city: Xinxiang

first: Tianhan

last: Li

state: Henan

address: No.601, Hualan Road

institute: Xinxiang Medical University

summary: Background: The adaptor protein Linker for activation of T cell (LAT) is a key signaling hub used by the T cell antigen receptor. Mice with a mutation at the LAT-PLCγ1 binding site (Y136) have a defect in thymocyte development due to dampened TCR signaling. CD4 + T cells that do reach the periphery are hyper-activated and skewed to Th2. Over time, these mice develop an autoimmune-like syndrome, characterize by overproduction of Th2 cytokines, T cell infiltration into various organs, and B cell activation, isotype switching, and autoantibody production. In this study, we established LatY136F and   LatY136F-CD45 KO  mice and using them to investigate to role of CD45 in  TCR signalling via flow cytometry and scRNA sequencing. Conclusion: Knockout CD45 in LatY136F mice affact T cell activation

overall_design: For scRNA-seq analysis of T cells, 8-9 weeks old LatY136FCD45-KO and LatY136F mice were sacrificed. Single cell suspension from spleens were stained with antibody CD4-PE-cy7 and CD3-FITC . After washing with 1 mL FACS buffer two times, cells were resuspended with Sytox blue and CD3+CD5+ cells were sorted and subjected to the BD Rhapsody Express system. Then cDNA and sample tag libraries were built with BD Rhapsody whole transcriptome amplification (WTA) reagent kit (BD Bioscience, Cat: 633733, 633773, 633801, 664887) following manufacturer’s instructions, and sequenced on an illumine Novaseq 600 sequencer. Pair-end Fastq files of sample tag and WTA data were processed via BD RhapsodyTM analysis pipline v2.0, and the resultant dataset was mainly analysis using SeGeqTM software, which contain Lex-BDSMK and Seurat v4.04 plugin components.

first: Yinming

last: Liang

first: Lichen

last: Zhang

first: Liaoxun

last: Lu


title: Direct comparison of Cdkn2a and p53 loss reveals global transcriptomic differences, including tumor suppressor dependency on pentose phosphate pathway in MPNST

status: Public on Aug 01 2025

city: Iowa City

first: Rebecca

last: Dodd

state: IA

address: 375 Newton Rd MERF 5241D

department: Internal Medicine

country: USA

institute: University of Iowa

type: Expression profiling by high throughput sequencing

summary: Malignant Peripheral Nerve Sheath Tumors (MPNSTs) are aggressive and chemo-resistant sarcomas with poor overall survival. Loss of tumor suppressors CDKN2A (~80%) or P53 (~20%) is a signature event in MPNST development. Here, we use CRISPR/Cas9 somatic tumorigenesis mouse models to mechanistically compare CDKN2A and P53 loss transcriptomic and metabolic differences, leading to therapeutic vulnerabilities in MPNSTs. Multi-omic analyses identified the pentose phosphate pathway (PPP) and regulation of NADPH metabolism as critical metabolic vulnerabilities in the CDKN2A-deleted MPNSTs. Disruption of glucose-6-phosphate dehydrogenase (G6PD), the rate-limiting step in the PPP, slowed CDKN2A-deleted MPNST growth, yet sensitized both genotypes of MPNSTs to standard-of-care chemotherapy. Moreover, the redox-regulated transcription factor NRF2 controlled G6PD activity in these tumors. Genomic analysis of patient samples showed a NRF2 gene signature that correlated with tumor transformation, further underscoring this pathway as a therapeutic target. This work identifies the G6PD/NADPH axis as a central metabolic vulnerability in MPNSTs.

overall_design: To better understand the transcriptomic differences between loss of tumor suppressors CDKN2A and P53, we derived mouse Malignant Peripheral Nerve Sheath Tumors (MPNSTs) primary cell lines (Individual tumor for each cell line). Tumors were developed utilizing CRISPR/Cas9 somatic tumorigenesis models of Nf1/Cdkn2a-deleted and Nf1/p53-deleted autochthonous MPNSTs in genetically identical, wild-type mice (129 Sv/Jae). Adenovirus containing gRNAs targeting either Nf1 and Cdkn2a or Nf1 and p53 and contains full length Cas9 were injected into the sciatic nerve. Tumors develop in 3-4 months. Tumors were dissociated and plated to develop cell lines. Three cell lines of each genotype (Nf1-/-; Cdkn2a-/- and Nf1-/-; p53-/-) were submitted for RNA sequencing.

first: Gavin

last: McGivney

middle: D

first: Eric

middle: B

last: Taylor


title: Circadian Gene BMAL1 Regulation of Cell Senescence in Thyroid aging [RNA-Seq]

city: Guangzhou

first: Dandan

last: Zong

address: No.106, Zhongshan 2nd Road

country: China

institute: Guangdong Provincial People’s Hospital

summary: As the global aging society intensifies, the incidence of thyroid diseases among the elderly is increasing annually, with hypothyroidism being particularly common. Studies have shown that in healthy elderly individuals, thyroid-stimulating hormone (TSH) levels are significantly elevated, while thyroid hormone (TH) levels are notably normal or decreased. However, the molecular mechanisms underlying thyroid aging and function remain unclear. To understand thyroid aging, it is essential to study the molecular and functional characteristics of various thyroid cell types during the aging process. We conducted single-cell sequencing of thyroids from different age groups and identified eight typical cell types and five thyroid epithelial cell subtypes (EPI). During aging, the expression levels of thyroid hormone synthesis-related genes (TSHR, TG, TPO) increased, suggesting that EPI cells adjust their gene expression patterns in response to elevated TSH. With advancing age, rhythmic disruption and cellular senescence signals accumulated in thyroid. Further analysis indicated that the senescent EPI cell subpopulation (CDKN1A_EPI) exhibited functional decline. Additionally, we unexpectedly found that the expression of the core circadian gene BMAL1 (ARNTL) was downregulated in the CDKN1A_EPI cells of elderly individuals. To verify this finding, we used a thyroid-specific knockout mouse model and found that BMAL1 downregulation inhibited NFKBIA expression, exacerbating cellular senescence. Finally, cell line knockout experiments and transcriptome sequencing further confirmed that BMAL1 knockout led to decreased expression of NF-kB Inhibitor Alpha (NFKBIA), a key mechanism driving thyroid cell senescence. This discovery not only reveals the relationship between thyroid cell aging and circadian rhythm disruption but also enriches our understanding of the mechanisms underlying thyroid aging.

overall_design: Changes in gene expression after knockout of the bmal1 gene in a normal thyroid cell line

first: Haixia

last: Guan


title: Circadian Gene BMAL1 Regulation of Cell Senescence in Thyroid aging [scRNA-Seq]

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: this study aims to systematically analyze the cellular composition and gene expression characteristics of pathologically normal thyroid tissues from different age groups through single-cell RNA sequencing.We collected thyroid tissues from young wild-type, old wild-type, and young mutant mice under identical light-dark cycles (12 hours light/12 hours dark) for single-cell transcriptome sequencing.


title: circRNA Microarray Service for 6 mouse samples

city: wuhan

first: yikang

last: yuan

address: Luoyu Road, Hongshan District

institute: Wuhan University Stomatological Hospital

summary: We have completed the Arraystar Mouse circRNA Array v2 analysis of the 6 samples that you submitted. Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols. Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were hybridized onto the Arraystar Mouse circRNA Array v2 (8x15K, Arraystar). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

overall_design: Six samples were included and divided into two groups. One group was exposed to 3% sevoflurane for a single 4-hour period at 7 days postpartum in mice, while the other group was not exposed to sevoflurane.

first: mian

last: peng

first: bingrui

last: xiong

first: qianwen

last: he


title: Effect of  knockdown of RPLP0P2 on gene expression in RKO cells

city: Hangzhou

first: Hang

last: Yuan

address: 158 Shangtang Road, Hangzhou, Zhejiang,China

institute: Zhejiang Provincial People's Hospital

summary: We found that RPLP0P2 is subject to m6A modification. In addition, knockdown of METTL3 decreased the RNA level of RPLP0P2, suggesting that m6A modification may promote RPLP0P2 RNA stability. Furthermore, RNA pulldown assay indicated that the reader of m6A modified RPLP0P2 was IGF2BP2, and mutation of m6A modified site of RPLP0P2 destroyed its interaction with IGF2BP2. Finally, RPLP0P2 activated Notch signaling pathway and promoted the stemness of CRC cells.

overall_design: To investigate the function of RPLP0P2 on colon cancee progression, we knockdown RPLP0P2 by shRNA


title: Histone H3K27 acetylation mediated by KAT8 maintains antiviral immunity in shrimp trained with inactivated WSSV

city: Qingdao

first: Li-Xia

last: Lv

address: Ao Shanwei 72

institute: Shandong University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The phenomenon of trained immunity, which facilitates vaccine development for disease control, has been identified in shrimp; however, the mechanism remains elusive. In the present study, we found that histone H3K27 acetylation (H3K27ac) mediated by the lysine acetyltransferase KAT8 plays an important role in preventing white spot syndrome virus (WSSV) infection in the shrimp Marsupenaeus japonicus. We then successfully established a model of trained immunity via the use of UV-inactivated WSSV to explore the underlying mechanism(s) in shrimp. In UV-WSSV-trained shrimp, the glycolysis and tricarboxylic acid (TCA) cycle metabolic pathways were enhanced and acetyl-CoA concentrations were increased. As the acetyl group donor, acetyl-CoA promotes KAT8 activity to increase H3K27 acetylation. H3K27ac is deposited at the promoter region of the transcription factor Dorsal to facilitate its expression and then Dorsal promotes the expression of an interferon-like cytokine, Vago5, and antimicrobial peptides that act against WSSV infection. H3K27ac is also deposited at the promoter region of hexokinase 2 and isocitrate dehydrogenase, which positively regulates glycolysis and the TCA cycle in a feedforward manner. Our results reveal a novel mechanism of trained immunity induced by UV-WSSV in shrimp and provide a theoretical basis for the development of antiviral vaccines for disease control in shrimp aquaculture.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP‑seq) for histone modification H3K27ac in hemocytes from UV-WSSV-trained shrimp, PBS-trained shrimp were used as controls


title: Comparison of the responses of alveolar macrophages from rats, mice and humans following particle overload [mouse]

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

country: Belgium

institute: Université catholique de Louvain

summary: Chromic inhalation of poorly soluble low toxicity particles, like titanium dioxide or carbon black, at high exposure levels leading to particle overload in alveolar macrophages, can induce chronic inflammation and lung cancer in rats, but not in mice. Whether this rat adverse response is predictive for humans remains unsettled for more than 40 years. In order to clarify the human relevance of the adverse rat response to particle overload, primary rat, mouse and human alveolar macrophages were exposed in vitro to overload of titanium dioxide or carbon black particles, and their activation profile was analyzed by RNAseq. We report, here, a robust transcriptomic signature of poorly soluble low toxicity particle overload in rat alveolar macrophages in vitro ,which was not observed in mouse macrophages. A similar but markedly lower response was recorded in human macrophages.

overall_design: Primary mouse alveolar macrophages were exposed in vitro for 4 days to control, non-overload or overload conditions of Printex90 (carbon black) or G1-1 (titanium dioxide) particles. For each condition, three replicates were analyzed

first: Laeticia

last: Perez

first: Bertrand

last: Bearzatto

first: François

last: Huaux

first: Dominique

last: Lison


title: Transcriptional landscape of Camellia sinensis roots at single- nucleus resolution

city: Nanjing

first: shunkai

last: Hu

state: Jiangsu Province

address: Nanjing Agricultural University, Weigang No. 1, Xuanwu District, Nanjing

department: College of Horticulture

institute: Nanjing Agricultural University

summary: In summary, this study identifies most cell types in the root tips of the tea plant through single-nucleus transcriptomic analysis, establishing marker genes and cell type-specific regulatory programs. The evolutionary conservation and divergence in cell type and species-specific gene expression between tea plant and Arabidopsis provide new insights into the functions and evolution of cell types in tea plant. And it provides a detailed transcriptomic overview of the main cell types at the root tips of the tea plant at single-nucleus resolution.

