni

first: David

last: Bryder


title: Integrated long-read transcriptomic profiling of peripheral blood from ankylosing spondylitis patients reveals regulatory shifts and core genes associated with programmed cell death

city: Zhengzhou City

first: Xue

last: Cao

state: Henan Province

address: No. 7, Weiwu Road, Zhengzhou City, Henan Province

institute: Henan Provincial People's Hospital

summary: Ankylosing spondylitis (AS) is a chronic immune-mediated arthritis marked by persistent inflammation and progressive structural damage. Although dysregulation of programmed cell death (PCD) is increasingly recognized in AS pathogenesis, the full spectrum of transcript-level regulation remains unclear. Here, we employed Oxford Nanopore Technologies (ONT) long-read RNA sequencing to comprehensively profile peripheral blood transcriptomes from six AS patients and six matched healthy controls. Our analysis identified 1,088 differentially expressed genes (DEGs) and 1,812 differentially expressed transcripts (DETs), with upregulated transcripts enriched in apoptosis, autophagy, and transcriptional regulation. We further detected 50 transcripts with significant differential usage and 304 alternative splicing events affecting immune- and PCD-related genes, including FCGR2B, TLR2, and STAT5B. Integrative multi-omic analysis revealed 26 core genes, such as NAMPT, GATA2, and DDIT3, showing consistent dysregulation at gene, isoform, and splicing levels, highlighting convergent regulatory networks underlying immune imbalance and cell death in AS. These findings provide the first isoform-resolved transcriptomic landscape of PCD regulation in AS, revealing extensive regulatory complexity and novel core genes that may represent promising targets for future mechanistic and therapeutic studies.

overall_design: ONT-based long-read RNA sequencing to systematically profile peripheral blood transcriptomes from AS patients and matched healthy controls (HC).

first: Panlong

last: Li

first: Haoran

last: Peng


title: Social isolation primes anxiety via a hippocampal iron-α-synuclein cascade

first: Zhuo

last: Wang

address: 382 Waihuan East Road, Panyu District, Guangzhou City, Guangdong Province

summary: This study reveals a novel mechanism linking social isolation to anxiety through a glucocorticoid (GC)-driven, ventral hippocampal (vHip)-specific iron-α-synuclein (α-Syn) axis. Social isolation activates glucocorticoid receptors (GRs) in vHip pyramidal neurons, which upregulate transferrin receptor 1 (TfR1) to promote iron accumulation. Elevated iron induces α-Syn overexpression, thereby enhancing presynaptic glutamate release and neuronal hyperexcitability in the vHip; this ultimately drives anxiety-like behaviors. Gain-of-function/loss-of-function experiments confirm that TfR1 and α-Syn are essential for this pathway, while intranasal iron chelation or α-Syn inhibition rescues both neural and behavioral abnormalities. These findings establish the GR-TfR1-α-Syn axis as a therapeutic target for social stress-related anxiety, which bridges metallobiology and psychiatric pathophysiology.

overall_design: RNA-seq profiles were generated from the ventral hippocampus tissues of (Camk2a-Cre, C57BL/6) mice following 28 days of housing under three conditions: group housing, social isolation, and neuronal-specific Nr3c1 knockdown combined with social isolation.

first: Sifan

last: Yang

first: Yuhan

last: Zhang

first: Jinhui

last: Zhao


title: Lactate deficiency-induced early embryonic arrest is mitigated through malate-aspartate shuttle

city: Jinan

first: Tiantian

middle: tian

last: Deng

address: Jinan Qianfoshan street

institute: Shandong University

summary: During assisted reproductive technology (ART) procedure, approximately one third to half of the in vitro fertilization (IVF) derived embryos cannot reach the blastocyst stage, and about 10% arrest at the early cleavage stage. Early mammalian embryos obtain nutrients from maternal environment to fulfill the energy requirements of growth and development, and lactate is one of the major substrates of embryo energy metabolism. To explicitly reveal the energy metabolism in early embryogenesis, we inhibited the production and uptake of lactate at the zygote stage, and found it resulted developmental arrest, impaired mitochondrial activity and reduced NAD+/NADH ratio. By activating the malate-aspartate shuttle (MAS), the developmental arrest was rescued through the restoration of NAD+/NADH balance. Therefore, we demonstrate that maternal LDHB plays an essential role from 4- to 8-cell stage that it converts lactate from pyruvate to generate NAD+, and MAS activation is responsible for the re-equilibrium of NAD+/NADH. Our study discusses the association of metabolic flexibility and developmental regulation, and deepens our understanding of the metabolic mechanism of embryonic development.

overall_design: For single-cell transcriptome sequencing, six 4-cell mouse embryos were collected from each untreated (control) and LDHB inhibition group, with three replicates for each group.

