title: Macrophage-derived IL-1β controls metabolic reprograming in distinct fibroblast progenitors to determine cell fate during wound healing

city: ChangChun

first: Zhengwen

last: An

state: JiLin

address: HeGuang Road 763

department: Department of Oral Biology

institute: Jilin University

summary: Compare with facial skin, oral mucosa has a high regenerative capacity and rapid healing efficiency, which has long been recognized as an ideal system of wound resolution. To decipher the underlying molecular mechanisms fostering this optimal healing process, we created a parallel injury model for both the oral and facial skin within the same mice. Utilizing single-cell transcriptomics (scRNA-seq) analysis, we were able to illuminate the diverse cell populations and the intricate cell-to-cell interactions taking place at a single cell level. Leveraging tools such as CytoTRACE, along with cell trajectory and RNA velocity analyses, we pinpointed fibroblast progenitors. Through the employment of GSEA and CellChat analyses, corroborated by flow cytometry and immunofluorescence staining, we demonstrated that IL-1β derived from macrophages augments oxidative phosphorylation in Il1rl1+ progenitors in skin. This points to a rapid response mechanism facilitated by heightened cell-cell interactions through IL-1β signals. We elucidated that the underlying mechanism involves a metabolic reprogramming in oral Il1rl1+ fibroblast progenitors driven by IL-1β/IL1R1, triggering the activation of the NFκB signaling pathway. This shift transitions the metabolic state from glycolysis to oxidative phosphorylation, favoring stem cell differentiation over proliferation and consequently accelerating wound healing in the oral mucosa.

overall_design: WT mice (n=5, 6~8 weeks) were anesthetized via intramuscular injection and the wound was inflicted using a 1.5 mm punch biopsy (Miltex, York, Inc. PA, USA) in the buccal mucosa, with the same size wounds created in the facial skin of the same mouse. At 48h after injury, the oral mucosa and skin wounds were harvested by 3.0 mm punch biopsy for scRNAseq analyse.

first: Huanyu

last: Luo

first: Xiaoyi

last: Yu

first: Hongchen

last: Sun


title: Novel ovarian cancer PD-1+ NK cell subsets, targetable by combined immune-checkpoint blockade

status: Public on Sep 03 2025

city: Genoa

first: Matteo

last: Bozzo

address: Viale Benedetto XV, 5

department: Department of Earth, Environmental and Life Sciences

country: Italy

institute: University of Genoa

type: Expression profiling by high throughput sequencing

summary: Ovarian cancer (OC) is the fifth leading cause of cancer-related death and High-Grade Serous Ovarian Carcinoma (HGSOC) is its most common histotype. Current therapies are ineffective, and most patients develop a recurrence within a few years. Moreover, if outstanding results can be obtained with immune-checkpoint blockade strategies (mainly PD-1/PD-L axis) in immunotherapeutic protocols for several aggressive tumors, clinical trials didn’t show good results with HGSOC patients so far. Here we analysed, by multiparametric flow cytometry, NK cells derived from peripheral blood, peritoneal fluid, tumor tissue, and metastatic tissue of a large cohort of HGSOC patients, in order to define how NK cells could be leveraged to improve HGSOC immunotherapy. We identified new PD-1+NK subsets occurring in HGSOC patients, but absent in healthy donors, characterized by a CD56dimNKG2A+KIR+/-NKp46+CD57low phenotype and ineffective anti-tumor response against autologous HGSOC cells. This impairment could be rescued by treatment with a combination of anti-PD-1/PD-Ls, NKG2A, and KIRs mAbs. PD-1+ NK cells were enriched in the metastatic niche and high levels of tumor-infiltrating PD-1+ NK cells correlate with a worse outcome, suggesting a role for PD-1 in metastatic promotion/progression. Our data demonstrate the existence of novel tumor-infiltrating PD-1+ NK cell subsets in HGSOC patients, which are inversely related to patient outcome, showing the importance of these NK subsets. These subsets show indeed impaired anti-tumor activity, which can be rescued by combined ICs blockade, paving the way for more successful NK cell-based immunotherapy in OC patients.

overall_design: We performed RNAseq analysis of subsets of NK cells (both PD-1+ and PD-1-) purified by FACS from three female healthy donors and two High-Grade Serous Ovarian Carcinoma (HGSOC) patients.

first: Marco

last: Greppi

first: Silvia

last: Pesce

first: Patrizio

last: Castagnola

first: Simona

last: Candiani

first: Emanuela

last: Marcenaro


title: Loss of the lipid transfer protein STARD7 triggers metabolic reprogramming and an epigenetic-mediated cell cycle arrest in breast cancer

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

country: Belgium

institute: University of Liège

summary: Cancer cells have to constantly adapt their metabolism to support aberrant cell proliferation. However, the functional link between metabolic reprogramming and cell cycle progression remain largely unexplored. Mitochondria rely on the transfer of multiple lipids from the endoplasmic reticulum (ER) to their membranes to be functional. Several mitochondrial-derived metabolites influence cancer cell proliferation by modulating the epigenome. Here we show that the loss of STARD7, a lipid transfer protein whose expression is enhanced in breast cancer, leads to a profound metabolic reprogramming characterized by the increased synthesis of Carnitine derivatives and S-Adenosyl-L-methionine (SAM). Elevated SAM levels causes the accumulation of H3K27 trimethylation, a repressive mark, on many gene promoters coding for candidates involved in cell cycle progression and in the response to oxidative stress. As a result, STARD7 deficiency triggers cell cycle arrest, at least through defective ERa- and EGFR-dependent signaling pathways as well as to autophagy and ciliogenesis. Collectively, our data define STARD7 as a critical candidate involved in cell cycle progression in breast cancer.

overall_design: RNAseq for 3 different conditions, one shCtrl and two different shSTAR7 KD derivatives. All conditions are in triplicates.

first: Ewelina

last: Dondajewska

first: Kateryna

last: Shostak

first: Alain

last: Chariot


title: The miRNA cargos and roles of small extracellular vesicles from cochlear explants in a model of cisplatin-induced ototoxicity

city: Nanjing

first: Jingru

last: Ai

state: Jiangsu

address: No. 2, Sipai Lou, Xuanwu District, Nanjing 210096, China.

country: China

institute: Southeast University

type: Non-coding RNA profiling by high throughput sequencing

summary: Small extracellular vesicles (sEVs) play an important role in intercellular communication as well as pathological development. To explore the roles of sEVs in the progression of cisplatin-induced ototoxicity, we isolated sEVs from the conditioned culture medium of cisplatin-induced cochlear explants (Cis-sEVs) and the control group (Ctrl-sEVs) and profiled their miRNA cargos using small RNA sequencing

overall_design: The cochlear explants treated with 50 μM cisplatin or an equal volume of PBS for 48 h were used to build an ex vivo cisplatin-induced ototoxicity model.The sEV-free FBS medium was used to culture the cochlear explants. The conditioned culture supernatant was collected and stored at 4℃, and sEVs were isolated from the supernatant within one week.To explore the differentiation of miRNA molecular profiles between the Cis-sEV and Ctrl-sEV groups, small RNA-seq analysis was performed with three biological replicates in each group. The sEVs isolated from around 80 cochlear explants from each sample were used for small RNA sequencing.

first: Shasha

last: Zhang

first: Mingchen

last: Dai

first: Pei

last: Jiang

first: Jingyuan

last: Huang

first: Hairong

last: Xiao

first: Meiling

first: Yanqin

last: Lin

first: Yintao

last: Wang

first: Xujun

last: Tang

first: Wei

last: Tong

first: Renjie

last: Chai


title: 5-HT6R-ATR-Primary Cilia Network Supports Memory Extinction

city: Xi'an

first: Junlin

last: Liu

address: No. 76 Yanta West Road

institute: Xian Jiaotong University

summary: Drug addiction represents a pathological form of learning and memory with profound implications for individuals and society. The serotonin receptor 5-HT6R, uniquely expressed on primary cilia, is associated with neurological development, cognitive impairments, emotional disorders, and reward memory for cocaine and nicotine. However, its role in morphine-related reward memory remains unclear. This study demonstrated that 5-HT6R expression was downregulated during the early stage of morphine-induced conditioned place preference (CPP) extinction but returned to baseline levels later, with no significant changes observed during CPP establishment or reinstatement. Knocking down 5-HT6R accelerated CPP extinction, while overexpression prolonged the process. Furthermore, primary cilia defects within the mPFC were noted during the early stage of CPP extinction, and the removal of primary cilia expedited this process. Finally, ATR was identified as a novel target molecule of 5-HT6R, and the 5-HT6R-ATR-primary cilia network was found to regulate morphine-induced CPP extinction, offering new insights for opioid addiction therapy.

overall_design: Toidentify potential targets resulting from the downregulation of 5-HT6R and mechanistic pathways involved in the extinction of morphine-induced CPP

first: Chunxia

last: Yan


title: Transcriptional analysis of the impact of BMPR2 loss and BMP9 treatment on pulmonary artery endothelial cells

city: Kingston

first: Mark

middle: L.