overall_design: To conduct snRNA-seq analysis on tea plant roots, nuclei were extracted and purified from the tender root tips of the tea plant. Initially, the raw data were processed using Cell Ranger, the official analysis software of 10x Genomics, for data filtering, alignment, quantification, and identification of recovered cells, ultimately yielding a gene expression matrix for each cell.

first: Shunkai

first: Xinghui

last: Li


title: Hepatic progenitor cell-originated ductular reactionfacilitates liver fibrosis through activation of hedgehogsignaling

city: shanghai

first: Jiamei

last: Chen

address: zhangheng road,pudong district,shanghai

institute: shuguang hospital

summary: Background: It is poorly understood what cellular types participate in ductular reaction (DR) andwhether DR facilitates recovery from injury or accelerates hepatic fibrosis. The aim of this study is to gaininsights into the role of hepatic progenitor cell (HPC)-originated DR during fibrotic progression.Methods: DR in liver specimens of PBC, chronic HBV infection (CHB) or NAFLD, and four rodentfibrotic models by different pathogenic processes was evaluated. Gli1 expression was inhibited in rodentmodels or cell culture and organoid models by AAV-shGli1 or treating with GANT61.Results: Severity of liver fibrosis was positively correlated with DR extent in patients with PBC, CHB orNAFLD. HPCs were activated, expanded, differentiated into reactive cholangiocytes and constituted“HPC-originated DR”, accompanying with exacerbated fibrosis in rodent models of HPC activation &proliferation (CCl4/2-AAF-treated), Μdr2-/- spontaneous PSC, BDL-cholestatic fibrosis orWD-fed/CCl4-treated NASH-fibrosis. Gli1 expression was significantly increased in enriched pathways invivo and in vitro. Enhanced Gli1 expression was identified in KRT19+-reactive cholangiocytes. SuppressingGli1 expression by administration of AAV-shGli1 or GANT61 ameliorated HPC-originated DR andfibrotic extent. KRT19 expression was reduced after GANT61 treatment in sodium butyrate-stimulated WB-F344 cells or organoids or in cells transduced with Gli1 knockdown lentiviral vectors. In contrast,KRT19 expression was elevated after transducing Gli1 overexpression lentiviral vectors in these cells.Conclusions: During various modes of chronic injury, Gli1 acted as an important mediator of HPCactivation, expansion, differentiation into reactive cholangiocytes that formed DR, and subsequentlyprovoked hepatic fibrogenesis.

overall_design: To systematically investigate the mechanisms of hepatic progenitor cell activation, expansion, differentiation intocholangiocytes, a transcriptomic assay was performed in WT mice and Μdr2-/- mice. Comparative gene expression profiling analysis of RNA-seq data for liver samples of WT mice and Μdr2-/- mice.

first: Yonghong

first: Jian

last: Wu

first: Ping

last: Liu


title: Transcriptomic changes in Human Umbilical Vein Endothelial Cells (HUVEC) after exposure to Tumor Necrosis Factor-Alpha(TNF-a), AdipoRon, and Sphingosine Kinase Inhibitor (SKI-I)

first: Vinnyfred

last: Vincent

address: 431 Newton Rd

summary: Endothelial dysfunction is one of the earliest manifestations of atherosclerosis development. Adiponectin, a hormone secreted by adipose tissue with insulin-sensitizing and anti-inflammatory properties, offers protection against atherosclerosis. The pleiotropic effects of adiponectin are thought to be mediated by the ceramidase activity of adiponectin receptors. Adiponectin has been shown to reduce ceramide levels in endothelial cells. Still, the effects of adiponectin on other sphingolipids and endothelial lipid metabolism are not completely elucidated. This study investigated the metabolic and sphingolipid alterations in endothelial cells linked to the protective effects of adiponectin against endothelial dysfunction. Human Umbilical Endothelial Cells (HUVECs) were treated with Tumor Necrosis Factor-alpha (TNF-α) to induce endothelial dysfunction. AdipoRon and SKI-I were used to study the effects of adiponectin and sphingosine kinase inhibition in HUVECs. Metabolic changes and sphingolipid alterations were assessed to understand changes in lipid metabolism, and RNA sequencing was used to quantify the transcriptomics changes.

overall_design: To identify the effects of Tumor Necrosis Factor-Alpha(TNF-a),  AdipoRon, and Sphingosine Kinase Inhibitor (SKI-I) on Human Umbilical Vein Endothelial Cells (HUVECs), we treated HUVECs with TNF-a, AdipoRon and SKI-I and cominations of these for 12 hours

first: Himani

last: Thakkar

first: Atanu

last: Sen

first: Ashutosh

last: Bansal

first: Ujjalkumar

last: Subhash Das

first: Abishek

last: Gunasekaran

first: Neerja

last: Bhatla

first: Thirumurthy

last: Velpandian

first: Archna

last: Singh


title: RNA-seq of sorted murine long-term hematopoietic stem cells segmented on CUX1 levels with and without CUX1 knockdown

city: Chicago

first: Tanner

middle: Clark

last: Martinez

state: IL

address: 900 E 57th Street Chicago, IL, 5220A LB35

department: Pathology

institute: University of Chicago

summary: Hematopoietic stem cells (HSCs) possess properties of both self-renewal and multipotent differentiation; however, the regulation of these opposing properties remains elusive. Using a novel reporter mouse, we demonstrate the dose-dependent role of the transcription factor, CUX1, in HSC fate. As CUX1 levels naturally rise, HSCs gradually lose repopulating capacity. CUX1 knockdown reverses this process and reverts HSCs to an earlier cell state—restoring the transcriptome, chromatin accessibility, repopulating capacity, and self-renewal ability of HSCs with normally low CUX1 levels. In the absence of CUX1, endogenous retroelements (EREs) are aberrantly expressed, leading to a cell-intrinsic inflammatory response, which contributes to CUX1-dependent HSC activity. Likewise, loss of the transcription factor IRF1 attenuates CUX1-mediated HSC reprogramming. This mechanism could be relevant to leukemogenesis as acute myeloid leukemias with CUX1 deletions upregulate EREs and the interferon response. Our findings attribute CUX1 and innate immune activation to the complex molecular underpinnings of HSC fate decisions.

overall_design: RNA-seq of long-term hematopoietic stem cells segmented on CUX1 levels. RNA-seq of segmented long-term hematopoietic stem cells after 3 days of ex vivo CUX1 knockdown.

first: Megan

middle: E

last: McNerney

middle: C


title: Identification of S100A9 as a target for diagnosis and treatment of Crohn’s Disease after Vedolizumab treatment failure

city: 河南省

first: 艳茹

last: 张

address: 金水区经八路

institute: 郑州大学第二附属医院

summary: Recent advances in Whole-Transcriptome Sequencing technologies enable the complete sequencing of entire genomes and allow us to analyze a number of disease genome profiles. In our study, whole-transcriptome sequencing was performed based on the peripheral blood leukocytes of patients in the Non-responsders group (contain 5 CD patients who are nonresponse to vedolizumab treatment) and the Rseponders group (contain 3 CD patients who are response to vedolizumab treatment). Subsequently, differential messenger RNA (mRNA), circRNA and lncRNA expression analysis was performed of  the Non-responsders and Responders groups, followed by functional interaction prediction analysis. This study may provide novel insights into the molecular basis of initiation and progression of IBD, and provide potential biomarkers for distinct prognostic and therapeutic implications.

overall_design: To make the next treatment plan for unresponsive patients and select Vedolizumab for the right Crohn’s patients to achieve precise treatment and better treatment persistence，this study used the Peripheral blood leukocyte samples which were from eight CD patients (five non-responders and three responders; age range: 18–52 years, mean age: 28.5 years) who accepted Vedolizumab treatment at the Second Affiliated Hospital of Zhengzhou University. Using a week’s worth of observational scoring, the Crohn’s Disease Activity Index (CDAI) is an essential indicator for calculating how active a patient’s condition is. We defined responder as a patient with a CDAI <150 along with a Simple Endoscopic Score for Crohn’s Disease (SES-CD) <5 assessed at least 14 weeks after the initial administration of vedolizumab; conversely, we rated it as a failure to respond if the patient did not meet the aforementioned criteria or suffered a dose increase that was not due to weight gain. All of the sections were graded according to their histological characteristics with the help of a pathologist.

first: Yanru

last: Zhang

first: Zhe

first: Baisui

last: Feng


title: Single-cell RNA-Seq characterization of CUX1 levels in murine hematopoietic stem cells.

overall_design: Single-cell RNA-Seq of sorted murine long-term hematopoietic stem cells and hematopoietic progenitors. In a second experiment, murine LT-HSCs were sorted and segemented on initial CUX1 levels. CUX1 knockdown was performed ex vivo for five days.


title: Detection of statistically robust interactions from diverse RNA-DNA ligation data [nucRNA-seq]

city: Frankfurt

first: Simonida

last: Zehr

state: Hesse

address: Theodor-Stern-Kai 7

department: Institute for Cardiovascular Physiology

country: Germany

institute: Goethe University, Frankfurt am Main, Germany,

summary: Chromatin-localized RNAs play diverse roles in gene regulation and nuclear architecture. Mapping genome-wide RNA-DNA interactions is possible using a variety of molecular methods, including using bridging oligonucleotides to ligate RNA and DNA in proximity. While molecular methods have progressed, a robust computational method for calling biologically meaningful RNA-DNA interactions from these data is lacking. Herein, we present RADIAnT, a reads-to-interactions pipeline for analyzing RNA-DNA ligation data. RADIAnT calls interactions against a dataset-specific, unified background which considers RNA binding site-TSS distance and genomic region bias. By scaling the background with RNA abundance, RADIAnT is sensitive enough to detect specific interactions of lowly expressed transcripts, while remaining specific enough to discount false positive interactions of highly abundant RNAs. RADIAnT outperforms previously proposed methods in the accurate recall of genome-wide Malat1-DNA interactions, and in a use-case, was utilized to identify dynamic chromatin-associated RNAs in the physiologically- and pathlologically-relevant process of endothelial-to-mesenchymal transition.

overall_design: nucRNA-sequencing was performed on 3 HUVEC replicates, once in wildtype (endothelial) phenotype (CTL), once after IL-1β + TGF-β induced phenotypic switch to mesenchymal-like cells (EMT).

first: Sandra

last: Seredinski

first: Matthias

middle: S

last: Leisegang

first: Ralf

middle: P

last: Brandes

first: Marcel

middle: H

last: Schulz

first: Timothy

last: Warwick


title: ATAC-Seq of sorted murine LT-HSCs segemented on intial CUX1 levels with and without CUX1 knockdown.

overall_design: ATAC-Seq of sorted murine long-term hematopoietic stem cells cultured ex vivo for five days. LT-HSCs were segmented on initial CUX1 levels. Addition of doxycycline drives expression of either a control shRNA or an shRNA targetting CUX1.