first: Keliang

last: Wu

first: Boyang

last: Liu


title: High resolution maps of nucleosome position and interactions [II]

first: Axel

last: Delamarre

address: 411 E 67th st

institute: MSKCC

summary: Chromatin plays a pivotal role in genome expression, maintenance, and replication. To better understand chromatin organization, we developed a novel proximity-tagging method which assigns unique DNA barcodes to molecules that associate in 3D space. Using this method – termed Proximity Copy Paste (PCP) – we mapped the connectivity of individual nucleosomes in Saccharomyces cerevisiae. We show that chromatin is predominantly organized into regularly spaced nucleosome arrays. The properties of the arrays differs according to transcriptional activity with short delocalized arrays dominating the most highly transcribed genes. Additionally, by mapping long-range, multi-way interactions we provide evidence for the longstanding hypothesis that metaphase chromosomes are compacted by arrayed cohesin hubs. Using single-molecule nuclease footprinting data we define distinct chromatin states within a mixed population to show that noncanonical nucleosomes are a stable feature of chromatin. PCP is a versatile method allowing the connectivity of individual molecules to be mapped at high-resolution

overall_design: PCP experiment in synchronized cells in G1 or in G2/M. Asynchronous cells in control conidion or after depletion of chromatin remodelers RSC (sth1) and SWI/SNF (snf2)


title: Gene expression profile at single cell level of articular cartilage superficial cells from pulse and trace labeled tdTomato+ cells from Procr-CreER;tdTomato mice.

first: Dandan

address: 1239 Siping Road, Yangpu District

institute: Tongji University

summary: Characteristics of the chondroprogenitors cells remain unidentified. Here we identified a chondroprogenitor population, which specifically expresses Procr, and used single cell RNA sequencing (scRNA-seq) to analyze the diversity and differentiation of Procr-lineage cells in articular cartilage.

overall_design: Articular cartilage cells from pulse and trace labeled tdTomato+ cells were isolated from Procr-CreER;tdTomato mice by Fluorescence-activated cell sorting (FACS) with APC-conjugated CD31, CD45, and Ter119 antibody and analyzed using scRNAseq.

first: Rui

last: Yue

first: Qiaoling

last: Zhu

first: Wanyu

last: Shi


title: SWI/SNF ATPase SPLAYED modulates ABA catabolism and GA biosynthesis in ABA-inhibition of seed germination

city: La Jolla

first: Po-Kai

last: Hsu

address: 9500 Gilman Dr

department: Cell and Developmental Biology

institute: UC San Diego

summary: The phytohormone abscisic acid (ABA) promotes seed dormancy and inhibits seed germination and seedling development. It remains unclear how chromatin remodeling influences ABA responses. In the present study, an artificial microRNA targeting two Sucrose Non-Fermenting 2 (SNF2)-family chromatin remodeling ATPases, SPLAYED (SYD) and PHOTOPERIOD-INDEPENDENT EARLY FLOWERING1 (PIE1), was identified through unbiased forward genetic screenings of artificial microRNA (amiRNA)-expressing pooled seed libraries exhibiting ABA-insensitive seed germination. T-DNA insertional mutants of syd and pie1, along with amiRNA-expressing knockdown lines amiR-SYD and amiR-PIE1, confirmed that SYD, but not PIE1, is essential for promoting ABA-inhibition of seed germination. Transcriptome analyses revealed that the ABA catabolism gene CYP707A3 and the gibberellin (GA) biosynthesis genes GA20OX2, GA20OX3, GA3OX2, GA3OX3, and GA3OX4 were upregulated in amiR-SYD mutant seeds compared to control seeds under ABA treatment during germination. The ABA hyposensitivity observed in amiR-SYD mutants was reversed by treatment with uniconazole, an inhibitor of ABA catabolism and GA biosynthesis, suggesting that the reduced ABA sensitivity in amiR-SYD mutants results from increased ABA degradation and GA production. These findings demonstrate that the SYD-associated chromatin remodeling complex positively regulates ABA responses during seed germination, unlike its close homolog BRAHMA (BRM), which acts as a negative regulator of the ABA response.

overall_design: Expression profiling of amiR-HsMYO control and amiR-SYD seeds germinated under control and ABA conditions for 24 hrs.

middle: K

first: Julian

middle: I

last: Schroeder


title: LncRNA RP11-284N8.3 regulates the expression and alternative splicing of genes associated with sepsis-induced acute lung injury

first: Xue

summary: Sepsis-induced acute lung injury (ALI) poses a significant threat to human health,  necessitating further investigation into its underlying mechanisms. Long noncoding RNAs (lncRNAs) have emerged as key regulators in various diseases, including sepsis. In our prior research, we observed significant downregulation of lncRNA RP11-284N8.3 in the blood samples of sepsis patients. Herein, we elucidate the functional role and regulatory molecular targets of RP11-284N8.3 in lipopolysaccharide (LPS)-exposed BEAS-2B cells. Initially, we found that LPS treatment notably repressed RP11-284N8.3 expression. However, overexpression of RP11-284N8.3 significantly promoted cell proliferation, inhibited apoptosis, and attenuated IL-1β expression in response to LPS stimulation, indicative of its anti-inflammatory properties. Further RNA-seq analysis revealed that RP11-284N8.3 might have contributed to the significant down-regulation of genes associated with the inflammatory response, while genes related to cell cycle/division and apoptosis underwent alternative splicing (AS) deregulation. Finally, RT-qPCR was used to validate differentially expressed genes (DEGs) (ICAM5, GDF15, NECTIN4,  SERPINB2) and AS genes (IL24, APEX1, PVT1, HNRNPUL1) regulated by RP11-284N8.3,  consistent with transcriptome changes. In summary, RP11-284N8.3 has a significant global regulatory effect in LPS-treated BEAS-2B cells and its possible protective role against sepsis-induced ALI. We propose RP11-284N8.3 and its downstream targets as potential therapeutic targets for sepsis management in the future.