last: Ormiston

state: Ontario

address: 18 Stuart Street

country: Canada

institute: Queen's University

summary: Pulmonary arterial hypertension (PAH) is a disease of the pulmonary endothelium associated with mutations in BMPR2, the gene encoding the bone morphogenetic protein (BMP) type II receptor (BMPR-II). Loss of BMPR-II in the pulmonary endothelium has been shown to alter the functional response of the endothelium to BMP9 treatment from growth suppression in healthy cells, to hyperproliferation with the loss of BMPR-II. To investigate the molecular mechanisms underlying this phenotypic switch, we performed RNA sequencing on total RNA isolated from primary human pulmonary artery endothelial cells treated with or without BMP9 following BMPR2 knockdown or control.

overall_design: To investigate the role of BMPR2 loss and BMP9 treatment in the pulmonary endothelium, primary human pulmonary artery endothelial cells (HPAECs) were treated with or without 1ng/mL of BMP9 for 24 hours following the siRNA mediated knockdown of BMPR2 or control siRNA treatment.

middle: L


title: Circular RNA profiling identifies circ5078 as a BMPR2-derived regulator of endothelial translation

summary: Germline loss-of-function BMPR2 mutations are the leading genetic cause of pulmonary arterial hypertension (PAH) and are strongly linked to aberrant endothelial proliferation and impaired translational stress responses. While these effects are generally attributed to a loss of the type-II bone morphogenetic protein receptor (BMPR-II), we used circular RNA profiling to identify circ5078, a BMPR2-derived circular RNA that regulates endothelial translation and cellular phenotype. circ5078 and linear BMPR2 mRNA exert opposing effects on endothelial proliferation and stress granule formation, while influencing the translational efficiency of multiple genes by regulating ribosome assembly and translational initiation. In PAH patient-derived endothelial cells lacking linear BMPR2 mRNA, circ5078 depletion rescued impaired translational stress responses by rebalancing circular to linear transcript levels, independent of BMPR-II protein. By identifying circ5078 as a functional BMPR2 gene product, this work reveals interdependent roles for both linear and circular BMPR2 transcripts as regulators endothelial translation and proliferation

overall_design: To investigate the role of BMPR2 derived RNAs on endothelial translation, primary pulmonary artery endothelial cells were treated with siControl, siLinear, si5078 or siLinear+5078. Lysates from these cells were separated on 10-45% sucrose gradients, and equal volumes of RNA from fractions 8-13 were pooled and sequenced, alongside samples representing the total input to sucrose gradients.

first: M

middle: M

last: VandenBroek

first: Mackenzie

middle: C

last: Sharp

first: Patrick

last: Thompson

first: Emmanuel

last: Fagbola

first: Douglas

last: Quilty

first: Jeffrey

middle: D

last: Mewburn

first: Anne

last: Theilmann

first: Stephen

last: Archer

first: Neil

last: Renwick


title: Ascites extracellular vesicle microRNA profiles of platinum-resistant high-grade serous ovarian carcinoma

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

country: Japan

institute: Nagoya University

summary: Ovarian cancer is one of the leading causes of death in females in the world. High-grade serous ovarian carcinoma (HGSOC) is the most common histological subtype, and the platinum-resistance is a clinical challenge. HGSOC frequently spreads to the peritoneal cavity and causes carcinomatous peritonitis. Extracellular vesicles (EVs) are lipid-bilayer nanoparticles containing various bioactive molecules. Thus, EVs mediate cell-to-cell communication and contribute to cancer progression. Moreover, EVs stably exist in the body fluid, including serum and ascites. This study investigated the ascites EV miRNA profiles of platinum-resistant and platinum-sensitive HGSOC.

overall_design: Archival fresh frozen ascites samples at the Hyogo Prefectural Cancer Center Biobank were used for analysis. Ascites-derived EVs were purified using the ultracentrifuge, and total RNA was extracted. Then, small RNA libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA). Finally, single-end reads were performed on the Illumina NextSeq.

first: Kazuhiro

last: Suzuki

first: Akira

last: Yokoi


title: Nuclear receptor coregulator NRIP1 R448G modulates T cell gut-homing and Teff:Treg balance to control intestinal inflammation [scRNA-seq]

city: Cambridge

first: Ramnik

last: Xavier

state: MA

address: 415 Main Street

country: USA

institute: Broad Institute of MIT and Harvard

summary: Nuclear receptors (NRs) are crucial to integrate metabolite sensing and immune responses in the gut. Nuclear receptor-interacting protein 1 (NRIP1) is an important coregulator of various NRs that has been implicated in inflammatory bowel disease risk, but mechanistic details of how NRIP1 controls NR activities mediating immune homeostasis and inflammation remain elusive. We unveil pleiotropic functions of NRIP1 in distinct CD4+ T cell subsets during intestinal inflammation. We demonstrate that a coding risk variant, NRIP1 R448G, promotes activated CD4+ T cell gut homing and inflammatory cytokine production but impairs regulatory T cell  stability, ultimately leading to exacerbated intestinal inflammation. Mechanistically, NRIP1 acts as a corepressor in retinoic acid signaling by modulating VDR (vitamin D receptor) expression and BATF (Basic leucine zipper transcription factor, ATF-like) activity. Our study reveals the impacts of NRIP1 on CD4+ T cells in immune regulation during intestinal inflammation, providing insights into mechanisms by which an NR coregulator controls immune homeostasis and tissue inflammation.

overall_design: Mouse splenic naïve CD4+ T cells were purified using EasySep™ Mouse Naïve CD4+ T Cell Isolation Kit (STEMCELL). Cells were then stimulated by plates coated with 2μg/ml anti-mouse CD3e and 2μg/ml anti-mouse CD28 antibodies, with or without 100nM atRA supplement in full RPMI 1640 medium. Cells were harvested on day 3 and submitted for 10x genomics single-cell multiome sequencing.

first: Xiangjun

last: Chen

first: HeeSeung

last: Hwang

first: Lingjia

last: Kong

first: Orr

last: Ashenberg

first: Elizabeth

middle: A

last: Creasey

first: Daniel

middle: B

last: Graham

middle: J


title: Genome-wide profiling of TFEB targets in melanoma

city: Oxford

first: Pakavarin

last: Louphrasitthiphol

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

country: United Kingdom

institute: Ludwig Institute for Cancer Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Unlike MITF-M, the melanocyte-specific isoform of MITF, TFEB, TFE3 and non-melanocyte MITF isoforms are regulated primarily by mTORC1-mediated phosphorylation at the lysosome that promotes their cytoplasmic retention. As low levels of glucose or amino acids trigger down-regulation of MITF, it is likely that on nutrient limitation some MITF functions are assumed by TFE3 and TFEB, enabling MITFLow melanoma cells to survive and proliferate. The role TFEB and TFE3 in melanoma biology and their impact on MITF-driven proliferation is poorly understood.

overall_design: 501mel melanoma cell lines engineered to express ectopic-doxycycline-inducible-HA-epitope-tag TFEB. Cells were then treated with 5ng Dox overnight to attain expression of ectopic TFEB that was comparable to the endogeneous level. The following day cells were treated with 250nM Torin1 or control for 6h. Samples were then processed as described below.

first: Érica

last: Aparecida de Oliveira

first: Colin

middle: R

last: Goding


title: TFEB and TFE3 are key regulators of melanoma biology

overall_design: B16/F10-luc2 mouse melanoma cells were obtained from Caliper Life Sciences (Hopkinton, MA, USA). B16F10-luc2_Mitf_sKO were generated as described in PMID: 33789714. Tfeb and Tfe3 KO were generated using guides tfe3 CGTAGAAGCTGTCAGGATCG and tfeb TGGACACGTACTGTCCACCT. KO cells were clonally isolated and validated.

first: Diogo

last: Dias


title: Nuclear receptor coregulator NRIP1 R448G modulates T cell gut-homing and Teff:Treg balance to control intestinal inflammation [scATAC-Seq]


title: Spatial transcriptomics for platinum-resistant high-grade serous ovarian carcinoma

summary: Ovarian cancer is one of the leading causes of death in females in the world. High-grade serous ovarian carcinoma (HGSOC) is the most common histological subtype, and the platinum-resistance is a clinical challenge. Moreover, JAK1-related inflammation may contribute to the platinum-resistance. This study investigated the spatial gene expression profiles of JAK1-high and -low expressed HGSOC.

overall_design: Archival Formalin-fixed paraffin embedded (FFPE) tissues at the Hyogo Prefectural Cancer Center Biobank were used for analysis. The expression of JAK1 was confirmed by immunohistochemistry. According to the Visium FFPE protocol, the spatial transcriptome analysis was conducted by CyberomiX (Kyoto, Japan).