title: Comparative single-cell analysis of esophageal cancer subtypes reveals cellular distinctions explaining varied immunotherapy responses

city: Seodaemun-gu

first: Insuk

last: Lee

state: Seoul

address: 50 Yonsei-ro

department: Biotechnology

country: South Korea

institute: Yonsei University

summary: Esophageal cancer comprises two main subtypes: esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC). Previous studies revealed their distinct genomic characteristics, sharing similarities with head and neck squamous cell carcinoma (HNSCC) and gastric adenocarcinoma (GAC) for ESCC and EAC, respectively. This study compares ESCC and EAC at single-cell resolution to identify factors explaining differences in immunotherapy response rates. We performed comparative single-cell transcriptome analysis for four cancer types near the esophagus using data from 35 patients with ESCC, EAC, HNSCC, or GAC. Malignant epithelial cells showed distinct separations between subtypes based on histological origins. We identified enrichment of CXCL13+ CD8+ T cells and CXCL9+CXCL10+ TAMs in ESCC and HNSCC, promoting a hot-tumor environment through interferon-γ pathways. Conversely, hypoxia and cold-tumor related populations, such as heat-shock protein high CD8+ T cells and MARCO+ TAMs, were enriched in EAC and GAC. These immune subsets' expression signatures predicted immunotherapy responses across diverse cancer types.

overall_design: Libraries were prepared using the Chromium controller following the protocol outlined in the 10x Chromium Next GEM Single Cell 5-v2 Cell Surface Protein User Guide (CG000330). Initially, cell suspensions were diluted with nuclease-free water to achieve a targeted cell count of 10,000. These suspensions were then mixed with master mix and loaded with Single Cell 5′ Gel Beads and Partitioning Oil into a Next GEM Chip K. Within the droplets, RNA transcripts from single cells were uniquely barcoded and reverse-transcribed. The purified libraries were quantified using qPCR following the qPCR Quantification Protocol Guide (KAPA) and qualified using the Agilent Technologies 4200 TapeStation. Finally, the libraries were sequenced on the HiSeq platform (Illumina) according to the specified read length in the user guide.

first: Seungbyn

last: Baek

first: Junha

last: cha

first: Min-Hee

last: Hong

first: Gamin

last: Kim

first: Yoon

middle: W

last: Koh

first: Dahee

first: Martin

last: Hemberg

first: Seong

middle: Y

last: Park

first: Hye

middle: R


title: Lipa regulates myeloid differentiation and is essential for intra-plaque macrophage accumulation during atherosclerosis

first: Tianhan

last: Li

summary: Lysosomal acid lipase (Lipa), which is primarily produced in the liver, has been identified as one of the earliest and most impactful genetic factors linked to human coronary artery diseases. Despite its original source, it is also found to be highly expressed in macrophages. However, the functional importance of Lipa in macrophages has been largely unknown. Notably, individuals with certain risk alleles demonstrate elevated Lipa expression in monocytes and macrophages, but lower levels of hepatic and plasma Lipa, indicating a potential regulatory role of Lipa on atherosclerosis through its impact on macrophages. The development of atherosclerosis in genetic models lacking Lipa has presented challenges. Our hypothesis is that Lipa deficiency may influence atherosclerosis development by affecting macrophages. In order to investigate this, we established Lipa-deficient mice on an ApoE-knockout background, providing a model that enables us to evaluate the influence of Lipa on atherosclerosis. In our experiments, we observed hepatosplenomegaly and increased myeloid cell differentiation in Lipa−/−ApoE−/− mice fed a high-fat diet, which aligns with observations in humans with LIPA deficiency. Surprisingly, we also discovered that Lipa deficiency led to a significant inhibition of atherosclerosis in both Lipa+/−ApoE−/− and Lipa−/−ApoE−/− mice. Mechanistically, we found that such inhibition was linked to a notable reduction in foam cell formation and macrophage accumulation within atherosclerotic plaques. Notably, reduced Lipa expression in Lipa+/−ApoE−/− mice influenced foam cell formation and macrophage accumulation, but did not impact hepatic lipid metabolism or macrophage differentiation, as evidenced by flow cytometry and single-cell RNA-sequencing. These findings highlight a novel role for Lipa in modulating macrophage behavior during atherosclerosis, suggesting that Lipa may serve as a promising therapeutic target for the treatment of atherosclerosis.

overall_design: Single cell suspension from spleens were firstly stained with antibody CD45.2-PE and BD™ Ms Single Cell Sample Multiplexing Kit (BD Bioscience, Cat: 633793). After washing with 1 mL FACS buffer two times, cells were resuspended with Sytox blue and CD45.2+CD5-CD19-Ly6G- cells were sorted and subjected to the BD Rhapsody Express system. Then cDNA and sample tag libraries were built with BD Rhapsody whole transcriptome amplification (WTA) reagent kit (BD Bioscience, Cat: 633733, 633773, 633801, 664887) following manufacturer’s instructions, and sequenced on an illumine Novaseq 600 sequencer. Pair-end Fastq files of sample tag and WTA data were processed via BD RhapsodyTM analysis pipline v2.0, and the resultant dataset was mainly analysis using SeGeqTM software, which contain Lex-BDSMK and Seurat v4.04 plugin components.

first: Juanjuan

last: Qiu

first: Yinming

last: Liang

first: Rong

last: Huang

first: Zhongshu


title: Beta-Adrenergic Stimulation and MYH7 G256E Mutant Gene Dosage Drive Hypertrophic Cardiomyopathy Phenotype Penetrance

city: STANFORD

first: Paul

last: Heinrich

address: 265 CAMPUS DRIVE

department: Cardiovascular Insititute

institute: Stanford University

summary: We characterized the baseline transcriptomic phenotype of day30 iPSC-Cardiomyocytes carrying hypertrophic cardiomyopathy associated heterozygous mutations MYH7 G256E and H251N using scRNAseq. We additionally analzyed trancriptomic signatures of HOM MYH7 G256E iPSC-CMs, and of HET MYH7 G256E iPSC-CMs after isopreterenol treatment.

overall_design: Our study includes the data of 7 independent scRNAsequencing runs using 10X Genomics characterizing the trancriptomic signature of the H251N and G256E mutation in iPSC-CMs. Individual conditions for each run is specified below. 10X CellPlex Feature barcoding technology was used to multiplex samples 2-7 for scRNAseq. Antibody-based labeling of CD29 and B2M and single indexing was used to multiplex sample 1. Please refer to each scRNAseq batch information for de-multiplexing settings used for this study. In the raw data, the FB files contain feature barcode sequencing information for sample multiplexing, while the GE files contain gene expression sequencing information.

first: Soah

first: Sean

middle: M

last: Wu


title: Detection of statistically robust interactions from diverse RNA-DNA ligation data [RADICL-seq]

first: Simonida

last: Zehr

overall_design: RADICL-sequencing was performed on HUVEC batch 405Z013, once in wildtype (endothelial) phenotype (CTL), once after IL-1β + TGF-β induced phenotypic switch to mesenchymal-like cells (EMT).

first: Sandra

last: Seredinski

first: Matthias

last: Leisegang

first: Ralf

last: Brandes

first: Marcel

first: Timothy


title: Effect of recombinant IGLL5 treatment on gene expressing of high endothelial venules

first: Mingjie

last: An

address: Yanjiang Road

institute: Sun-Yat Sen university

summary: High endothelial venules (HEVs) are key component in the formation of tertiary lymphatic structure. Our previous studies have shown that IGLL5+B cells adhere to and inhibit the functional phenotype of HEVs. In addition, we found that IGLL5 binds to the LTβR receptor on the membrane of HEVs.

overall_design: In order to further investigate the effect of IGLL5-LTβR binding on the downstream signaling pathway of HEVs, we stimulated HEVs cells by IGLL5 recombinant protein in vitro. Gene expression profiling analysis was performed using  HEVs cells in 3 separate experiments.

first: Tianxin

last: Lin

first: Changhao

last: Chen


title: Maternal high-fat diet alters Tet-mediated epigenetic regulation during heart development [ATAC-Seq]

city: Houston

first: Yuhan

last: Yang

address: 2121 W. Holcombe Blvd.

institute: Texas A&M University

summary: Our study suggested a direct link between maternal high-fat diet exposure and TET-mediated epigenetic regulation during heart development. Furthermore, we also uncovered beneficial effects of maternal vitamin C intake to protect heart development under maternal obesity conditions

overall_design: We collected E15.5 embyronic hearts from C57/BL6 WT dams fed with either normal diet(injected with vitamin C or PBS) or high-fat diet (injected with vitamin C or PBS) for RNA-Seq and ATAC-Seq

first: Logan

last: Rivera

first: Shaohai

last: Fang

first: Maryn

last: Cavalier

first: Ashley

last: Suris

first: Yubin

last: Zhou

first: Yun


title: Comparison of gamma-radiation-responsive transcriptomes between Arabidopsis thaliana (ecotype Col-0) wild type and two ago2 mutant lines.

city: Jeongeup-si

first: Jin-Hong

last: Kim

state: Jeonbuk-do

address: 29 Geumgu-gil

institute: Korea Atomic Energy Research Institute

summary: To compare the gamma-radiation-responsive transcriptone between wild-type and ago2 mutant lines (SALK_003380 and SALK_037548), we performed whole-genome expression microarray profiling using mock seedlings as controls and gamma-irradiated seedlings as test samples.

overall_design: Fourteen-day-old seedlings of wild-type and ago2 mutant lines were irradiated with gamma radiation for 4 hours at a dose rate of 50 Gy/hour, and gamma radiation-responsive transcripts were measured 24 hours after irradiation using whole-genome expression microarrays.


title: Physiological, biochemical and transcriptomic analyses reveal the mechanism of variation in color traits in Panax japonicus fruits

city: guiyang

first: Xilun

last: Huang

state: guizhou

address: 180 North Baoshan District Road, Yunyan District

institute: Guizhou Normal University

summary: Panax japonicus C. A. Mey. is a rare and endangered Class II important protected wild medicinal plant in China with a wide range of pharmacological activities. The development of the fruit is special, only the apical capitulum can develop into fruit normally, and the colour trait changes during the maturation process showed a pattern from green to red and from red to purple-black.

overall_design: In order to reveal the phenomenon of colour trait changes during fruit development, this paper analyzed the correlation between colour trait changes and pigment contents (chlorophyll, carotenoids) and secondary metabolite contents (anthocyanosides, flavonoids, and total phenols) of the fruits, and used transcriptome sequencing to explore the correlation between colour trait changes and synthetic genes, and then verified the fluorescence quantification with qRT-PCR. Transcriptome sequencing obtained transcriptome data of 15 samples from five periods of colour trait changes in Panax japonicus fruits

first: Xi

middle: L

first: Ting

middle: t

last: Tang

first: E

last: Liang

first: Lai

last: Zhang


title: Maternal high-fat diet alters Tet-mediated epigenetic regulation during heart development [RNA-Seq]


title: Transcriptome of Synechocystis sp. PCC 6803 strains with high light tolerance

city: Planegg

first: Weiyang

address: Großhaderner Straße 2

department: Biologie I, Botanik

institute: Ludwig-Maximilians-Universität München

summary: Several strains with increased high light tolerance were previously generated by adaptive laboratory evolution from Synechocystis sp. PCC 6803 WT strain. The high light tolerance in each strain was caused by a few non-synonymous point mutations. Reintroduction of the corresponding point mutation in WT conferred enhanced tolerance to high light. Here, we characterized the responses at the transcriptional level using RNA-Seq approach to identify genes associated with the HL tolerance.

overall_design: The pre-cultured Synechocystis cells under control light (50 μmol photons per m-2 s-1) were harvested, and inoculated into fresh liquid BG11 medium at an OD = 0.05 to grow photoautotrophically under control light , moderate high light (700 μmol photons per m-2 s-1) or strong high light (1,200 μmol photons per m-2 s-1) for one week. Three biological replicates of each strain under different light conditions were collected. And then, the RNA were extracted from all samples and used for RNA-Seq analysis.