overall_design: RNA-seq of RP11-284N8.3 overexpression versus control in BEAS-2B cells aims to comprehensively characterize the functional role of lncRNA RP11-284N8.3 in lipopolysaccharide (LPS)-induced ALI through transcriptomic (RNA-seq) analyses, including differentially expressed gene (DEG) and alternative splicing (AS) profiling.

first: Yanwei

last: Cheng

first: Ning

last: Ding


title: Nephron segmentation and patterning in kidney organoids can be modulated by distinct FGF subfamily members

city: Melbourne

first: Allara

last: Zylberberg

state: VIC

address: Murdoch Children's Research Institute, Royal Children's Hospital, 50 Flemington Rd, Parkville VIC 3052

department: Stem Cell Medicine

country: Australia

institute: Murdoch Children's Research Institute

summary: Human pluripotent stem cell-derived kidney organoids replicate embryonic nephrogenesis in a 3D-culture system. Recent advances suggest that refining the culture environment to replicate spatiotemporal cues present during embryonic organogenesis improves patterning. Here, this paradigm was applied to FGF signalling, a key regulator of embryonic nephron progenitor maintenance, nephrogenesis and ureteric branching. Both FGF8b and FGF10 signalling is sufficient to support nephrogenesis, with each having distinct effects on nephron patterning. FGF10 enhanced the initial WT1+ mesenchymal population, leading to proximally biased nephrons, while FGF8b biased toward early distal patterning, leading to the formation of cells with connecting segment identity. The addition of both FGF8b and FGF10 together had an additive effect, leading to a balance of proximal and distal patterning. This differential patterning was retained in tissue transplanted under the murine renal capsule, with FGF8b-treated organoids displaying increased distal/connecting segments. These findings highlight plasticity during organoid nephrogenesis that can be modulated by FGF signalling and identify an approach to refine nephrogenesis toward key cell types.

overall_design: Single cell suspensions of each condition were fixed with formaldehyde (ProSciTech C004) and additive according to the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10x Genomics). Fixation was performed at 4oC overnight, and after addition of the buffer, fixed cells were stored at -80oC until processing. The four barcode version of the Chromium Fixed RNA Kit, Human Transcriptome (10x Genomics) was used to barcode all 8 samples, giving 2 libraries. Post hybridisation washes were completed individually for each barcoded sample, according to the manufacturer’s protocol. Cell counting was completed using InvitrogenTM ReadyCountTM Green/Red Cell Viability Stain (Thermo Fisher Scientific) and the Countess 3 Automated Cell Counter (Thermo Fisher Scientific). A target of 10,000 cells per sample was combined for a total of 40,000 cells per library.

first: Emma

last: Scully

first: Pei Xuan

last: Er

first: Hannah

last: Baric

first: Michelle

last: Scurr

first: Mian

last: Xie

first: Thanushi

last: Peiris

first: Sara

middle: E

last: Howden

first: Kynan

middle: T

last: Lawlor

first: Melissa

middle: H

last: Little


title: Transcriptional profile of mammary mouse MMTV-PyMT tumors and mammary gland from FVB/N mice

city: Glasgow

first: Robin

last: Shaw

address: Switchback Road

institute: CRUK Scotland Institute

summary: To characterise the metabolic landscape of metastatic breast cancer we investigated differences in metabolites between the serum of MMTV-PyMT (Mouse Mammary Tumor Virus long terminal repeat upstream of a cDNA sequence encoding the Polyoma Virus middle T antigen) mice and their wild-type counterparts (https://doi.org/10.1101/2024.07.02.601676). Here we provide matched transcriptomic data on the primary mammary tumors from MMTV-PyMT mice and the mammary gland from FVB/N mice

overall_design: Transcriptomics from n=31 primary mammary tumors from MMTV-PyMT mice and the n=8 mammary gland from FVB/N (Friend Virus B NIH Jackson) mice. Ribodepletion Total RNA sequenced on Illumina NextSeq 500 platform.

first: Cassie J

last: Clarke

first: William

last: Clark

first: Ann

last: Hedley


title: Transcriptional analysis of cell lines derived from primary mammary tumors and lung micrometastases

summary: Cell lines were derived from either, (1) mammary tumors from the MMTV-PyMT genetically engineered mouse model, (2) mammary tumors resulting from syngeneic transplantation (of cells described in 1) and primary tumor resection, or (3) isogenic cell lines derived from lung metastasis that occurred following resection of the primary tumors dsecribed in approach 2.

overall_design: Three conditions: Primary tumor (mammary gland), fat pad tumor, whole lung. Each condition split across cell lines: YEJH and YEJG.