title: Integration of transcriptomics, proteomics, phosphoproteomics analysis for characterization of pulmonary arterial hypertension in Chinese people

city: xuzhou

first: tianya

last: liu

address: 99 Huaihai West Road,xuzhou,jiangsu province

institute: Affiliated Hospital of Xuzhou Medical University

summary: Pulmonary arterial hypertension (PAH), a fatal disease, is characterized by pulmonary vascular remodeling and vascular resistance. However, the molecular mechanisms underlying the pathogenesis of PAH remained to be incompletely understood. RNA-seq, 4D Label-free proteomics and phosphoproteomics were used to detect the levels of mRNA, proteins, and phosphoproteins in lung tissues from PAH patients, respectively. Parallel reaction monitoring (PRM) was carried out to verify the expression of the differentially expressed proteins. In total, 967 differentially expressed genes (|log2FoldChange|>1 and p<0.05), 764 differentially expressed proteins and 411 phosphoproteins were observed after data filtering (|log2FoldChange|>1 and p<0.05) in lung tissues of PAH patients as compared with the control group. Integrated analysis of the three omic measures revealed that the biological processes involving inflammation, ion channel and metabolism were closely associated with PAH. Several signaling pathways, such as ferroptosis, HIF-1, PI3K-AKT, and Rap1 might be related to the development of PAH. This study combined multi-omics characteristic profiling to find out the changed genes or proteins that contributed to a detailed pathogenic of PAH. It would have the benefit of looking for the novel and effective treatment targets and therapeutic drugs for PAH patients.

overall_design: To detect the levels of mRNA, in lung tissues from PAH patients.

first: Tianya

last: Liu

first: Siqi

last: Zhou

first: Rui

last: Wang

first: Zhiping


title: A promoter-dependent upstream activator augments CFTR expression in diverse epithelial cell types

city: Cleveland

first: Ann

last: Harris

state: OH

address: 2109 Adelbert Rd

department: Genetics and Genome Sciences

institute: Case Western Reserve University

summary: The cystic fibrosis transmembrane conductance regulator (CFTR) gene encodes an anion-selective channel found in epithelial cell membranes. Mutations in CFTR cause cystic fibrosis (CF), an inherited disorder that impairs epithelial function in multiple organs. Most men with CF are infertile due to loss of intact genital ducts. Here we investigated a novel epididymis-selective cis-regulatory element (CRE), located within a peak of open chromatin at -9.5 kb 5’ to the CFTR gene promoter. Activation of the -9.5 kb CRE alone by CRISPRa had no impact on CFTR gene expression. However, CRISPRa co-activation of the -9.5 kb CRE and the CFTR gene promoter in epididymis cells significantly augmented CFTR mRNA and protein expression when compared to promoter activation alone.  This increase was accompanied by enhanced chromatin accessibility at both sites. Furthermore, the combined CRISPRa strategy activated CFTR expression in other epithelial cells that lack open chromatin at the -9.5kb site and in which the locus is normally inactive. However, the -9.5 kb CRE does not function as a classical enhancer of the CFTR promoter in transient reporter gene assays.  These data provide a novel mechanism for activating/augmenting CFTR expression, which may have therapeutic utility for mutations that perturb CFTR transcription.

overall_design: Single guide RNAs (sgRNAs) targeting the -9.5 Kb DHS and the -44 Kb DHS were designed using Benchling. Two sgRNAs were used for each DHS. The sgRNA targeting CFTR promoter was described elsewhere (Mendenhall, 2021, Sharma et al., 2021).  sgRNAs were cloned into the pSPgRNA plasmid (Addgene #47108 (Perez-Pinera et al., 2013)) and transfected with the SP-dCas9-VPR plasmid (Addgene #63798, a gift from George Church (Chavez et al., 2015))  into HEP cells (Coleman and Harris 1991) with Lipofectamine 3000 (ThermoFisher). Cells were processed for ATAC-seq 48h post-transfection. Omni-ATAC was performed as described in Corces et al. 2017.

first: Giuliana

last: Coatti

first: Shih-Hsing

last: Leir


title: Transcriptome analysis of bulk-HSCs, LT-HSCs and ST-HSCs.

city: Kobe

first: Katsuyuki

last: Nishi

state: Hyogo

address: 1-5-6 Minatojima-minamimachi, Chuo-ku

institute: Kobe University Graduate School of Medicine

summary: Here, we used bulk-RNAseq of bulk-HSCs (Lineage-c-Kit+Sca-1+CD150+CD34-/loFlk2- ), LT-HSCs (Hoxb5+Lineage-c-Kit+Sca-1+CD150+CD34-/loFlk2- ), and ST-HSCs (Hoxb5-Lineage-c-Kit+Sca-1+CD150+CD34-/loFlk2- ) from young (2-3 months) or aged (23-25 months) mice to compare age-associated transcriptomic changes.

overall_design: cDNA libraries were prepared from bulk-HSCs, ST-HSCs and LT-HSCs using a KAPA RNA HyperPrep kit with RiboErase (HMR) and sequenced using a Hiseq 1500 (Illumina) to obtain 2 × 127 basepair (bp) paired-end reads. Three replicates were sequenced for each population.

first: Masanori

last: Miyanishi


title: A wound-responsive transcription factor, OsWRKY53 dictates downstream wound responses upon OsPep2 perception

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: UAS-GKVK Campus

country: India

institute: National Centre for Biological Sciences - TIFR

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

overall_design: Refer to individual Series


title: Noninvasive focused ultrasound non-specifically activating spleen immunological function to universally suppress tumor proliferation: a new strategy for cancer immunotherapy

city: Xi’an

first: Wei

last: Dong

address: No.157#, The West 5th Road

department: The Second Affiliated Hospital

institute: Xi’an Jiaotong University

summary: CD8 T cells were sorted from the spleen using the Beckman Kurt MoFlo Astrios ultra high speed flow cytometry sorting system. Subsequently, general transcriptome sequencing was performed when the positive cell rate was greater than 90% detected by flow cytometry. The cDNA library construction and sequencing of all RNA samples were performed by Shanghai Ouyi Biomedical Technology Co., LTD. Transcriptome sequencing was performed to screen differentially expressed genes (DEGs). Then, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were applied to annotate the function of the DEGs. The results revealed that FUS firstly regulated calcium-related signaling pathways to further modulate other signaling pathways, such as ECM-receptor interaction, PI3K-AKT signaling pathway, Rap1 signaling pathway and Hippo signaling pathway to promote immune cell proliferation, migration and activation to suppress cancer cell deterioration.

overall_design: CD8 T  cells (CD45+ CD3+ CD8a+) were sorted from the spleen using the Beckman Kurt MoFlo Astrios ultra high speed flow cytometry sorting system (MoFlo Astrios EQ, Beckman Coulter, lnc, USA). Subsequently, general transcriptome sequencing was performed when the positive cell rate was greater than 90% detected by flow cytometry (CytoFLEX LX, Beckman Coulter Life Sciences, USA). RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).


title: Functional transitions of the Aspergillus fumigatus iron regulator HapX are governed by conserved domains cooperatively binding [2Fe-2S] clusters

city: Innsbruck

first: Hubertus

last: Haas

state: Tyrol

address: Innrain 80/82

department: Institute of Molecular Biology

country: Austria

institute: Medical University of Innsbruck

summary: Accurate sensing of cellular iron levels is vital, as this metal is essential but toxic in excess. The iron-sensing transcription factor HapX is crucial for virulence of Aspergillus fumigatus, the predominant human mold pathogen. Its absence impairs growth under iron limitation and excess, but not under moderate iron availability, suggesting that HapX switches between three states to adapt to varying iron availability. This study suggests that the HapX state transitions are regulated by different propensities of four phylogenetically conserved cysteine-rich regions (CRRs) to coordinate [2Fe-2S] clusters resulting in cumulative occupancies depending on iron availability. The iron starvation state features no [2Fe-2S] clusters in any of the CRRs, the iron sufficiency/”neutral” state features clusters in CRR-B and/or -C, and the iron excess state has clusters in CRR-A, -B, and -C, while CRR-D plays a minor role. Combinatorial mutation of CRR-B and -C inhibited growth by locking HapX in the iron starvation state, leading to uncontrolled iron uptake and repression of iron-consuming pathways and iron detoxification. This growth defect was partially rescued by removing the C-terminal 27 amino acids, which are crucial for the iron starvation state and contain a degron. Noteworthy, the HapX iron starvation state induced several gene clusters encoding secondary metabolites.

overall_design: RNA-seq profiling of fungal strains encoding the native hapX and the hapXA/B/C/D allele, which is characterized by the simultaneous mutation of all four cysteine-rich regions (CRR); both alleles are under control of the xylose-inducible xylanase promoter (xylP); fungal liquid cultures were grown at 37 °C under iron sufficient conditions without xylose supplementation for 17 h, followed by 1 h incubation in the presence of 0.1% (w/v) xylose for xylP induction;

first: Simon

last: Oberegger

first: Matthias

last: Misslinger

first: Isidor

last: Happacher


title: MicroRNA sequencing for platinum-resistant high-grade serous ovarian carcinoma

first: Kosuke

last: Yoshida

summary: Ovarian cancer is one of the leading causes of death in females in the world. High-grade serous ovarian carcinoma (HGSOC) is the most common histological subtype, and the platinum-resistance is a clinical challenge, In this study, we investigated the microRNA (miRNA) profiles of platinum-resistant and platinum-sensitive HGSOC.