title: Isoflurane Aggravates Pre-Existing Proteotoxicity in Adult Nematodes by Modulating Mitophagy

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

summary: Post operative delirium (POD) is an acute complication characterized by fluctuating attention and confusion which may develop and persist into cognitive decline. POD is most commonly observed in elderly patients, particularly those with preexisting cognitive impairments. Isoflurane, as a widely used volatile anesthetic, is associated with POD. Utilizing the nematode C. elegans, we found that isoflurane enhances protein aggregation and long-lasting decline in protein homeostasis (proteostasis) of adult animals that express neurodegeneration-causing, abnormally long poly-glutamine stretches. Isoflurane-induced proteostasis impairments are dependent on the aging-regulating transcription factors DAF-16/FOXO and SKN-1/NRF. We also show that reducing the activity of a certain mitophagy mechanism and inducing mitochondrial biogenesis protect worms that exhibit weakened proteostasis, from isoflurane-induced proteotoxicity. Our observations provide a novel insight into the mechanism that links isoflurane and POD, and highlight the potential of mitophagy modulators as alleviators of POD in elder patients with preexisting cognitive impairments.

overall_design: 4 synchronized groups of AM140 worms were included in the experiment: Animals were grown from hatching on EV bacteria or on bacteria that express YFP RNAi at 20C. These worms express polyQ-YFP uninterruptedly and thus, were challenged by high / low levels of proteotoxicity. At day 5 of adulthood, half of the worms of each group were exposed to isoflurane while the other half was not.

first: Ehud

last: Cohen

first: Tayir

last: Elami

first: Vijigisha

last: Srivastava

first: Huadong

last: Zhu

first: Reut

last: Bruk-Haimson

first: Irit

first: Einav

last: Gross

first: Idit

last: Matot


title: Fusobacterium nucleatum-driven mitophagy facilitates endosymbiosis in macrophages and promotes esophageal squamous cell carcinoma metastasis

city: Guangzhou

first: Fangfang

last: Chen

state: Guangdong

address: No.132 Waihuandong Road, University Town

department: School of Pharmaceutical Sciences

institute: Sun Yat-sen University

summary: The facultative intracellular bacterium Fusobacterium nucleatum (Fn) mediates tumorigenesis and progression in esophageal squamous cell carcinoma (ESCC). The intracellular survival strategy of Fn and whether Fn can spread through cell‒cell contact in intratumoral tissues and, if so, the underlying mechanisms and implications are currently unknown. Here, we observed that Fn accumulates in macrophages from ESCC tumors and paracancerous normal tissues. We further found that Fn-induced macrophage mitophagy through the PINK1-Parkin-independent pathway decreases excessive mitochondrial ROS production to promote survival. Furthermore, Fn drives a biphasic metabolic switch between glycolysis and oxidative phosphorylation in macrophages to support the bioenergetic demands of survival. Notably, Fn is carried and delivered to tumors by macrophages, where it promotes tumor metastasis via the CCL2-CCR2 axis in ESCC. Treatment with a mitochondrial division inhibitor (mdivi-1) reduced the intracellular Fn concentration and inhibited Fn-positive tumor metastasis in mice. These findings indicate that mitophagy inhibitors or mitophagy machinery targeting may serve as efficient therapeutic strategies to treat Fn-positive tumors.

overall_design: To explore how tumor cells transmit Fn to macrophages, we performed transcriptome profiling experiments in Fn-infected ESCC cell line.

first: Han

last: Xiao

first: Xiaoyun

last: Pan

first: Tongfang

first: Yiqiu

last: Li

first: Shengxin

first: Songhe

last: Guo

first: Ge


title: Detection of statistically robust interactions from diverse RNA-DNA ligation data [ATAC-seq]

first: Simonida

last: Zehr

overall_design: ATAC-sequencing was performed on 3 HUVEC replicates, once in wildtype (endothelial) phenotype (CTL), once after IL-1β + TGF-β induced phenotypic switch to mesenchymal-like cells (EMT).

first: Sandra

last: Seredinski

first: Matthias

last: Leisegang

first: Ralf

last: Brandes

first: Marcel

last: Schulz

first: Timothy

last: Warwick


title: TRIM24 as therapeutic target in endocrine treatment resistant breast cancer (ChIP-Seq)

city: Amsterdam

first: Wilbert

last: Zwart

state: Noord-Holland

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute

summary: While ERα+ breast cancer treatment is considered effective, resistance to endocrine therapy is common. Since ERα is still the main driver in most therapy-resistance tumors, alternative therapeutic strategies are needed to disrupt ERα transcriptional activity. In this work, we position TRIM24 as therapeutic target in endocrine resistance, in its role as key player of the ERα transcriptional complex. TRIM24 interacts with ERα and other well-known ERα-cofactors to facilitate ERα chromatin interactions, and allows for maintenance of active histone marks including H3K23ac and H3K27ac. Consequently, genetic perturbation of TRIM24 abrogates ERα-driven transcriptional programs and reduces tumor cell proliferation capacity. Using a recently-developed degrader targeting TRIM24, ERα-driven transcriptional output and growth was blocked, effectively treating not only endocrine-responsive cell lines, but also drug resistant derivates thereof as well as cell line models bearing activating ESR1 point mutations. Finally, using human tumor-derived organoid models, we could show efficacy of TRIM24 degrader in the endocrine responsive and resistant setting. Overall, our study positions TRIM24 as a central component for integrity and activity of the ERα transcriptional complex, with degradation-mediated perturbation of TRIM24 as promising therapeutic avenue in the treatment of primary and endocrine resistance breast cancer.

overall_design:
ERα and TRIM24 ChIPs in MCF7 WT cells in full-media. 2 biological replicates for ERα ChIPs and 3 biological replicates for TRIM24 ChIPs. ERα, H3K23ac and H3K27ac ChIPs in TRIM24-KO and NT MCF7 cells, in full-media. 3 biological replicates for each ChIP.
p-Ser RNA POLII CTD ChIP-seq. Experiment was performed in both TRIM24-KO (clone A and B) and Non-target (NT1 and NT2) MCF7 cells in FBS conditions. 3 biological replicates for each condition was performed.
TRIM24 ChIP-seq in MCF7 WT cells treated with DMSO or E2 (10nM) for 3hours

first: Nuno

last: Padrão

first: Sebastian

last: Gregoricchio

first: Nils

last: Eickhoff

first: Lara

last: Luzietti

first: Jing

last: Dong

first: Daniela

last: Bossi

first: Tesa

last: Severson

first: Joseph

last: Siefert

first: Maria

last: Collier

first: Arianna

last: Calcinotto

first: Laki

last: Buluwela

first: Simak

last: Ali

first: Leonie

last: Young

first: Jean-Philippe

last: Theurillat

first: Damir

last: Varešlija


title: Highly-metastatic colorectal cancer cell released Nidogen 1-Enriched Extracellular Vesicles promote liver metastasis by activating hepatic stellate cells and forming the neutrophilextracellulartraps

city: jinan

first: liu

last: jialiang

address: wenhuaxi road

institute: shandong university

summary: The liver is frequently affected by metastasis in colorectal cancer patients; however, the precise interaction between the liver microenvironment and metastatic colorectal cancer cells remains elusive. Our study reveals that NID1, present in extracellular vesicles (EVs) derived from metastatic colorectal cancer, plays a pivotal role in promoting colorectal cancer liver metastasis (CRLM). EV-NID1 facilitates epithelial-mesenchymal transition (EMT) in colorectal cancer cells by modulating EMT-associated genes. Moreover, EV-NID1 activates hepatic stellate cells (HSCs), which in turn stimulate neutrophil infiltration and induce the formation of neutrophil extracellular traps (NETs) within the hepatic metastatic microenvironment via interleukin 11 (IL-11) secretion. This process ultimately reshapes the tumor microenvironment (TME) and fosters the establishment of a metastatic niche conducive to CRLM. Notably, targeted inhibition of IL-11 signaling using anti-IL-11 monoclonal antibodies effectively suppresses EV-NID1-induced liver metastasis in a murine model. In summary, our findings elucidate the mechanism underlying EV-NID1-mediated regulation of CRLM, presenting a promising therapeutic target for intervention in this disease.

overall_design: 1. In order to study the characteristics of metastatic colorectal cancer cells, we screened high metastatic cell lines by spleen injection of SW480 cells, and through three rounds of screening, we obtained a high metastatic colorectal cancer cell line named SW480-LM3, and the parental cells were SW480-P;2.To investigate the effect of exosome-derived NID1 protein on hepatic stellate cells LX-2, hepatic stellate cells were incubated for 48 hours using exosomes containing NID1, designated EV-XP-NID1-LX-2, and control EV-XP-LX-2;3.To investigate the effect of the exosomal pathway on epithelial mesenchymal transition in colorectal cancer cell lines, SW480 colorectal cancer cell line overexpressing NID1, named LV5-NID1, was treated for 72 hours using GW4869, and the control group was LV5.


title: Transcriptional response induced by knockdown of HUWE1 in human HEK293T cells

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

summary: siHUWE1-downregulated proteins have higher-than-average insolubility, suggesting that HUWE1 stabilizes proteins with high insolubility

overall_design: RNA-sequencing data from human HEK293T cells treated with siRNAs for HUWE1 or control non-targeting (NT) siRNAs. For each condition, 4 biological replicates were analyzed.

first: Liam

last: Hunt

first: Kaiwen

last: Yu

first: Kanisha

last: Kavdia

first: Vishwajeeth

last: Pagala

first: Yingxue

last: Fu

first: Suresh

last: Poudel

first: Xusheng

first: Junmin

last: Peng

first: Fabio

last: Demontis


title: Myeloid cell states determine reinstatement of original immune environments in recurrent ovarian cancer

city: Lausanne

first: Aspram

last: Minasyan

address: Bugnon 25A

country: Switzerland

institute: Ludwig Institute for Cancer Research / CHUV

summary: Immunotherapy has produced disappointing results in recurrent ovarian cancer (OC). However, the prognostic value of tumour-infiltrating lymphocytes (TILs) is grounded on the analysis of treatment-naive tumours. To understand the immunobiology of recurrent cancers, and their evolution, we profiled 170 patient-matched primary-recurrent OC samples from 69 patients of two independent cohorts. By capturing heterogeneous TIL distributions, we identified four immune phenotypes associated with differential prognosis, TILs states and TILs:myeloid networks, which dictate malignant evolution after chemotherapy and recurrence. Notably, recurrent tumours recapitulate the immunogenic patterns of original cancers. Mirroring inflamed human OC, preclinical recurrent Brca1mut tumours maintained activated TILs:dendritic cells (DCs) niches and immunostimulatory tumour-associated macrophages (TAMs). Conversely, recurrent Brca1wt tumours displayed loss of TILs:DCs niches and accumulated immunosuppressive myeloid networks featuring Trem2/ApoEhigh TAMs and Nduf4l2high/Galectin3high malignant states. Our study highlights that persistent immunogenicity in recurrent OC is governed by the crosstalk between dissimilar myeloid cells and TILs, which is BRCA-dependent.

overall_design:
scRNA-seq of mouse ovarian cancer models: Trp53-/- Brca1-/- (hereby referred as Brca1mut) or Trp53-/- Brca1+/+ (or Brca1wt). We characterized solid tumors at baseline (referred as primary tumors) and relapse after chemotherapy treatment (referred as recurrent tumors). Therefore, the experiment included 4 arms and the single-cell samples belonging to each arm are assigned below:

Brca1wt primary: group BRCA-A (mice A1-A5 and A_pooled) and group BRCA-B (mice B7-B10 and B_pooled).