first: Michalis

last: Gounis


title: Prostaglandin and prostacyclin regulation of Th1 responses [ptgir_ko]

city: Bethesda

first: Ayden

last: Case

state: MD

address: 10 Center Dr

institute: NHLBI

summary: Metabolic reprogramming is an integral component of normal Th1 induction and contraction. Whereas Th1 inducing signals are largely defined, the pathways underlying timely Th1 contraction remain poorly understood. Here, we show that a CD4+ T cell-intrinsic prostanoid lipid mediator production and signaling machinery, controlled by cell-autonomous complement C5, governs the Th1 shutdown program.

overall_design: This was a three part study. First, human CD4 T cells were stimulated with anti-CD3+46 in the presence or absence of a C5AR double receptor antagonist and microarray analysis performed. Second, CD4 T cell from WT or PTGIR-/- mice were stimulated for 2 hours and bulk RNA-sequencing was performed. Third, human CD4 T cells were isolated, treated with PTGIR or PTGIS siRNA, stimulated with anti-CD3+46, and IFNG-IL10- (DN), IFNG+IL10- (IFNG) populations were sorted before RNA-sequencing.

first: Jack

last: Bibby

first: Jubayer

last: Rahman

first: Claudia

last: Kemper


title: Prostaglandin and prostacyclin regulation of Th1 responses [ptgir_ptgis_sirna]


title: Genome-Wide Mapping of E2F1 Transcription Factor Binding Sites Across Human and Epstein-Barr virus (EBV) Chromosomes

city: Kolkata

first: Joyanta

last: Biswas

state: West Bengal

address: Street-358, Action Area-1, Newtown

department: Institute of Health Sciences

country: India

institute: Presidency University

summary: E2F1, the first member of E2F family transcription factors, plays a central role in cell cycle progression, DNA-damage response and apoptosis. Accumulating evidence indicates that E2F1 regulates replication of several DNA viruses. We and others previously described deregulated E2F1 expression during Epstein-Barr virus (EBV) induced B-cell transformation and its role in survival of transformed B-lymphocytes in response to DNA-damage signals. In addition, global transcriptomic analyses (GSE235941, GSE237484) reveal that E2F1 expression is transcriptionally activated during EBV latent infection in B-lymphocytes but suppressed during lytic-cycle reactivation. However, the precise regulations by which E2F1 sustains EBV latent to lytic switch remains unanswered. Given that E2F activity is often deregulated by infection with DNA viruses, the main objective of our study was to investigate the genome-wide occupancy of E2F1 on both cellular and viral gene promoters, driving  EBV pathogenesis.

overall_design: Chromatin immunoprecipitation was performed using E2F1 specific antibody (KH95, Invitrogen) in two in vitro EBV transformed lymphoblastoid cell lines (LCL#1 and LCL#89) followed by sequencing analyses on the Illumina HiSeq2500 platform.

first: Samaresh

last: Malik

first: Abhik

last: Saha


title: Unveiling Host and EBV Gene Expression Dynamics Following E2F1 Knockdown in P3HR1 Cells

summary: E2F1, a member of E2F family transcription factors, is involved in the transcriptional regulation of genes required for G1 to S phase transition of the cell cycle, DNA replication and DNA repair along with apoptosis in response to DNA damage signals. Studies suggest that several DNA viruses deregulate E2F1 functions to modulate their replications. Our previous global transcriptomic analyses (GSE235941, GSE237484) reveal that E2F1 expression is transcriptionally activated during EBV latent infection in naïve B-lymphocytes but suppressed during reactivation into lytic-cycle replication. We hypothesize that EBV controls E2F1 expression to regulate its latent to lytic switch. To gain insights into the E2F1 mediated global transcriptional network of both cell and viral gene expressions in response to EBV lytic cycle induction, we knocked-down E2F1 in EBV positive P3HR1 cells and subjected to RNA-Seq analyses with or without lytic cycle inducer. The primary goals of our work were to identify the key cell pathways and the differential expression patterns of EBV latent and lytic genes upon E2F1 depletion. Our findings support the hypothesis that EBV controls latent to lytic switch by critically monitoring E2F1 expression, providing clues for therapeutic intervention.

overall_design: E2F1 was knockdown in an EBV positive Burkitt’s lymphoma P3HR1 cells using specific Sh-RNA sequence in pTripZ, a doxycycline (DOX) inducible lentiviral vector. Additionally, E2F1 WT (minus DOX) / E2F1 KD (plus DOX) P3HR1 cells were either left untreated or treated with the combination of 3 mM sodium butyrate and 20 ng/ml 12-O-tetradecanoylphorbol-13-acetate (TPA). 72h post-treatment cells were harvested and subjected to RNA isolation, cDNA synthesis, library generation followed by RNA sequencing analyses on the Illumina NovaSeq 6000 platform.