overall_design: Archival fresh frozen samples at the Hyogo Prefectural Cancer Center Biobank were used for analysis. Total RNA was extracted from the samples, and small RNA libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA). Finally, single-end reads were performed on the Illumina MiSeq.

first: Kazuhiro

last: Suzuki

first: Akira

last: Yokoi


title: Nuclear receptor coregulator NRIP1 R448G modulates T cell gut-homing and Teff:Treg balance to control intestinal inflammation.

first: Ramnik

last: Xavier


title: Transcriptional Signatures of Wild-type and F508del-CF HL-60 Cell Lines and their Differentiated Neutrophils

city: New Orleans

first: Guoshun

state: LA

address: CSRB 607, 533 Bolivar Street

institute: Louisiana State University Health Sciences Center

summary: This study performed single-cell RNA sequencing (scRNA-seq) analyses on gene transcriptions of parental Wild-type and F508del-CF HL60 cell lines, and their DMSO-derived neutrophils with or without LPS stimulation.

overall_design: There are 6 groups of cells subjected to scRNA-seq: 1) Parental wild-type HL-60 cell line (WT_HL-60); 2) Parental F508del-CF HL-60 cell line (CF_HL-60); 3) Neutrophils differentiated from wild-type HL-60 cell line (WT_dHL-60); 4) Neutrophils differentiated from CF-F508del HL-60 cell line (CF_dHL-60); 5) WT_dHL-60 stimulated with LPS (WT_dHL-60_LPS); and 6) CF_dHL-60 stimulated with LPS (CF_dHL-60_LPS). For differentiation induction, 1.25% DMSO was added to the complete RPMI-1640 culture medium for 5 days with a medium replenishment at Day 3. For LPS stimulation, Pseudomonas aeruginosa LPS (42.67 ug/ml) was added for 16 hours.

first: Yawen

last: Hu


title: Lung disease death predictor gene expression

city: New York

first: Shanaz

middle: Adi

last: Ghandhi

state: NY

address: 630, W 168th street

department: Center for Radiological Research

institute: Columbia University Medical Center

summary:
Towards individual radiosensitivity / late radiation injury: Dose estimates provide only a general idea of the average radiation injury expected across a population. Predictors of individual radiation injury response and outcome will be even more useful. Building on our successful studies of blood-based transcriptomic predictors for individualized radiation-induced ARS mortality, we will assess the utility of gene expression biomarkers for the individualized prediction of later mortality from lung injury. We will develop signatures of injury and recovery, and use mouse models to investigate the impact of inflammatory pathways on our biodosimetric signatures.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at two time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for blood cell response to radiation and for identification of survival biomarkers for delayed lung injury

first: S

last: Amundson


title: ChIP-Seq CEBP-β of pig endometrial tissues

city: wuhan

first: yan

last: sun

address: No. 1, Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

summary: Transforming the endometrial luminal epithelium (LE) into a receptive state is a requisite event for successful embryo implantation. This study suggests the role of a transcription factor in regulating endometrial LE receptivity.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) CEBP-β  for on pig endometrial tissues in day 12 and 15 of pregnancy

first: Mei

last: Yu

first: Yan

last: Sun

first: Yifen

last: Yang

first: Ziran

last: Jiang


title: Inhibition of nonsense-mediated decay in TDP-43 deficient neurons reveals novel cryptic exons

status: Public on Sep 02 2025

city: Baltimore

first: Irika

middle: R.

last: Sinha

state: MD

address: 720 Rutland Ave Room 567

institute: Johns Hopkins University

summary: Transactive response DNA binding protein 43 kDa (TDP-43) is a protein that regulates splicing, the loss of which underlies the pathophysiology of a variety of neurodegenerative disorders, including amyotrophic lateral sclerosis and frontotemporal dementia (ALS-FTD). In disease states, TDP-43 is cleared from the nucleus of neurons, leading to the loss of its splicing repressor function and the aberrant inclusion of cryptic exons. Frequent inclusion of premature termination codons (PTCs) by cryptic exons leads to degradation of cryptic mRNA by nonsense-mediated mRNA decay (NMD). However, detection of cryptic exons relies on inefficient NMD; therefore cryptic exons efficiently targeted and eliminated by NMD remain undetectable through conventional RNA-sequencing. Here we generated a comprehensive set of neuronal targets of TDP-43 in human IPSC-derived i3Neurons (i3N) by combining TDP-43 knockdown with inhibition of several factors regulating NMD, and identified various cryptic exons that were either underestimated or entirely undetected by TDP-43 knockdown alone.

overall_design: RNA-seq profiling of i3Neurons with and without TARDBP Knockdown and NMD inhibition

first: Yingzi

last: Ye

first: Philip

last: Wong

first: Shuying

first: Jonathan

middle: P

last: Ling


title: Mapping regulatory elements from transcription initation data

city: Copenhagen

first: Robin

last: Andersson

address: Ole Maaloes Vej 5

department: Department of Biology

country: Denmark

institute: University of Copenhagen

summary: Determining enhancer and promoter activities is important for modeling gene regulation and interpreting the impact of genetic variation on disease. Studying regulatory element activity genome-wide has been challenging, partly due to a lack of benchmarks. Here, we systematically evaluate CAGE for detecting active regulatory elements and present PRIME, a framework for analyzing regulatory elements from transcription initiation data. We assess nuclear RNA CAGE (nucCAGE) versus total RNA CAGE using fine-mapped eQTLs, likely pathogenic variants, and CRISPRi loci. Transcribed loci identified by PRIME on CAGE data show superior performance in detecting active regulatory elements compared to transcription run-on assays, and nucCAGE improves recall. Importantly, nucCAGE maintains the ability of CAGE to study promoter activities at base-pair resolution. These assays and computational tools will aid in understanding gene regulatory circuits and interpreting pathogenic variants.

overall_design: Transcription initiation was profiled in 5 human cell lines (i.e., A549, HCT116, GM12878, HepG2, K562) using CAGE. Selected samples were subjected to 1) nuclear extraction by applying osmotic pressure and sheer forces or 2) transcriptional perturbation by applying triptolide. Libraries were prepared from defined numbers of input cells to allow comparability of results and sequenced to acquire strand-specific transcription start site signals to summarize promoter and enhancer activities.

first: Hjörleifur

last: Einarsson

first: Natsuda

last: Navamajiti

first: Christian

middle: S

last: Vaagensø

first: Robert

last: Krautz


title: Chronic exposure of PFOS at environmental-relevant concentration promotes TNBC aggressive phenotypes

city: 苏州市

first: hongjin

last: huo

address: 江苏省苏州市工业园区仁爱路199号苏州大学独墅湖校区

institute: Suzhou Medical College of Soochow University

summary: The purpose of this project was to investigate the effects of chronic PFOS exposure at encironmental-relevant concentration on triple negative breast cancer cells.

overall_design: Murine triple negative breast cancer cells (4T1 cells) were exposed to 0 nM or 100 nM PFOS  for 35 passages.RNA was subsequently isolated and RNA-sequencing method was uesd to analyze changes in gene expression.

first: Hongjin

last: Huo

first: Wei

last: Wei

first: Dongxuan

last: Wang

first: Xingxi

last: Song

first: Fei


title: System biology reveals a mechanism associated with protection by the co-immunization of DNA and protein in the same anatomical site

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

department: Medicine

institute: Northwestern University

summary: System immunology was used to identify  the mechanisms  linked to the immunogenicity and protective efficacy of an HIV vaccine comprised of Env and Gag DNA and Env proteins by co-administration of the vaccine components in the same muscles or by separate administration of DNA and protein in contralateral sites in female rhesus macaques. Interestingly, only macaques in the co-administration vaccine group were protected against SHIV CH505 acquisition after repeated low-dose intravaginal challenge and showed 67% risk reduction per exposure. Macaques in the co-administration group developed higher migratory monocytes (CXCR4+ monocytes with increased LYN expression) from blood to lymph nodes. The heightened frequency of those migratory monocytes was associated with heightened ADCC pre-challenge and with decreased risk of acquisition. These data suggest that monocytes migration is key to the simultaneous recognition, processing and presentation of DNA+Env protein in the same draining lymph nodes to confer protective immunity.

overall_design: Blood bulk RNA-seq (paired-end strand-specific) for 505 samples and 24 controls. Samples were collected from 20 rhesus macaques that receive DNA and protein in both legs and 19 rhesus animals that received DNA and protein in different legs

first: Michael

last: Gale

first: Rafick-Pierre

last: Sekaly

first: Barbara

last: Felber

first: George

middle: N

last: Pavlakis


title: RUNX1 mediating the effects of TGFβ stimulation in cholangiocytes

city: Richmond

first: Grayson

middle: Welch

last: Way

email: waygw@vcu.edu, waygw@outlook.com

state: Virginia

address: 1217 E Marshall Street Room 534

department: Microbiology and Immunology

institute: VCU

summary: Cholestatic liver diseases, such as primary sclerosing cholangitis (PSC), are characterized by biliary fibroinflammation. Transforming growth factor-β (TGFβ) activated cholangiocytes release signals that recruit immune cells to drive inflammation and activate myofibroblasts to deposit the extracellular matrix (ECM). TGFβ signaling interacts with RUNX1 transcription factor. However, the role of RUNX1 has not been investigated in biliary fibroinflammation. Here we used mouse large biliary epithelial (MLE) cells that were treated with TGFβ (10ng/mL). ChIP-seq was performed followed by pathway analysis of genes associated with regions of RUNX1 binding.