Brca1wt recurrent: group BRCAP1 (mice P1_3, P1_13, and P1_pooled) and group BRCAP2 (mice P2_1, P2_47, and P2_pooled).

Brca1mut primary: group BRCA-C (mice C11-C15 and C_pooled) and group BRCA-D (mice D16-D20 and D_pooled).

Brca1mut recurrent: group BRCAB1 (mice B1_21, B1_23, and B1_pooled) and group BRCAB2 (mice B2_28, B2_29, and B2_pooled).

Note: This represents a multiplexed sc RNAseq assay (see methods). Most cells were successfully de-multiplexed to individual mice. Unassigned cells from each group of the corresponding experimental arm were grouped as additional "pooled" sc samples.

first: Eleonora

last: Ghisoni

first: Alizée

middle: J

last: Grimm

first: Noémie

last: Fahr

first: Mathieu

last: Desbuisson

first: Denarda

last: Dangaj


title: Transcriptome analysis of gene expression in control and circFUT8 Knockdown MK cultures at day 13.

city: Chongqing

first: Huang

last: Wu

state: Chongqing

address: 10 Changjiang Access Road

department: Department of Blood Transfusion

institute: Daping Hospital, Army Medical University

summary: We have used RNA-seq to explore  gene expression profiles in  control and circFUT8 Knockdown MK cultures at day 13.

overall_design: Three biological replicates for control and circFUT8 Knockdown MKs.


title: TRIM24 as therapeutic target in endocrine treatment resistant breast cancer

first: Wilbert

last: Zwart

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

overall_design: Refer to individual Series

first: Padrão

last: Nuno

first: Zwart

last: Wilbert


title: CmMYB113 and CmMADS26 interact to regulate ethylene synthesis and sucrose accumulation in oriental melon fruit

city: Shenyang

first: Hongyan

last: Qi

state: Liaoning

address: No.120 Dongling Road, Shenhe District

institute: Shenyang Agricultural University

summary: Sugar content is one of significant marks of fruit quality, and understanding the regulatory mechanism of sucrose accumulation is fundamental for breeding excellent melon fruit. As indicated by the co-expression network analysis, we distinguished a MYB transcription factor, CmMYB113, whose expression responds to oriental melon (‘HS’ (high-sucrose cultivar) and ‘LW’ (low-sucrose cultivar)) fruit ripening. Agrobacterium-mediated transient transformation injection and stable genetic transformation system confirmed that CmMYB113 promoted the sucrose accumulation and ethylene synthesis by up-regulating the expression of CmACO1 and CmSPS1 in oriental melon fruit. What’s more, we also identified a MADS transcription factor from the transcriptome, CmMADS26, which is highly expressed during melon fruit ripening. Intriguingly, CmMADS26 could directly bind to the promoter of CmACO1 to promote its transcription, and CmMYB113 physically interacted with CmMADS26 in yeast and tobacco leaves. Our findings give new bits of knowledge into the regulatory mechanisms by which MYB and MADS transcription factors interact to regulate melon fruit ripening and sucrose accumulation.

overall_design: To investigate the molecular mechanism of sucrose accumulation differences in oriental melon fruit of different varieties, RNA-seq was performed on samples from four developmental stages of two oriental melon varieties to screen differentially expressed genes and transcription factors

first: Ge

last: Gao

first: Fan

last: Yang

first: Jingyue

last: Guan

first: Yinhan

last: Sun

first: Cheng

last: Wang


title: Extracellular Granzyme B directly drives Interferon-stimulated genes expression in macrophages.

city: Hefei

first: Qi

middle: wu

last: Bian

state: Anhui

address: Division of Life Sciences and Medicine, 443 Huangshan Road

department: Life sciences and medicine

institute: University of Science and Technology of China

summary: Previous research indicate MIA propagates maternal inflammation to the fetal developing brain, that manifests as increased pro-inflammatory cytokines and activation of macrophages. Our data sugests that maternal Granzyme B released by aberrant decidual NK cells can reach to the fetal brain and instigate the activation of macrophages. To determine whether Gzmb can directly impact macrophages, we co-cultured murine microglial BV-2 cells with Gzmb for 20 hours, and then performed gene expression profiling analysis. We found that GzmB exposure directly induces a unique gene signature in microglia that includes the unexpected upregulation of multiple interferon-stimulated genes (ISGs).

overall_design: Murine microglial BV2 cells were stimulated for 20 hours using different treatments, including Ctrl, GZMB (500 ng/ml), amniotic fluid (AF, 50 μl), and AF (50 μl) + GZMB (500 ng/ml)

first: Qiwu


title: Addition of melanin concentration hormone and control in osteogenic differentiation of mesenchymal stem cells

city: Changsha

first: bin

last: guo

address: Xiangya street

institute: Xiangya Hospital

summary: Mice lacking melanin rich Hormone receptor will have osteoporosis, and there is MCH receptor expression on mesenchymal stem cells. In the cell experiment, we extracted bone marrow mesenchymal stem cells from mice, induced osteogenic differentiation, and added MCH for comparison with the cell control. The experimental group showed an increase in important factors such as RUNX2 for osteogenic differentiation.

overall_design:
Mesenchymal stem cells are extracted from mouse bone marrow, purified and identified, and then induced into osteogenic differentiation,
Divide into two groups and sample on the 8th day of inducing osteogenic differentiation.
Osteogenic differentiation induction solution formula: complete medium (containing 10% FBS ,89% MEM and 1% penicillin-streptomycin solution). Add to 50μM ascorbic acid, 10mM β- Glycerol phosphate and 100nM dexamethasone. Additional added to the experimental group 0.5μ M melanin concentration hormone.

first: Bin

last: Guo


title: Single-cell Sequencing of human induced pluripotent stem cells (hiPSC) during cardiac differentiation and EHM

city: Maastricht

first: Jana

last: Hegenbarth

state: Limburg

address: Universiteitssingel 50

department: Department of Molecular Genetics

institute: Maastricht University

summary: In this study, we set out to map the transcriptomes of human induced pluripotent stem cells (hiPSCs) that underwent in vitro cardiac-directed differentiation from pluripo- tency to mesodermal commitment to 2D beating heart muscle cultures and finally to 3D- engineered heart myocardium (EHM) rings at single cell resolution.

overall_design: HiPSc were differentiated into cardiomyocytes and collected at five timepoints during the differentiation process (d0, d3, d10,d25, EHM) and subjected to single-cell sequencing. Two caucasian cell lines were used to account for biological variation.

first: Jana-Charlotte

first: Federica

last: De Majo

first: Giulia

last: Spanò

first: Dena

last: Esfandyari Shahvar

first: Malte

last: Tiburcy

first: Wolfgang

last: Zimmermann

first: Monika

last: Stoll

first: Leon

last: De Windt


title: Gene expression profile of human monocyte-derived macrophage infected with mycobacterium avium infaction.

city: Kumamoto

first: Yoshihiro

last: Komohara

address: Honjo 1‐1‐1, Chuouku

department: Department of Cell Pathology

country: Japan

institute: Graduate School of Medical Sciences, Kumamoto University

summary: Macrophages infected with Micobacterium avium were also tested. The mRNA expression in control and infected macrophages were analysed.

overall_design: Macrophages (200000 cells/well in 6-well plate)  were infected with mycobacterium avium for 3 days and 7days. Based culture madium was DMEM/HamF12 medium supplemented with 10% FBS.


title: Whole-course Taming of Tumor-associated Macrophages from Central to Peripheral using Engineered Outer Membrane Vesicle Nanohybrids for Improved Immunotherapy [part 1: RNA-seq]

city: Beijing

first: Jie

last: Liang

address: beiyitiao 11, zhognguancun, beijing

institute: National Center for Nanoscience and Technology, Chinese Academy of Sciences

summary: Only regulation of tumor-associated macrophages (TAMs) in tumor microenvironment (TME) is always insufficient to achieve satisfactory clinical outcome, and training of central progenitor cells of TAMs in bone marrow is a potential approach. To achieve the whole-course taming of TAMs from central to peripheral, we developed nanohybrids containing bacterial outer membrane vesicle (OMV), GM-CSF and SIRPα-Fc fusion protein, which were coated with calcium phosphate (CaP) shell. The surface CaP coating endowed nanohybrids with safe circulation, allowing them to reach both bone marrow and TME. In bone marrow, OMV and GM-CSF together induced trained immunity of central progenitor cells, indicating by transcriptional alterations and epigenetic remodeling, which was inherited to peripheral TAMs. In peripheral TME, OMV and SIRPα-Fc triggered M1-like TAM phagocytosis with subsequent CD8+ T cell activation.

overall_design: RNA-Seq: GMPs and monocytes of 3 samples of each group were pooled when treated with PBS, OMV-SIRP, and OMV-SIRP-G. TAMs of 3 samples of each group in MC38 and B16-F10 bearing mice were pooled when treated with PBS, OMV-SIRP, and OMV-SIRP-G.

first: Xiao

last: Zhao

first: Guangjun

last: Nie


title: An MCH neuroendocrine circuit in lateral hypothalamus for bone mass regulation

first: Xiangming

last: Chen

state: Hunan

address: Xiangya Road，88

department: Department of Orthopedic

institute: Xiangya Hospital of Central South University

summary: Neuroendocrine regulation is essential for maintaining metabolic homeostasis. However, whether neuroendocrine pathway influence bone metabolism is unelucidated. Here, we identify a central neuroendocrine circuit that directly controls osteogenesis. Using virus based tracing, weidentify that melanin concentrating hormone (MCH) expressing neuronsin the lateral hypothalamus (LH) are connected to the bone.Chemogenetic activation of MCH neurons in the LH induces osteogenesis, whereas inhibiting these neurons reduces osteogenesis.Meanwhile, MCH is released into the circulation upon chemogenetic activation of these neurons. Single cell sequencing reveals that blocking MCH neurons in the LH diminishes osteogenic differentiation of bone marrow stromal cells (BMSCs). Mechanistically, MCH promotes BMSC differentiation by activating MCHR1 via PKA signaling and activating MCHR1 by MCH agonists attenuate osteoporosis in mice. By elucidating a brain-bone connection that autonomously enhances osteogenesis, these findings uncover the neuroendocrinological mechanisms governing bone mass regulation.

overall_design: Adult mice aged 6-8 weeks were anesthetized intraperitoneally using sodium pentobarbital (100 mg/kg) and gently secured to a stereotaxic frame (RWD Life Science, Shenzhen, China). A total volume of 200 nL of the virus suspension was loaded into a 1 ml-Hamilton syringe fitted with a needle made of glass electrode. The AAVs used were rAAV-hSyn-DIO-hM3D(Gq)-EGFP-WPRE-hGH polyA,rAAV-hSyn-DIO-EGFP-WPRE-hGH polyA rAAV-hSyn-DIO-hM4D(Gi)-EGFP-WPRE-hGH polyA, obtained from BrainVTA, Wuhan, China. The viral titer for all AAVs was maintained at 2.32-5.72E+12 PFU/mL. Mice(C57BL/6-Tg(Pmch-cre)1Rck/J) carrying genes specifically expressing CRE in pMCH cells come from JAXlab, The injection was performed at a rate of 20 nL/min into specific target locations (-0.58,0,-2.5 for the LH (bregma:-1.8 to -2.20 mm,lateral from midline:±1.27 to ±1.47 mm,depth:-4.55 to -4.75 mm). The surgical procedure adhered to the protocol outlined by Lowery and Majewska (reference 54). Following the surgery,a recovery period of at least 1 week was provided for the mice before commencing any experimental procedures. For chemogenetic activation and inhibition, clozapine-N-oxide (CNO) at a dosage of 1 mg/kg (MCE,34233-69-7) was administered intraperitoneally three weeks after viral expression. The injections were repeated every 48 hours for a duration of four weeks before serum and bone samples were collected for subsequent analysis. The AAV9 viruses were prepared in-house, ensuring their quality and consistency.