first: Sk Asif

last: Ali


title: Repurposing MDM2 Inhibitor RG7388 For TP53-Mutant NSCLC: A p53-Independent Pyroptotic Mechanism via ROS/p-p38/NOXA/Caspase-3/GSDME Axis

city: Weifang

first: lei

last: sun

address: 151 Guangwen Street

institute: shandong second medical university

summary: Non-small cell lung cancer (NSCLC) is highly malignant with limited treatment options due to the inherent tumoral heterogeneity and acquired resistance towards chemotherapy and immunotherapy. RG7388 was previously reported to have anticancer activity against TP53WT NSCLC which was designed as MDM2 inhibitor triggering p53/PUMA axis-dependent apoptosis. However, RG7388 exhibited p53-independent anticancer effect against TP53mutant NSCLC in our current research, the underlying mechanisms of which were still uncertain. Here, we reported that RG7388 specifically induced NOXA/Caspase-3 axis dependent apoptosis and gasdermin E (GSDME)-mediated secondary pyroptosis in TP53mutant NSCLC using in silico and multiple biological methods. Mechanically, we identified accumulated reactive oxygen species (ROS) served as the pivotal factor in NOXA upregulation and p38 MAPK pathway activation in RG7388 treated TP53mutant NSCLC by using two ROS scavengers N-acetylcysteine (NAC) and Ferrostatin-1 (Fer-1) respectively. Furthermore, pharmacologic inhibition of p38 MAPK signaling by SB203580 rescued RG7388 induced ROS-dependent NOXA accumulation and subsequent apoptosis and pyroptosis, thus suggesting a leading role of ROS/phosphorylated p38 MAPK (p-p38)/NOXA/Caspase-3 axis in RG7388 induced TP53mutant NSCLC cell death. Taken together, our work unraveled a novel mechanism of selective targeting of mutant p53 derived cancers via ROS/p-p38-mediated NOXA accumulation that could have potential therapeutic implications given the relative lack of direct mutant p53 targeting strategies in cancer. Moreover, A strong positive correlation between p-p38 and NOXA expression was confirmed by using an NSCLC tissue microarray and immunohistochemical (IHC) staining. Clinical data analysis suggested that the p-p38/NOXA axis could serve as a potential indicator for predicting overall survival (OS) in NSCLC patients.

overall_design: RNA-seq profiling with HCC827 or PC9 cells under the treatment of DMSO or RG7388 (60 μM) for 6 hours.


title: A noncanonical Pol III-dependent, Microprocessor-independent biogenesis pathway generates a germline enriched miRNA family

first: Katherine

last: McJunkin

state: Maryland

address: 50 South Dr

institute: NIDDK/ NIH

summary: MicroRNAs (miRNAs) are short RNAs that post-transcriptionally regulate gene expression. In canonical miRNA biogenesis, primary miRNAs are transcribed from intergenic loci or intronic regions by RNA polymerase II, sequentially cleaved by the Microprocessor complex and Dicer, and resulting mature miRNAs are loaded into Argonaute to repress target mRNAs. A minority of miRNAs are generated via noncanonical biogenesis pathways that bypass the Microprocessor and/or Dicer. Here, we describe a new Pol III-dependent, Microprocessor -independent, and Dicer-dependent biogenesis pathway exemplified by the mir-1829 family in C. elegans. Although the mir-1829 family loci reside in intronic regions of protein-coding genes, we show that the miRNAs are derived from independent Pol III transcripts. Unlike other Pol III-dependent miRNAs, the mir-1829 family small RNAs are the dominant species derived from their loci, rather than fragments of a larger functional noncoding RNA. These germline-enriched miRNAs are loaded in multiple miRNA Argonautes, including the recently-characterized germline Argonaute ALG-5, which we demonstrate is repressive when tethered to a reporter transcript. We extend these findings, identifying additional Pol III-transcribed and noncanonical small RNAs in C. elegans and human datasets, including human miR-4521. These young, noncanonical miRNAs may represent an early snapshot in the evolution of de novo miRNA genes.

overall_design: To determine the requirement of Dicer and RPC-1 in mir-1829 biogenesis as well as other miRNAs that may follow this novel biogenesis pathway (i.e. Pol III-transcribed, Microprocessor-independent, Dicer-dependent) in C. elegans and human. To determine which miRNAs are enriched in the germline by depleting Dicer solely in the germline in C. elegans.

first: Rima

last: Sakhawala

first: Reyhaneh

last: Tirgar

first: Karl-Frédéric

last: Vieux

first: Guoyun

last: Yu

first: Dustin

last: Haskell

first: Anna

last: Zinovyeva


title: Gene expression profile at single cell level of articular cartilage superficial cells from sham and dmm surgery mice and long bone periosteum cells  from steady state mice.

city: Shanghai

first: Dandan

last: Cao

summary: Characteristics of the chondroprogenitors cells remain unidentified. Here we identify a chondroprogenitor population, which specifically expresses Procr,and used single cell RNA sequencing (scRNA-seq) and bulk RNA-seq to analyze the diversity of Prcor+ cells in articular cartilage and periosteum.

overall_design: Articaular cartilage cells  from sham and DMM surgery mice were isolated by Fluorescence-activatedcell sorting (FACS) with  APC-conjugated CD31, CD45, and Ter119 antibody and analyzed using scRNAseq. Long bone periosteum cells from Prrx1-Cre;tdTomato;Col2.3-GFP were isolated by Fluorescence-activatedcell sorting (FACS) with  APC-conjugated CD31, CD45, and Ter119 antibody and analyzed using scRNAseq. Articaular cartilage cells from steady state mice were isolated for Procr+CD105- and Procr+CD105+ cells, and analyzed using RNAseq.