overall_design: MLE cells were plated to near confluence and treated with  TGFβ (10ng/mL) overnight. A RUNX1 polyclonal antibody (ThermoFisher PA5-19638) was used using a ChIP kit (Cell Signaling #900 Simple ChIP Enzymatic Chromatin IP Kit (Magnetic Beads)).

first: Aseem

last: Sayed Obaidullah

first: Way

last: Grayson

first: Wang

last: Jing

first: Carter

last: Christiane

first: Zhou

last: Huiping


title: scRNA-seq data of peritoneal immune cells from PTENα knockout and WT mice

city: Beijing

first: Weixuan

address: No. 38 Xueyuan Road, Haidian District

institute: Peking University

summary: To determine the changes in peritoneal immune cells upon PTENα deficiency, we performed scRNA-seq to analyze the peritoneal immune microenvironment in wild-type (WT) and PTENα knockout (KO) mice.

overall_design: Wild-type (WT) and PTENα knockout (KO) mice were placed on a high-fat diet beginning at 4 weeks of age and maintained for three months. To obtain peritoneal immune cells, mice were intraperitoneally injected with serum-free RPMI 1640 medium, and the lavage fluid was collected. CD45⁺ immune cells were then isolated by flow cytometry and subjected to single-cell RNA sequencing to profile the peritoneal immune microenvironment.

first: Linjiang

last: Han

first: Dan

last: Lv


title: 2B4 Co-Stimulation and Dasatinib Modulation  Enhance Anti-CD19 CAR-NK Cell Cytotoxicity

city: Ribeirão Preto

first: Matheus

middle: Henrique

last: dos Santos

state: SP

address: R. Ten. Catão Roxo, 2501

department: Oncology

country: Brazil

institute: University of Sao Paulo

summary: Chimeric Antigen Receptor (CAR)-cell-based therapies have shown remarkable achievements in cancer treatment, especially for hematological malignancies. In CAR-T cells, the costimulatory[P1]  domain is a key factor that significantly affects their therapeutic success. However, the effects of different costimulatory domains on the activation and performance of CAR-natural killer (CAR-NK) cells have not been sufficiently studied. We designed novel CAR constructs incorporating NK-specific costimulatory domains, such as 2B4 (CD244) and DAP12, to enhance CAR NK functionality. We evaluated their efficacy using in vitro cytotoxicity assays, cytokine profiling, and in vivo tumor models. We further investigated dasatinib, a tyrosine kinase inhibitor, as a pharmacological modulator of CAR NK cell activity. Short-term dasatinib exposure temporarily and reversibly suppressed CAR-NK activity yet enhanced function upon withdrawal. Accordingly, 2B4-DAP12 CAR-NK cells demonstrated superior tumor control and survival compared to conventional 4-1BBζ CAR-NK cells in vivo following dasatinib pretreatment. Our findings highlight that NK-optimized co-stimulation (2B4-DAP12) with reversible dasatinib pharmacological control synergistically enhanced CAR-NK cytotoxic function, providing an innovative strategy for next-generation cellular therapies.

overall_design: The cells were then co-culture against CD19+positive Nalm-6 cells for 4 hours. After co-culture, cells were magnetically separated and the RNA of CAR-NK cells were purified for differencial gene expression analisys.

middle: H

first: Virgínia

last: Picanço Castro


title: The role of BRCT domain from LmjPES in Leishmania major biology

city: Pamplona

first: Esther

last: Larrea

state: Navarra

address: CIMA Avda. Pio XII 55

country: Spain

institute: Institute of Tropical Health of Universidad de Navarra

summary: To investigate the implications of LmjPES BRCT domain overexpression in Leishmania major. We generated a strain of L. major constitutively overexpressing LmjPES BRC domain and we compared its gene expression with other L. major strain no-overexpressing this domain.The data showed a role of LmjPES BRC domain in genes related mainly to metabolic patways

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Leishmania major overexpressing and no-overexpressing LmjPES BRCT domain

first: Paul

last: Nguewa

first: Celia

last: Fernandez-Rubio


title: ChIP-seq in human trophoblast stem cells

city: Kumamoto

first: Hiroaki

last: Okae

address: 2-2-1 Honjo, Chuo-ku

department: Department of Trophoblast Research

institute: Kumamoto University

summary: Trophoblasts are multifunctional cells in the placenta and essential for normal pregnancy. Although trophoblast dysfunction can cause pregnancy complications, their underlying mechanisms remain unclear, and effective treatments are limited, partly because of the scarcity of appropriate experimental models. We previously reported the derivation of human trophoblast stem cells (hTSCs) from 1st-trimester placentas and blastocysts, providing a powerful tool to investigate human trophoblast development and function. However, the difficulty in deriving hTSCs from late-gestation placentas has limited their use in pregnancy complication research. Here we report a technique to derive hTSCs from term placentas based on the transient expression of a p53 dominant negative mutant, SALL4, and shRNAs against cyclin-dependent kinase inhibitors. Using this technique, we derived hTSCs from placentas obtained from patients with preeclampsia and reproduced key features of the disease.

overall_design: hTSCs were transduced with FLAG-SALL4 using lentivirus. ChIP was performed using ChIP Reagents (#318-07131; Nippon Gene, Tokyo, Japan) and an anti-FLAG antibody (1:100; #F3165; Sigma-Aldrich, St. Louis, MO, USA). Briefly, IP was performed in buffer containing 400 mM NaCl instead of 150 mM to reduce the background signal. ChIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (#E7645; New England Biolabs, Ipswich, MA, USA) and sequenced on an Illumina NovaSeq 6000 platform. Reads were trimmed using TrimGalore and aligned to the reference genome (UCSC hg38) using Bowtie 2 v2.2.5. SALL4-binding sites were identified using MACS2 v2.2.7.2.


title: Synthetic engineering demonstrates that synergy among enhancers involves an increase in transcriptionally productive enhancer-gene contacts [ChIP-Seq]

city: Santander

first: Alvaro

last: Rada-Iglesias

state: Cantabria

address: Albert Einstein 22, PCTCAN

institute: Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/University of Cantabria

summary: Enhancers are non-coding cis-regulatory elements that control the expression of distally located genes in a tissue- and time-specific manner. Recent studies indicate that enhancers can differ in their underlying genetic architecture and regulatory properties. However, these different types of enhancers were previously investigated under rather variable conditions (e.g. model organism, cell type, enhancer-promoter distance, type of target promoter, etc.), thus introducing confounding factors that make it difficult to discern the distinct regulatory properties of each enhancer type. To overcome these limitations, here we generated transgenic mouse embryonic stem cells (mESC) lines in which different types of synthetic enhancers (i.e. “typical” enhancer, CTCF-associated enhancer, enhancer cluster/super-enhancer) were built upon the same “core” neural enhancer and inserted at the same distance (i.e. 100 Kb) from a typical developmental gene (i.e. Gata6). Subsequently, the mESC lines were differentiated to systematically compare the regulatory properties of the different enhancer types under identical conditions. Regarding the CTCF-associated enhancer, our data revealed that the addition of a CTCF site to the “core” enhancer increased insulation and led to the formation of a smaller contact domain, while having a rather mild effect on enhancer-promoter contact frequency and target gene expression. On the other hand, in comparison to the “core” enhancer alone, the enhancer cluster synergistically increased target gene expression and burst fraction. Importantly, we found that, in contrast to previous models, the strong regulatory activity of the enhancer cluster can not be explained by changes in enhancer-promoter contact frequency or the formation of transcriptional condensates. Instead, our data suggest that the emergent regulatory properties of enhancer clustering preferentially entail an increase in RNA Polymerase II pause release and, thus, in the fraction of enhancer-promoter contacts that are transcriptionally productive.

overall_design: ChIP-seq pair end read samples for diferent histone marks and co-activators

first: Endika

last: Haro

first: Mariana

last: Iliadou

first: Shyam

last: Ramasasy

first: Thais

last: Ealo

first: Victor

last: Campa

first: Tomas

last: Pachano

first: Marieke

last: Oudelaar


title: m6A RNA modification controls reproductive development and metabolic adaptation in the human parasite Schistosoma japonicum [RNA-seq]

city: Shanghai

first: Guofeng

last: Cheng

state: Shanghai

address: #500, Zhennan Road, Shanghai

institute: Tongji University

summary: N6-Methyladenosine (m6A) is an abundant eukaryotic post-transcriptional mRNA modification, which plays pivotal role in regulating RNA metabolism. m6A is crucial for dynamic processes in many parasites, however, its presence, roles, and contribution to Schistosoma japonicum, a parasitic flatworm with a complex lifecycle involving dynamic transcriptional reprogramming, remain entirely unexplored. Here, we report the first evidence that m6A is abundant on S. japonicum RNA, and demonstrate its critical contribution to parasite biology. We identify the m6A writer as a crucial regulator of female reproductive development, including ovary morphogenesis and egg production, and in orchestrating metabolic reprogramming essential for survival and parasitism in male worms. Given the central role of eggs in host pathology and transmission, our findings uncover a key regulatory layer in schistosome biology and pinpoint m6A deposition as a potential target for anti-schistosomiasis interventions.