first: Guo

last: Bin

first: Yong

last: Zhu

first: Zhuoqun

last: Ren

first: Yuqi

last: Liu

first: Hao

last: Luo

first: Chao

first: Xucheng

last: Yang

first: Jianxi


title: Epithelial sodium channel inhibition as a targeted therapy for skin inflammation

city: Stanford

first: Marten

middle: CG

last: Winge

address: 269 Campus Dr

institute: Stanford University

summary: Inflammatory skin disease is characterized by a pathologic inflammatory interplay between skin cells and immunocytes and can result in disfiguring cutaneous lesions and systemic inflammation. Immunosuppression is often used to target the inflammatory component; however, these drugs are often expensive and associated with side effects. To identify novel targets, potentially impacting epidermal pathways, we carried out a non-biased informatics screen to identify drug entities with an inverse transcriptional signature to keratinocyte inflammatory signals. Using psoriasis, a prototypic inflammatory skin disease as model, we utilized pharmacologic, transcriptomic and proteomic characterization to find that benzamil, the benzyl derivative of the FDA-approved diuretic amiloride, effectively reversed keratinocyte-driven inflammatory signaling. Orthogonal validation across transgenic, chemically induced and xenograft models of skin inflammation indicate that benzamil perturbs pathogenic interactions between the small GTPase Rac1 and its adaptor NCK1, reduce STAT3 and NFκβ signaling and downstream cytokine production in keratinocytes. Inhibition of sodium channels prevents excess Rac1-NCK1 binding, rescues pro-inflammatory signaling pathways in patient keratinocytes without systemic immunosuppression, and can effectively be accomplished through both systemic and topical intervention. We show that small molecule inhibition of epithelial sodium channels is a potent novel therapeutic avenue for treating skin inflammation.

overall_design: To investigate the transcriptional effect of benzamil in vivo, we applied benzamil or DMSO to backand ears of imiquimod treated mice, or untreated control back skin for 6 days.

first: Leandra

middle: V

last: Jackrazi


title: TRIM24 as therapeutic target in endocrine treatment resistant breast cancer (RNA-Seq)

first: Wilbert

last: Zwart

summary: While ERα+ breast cancer treatment is considered effective, resistance to endocrine therapy is common. Since in therapy-resistance tumors, ERα is still the main driver, alternative therapeutic strategies are needed to disrupt ERα transcriptional activity. In this work, we describe TRIM24 as a key player of the ERα transcriptional complex. TRIM24 interacts with ERα and other well-known ERα-cofactors to facilitate ERα chromatin interactions, and allows for maintenance of active histone marks including H3K23ac and H3K27ac. Consequently, genetic perturbation of TRIM24 abrogates ERα-driven transcriptional programs and reduces tumor cell proliferation capacity. Using a recently-developed PROTAC targeting TRIM24, ERα-driven transcriptional output and growth was blocked, effectively treating not only endocrine-responsive cell lines, but also drug resistant derivates thereof as well as cell line models bearing activating ESR1 point mutations. Finally, using human tumor-derived organoid models, we could show efficacy of TRIM24 PROTAC in the endocrine responsive and resistant setting, with no response in ERα-negative organoids. Overall, our study positions TRIM24 as a central component for integrity and activity of the ERα transcriptional complex, with PROTAC-mediated perturbation of TRIM24 as promising therapeutic avenue in the treatment of primary and endocrine resistance breast cancer.

overall_design: RNA-seq in MCF7 TRIM24-KO (clone A and B) and NT (clone 1 and 2) cells in full-media. 3 biological replicates. RNA-seq in MCF7 WT cells treated with either 5μM of dTRIM24 (TRIM24 PROTAC, HY-111519) or vehicle (DMSO) in full-media. 3 biological replicates.

first: Nuno

last: Padrão

first: Nils

last: Eickhoff

first: Sebastian

last: Gregoricchio

first: Tesa

last: Severson

first: Joseph

last: Siefert

first: Lara

last: Luzietti

first: Leonie

last: Young

first: Maria

last: Donaldson Collier

first: Damir

last: Varešlija


title: Liver sinusoidal endothelial cells constitute a major route for hemoglobin clearance

city: Warsaw

first: Michal

last: Mikula

address: Roentgena 5

department: Experimental Oncology

country: Poland

institute: Maria Skłodowska-Curie National Research Institute of Oncology

summary: Hemolysis of senescent erythrocytes occurs in the spleen, resulting in hemoglobin (Hb) release. Several diseases are associated with an increased risk of erythrocyte rupture. Iron recycling from Hb and Hb detoxification have been attributed to the sequestration of Hb-haptoglobin complexes by macrophages, however, other routes of Hb clearance might exist. We identified liver sinusoidal endothelial cells (LSECs) as the major cell type that sequesters Hb. Hb uptake involves macropinocytosis and is independent of haptoglobin and the Hb-haptoglobin receptor CD163. LSECs expressed heme oxygenase 1 and hepcidin-controlled ferroportin and were the most efficient cellular scavengers of Hb at doses below the haptoglobin binding capacity. Erythrocyte transfusion assays demonstrated that while splenic red pulp macrophages are efficient in erytrophagocytosis, liver Kupffer cells and LSECs are primarily involved in the clearance of erythrocyte ghosts and Hb, respectively. Using time-course injections of high doses of Hb in mice, we detected transient hepatic iron retention, early induction of Hmox1 specifically in LSECs, and elevation of ferroportin levels. This was associated with transcriptional activation of LSEC Bmp6, followed by hepcidin-mediated transient hypoferremia. Injection of Hb and iron-citrate elicited distinct transcriptional signatures in LSECs and the early Bmp6 induction was phenocopied by erythrocyte lysis upon phenylhydrazine. Collectively, we propose that LSECs provide a key mechanism for Hb clearance, a function that establishes the spleen-liver axis for physiological iron recycling from Hb and contributes to heme detoxification during hemolysis, coupled with the induction of the BMP6-hepcidin axis that restores homeostasis.

overall_design: We analyzed in total 4 versus 4 RNA samples derived from FACS-sorted LSECs obtained from young female Balb/c mouse mice, intravenously injected with PBS or free hemoglobin (10 mg), respectively.

first: Gabriela

last: Zurawska

first: Zuzanna

last: Sas

first: Aneta

last: Jończy

first: Patryk

last: Slusarczyk

first: Raghunandan

last: Mahadeva

first: Marta

last: Chwałek

first: Izabela

last: Rumieńczyk

last: Kulecka

first: Kamil

last: Jastrzębski

first: Michał

first: Anders

last: Etzerodt

last: Miączyńska

first: Tomasz

last: Rygiel

first: Katarzyna

last: Mleczko-Sanecka


title: RNA sequencing profiling of circular RNA during during megakaryocyte maturation

first: Huang

last: Wu

summary: To profile the landscape of circRNAs during megakaryocyte differentiation, we conducted circRNA expression profiling analysis on day 6, day 9 and day 13.

overall_design: By day 13, CD34+ cells differentiated into mature MKs to extract total RNA. RiboMinus/RNaseR-treated RNA sequencing (RNA-seq) was performed. Total RNA from MK cultures at days 6, 9, and 13, Ribo minus RNA-seq were performed.


title: Hepatic Dyrk1b regulates systemic glucose homeostasis [mouse liver]

city: Shanghai

first: Lianju

last: Li

state: China

address: Xujiahui Road

institute: Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases

summary: Elucidation of the mechanisms controlling glucose homeostasis may deepen our understanding of the pathogenesis of T2DM and provide new therapeutic strategies for T2DM in the future. As reported, Dyrk1b is a pleiotropic protein and its genetic mutations are associated with blood glucose levels. However, the role of Dyrk1b in glucose metabolism is not well understood. Herein, we find that hepatic Dyrk1b overexpression in mice impairs the glucose tolerance and insulin resistance, whereas global Dyrk1b deficiency improves glucose metabolism of mcie. Dyrk1b overexpression in vitro blunts insulin signalling and glucose uptake. Collectively, our study uncovers a novel link between hepatic Dyrk1b and whole body glucose homeostasis.

overall_design: For better understanding of Dyrk1b’s function, RNA-seq analyses were performed on livers from C57 mice infected with adenovirus overexpressing mouse Dyrk1b (Ad-Dyrk1b) or control adenovirus (Ad-EGFP).

first: Ruixin

last: Liu

first: Jiqiu

last: Wang

first: Guang

last: Ning


title: Genes related to cell wall metabolisms are targeted by miRNAs in immature tomato fruits under drought stress

city: Bunkyo-ku

first: Tomiko

last: Asakura

state: Tokyo

department: Applied Biological Chemistry Graduate School of Agricultural and Life Sciences

institute: The University of Tokyo

type: Non-coding RNA profiling by high throughput sequencing

summary: The metabolism of tomato fruits changes when plants experience drought stress. In this study, we investigated changes in microRNA abundance and detected 32 miRNAs whose expression changes in fruit.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for normal condition and drought stress.

first: Hiroko

first: Mayui

last: Tanaka

first: Tomoko

last: Tamura

first: Yoshikazu

last: Saito

first: Takashi

last: Yamakawa

first: Keiko

last: Abe


title: Whole-course Taming of Tumor-associated Macrophages from Central to Peripheral using Engineered Outer Membrane Vesicle Nanohybrids for Improved Immunotherapy [part 2: ATAC-seq]

first: Jie

last: Liang

overall_design: ATAC-Seq: GMPs and monocytes of 3 samples of each group were pooled when treated with PBS, OMV-SIRP, and OMV-SIRP-G.

first: Xiao

last: Zhao

first: Guangjun

last: Nie


title: Transcriptome profiling of T47D cells expressing mutated forms of the receptor tyrosine kinase MET in response to HGF

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

summary: Effect of the hepatocyte growth factor (HGF) stimulation on gene expression in T47D cells expressing either MET WT, MET Exon14, MET S985A, MET V1001A or MET Y1003F.

overall_design: Comparisons of genes regulated by MET WT, MET Exon14, MET S985A, MET V1001A or MET Y1003F in response to HGF in T47D cell line.

first: Marie

last: Fernandes

first: David

last: Tulasne


title: Effect of Notch over-expression on murine liposarcoma cells

city: West Lafayette

first: Shihuan

last: Kuang

state: IN

address: 901 W State St

institute: Purdue University

summary: This RNA-seq analysis compares gene expression of a murine liposarcoma cell line with or without over-expression of Notch1 intracellular domain (NICD). The NICD overexpressing cell line (mLPS1) was derived from a corresponding mouse model that specifically express NICD in adipocytes, which leads to development of tumor resembling human dedifferentiated liposarcoma (LPS). From the mLPS1 cell line, a new cell line was derived after CRISPR-Cas9 mediated removal of the NICD expressing cassette (mLPS1-dNICD). Gene expression profiling analysis was performed on the mLPS1 and mLPS1-dNICD cells collected at three different passages.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mLPS1 cells mLPS1-dNICD cells.