first: Rui

last: Yue

first: Qiaoling

last: Zhu

first: Wanyu

last: Shi


title: High resolution maps of nucleosome position and interactions

first: Axel

last: Delamarre


title: Mouse embryonic fibroblasts - transcriptional analysis following uracil treatment

first: Robin

last: Shaw

summary: To characterise the metabolic landscape of metastatic breast cancer we investigated differences in metabolites between the serum of MMTV-PyMT mice (n=29) and their wild-type counterparts (n=9) (https://doi.org/10.1101/2024.07.02.601676). Uracil was identified as a metabolite that had a positive correlation with metastatic burden in tumor-bearing animals (p=0.030). Serum uracil was quantified as 10µM in tumor-bearing mice with no lung metastases, compared to 30µM in mice with >10 lung metastases. To understand the physiological effects of these uracil concentrations, mouse embryonic fibroblasts (MEFs) were cultured in the presence of 10µM and 30µM uracil and the cellular derived matrices (CDMs) deposited characterised. CDMs generated in the presence of 30uM uracil had increased fibronectin deposition and were able to support increased invasive capacity of PyMT tumor cells. We performed RNA-Seq on MEFs treated with 0uM v 10uM v 30uM to understand the transcriptional effects of these concentrations of uracil on fibroblasts.

overall_design: MEFs were plated to confluence, treated with 0µM, 10µM or 30µM uracil for 24 hours (37°C/5%CO2). Six samples per biological condition.

first: Cassie J

last: Clarke

first: William

last: Clark

first: Ann

last: Hedley


title: Phytic acid impairs macrophage inflammatory response in Echinococcus multilocularis infection

city: Vienna

first: Manuel

last: Salzmann

address: Lazarettgasse 14

department: Department of Medicine II, Division of Cardiology

country: Austria

institute: Medical University of Vienna

summary: The endoparasite Echinococcus multilocularis relies on immune evasion strategies to persist within its host. The laminated layer (LL) surrounding the parasite provides physical protection while modulating host immune responses. E. multilocularis’ immunomodulatory mechanisms are poorly understood and we explored the role of phytic acid, a known component of E. granulosus sensu lato. Here we show that phytic acid is also present in E. multilocularis and impairs macrophage inflammation. In vivo, inflammatory macrophages accumulate near the metacestode, yet do not express IL-6, indicating anti-inflammatory modulation. In vitro, phytic acid reduces pro-inflammatory cytokines such as IL-6, IL-1β, and TNF by lowering intracellular calcium levels in macrophages. This calcium-chelating effect is mirrored by the anti-inflammatory properties of an E. multilocularis metacestode extract, revealing a protein-independent immune modulation strategy. These findings suggest that phytic acid plays a crucial role in E. multilocularis’ ability to suppress host immune responses and supports the parasite's long-term survival.

overall_design: RNAseq of Mus musculus (C57BL/6JRj) livers that were orally infected with 1000 Echinococcus multilocularis eggs.

first: Philipp

last: Hohensinner

first: Laura

last: Boccuni


title: Spatial component of: CELSR3 deficiency leads to tic-related behaviors and dopaminergic alterations in the striatum

city: Salt Lake City

first: Philip

last: Moos

state: UT

department: Pharmacology & Toxicology

institute: University of Utah

summary: The gene CELSR3 (cadherin EGF LAG seven‐pass-G‐type receptor 3) has been recently recognized as a high-confidence risk factor for tic disorders (TD). Celsr3 mutant mice displayed tic-like grooming stereotypies and jerks, as well as sensorimotor gating deficits, which were opposed by TD therapies. Spatial transcriptomic analyses revealed that Celsr3 mutants featured abnormalities of the extracellular matrix in the striatum.  Notably, there are alterations in collagen and extracellular organization.

overall_design: Coronal sections from 4 distinct mice ( 2 from each group: Celsr3 WT and HZ) from FFPE preserved samples were analyzed by Visium Cytassist

first: Macro

last: Bortolato


title: CD30/CD30L is critical for Tfh cell differentiation and promotes antibody production against Plasmodium yoelii infection