overall_design: identification of differential expression genes after mettl3 KD, in two biological replicates

first: BIKASH

last: GIRI

first: ZIHAO

last: ZHANG


title: ScRNA-seq Links Dental Fibroblasts Heterogeneity with Mechanoresponsiveness

first: Lingyong

last: Jiang

address: No.639, zhi zao ju road

institute: Shanghai jiao tong University

summary: Periodontal ligament (PDL) and dental pulp (DP) share a common origin but have distinct biological and mechanical functions. We used ScRNA-seq to decipher cellular heterogeneity and their underlying molecular mechanisms.

overall_design: A single-cell comparison of digested human periodontal ligament (PDL) and dental pulp (DP) was performed using scRNA-seq.

first: Hongyuan

last: Xu

first: Qinggang

last: Dai

first: Anting

last: Jin

first: Yiling

last: Yang

first: Xiangru

last: Huang

first: Xijun

last: Wang

first: Xin

last: Gao

first: Siyuan

last: Sun

first: Yuanqi

last: Liu

first: Yanfei

last: Zhu

first: Steve

middle: F

last: Shen

first: Qian

last: Bian


title: Inhibition of USP5 offers potential targeted therapeutic strategies for t(8;21) AML through ubiquitin-mediated degradation of AML1-ETO

first: Zhi-xin

last: Li

address: No. 507 Zhengmin Road, Yangpu District

department: Department of Thoracic Surgery, Shanghai Pulmonary Hospital

summary: The AML1-ETO (AE) fusion protein is a key target for treating t(8;21) acute myeloid leukemia (AML). In this investigation, we identified ubiquitin-specific protease 5 (USP5) as the deubiquitinating enzyme of AE. USP5 knockdown decreased AML cell growth and induced differentiation both in vitro and in vivo. Additionally, we developed a high-throughput screening (HTS) method and identified a potent, selective USP5 inhibitor, WCY-8-67. This lead compound was identified as a selective USP5 inhibitor via targeting the ubiquitin-associated domain 2 (UBA2) region, and it also induced aggregation and precipitation of the target protein, leading to USP5 dysfunction. WCY-8-67 was exhibited excellent in vivo bioavailability and tolerability, and it effectively inhibited the growth of t(8;21) AML cell lines and the primary AML cells in animal models. Notably, in the patient-derived xenograft (PDX) model, this compound, when combined with 5-Azacytidine (5-Aza), demonstrated good safety and significant synergistic therapeutic effects. This study presented promising targeted therapeutic possibilities for the treatment of t(8;21) AML.

overall_design: RNA-seq profiling was performed on three groups of Kasumi-1 AML cells: USP5 knockdown (ShUSP5), AE knockdown (ShAE), and a control (ShNC) to explore the impact of AE and USP5 knockdown on gene expression and downstream signaling pathways. The aim was to identify differentially expressed genes (DEGs) and enriched signaling pathways between the experimental groups.

first: Lan

last: Ma

first: Kun

last: Zhang

first: Zixuan

first: Chenyang

first: Mengyuan

first: Ying

first: Yanli

last: Zhao

first: Ziqing

last: Gong

first: Ning

first: Mingming

last: Wei

first: Xiang

first: Jingfeng

last: Zhou

first: Shuangwei

first: Cheng

first: Guang


title: RNA-seq of Epithelial cells treated with siRNA and irradiation or cytokine treatment

city: Seoul

first: Yoon-Jin

last: Lee

address: Nowon GU

country: South Korea

institute: Korea Institute of Radiological & Medical Sciences

summary: RNA-seq of lung epithelial cells with EGFR or ErbB deletion, harvested 3 days after irradiation or cytokine treatment. RNA was extracted, libraries were prepared using a stranded RNA-seq protocol, and sequencing was performed on the Illumina platform.

overall_design: RNA-seq analysis of lung epithelial cells with EGFR or Erbb3 deletion, 3 days after irradiation or cytokine treatment.

first: Ji-Hee

last: Kim

first: Seo-Hyun

last: Choi

first: Jae-Kyung

last: Nam

first: Haeng Ran

last: Seo

first: Min-sik

last: Park

first: Inhee

first: Jeeyong


title: A platform for multisite immune profiling of premetastatic pancreatic cancer at single cell resolution

city: Durham

first: Peter

last: Allen

state: NC

address: 203 Research Dr., MSRB1 Rm. 475

department: Surgery

institute: Duke Medical Center

summary: Pancreatic ductal adenocarcinoma (PDAC) is characterized by exceedingly high rates of metastatic progression, with the liver representing the most common site of distant spread. Here, we established a platform for multisite immune profiling of human PDAC encompassing the tumor, peripheral circulation, and premetastatic liver, to more comprehensively study how various immune subsets might contribute to patient outcomes. METHODS: Tumor, liver, and blood samples were obtained from patients undergoing resection for non-metastatic PDAC. Derived immune cells underwent paired single-cell RNA and TCR sequencing. Immune composition, cell type functional profiles, and T cell clonal expansion patterns were evaluated across tissue sites. RESULTS: In total, 106,539 immune cells were sequenced, of which 85,748 met criteria for analysis. We identified 32 cell populations, of which seven demonstrated significant enrichment within a particular tissue. Functional profiling revealed tissue-specific differences in cell phenotypes. This included terminally differentiated exhausted CD8 T cells within the tumor, highly active Tregs within the premetastatic liver and tumor, and M1 versus M2 polarization of liver and tumor macrophage populations, respectively. Clonal expansion of T cells was greatest in the liver, which comprised predominantly mature CD8 T cells and MAIT cells. Within the tumor, expanded Treg clones were uniquely abundant, and while expanded clones could be tracked to the blood and premetastatic liver, many of these mapped back to known viral antigens. Leveraging previously validated gene sets, we predicted the tumor reactivity of intratumoral T cells using transcriptional signatures. We demonstrated a high degree of concordance between multiple independent signatures and tracked high-priority TCRs within the blood and liver. CONCLUSION: This study provides a platform, which has already been implemented into ongoing clinical protocols, for immune profiling of human PDAC across the sites most relevant to metastatic progression. Future applications of this work can monitor immune populations throughout metastatic progression to build a temporal database of immune phenotypes and track association with clinical outcomes.

overall_design: scRNA-seq profiling of triplicate liver tissues, pancreas tissue, and blood smaples from three patients with pancreatic adenocarcinoma.

first: Elishama

last: Kanu

first: Ashley

last: Fletcher

first: Daniel

last: Nussbaum

first: Erika

last: Crosby


title: The effects of Trichinella spiralis tropomyosin on breast cancer MCF-7 cells

city: Chengde

first: Miao

last: Liu

address: Nanyingzi Street

department: Department of Oncology

institute: Affiliated Hospital of Chengde Medical University

summary: The excretory-secretory proteins (ESPs) of Trichinella spiralis (T. spiralis) muscle larvae have been confirmed to exert antitumor effects by modulating host immune responses or directly acting on tumor cells. Our research group previously identified that the ESPs of T. spiralis muscle larvae contain multiple proteins potentially related to antitumor activity, among which tropomyosin (TM) has attracted our attention. This study aims to introduce TM from Trichinella spiralis (T. spiralis TM) into breast cancer MCF-7 cells via transfection technology. Furthermore, we investigated the impact of T. spiralis TM on the gene expression profile of MCF-7 cells through transcriptomics. Finally, the study systematically evaluated its regulatory effects on apoptosis, proliferation, and migration. We are the first to comprehensively evaluated the anticancer effects of T. spiralis TM on MCF-7 breast cancer cells. Our findings showed that T. spiralis TM increases apoptosis by activating the mitochondrial-mediated apoptosis pathway and inhibits cell migration and proliferation by downregulating the expression of important hub genes, including PRKACA, CDK3, VPS35, and BCAR1. These findings provide a novel theoretical basis for the application of molecules linked to Trichinella in tumor therapy and support for potential new targets.

overall_design: In our study, we constructed a eukaryotic expression plasmid containing T. spiralis TM and transfected it into the MCF-7 breast cancer cell line. We then used transcriptomics to assess the effects of T. spiralis TM on MCF-7 cells at the mRNA level and validated these findings experimentally.