first: Pei-Chieh

last: Tien

first: Xiyue

last: Chen


title: Targeting peroxiredoxin 2 prevents hepatocarcinogenesis in metabolic liver disease models

city: Strasbourg

first: Frank

last: Jühling

address: 3 Rue Koeberlé

institute: Université de Strasbourg, Inserm, Institut de Recherche sur Les Maladies Virales et Hépatiques UMR_S1110

summary: Chronic liver disease and hepatocellular carcinoma are a global health burden, causing approximately two million deaths globally per year. Treatment options for advanced liver disease are limited and strategy to prevent hepatocellular carcinoma (HCC) development are lacking. Peroxiredoxin 2 (PRDX2) PRDX2 is a soluble cellular enzyme that detoxify peroxides generated during oxidative stress. This protein is involved in the control of various physiological process including cell growth and differentiation by regulating numerous signaling pathways. PRDX2 was also reported to promote tumor growth including colorectal and breast cancers. Since its role in liver disease progression and HCC development is unknown, we therefore further explored the role of PRDX2. This study aims to understand the mechanistic events of Prdx2 KO on the cell circuits driving metabolic liver disease progression and HCC development. We induced a liver-specific Prdx2 KO in a Cas9 transgenic mouse model for NASH and HCC. Prdx2 gene was specifically targeted in hepatocytes by combining a Cre-dependent expression of the Cas9 endonuclease in the liver and the hepatic delivery of specific single guide (sg) RNA to hepatocytes using Adeno-associated virus 8 (AAV8) as vector. Chronic liver disease and HCC were thereafter induced by a single dose of diethylnitrosamine (DEN), followed by a 6-month choline-deficient L-amino acid-defined high-fat diet (CDAHFD). At the time of sacrifice, animals were anesthetized, weighted and a terminal blood collection was performed by cardiac puncture. Total RNA from mice liver were obtained using Tri Reagent (MRC) and Direct-zol RNA Miniprep kit (Zymo Research).

overall_design: Three biological replicates per mice group (sgCTRL, sgPrdx2). mRNA was isolated individually from each replicate. Three biological replicates from each mice group were sequenced and analyzed.

first: Emilie

last: Crouchet

first: Eugénie

last: Schaeffer

first: Laurent

last: Mailly


title: CUT&Tag of R-loops in Ube2t knockdown P19 cells

city: Jinan

first: Yongze

last: Yu

email: lwyyzsdu@163.com, lwyyzsdu@hotmail.com

state: Shandong

address: 文化西路44号国家辅助生殖与优生工程技术研究中心

institute: Shandong University

summary: DNA sequencing of libraries from CUT&Tag with R-loops antibody (S9.6) in Ube2t knockdown and control P19 cells

overall_design: To understand the role of UBE2T in resolving R-loops. Mouse P19 cells were used. Two kinds of Ube2t knockdown adenovirus were used. No antibody group was regarded as control sample.

first: Shidou

first: Yajuan

last: Yang

first: Weiwei

last: Xu


title: MNN45 is involved in Zcf31-mediated cell surface integrity and chitosan susceptibility in Candida albicans

city: Taipei

first: Ching-Hsuan

last: Lin

state: Taiwan

address: National Taiwan University, 1 Roosevelt Rd. Sec. 4

department: Department of Biochemical Science and Technology

country: Taiwan

institute: National Taiwan University

summary: To explore why zcf31Δ cells exhibited thicker cell wall, RNA sequencing was performed. By pairwise analysis, a total of 123 genes were differentially expressed between the wild-type (WT) and zcf31Δ strains based on the selection criteria of two-fold change in expression (Log2 fold change > 1 or < -1, P < 0.05). Among these, 55 and 68 genes were significantly upregulated and downregulated, respectively. GO Enrichment analysis showed these transcripts were mainly involved cell wall, cell membrane, cell adhesion and glycosyl transferase activity.

overall_design: Total mRNA extracted from wild-type (WT) and zcf31Δ strains was analyzed using RNA sequencing.

first: Hao-Sen

last: Chiang

first: Ji-Hong


title: Analysis on the transcriptomic profile in the mouse cerebellum with LINE-1 overexpression

city: New Haven

first: Takehiro

last: Takahashi

state: Connecticut

address: 300 Cedar Street TAC S630

institute: Yale University

summary: We report the transcriptomic profile of the cerebella of the mice in which a class of endogenous retroelements long interspersed nuclear elements-1 (LINE-1) is overexpressed with CRISPR-a modules targeting the promoter sequence of evolutionally young LINE-1 family. Transgenic mice for guide RNA targeting the LINE-1 promoter sequence were generated, crossed with another transgenic mice for dCas9-CRISPR-a module. The double transgenic mice presented with strong cerebellar ataxia phenotype as well as robust overexpression of LINE-1 in the cerebellum. The result of transcriptomic profiling of the cerebella in these mice showed close similarities of the dysregulated gene profiles in human cerebellar ataxia patients’ cerebella, suggesting the usefulness of these mice in the studies of the etiopathogenesis of human cerebellar ataxia.

overall_design: Analysis on the RNA expression profile in the cerebellum of 8-wk-old mice in which LINE-1 is activated (LINE-1a mice) and of control mice (dCas mice).

first: Eric

last: Song

first: Yong

last: Kong


title: Formation of an active epigenetic mark and its recycling is mediated by cell cycle-specific RNAs [RIP-seq]

city: Boston

first: Annalisa

last: Di Ruscio

address: 3 Blackfan Circle, Center of Life Science, Room 407

institute: Beth Israel Deaconess Medical Center, Harvard Medical School

summary: The mechanisms by which epigenetic modifications are established in gene regulatory regions of active genes remain elusive. The data presented show that the establishment and recycling of a major epigenetic mark, the acetylated form of the replacement histone H2A.Z, is regulated by cell cycle-specific long noncoding RNAs encoded in regions adjacent to the promoters of active genes. These transcripts, termed SPEARs (S Phase EArly RNAs), are induced in early S phase: their expression precedes that of the downstream genes on which they exert their regulatory action. SPEARs drive the modification and deposition of the acetylated form of histone H2A.Z by bringing together the replacement histone and the histone acetyl transferase TIP60. This widespread bimodal pathway constitutes a novel RNA-mediated mechanism for the establishment of epigenetic marks and cell-specific epigenetic profiles, thereby providing a unifying explanation for the accuracy and persistence of epigenetic marks on chromatin.

overall_design: All samples were done using the cell line HL-60. 1 replicate each.  RIP-Sequencing targetting acH2A.Z, H2A.Z and TIP60 with corresponding input.  RNA-Sequencing on nuclear extract, nuclear-extracts synchronized at S-Phase and nascent nuclear-extracts synchronized at S-Phase.  ChIP-Seq was performed targeting the acH2A.Z and H2A.Z histone marks with cells treated with DMSO, ACTD and DRB with appropriate controls.

first: Alexander

middle: K

last: Ebralidze

first: Simone

last: Ummarino

first: Emanuele

last: Monteleone

first: Daniel

middle: G

last: Tenen


title: Identification of key developmental genes regulated by ALX1 in human isogenic PSC model

last: Liao

state: MA

address: CRMT, Simches Research Center, CPZN 4400, 185 Cambridge Street

institute: MGH

summary: To identify the key developmental genes regulated by ALX1 in the neural crest cell stage, we establsihed isogenic PSC lines with different ALX1 genotype (patient-specific missense mutation, large deletion or control/wild-type). We then performed gene expression profiling analysis using data obtained from RNA-seq of cells of 3 different genotypes at PSC stage and NCC stage

overall_design: Comparative gene expression profiling analysis of RNA-seq data for H9 cells with different ALX1 genotype (knock-in, knock-out, and control).

first: Pan

last: Yeung

first: Casey

last: Tsimbal

first: Kenta

last: Kawasaki

first: Christopher

last: Stoddard

first: Yevgenya

last: Grinblat

first: Justin

last: Cotney


title: Formation of an active epigenetic mark and its recycling is mediated by cell cycle-specific RNAs

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

overall_design: Refer to individual Series


title: Formation of an active epigenetic mark and its recycling is mediated by cell cycle-specific RNAs [RNA-seq]


title: Effect of PFKFB3 overexpression on A549 in VSV infection.

city: Su Zhou

first: Shiyou

last: Wang

state: Jiang Su

address: Chong Wen street

department: Suzhou Institute of Systems Medicine

institute: Peking Union Medical College

summary: To investigate the function PFKFB3 in RNA virus infection, we established PFKFB3 overexpressed A549 cell lines and infected cells with VSV.

overall_design: PFKFB3 overexpressed A549 were established and infected by VSV.

first: Haijuan

last: Jiang

first: Lifen

last: Xie

first: Siying

last: Liu


title: Plasma transcriptome profile in patients with mild traumatic brain injury

first: Yen-Sung

last: Huang

address: Academia Sinica, No.128, Sec2,

department: Institute of Biomedical Sciences

institute: Academia Sinica

summary: Using next-generation sequencing (NGS) to identify plasma RNA biomarker in patients with mild traumatic brain injury.

overall_design: Identification of the plasma transcriptome profile in 3 patients with mild traumatic brain injury

first: Yen

first: Kai

last: Chen

first: Yung

last: Chiang


title: Transcriptome analysis of liver cirrhosis

city: kunming

first: Xiao

last: Kuang

state: yunnan

address: 374 Dianmian Avenue, Kunming, Yunnan

institute: The Second Affiliated Hospital of Kunming Medical University

summary: Liver cirrhosis is one of the leading causes of decreased life expectancy worldwide. However, the molecular mechanisms underlying the development of liver cirrhosis remain unclear. In this study, we performed a comprehensive analysis using transcriptome sequencing to explore the genes, pathways, and interactions associated with liver cirrhosis. We performed transcriptome sequencing of blood samples from patients with cirrhosis and healthy controls (1:1 matched for sex and age). For transcriptome analysis, we screened for differentially expressed miRNAs and mRNAs, analyzed mRNAs to identify possible core genes and pathways, and performed co-analysis of miRNA and mRNA sequencing results. And we validated differentially expressed microRNA (miRNA) and mRNAs using real-time quantitative polymerase chain reaction. Using a systems biology framework, We identified miRNAs and mRNAs that were differentially expressed in the blood of cirrhotic patients and healthy controls. And explored associated pathways as well as disease-specific networks.

overall_design: In this study, we screened for differentially expressed genes using microRNA (miRNA) and mRNA sequencing of blood samples from patients with cirrhosis and healthy controls (1:1 matched for sex and age) and analyzed them using bioinformatics tools. Pathways and key biomarkers associated with cirrhosis were identified and their relationship with the disease was investigated.

first: Wenlin

last: Tai


title: Transcriptome of PBMC from Zika virus patient

summary: To investigate the transcriptome change in Zika virus infection, PBMCs of patient who was infected with Zika virus in Guangzhou were collected and sequenced.

overall_design: PBMCs of patient who was infected with Zika virus in Guangzhou at 3 days, 7 days, 10  days, 1 month and 3 months post infection were collected and sequenced.


title: The CTCF paralog CTCFL disrupts cohesin at active promoters.