city: Shenyang

first: Li

last: Zheng

state: Liaoning

address: No.77 Puhe Road

department: Immunology

institute: China Medical University

summary: Host resistance to malaria parasite infection relies on the establishment of a moderate and sequential adaptive immune response. The production of specific antibodies is critical for parasite clearance. CD30 and CD30L are respective members of the tumor necrosis factor (TNF) receptor superfamily and TNF superfamily; and are expressed on the surface of various immune cells and tissue cells. In mice infected with a non-lethal Plasmodium yoelii strain, CD30/CD30L expression was significantly increased. Using CD30L-deficient (CD30L−/−) mice, we found that the CD30/CD30L interaction played a crucial role in the activation of T follicular helper (Tfh) cells and germinal center (GC) B cells. During P. yoelii infection, CD30L−/− mice developed a weaker humoral response with reduced differentiation of Tfh cells, decreased secretion of IL-21, impaired formation of GCs, a lower number of antibody-secreting cells, and reduced production of antibodies. Supplementing the CD30L−/− mice with recombinant IL-21 (rIL-21) restored the number and proliferation of Tfh cells, but it did not completely restore the humoral immune response. The expression of IL-21R on CD4+ T cells and B cells in CD30L−/− mice during infection was significantly lower than that in wild-type mice; and supplementation with rIL-21 did not increase IL-21R expression on T and B cells. Therefore, we conclude that the CD30/CD30L receptor-ligand pair are key molecules for Tfh cell differentiation and maintenance of the Tfh-GC B cell response, which are needed for the establishment of humoral immunity against P. yoelii blood-stage infection.

overall_design: We used transcriptomic data analysis to examine the key shifts in genetic signatures that derail the immune states in the absence of the CD30/CD30L signaling pathway.We performed gene expression profiling analysis using data obtained from RNA-seq of two groups, WT and CD30L-/- at day 10 post infection. Each group has 3 mice.

first: Wenting

last: Liu

first: Shijie

last: Yao

first: Yan

last: Zhao

first: Yaming

last: Wu

first: Zifang

first: Ting

last: Liao

first: Xiaoliang

last: Zhou

first: Liwang

last: Cui


title: Hybrid Antibiotics for Persistent Infections

city: Memphis

first: Richard

last: Lee

state: TN

address: 262 Danny Thomas Place

department: Department of Chemical Biology and Therapeutics

institute: St. Jude Children's Research Hospital

summary: The goal of this project is to develop a new class of urea-depsipeptide (UDEP) antibiotics to treat prosthetic joint infections (PJI). UDEPs kill bacteria through activation of the ClpP protease, causing cells to self-digest. This unique activating mechanism allows UDEPs to kill biofilms and non-growing persister cells, which are prevalent in PJI and explain why current antibiotics are largely ineffective. Current therapies involve weeks to months of antibiotic treatment, debridement surgeries, and medical device replacement. UDEPs have the potential to minimize surgical interventions due to PJI and improve patient care. PJI are primarily caused by the Gram-positive pathogens Staphylococcus aureus and epidermidis and the UDEPs are potently active against these pathogens, including multi-drug resistant strains. A recent advance in our UDEP medical chemistry program yielded a new compound which has improved safety, solubility, and bone penetration compared to first generation UDEPs. A preliminary study found that the compound was effective in a K-wire femur medullary canal implant model of PJI, which is known to be difficult to treat. In this project, we will evaluate if the compound is an acceptable pre-clinical candidate for PJI by testing it in a series of in vitro and in vivo studies focused on this indication. Specifically, the aims are to 1) scale up the compound; 2) determine the microbiological and biofilm killing effect against the main pathogens isolated from PJI; and 3) determine the efficacy of the compound in mouse and rabbit models of PJI.

overall_design: mRNA profiles of Staphylococcus aureus subsp. aureus ATCC 33591 strains (wild-type, ARI-4206 resistant, and Rifampin resistant strains) after exposure to 1/2 minimal inhibitory concentration of ARI-5192 (0.5 mg/L), ARI-4206 (0.125 mg/L), Rifampin (0.004 mg/L) or DMSO for 30 minutes.

first: Micheal

middle: D

last: LaFleur

first: Gregory

middle: A

last: Phelps

first: Nicole

last: Chumbler

first: Chritine

last: Dunn


title: To identify differentially expressed genes in ventricular tissue between wildtype control and the 6-month-old mtorxu015/+ mutant, Tg(cmlc2:tfeb) transgenic zebrafish at six months.

city: Baltimore

first: Yuji

last: Zhang

address: 660 W. Redwood Street

institute: University of Maryland

summary: To seek molecular mechanisms underlying the mechanisms of mutant genotypes by comparing them witht he wild types, we performed whole transcriptome RNA-sequencing experiments using ventricular tissue isolated from 6-month-old mtorxu015/+ mutant, Tg(cmlc2:tfeb) transgenic zebrafish,and corresponding WT siblings.

overall_design: Total RNA was extracted from dissected ventricular tissue of 6-month-oldmtorxu015/+ mutant, Tg(cmlc2:tfeb) transgenic and corresponding  WT siblings.

first: Yonghe

last: Ding

first: Xiaolei

last: Xu


title: CELSR3 deficiency leads to tic-related behaviors and dopaminergic alterations in the striatum

first: Philip

middle: J

last: Moos

summary: The gene CELSR3 (cadherin EGF LAG seven‐pass-G‐type receptor 3) has been recently recognized as a high-confidence risk factor for tic disorders (TD). Celsr3 mutant mice displayed tic-like grooming stereotypies and jerks, as well as sensorimotor gating deficits, which were opposed by TD therapies. Single-nucleus transcriptomic analyses revealed that Celsr3 mutants featured a unique group of eccentric striatal projection neurons. Notably, the Drd3 gene, encoding the dopamine D3 receptor, was significantly upregulated in these cells as well as striosomal D1-positive neurons, while it was reduced in calretinin-positive GABAergic interneurons.