first: Yalun

last: Guo


title: CRISPR/Cas9-Mediated PTPRZ1 Knockout Suppresses LUSC Proliferation with Genome-Wide Off-Target Analysis

city: Xi'an

first: Yihui

last: Zhang

state: Shanxi

address: No.229 Taibai North Road

institute: Northwest University

summary: To investigate the potential role of the PTPRZ1 in tumor development, we leveraged CRISPR/Cas9 to perform knockout experiments in two distinct LUSC cell lines, H520 and HCC95, both characterized by high cellular expression of the gene. Following the disruption of PTPRZ1, we observed a significant reduction in the proliferation of both LUSC cell lines, as indicated by the Cell Counting Kit-8 (CCK-8) assay .To comprehensively assess potential off-target effects of the CRISPR/Cas9 editing, we conducted whole-genome sequencing comparing the HCC95-NC and HCC95-KO-PTPRZ1cell lines, which enabled genome-wide evaluation of editing specificity

overall_design: WGS of the HCC95-NC and HCC95-KO-PTPRZ1 cells.

first: Jie

last: Wang

first: Yongqiang

last: Ning


title: RNA-seq of mouse lung tissue after irradiation

first: Yoon-Jin

summary: High-dose ionizing radiation-induced pulmonary injury. To characterize these changes, we performed RNA sequencing (RNA-seq) on lung tissues isolated from mice exposed to 90 Gy irradiation. Samples were collected at 8, 11, and 14 days post-irradiation, and non-irratied controls. RNA was extracted and libraries were prepared using a stranded RNA-seq protocol, followed by sequencing on the Illumina platform. 해석

overall_design: RNA sequencing (RNA-seq) analysis conducted on selectively sampled lung tissues exclusively from irradiated areas during the 8 to 14-d period postirradiation

first: Ji-Hee


title: Transcriptome profiling of A375SM melanoma cells following PRAME and BAP1 knockdown

first: Hyeon Ho

last: Heo

address: 209 Neungdong-ro, Gwangjin-gu

department: Department of Integrative Bioscience and Biotechnology

institute: Sejong University

summary: To investigate the transcriptomic changes associated with PRAME and BAP1 knockdown, RNA-seq was performed on A375SM melanoma cells stably expressing shRNA targeting PRAME (shPRAME), BAP1 (shBAP1), or a non-targeting control (shEmpty). This study aims to understand the role of PRAME and BAP1 in gene regulation and melanoma progression.

overall_design: RNA-seq was performed on A375SM melanoma cells stably expressing shRNA targeting PRAME (shPRAME), shRNA targeting BAP1 (shBAP1), or a non-targeting control shRNA (shEmpty). Transcriptomic changes in shPRAME and shBAP1 cells were compared with shEmpty(non-targeting control).

first: Soo-Jong

last: Um


title: Overcoming CXCR4-mediated T cell exclusion potentiates antitumor cytotoxicity in fibrolamellar carcinoma

city: Ithaca

first: Praveen

last: Sethupathy

address: 618 Tower Rd

institute: Cornell University

summary: Fibrolamellar carcinoma (FLC) is a rare liver cancer affecting young adults without underlying liver disease and is characterized by the DNAJB1-PRKACA fusion oncogene. Despite its immunogenicity, FLC shows limited response to immunotherapy. To investigate the mechanisms of immune resistance, we performed single-nucleus RNA sequencing on human FLC and matched adjacent non-tumor liver samples. Our analyses revealed dysregulated stromal-immune interactions, including CXCL12+ myofibroblast signaling that restricted T cell infiltration. Using complementary approaches, we found that CXCR4 inhibition enabled T cell entry into tumors, while PD-1 blockade enhanced T cell effector function. Combination treatment synergistically increased tumor cell death in a human tumor slice culture system. These results define mechanisms of immune evasion in FLC and provide preclinical support for combined CXCR4 and PD-1 blockade as a potential therapeutic strategy.

overall_design: Single-nucleus RNA-seq was performed on human fibrolamellar carcinoma (primary and metastatic) and matched adjacent liver. Nuclei were processed with Parse Evercode Mega WT v3, generating pooled sublibraries via combinatorial barcoding. Pooled libraries were sequenced (paired-end) on an Illumina NovaSeq 6000; raw multiplexed reads are deposited in SRA, and processed count matrices and cell-level annotations are provided here in GEO.

first: Jason

last: Carter

first: Lindsay

middle: K

last: Dickerson

first: Andreas

last: Stephanou

first: Sheela

last: Damle

first: Kristin

middle: E

last: Goodsell

first: Sara

last: Daniel

first: Kevin

last: Sullivan

first: Bo

last: Shui

first: Xiuyun

last: Jiang

first: Heidi

middle: L

last: Kenerson

first: Renske

last: E van den Bijgaart

first: Alaa

last: Farghli

first: Yongjun

first: Emily

last: Beirne

last: Labadie

first: Jack

last: Cernak

first: Sardar Shahmir

last: Chauhan

first: Jose

last: Mario Bello Pineda

first: Annalyssa

last: Long

first: Anna

last: Elz

first: Evan

middle: W

last: Newell

first: Teresa

last: Kim

first: Kimberly

last: Riehle

first: Raymond

last: Yeung

first: Shreeram

last: Akilesh

first: Ian

last: Crispe

last: Barry

first: Venu

middle: G

last: Pillarisetty


title: Spatio-molecular gene expression reflects dorsal anterior cingulate cortex structure and function in the human brain [snRNA-seq]

first: Keri

last: Martinowich

state: Maryland

address: 855 N Wolfe St Suite 300

institute: Lieber Institute for Brain Development

summary: In the human brain, the dorsal anterior cingulate cortex (dACC) plays a key role in the reward pathway, which is connected to drug addiction, substance abuse, and some psychiatric disorders. Specific cell types in the dACC are associated with these disorders, but the breakdown of cell populations and their relative positions are unknown. Uniquely, the dACC has agranular laminar structure due to a lack of layer IV, which relates to distinct biological functions. We generated a human dACC spatial transcriptomic map by integrating 10x Genomics Visium Spatial Gene Expression data from ten neurotypical donors and combining this map with corresponding 10x Genomics Chromium Single Cell Gene Expression data. We utilized nonnegative matrix factorization (NMF) to discover various gene programs, which shed light on von Economo neurons (VENs) in Layer V of the dACC.To better understand the molecular landscape of this region, we compared it with the dorsolateral prefrontal cortex (dlPFC) region in the same ten donors. The brain’s structure and function are closely connected, so our precise pairing of gene expression to spatial information sheds light on how dysregulation in the dACC relates to psychiatric disorders.

overall_design: We obtained tissue blocks of postmortem human brain containing dACC from 10 neurotypical adult brain donors. We used the 10x Genomics Visium and 3’ Single Cell Gene Expression platforms to generate paired spatial transcriptomics and single-nucleus RNA-seq data of the human dACC. We performed a second spatial transcriptomics experiment using the Visium Spatial Proteogenomics (Visium-SPG) platform for four of the 10 donors.

first: Kinnary

last: Shah

first: Michael

last: Totty

first: Ryan A.

last: Miller

first: Heena R.

last: Divecha

first: Sang Ho

last: Kwon

first: Svitlana V.

last: Bach

first: Sanjana

last: Tyagi

first: Madeline

last: Valentine

first: Joel E.

last: Kleinman

first: Atharv

last: Chandra

first: Madhavi

last: Tippani

first: Kristen R.

last: Maynard

first: Thomas M.

last: Hyde

first: Stephanie C.

last: Page

last: Hicks


title: Generation and characterization of iPSC derived microglia from blood derived PBMCs for in vitro modeling of stimuli-specific neuroimmune responses

city: Indianapolis

first: Joshua

last: Kulas

state: IN

address: 1210 Waterway Blvd Ste. 2000

institute: IBRI

summary: Microglia are highly specialized brain immune cells which express several genes known to influence the risk of developing Alzheimer’s disease. While interest in harnessing the potential neuroprotective functions of microglia using targeted therapeutics is high, it remains challenging to test emerging tool molecules for their potential biological effects in physiologically relevant model systems. Here we describe the generation of iPS cell lines from donor somatic cells (PBMCs) using non-integrating episomal reprogramming vectors for the downstream stepwise differentiation of iPSC-derived microglia (iMG). We find that our stepwise differentiation protocol reproducibly generates iMG expressing several microglia signature genes. Moreover, these iMG are highly morphologically and transcriptionally dynamic. We challenge iMG with diverse stimuli and find that iMG respond to myelin debris by robustly changing lipid metabolism and upregulating several chemokines including CXCL10. While iMG express both TREM2 and DAP12, neither Interleukin 4 mediated upregulation of TREM2 or TREM2 binding by an antibody tool molecule caused an increase in the phagocytosis of myelin debris. Interestingly, we find the TREM2 binding antibody induces a consistent transcriptional response resulting in the upregulation of several chemokines. We conclude iMG are a flexible model system which can be used to explore the biological response of human microglia-like cells to specific physiological stimuli and to test emerging tool molecules for their transcriptional and functional impacts.

overall_design: ultra low-total RNAseq of iMG stimulated with either the TREM2 agonist antibody (1 μg/mL), IgG antibody (1 μg/mL), myelin debris (5 μg/mL), TREM2 agonist antibody with myelin debris, or IgG with myelin debris, using untreated iMG as a control


title: Spatio-molecular gene expression reflects dorsal anterior cingulate cortex structure and function in the human brain [spatial transcriptomics]

city: Baltimore

last: Martinowich


title: Integrative analysis of mRNA stability regulation uncovers a metastasis-suppressive program in breast cancer