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

country: United Kingdom

institute: MRC London Institute of Medical Sciences


title: Single-cell RNA sequencing of Medicago truncatula roots after exposure to Ensifer meliloti (formerly Sinorhizobium meliloti)

city: Gainesville

first: Matias

last: Kirst

address: 367 Newins-Ziegler Hall, PO Box 110410

institute: University of Florida

summary: Single-cell RNA sequencing of Medicago truncatula roots was generated from nuclei using the 10X Genomics' Chromium technology. Roots were harvested and processed 24h after exposure to Ensifer meliloti (formerly Sinorhizobium meliloti).

overall_design: Two independent experimental replicates were analyzed. Each replicate consisted of nuclei extracted from a pool of ~ 150 root segments exposed to Ensifer meliloti for 24 hrs. Each replicate was sequenced two times.

first: Daniel

last: Conde

first: Paolo

last: Triozzi

first: Wendell

last: Pereira

first: Kelly

last: Balmant

first: Henry

last: Schmidt

first: Thomas

middle: B

last: Irving

first: Sanhita

last: Chakraborty

first: Sara

middle: A

last: Knaack

first: Sushmita

last: Roy

last: Dervinis

first: Jean-Michel

last: Ané


title: The CTCF paralog CTCFL disrupts cohesin at active promoters. [mouse]

summary:
Analysis of gene expression changes in mouse ES cells expressing FLAG-CTCFL
There are 6 samples. 3 control Vector mouse ES cells biological replicas and 3 FLAG-CTCFL ES cells biological replicas.

overall_design: ES cells transfected with a vector expressing FLAG-CTCFL or Control Vector were grown in serum containing medium. Three biological replicates of each condition were collected and RNA was extracted. Microarray samples were prepared following the manufacturers instructions (Affymetrix) using 200ng of total RNA. Microarry samples were hybridized to Affymetrix GeneChip Mouse Gene 1.0 ST Arrays

first: Hegias

last: Mira-Bontenbal

first: André

last: Faure

first: Matthias

last: Merkenschlager


title: Formation of an active epigenetic mark and its recycling is mediated by cell cycle-specific RNAs [ChIP-seq]

first: Annalisa

last: Di Ruscio

first: Alexander

last: Ebralidze

first: Simone

last: Ummarino

first: Emanuele

last: Monteleone

last: Tenen


title: Sodium taurocholate co-transporting polypeptide deficiency attenuates hepatocarcinogenesis in mice

first: Wenhui

last: Li

address: 7 Science Park Road ZGC Life Science Park

institute: National Institute of Biological Sciences

summary: Sodium taurocholate co-transporting polypeptide (NTCP) is a liver specific bile acid (BA) transporter; this transporter also serves as a functional receptor for hepatitis B virus (HBV) and hepatitis D virus (HDV). Here, we generated mouse models to investigate the role of NTCP in hepatocarcinogenesis. We report that NTCP-deficient (Slc10a1-/-) mice with long-term hypercholanemia do not develop spontaneous hepatocellular carcinoma (HCC). Using a diethylnitrosamine (DEN)-induced mouse model of HCC, we found that Slc10a1-/- mice exhibited fewer liver tumors, while transgenic mice constitutively overexpressing mouse NTCP in hepatocytes Tg(mNTCP-C9) experienced increased tumor burdens. Intriguingly, the subset of male Slc10a1-/- mice with hypercholanemia exhibited a hepatic female-biased gene expression. Importantly, a majority of the human homologs of genes with significantly hepatic female-biased expression were found to be correlated with improved prognosis in human patients with liver cancer. Our ﬁndings indicate that pharmacological manipulation of NTCP function can have a clinical impact on decreasing risk of development or decreasing risk of death liver cancer.

overall_design: Methods: Liver mRNA profiles of 8-week old male and female wild-type (WT) and sodium taurocholate cotransporting polypeptide knockout (Slc10a1-/-) mice (2-6 replicates respectively), and 6-month-old male WT and Tg(mNTCP-C9) (5 replicates respectively) were generated respectively by deep sequencing using Illumina Hiseq-2500 platform.

first: Hanqing

last: Zhao


title: PIWIL2 downregulation in colon cancer promotes transposon activity and pro-tumorigenic phenotypes

status: Public on Jul 31 2025

city: Charleston

first: Antonis

last: Kourtidis

state: SC

address: 173 Ashley Avenue

department: Regenerative Medicine and Cell Biology

institute: Medical University of South Carolina

summary: Reactivation of transposable elements (TEs) in somatic tissues, particularly of LINE-1, is associated with disease by causing gene mutations and DNA damage. Previous work has shown that the PIWI pathway is crucial for TE suppression in the germline. However, the status and function of this pathway is not well characterized in differentiated somatic cells and there is lack of consensus on the role of the pathway in somatic tumorigenesis. To shed light on this conundrum, we examined the PIWI pathway in colon cancer through combining bioinformatic analyses and cell-based assays. Shifted Weighted Annotation Network (SWAN) analysis revealed that the pathway experiences significant allelic losses in colon cancer and that PIWIL2, the main catalytic component of the pathway responsible for TE silencing, experiences the highest percent deletions. PIWIL2 is downregulated in colon tumors of advanced stage, nodal metastasis, and in certain subtypes, correlating with poor survival, while it is also downregulated in ulcerative colitis, an inflammatory bowel disease that predisposes to colon cancer. PIWIL2 depletion in colon epithelial Caco2 cells leads to increased anchorage-independent growth, loss of transposon-targeting - non-canonical - piRNAs, increased LINE-1 levels and activity, and in DNA damage, altogether highlighting a tumor-suppressing role of PIWIL2 in the colon.

overall_design:
Caco2 wild type cells and Caco2 cells with a CRISPR/Cas9 - mediated PIWIL2 knckout were grown to confluency and RNA was isolated by adding 1ml of Trizol (Invitrogen # 15596018), incubating the sample at RT for 5 minutes then using the PureLink RNA mini kit (Invitrogen #12183018A) for total RNA, using the whole transcriptome protocol of the kit. Final RNA concentrations and purity were determined by using a NanoDrop spectrophotometer.  short RNA sequencing was performed using the NovaSeq SE50 strategy. Sequenced reads were first processed using Cutadapt (v1.15) to trim the 3′ adapter sequence (5′-AGATCGGAAGAGCACACGTCT-3′). Adapter-trimmed reads were analyzed using the piPipes small RNA pipeline to quantify transposon-mapped reads and normalize sense and antisense counts as counts per million (CPM) uniquely mapped to the hg19 genome(Han et al., 2015b). In parallel, reads were aligned to Repbase and known piRNA clusters using Bowtie2(Langmead and Salzberg, 2012, Langmead et al., 2019) and only successfully aligned reads were retained. These reads were then assessed for size distribution and 5′ nucleotide signature using the TBr2_basicanalyses.pl script (Rosenkranz et al., 2015).
smallRNA-Seq

first: Alyssa

last: Risner

first: Vamsi

last: Gangaraju


title: The CTCF paralog CTCFL disrupts cohesin at active promoters. [human]

first: Gopuraja

last: Dharmalingam

summary:
Analysis of gene expression changes in human K562 cells depleted of hCTCFL
There are 6 samples. 3 control K562 cells biological replicas and 3 K562 depleted of CTCFL by siRNA biological replicas.

overall_design: K562 cells were transfected with siRNAs targeting hCTCFL or contro siRNAs.  Three biological replicates of each condition were collected and RNA was extracted.  Microarray samples were prepared following the manufacturers instructions (Affymetrix) using 200ng of total RNA. Microarry samples were hybridized to Affymetrix GeneChip Human Gene 1.0 ST Arrays


title: Memory-like T cells emerge early in circulation after gene therapy for SCID-X1 [Bisulfite-Seq]

city: Memphis

first: Tian

last: Mi

address: 262 Danny Thomas Pl MS351

department: Immunology

institute: St. Jude Children's Research Hospital

type: Methylation profiling by high throughput sequencing

summary: Studying the emerging immune system after successful gene therapy for X-linked severe combined immunodeficiency (SCID-X1) in infants provides a unique opportunity to characterize human T cell development. Here we report our longitudinal analysis of T cells isolated from the peripheral blood of SCID-X1 patients after treatment with gene-transduced autologous CD34+ cells. We observed an early enrichment of memory-like T cells, which was intriguing given that newly generated T cells were unlikely to have previously encountered their cognate antigen. Single-cell RNA sequencing of the emerging and established T cell pool identified a subset of memory-like cells enriched for NKG2A expression that contained innate-associated transcriptional profiles. Genome-wide epigenetic profiling of the de novo memory-like NKG2A+ T cell subset confirmed an epigenetic permissivity of this locus along with programs indicating a poised effector response. Consistent with the epigenetic profile, ex vivo stimulation of NKG2A+ T cells with IL-12 and IL-18 resulted in antigen-independent IFNg expression. Collectively, these data suggest that NKG2A+ innate memory-like T cells develop early in human life and are epigenetically poised to rapidly elicit effector cytokines in an antigen-independent manner.

overall_design: 2 replicates of SCID NKG2Apos samples, 2 replicates of SCID NKG2Aneg samples, 1 replicate of HD NKG2Apos sample, 1 replicate of HD NKG2Aneg sample

first: Anoop

last: Vasandan

first: Hossam

last: Abdelsamed

first: Shannon

last: Boi

first: Caitlin

last: Zebley

first: Ben

last: Youngblood


title: Restoring Taxane Efficacy in Castration Resistant Prostate Cancer Through Targeting Menin

city: Istanbul

first: Hamzah

last: Syed

address: Rumelifeneri Yolu

department: School of Medicine

country: Turkey

institute: Koç University

summary: Prostate cancer (PC) typically depends on hormones for growth, with androgen deprivation therapy (ADT) serving as the primary treatment. However, many patients progress to a castration-resistant (CR) stage, where their tumor becomes unresponsive to ADT. Despite the common use of conventional chemotherapeutics like taxanes (docetaxel, cabazitaxel), the majority of patients experience recurrence. To uncover the mechanisms underlying the drug-resistant phenotype, we developed docetaxel-resistant CRPC cell lines, and  through a drug library screen, we identified MLL-Menin and MLL-WDR5 inhibitors that overcome taxane resistance and significantly induced G2/M arrest and apoptosis. To determine the roles of individual proteins in the MLL complexes, we silenced several MLL partner proteins , and the absence of Menin and LEDGF particularly halted the growth of the resistant cells while showing no significant effect on parentals. Notably, parental cells with Menin silencing failed to develop resistance even after prolonged exposure, unlike their Menin-expressing counterparts, highlighting the critical role of Menin in the resistance process. Menin knockouts were analyzed through RNA-sequencing, and several gene sets, including E2F targets, G2/M checkpoints, and mTORC1 pathways, were found to be negatively regulated in taxane-resistant cells. The ablation of Menin led to a reduction in mTOR levels, and ChIP-qPCR analysis confirmed that Menin was enriched on the mTOR promoter. According to TCGA clinical data, the correlation between MEN1 and mTOR became stronger as the disease advanced to metastatic stages. Furthermore, the combination of the mTOR inhibitor Torin1 and docetaxel enhanced the sensitivity of our resistant cells. Menin deficiency reduced cell proliferation and key expression of cell cycle genes (Cyclin D1, CDK20). Rescue experiments reversed these effects, and Menin showed significant enrichment of the Cyclin D1 and CDK20 promoters. Finally, Menin loss impaired docetaxel resistant CRPC growth in our in vivo model. Our data demonstrate the essentiality of Menin for docetaxel resistance and suggest a combined approach targeting both Menin and mTOR to improve taxane therapy responses. Additionally, Menin regulates some key cell cycle genes to promote the G1/S transition, emphasizing its critical role in cell cycle regulation and the growth of taxane-resistant CRPC.

overall_design: To understand the molecular mechanisms underlying Menin-mediated inhibition in taxane-resistant CRPC, we aimed to analyze the transcriptome of Du145-P and Du145-DtxR cells following Menin knockout.  We conducted gene expression profiling using RNA-seq data from both non-target guided and Menin-guided Du145-P and Du145-DtxR cells.

first: Ipek

last: Bulut

first: Buse

last: Cevatemre

first: Neslihan

last: Yuksel-Catal

first: Tamer

middle: T

last: Onder

first: Ceyda

last: Acilan


title: Memory-like T cells emerge early in circulation after gene therapy for SCID-X1 [scRNA-seq]

overall_design: 3 replicates of 14 week CD3 T cells, 4 replicates of 12 month CD3 T cells