overall_design: single-nuclei RNA sequencing from flash-frozen dissected striatal tissue from wild-type mice and Celsr3 heterozygous mice

first: Marco

last: Bortolato


title: Gene Signature-guided Drug Screening Identified Narciclasine as a Potential Therapeutic Drug for Renal Interstitial Fibrosis

city: Guangzhou

first: An

last: Xiao

address: JingXi street

department: Division of Nephrology

institute: Nanfang Hospital

summary: Chronic Kidney Disease (CKD) is characterized by progressive tubulointerstitial fibrosis (TIF), a condition not adequately addressed by existing therapies. To identify potential compounds that could slow or halt the progression of TIF, we established gene signatures of TIF using published human CKD renal transcriptome data, followed by high-throughput screening of compounds that could reverse TIF-associated gene expression using the LINCS L1000 database. The natural compound Narciclasine (Ncls), extracted from daffodils, was identified as a promising candidate. We validated the effects of Ncls on a TGF-β1-induced fibrosis model in vitro using mouse primary tubular epithelial cells (TECs) and rat fibroblast cell line (NRK49F). Results demonstrated that Ncls significantly inhibited the pro-inflammatory and pro-fibrotic effects induced by TGF-β1 in TECs. Additionally, in fibroblasts, Ncls markedly suppressed the proliferation and activation induced by TGF-β1. These findings not only confirm the therapeutic potential of Ncls in managing TIF but also highlight the efficacy of gene signature-based screening in identifying drugs for the treatment of CKD.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: We utilized isolated mouse primary tubular epithelial cells (TECs) and the rat kidney fibroblast cell line (NRK49F) to validate the effects of Narciclasine (Ncls) on TGF-β1-induced pro-fibrotic responses in vitro. Ncls was diluted to a final concentration of 20 nM in serum-free DMEM/F12 medium. TECs were pre-incubated in this solution for 2 hours. Subsequently, TGF-β1 was added to achieve a concentration of 5 ng/ml in the medium, and the cells were co-stimulated with Ncls for 24 hours. The control group contained only the medium, without the addition of TGF-β1 or Ncls. Cell samples were then collected for RNA-seq analysis. Experimental samples were organized into three groups with three biological replicates each: Control TECs (Con_TECs), TECs stimulated with TGF-β1 alone (Tgfb_TECs), and TECs co-stimulated with TGF-β1 and Ncls (T+N_TECs). The experimental procedure for NRK49F cells mirrored that of the TECs. Experimental samples for NRK49F were also divided into three groups with three biological replicates each: Control 49F (Con_49F), 49F cells stimulated with TGF-β1 alone (Tgfb_49F), and 49F cells co-stimulated with TGF-β1 and Ncls (T+N_49F).

first: Xiaomei

last: Chen


title: Hypoxia-inducible Factor 1α Mediated Lactylation to Enhance Inflammatory Response during Hypoxia induced lung dysfunction [RNA-seq]

city: Beijing

first: Yubing

last: Zeng

address: 9 Dongdan Santiao, Dongcheng District,

institute: Peking union medical college

summary: Hypoxia can result in tissue dysfunction, metabolic alterations, and structural damage within the pulmonary tissue, thereby impacting lung ventilation and air exchange. The identification of Hypoxia-inducible factor (Hif) 1α as a pivotal mediator in the inflammatory cascade subsequent to hypoxia induction has been established. However, the mechanism remains elusive. To delve deeper into this phenomenon, we have developed a murine model of sustained hypoxia and utilized nanocarriers for the delivery of lentivirus Hif-1α for knockdown purposes. Our findings suggest that under conditions of sustained hypoxia, knockdown of Hif-1α effectively ameliorated SpO2 levels and attenuated lung injury in our murine model. We observed that Hif-1α-mediated Histone Lactylation was evident in the lungs exposed to sustained hypoxia. Through RNA-seq and ChIP-seq profiling, we determined that upregulation of Hif-1α expression in sustained hypoxic lung tissue is essential for inducing lactylation enrichment of inflammatory response genes. Furthermore, knockdown of Hif-1α returned to normal inflammatory cytokines (e.g. TNF-α, IL-6 and IL-1β). Analysis of plasma metabolites from individuals experiencing restrictive/ obstructive lung disease revealed a significant enrichment of the Warburg effect within the sustained hypoxic group. Thus, our study provides compelling evidence supporting the notion that targeting Hif-1α-mediated histone lactylation may represent a promising therapeutic strategy for managing sustained hypoxia-induced lung injury.

overall_design:
To investigate the function of sustain hypoxia in mouse lung tissues,we established the model of substain hypoxia in mice.Besides,we knocked down Hif-1αin sustain hypoxia mice.
We then performed gene expression profiling analysis using data obtained from RNA-seq of lung tissues in mice.

first: Youjia

last: Wei

first: Chen

first: Xiaolin

last: Ma

first: Yiqing

last: Miao

first: Chunmei

last: Zhu

first: Shan

last: Wang