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

institute: UCSF

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

overall_design: Refer to individual Series


title: Regulation of the NSL complex by TAF4A is critical for genome stability and quiescence of skeletal muscle stem cells

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

summary: Acetylation of lamin A/C by the NSL complex, containing MOF and KANSL2, is instrumental for maintaining nuclear architecture and genome stability, but the mechanisms controlling expression of NSL complex components in different cell types are poorly characterized. Here, we describe that TAF4A, primarily known as a subunit of the general transcription factor TFIID, is critical for cell type-specific regulation of Kansl2 in MuSCs. Inactivation of Taf4a in MuSCs reduces expression of Kansl2 and alters post-translational modification of lamin A/C, thereby decreasing the stiffness of MuSC nuclei and disrupting the nuclear architecture. Using CUT&RUN technique, we found that TAF4A together with the heterotrimeric transcription factor NF-Y controls Kansl2 expression. In addition to destabilization of the nuclear architecture, reduced expression of Kansl2 in Taf4a-mutant MuSCs changes expression of numerous genes involved in chromatin regulation. The subsequent loss of heterochromatin and MuSC activation, in combination with pronounced genomic instability, activates MuSCs and impairs MuSC proliferation, which depletes the stem cell pool and abolishes skeletal muscle regeneration. We conclude that TAF4A-NF-Y-dependent transcription regulation safeguards heterochromatin and genome stability of MuSCs via the NSL complex.

overall_design: We examined chromatin structure using ATAC-seq in control and Taf4a mutant MuSCs

first: Angelina

middle: M

last: Georgieva

first: Stefan

last: Günther


title: Conserved Noncoding Cis-Elements Associated with Hibernation Modulate Metabolic and Behavioral Adaptations in Mice

city: Salt Lake City

first: Chris

last: Gregg

state: UT

address: 20 South 2030 East

department: Neurobiology and Anatomy

institute: University of Utah


title: Conserved Noncoding Cis-Elements Associated with Hibernation Modulate Metabolic and Behavioral Adaptations in Mice [CUT&Run]

summary: Conserved cis-elements tied to hibernator evolution affect diverse metabolic traits in mice.

overall_design: Define DNA sequences in the mouse genome bound by Irx3.

first: Susan

last: Steinwand

first: Elliott

last: Ferris

first: Cornelia

last: Hörndli

first: Jared

last: Emery

first: Josue

middle: D

last: Gonzalez Murcia

first: Riley

middle: J

last: Spotswood

first: Adriana

middle: C

last: Rodriguez

first: Amandine

last: Chaix

first: Alun

last: Thomas

first: Crystal

last: Davey


title: m6A RNA modification controls reproductive development and metabolic adaptation in the human parasite Schistosoma japonicum [m6a-seq]

first: Guofeng

last: Cheng

overall_design: identification of m6A modifcation in Schistosoma japonicum and differential expression genes after mettl3 KD, in three biological replicates

first: BIKASH

last: GIRI

first: ZIHAO

last: ZHANG


title: Engineering a superactivator of smooth muscle gene expression with the Myocardin condensate forming region [RNA-seq]

city: Dallas

first: kenian

last: chen

state: TX

address: 5323 Harry Hines Boulevard

department: Population and Data Science

institute: UTsouthwestern

summary: Differentiation of smooth muscle cells (SMCs) is accompanied by the expression of a battery of genes controlled by serum response factor (SRF), a ubiquitous transcription factor with weak intrinsic transcriptional activity. Myocardin (MYOCD) is a potent transcriptional coactivator that activates smooth muscle differentiation through its association with SRF. MYOCD forms condensates through its highly disordered transcription activation domain (TAD), whereas SRF displays a diffuse distribution within the nucleus. SRF is recruited to nuclear condensates by the TAD of MYOCD (MYOCD-TAD), thereby triggering the smooth muscle gene program. Swapping the weak TAD of SRF with that of MYOCD enables SRF to form condensates and acquire the ability to reprogram fibroblasts to SMCs. SRF-MYOCD-TAD chimeric protein exhibits stronger transcriptional activity on smooth muscle genes than MYOCD. Using protein proximity labelling, quantitative proteomics and super-resolution confocal microscopy, we show that MYOCD-TAD condensates aggregate chromatin remodelers, RNA polymerases, and mRNA processing factors to drive smooth muscle gene expression. These findings provide insights into the mechanisms whereby nuclear condensates promote tissue-specific gene expression and point toward a strategy for engineering superactivators leveraging transcriptional condensates.

overall_design: Comparative gene expression profiling analysis of RNA-seq data and chromatin occupancy and chromatin accessibility (H3K27ac) by ChIP-seq data for 10T1/2 cells reprogrammed by GFP (control), SRF, and SRF chimeric mutants (SRF-MYOCD-TAD, SRF-MYOCD-TAD-FWY/A, SRF-FUSN).

first: Peiheng

last: Gan

first: Akansha

last: Shah

first: Svetlana

last: Bezprozvannaya

first: Kenian

last: Chen

first: Qianqian

last: Ding

first: Hui

last: Li

first: Xinyi

last: Zhou

first: Ning

last: Liu

first: Eric

last: Olson


title: Engineering a superactivator of smooth muscle gene expression with the Myocardin condensate forming region [ChIP-seq]


title: Distinct hepatocyte adaptations during gestation and lactation [pregnant_liver_mm10_nuclei]

city: Beijing

first: Cheng-ran

last: Xu

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

department: School of Basic Medical Sciences

institute: Peking University

summary: Using high-resolution single-cell RNA sequencing, we systematically characterized hepatocyte adaptations in mice across pregnancy and postpartum stages. We discovered a cyclical hepatocyte trajectory (“pregnancy clock”) governing metabolic changes during gestation and postpartum recovery, which reverted to pregestational states in non-lactating mice. Lactation induced a distinct branching trajectory characterized by elevated lipid synthesis and export. Deletion of gp130 disrupted hepatic adaptations during pregnancy, impairing fetal growth, whereas ACSS2 deficiency postpartum disrupted lipid export, affecting milk quality and offspring growth.

overall_design: To comprehensively investigate hepatocyte state transitions throughout gestational (G) and postpartum (P) periods, we isolated single hepatocytes from maternal C57BL/6J mice mated at approximately 8 weeks of age. Single-cell RNA sequencing (scRNA-seq) was conducted across continuous reproductive stages, encompassing both lactating (L) and non-lactating (NL) phases.

first: Li

last: Yang

first: Yu

last: Zhang

first: XinXin

last: Yu

first: YuHeng

first: Shuang

last: He

first: Liu

first: TongYun

last: Mao

first: JunGe

first: Ying

last: Wu

first: QiQi

last: Zheng

first: ChengRan


title: Distinct hepatocyte adaptations during gestation and lactation [pregnant_liver_mm10]


title: Conserved Noncoding Cis-Elements Associated with Hibernation Modulate Metabolic and Behavioral Adaptations in Mice [RNA-seq]

first: Chris

last: Gregg

overall_design: Knock out conserved potential cis elements tied to hibernation and test for changed to gene expression.

first: Susan

last: Steinwand

first: Elliott

last: Ferris

first: Cornelia

last: Hörndli

first: Jared

last: Emery

first: Josue

last: Gonzalez Murcia

first: Riley

last: Spotswood

first: Adriana

last: Rodriguez

first: Amandine

last: Chaix

first: Alun

last: Thomas

first: Crystal

last: Davey


title: Temporal transcriptomics of human 3D neuromuscular cultures reveal key signatures of neuromuscular junction development

city: Wuerzburg

first: Patrick

last: Lüningschrör

address: Versbacher Str. 5

department: Institute of Clinical Neurobiology

institute: University Hospital Wuerzburg

summary: The principal organization of mammalian neuromuscular junctions (NMJs) shares essential features across species, yet human NMJs (hNMJs) exhibit distinct structural and physiological properties. While recent advances in stem cell-based systems have significantly improved in vitro modeling of hNMJs, the extent to which these models recapitulate in vivo development remains unclear. Here, we performed spatial transcriptomic analysis of human 3D neuromuscular co-cultures, composed of iPSC-derived motoneurons and 3D skeletal muscle engineered from primary myoblasts. We found the transcriptomic analysis follows a temporally coordinated gene expression program underlying NMJ maturation. The model recapitulates key transcriptional features of NMJ development, including early myoblast fusion, sequential upregulation of presynaptic and postsynaptic maturation genes, and late-stage induction of embryonic AChR subunits.  Importantly, consistent transcriptional dynamics across two independent hiPSC lines and differentiation protocols confirm the reproducibility and robustness of this system. This study provides a valuable transcriptomic resource and demonstrates that human 3D neuromuscular co-cultures are a robust and physiologically relevant model for investigating human NMJ development, function, and disease.

overall_design: This project aims to perform Bulk RNA sequencing from two different lines of 3D Neuromuscular Co-culture at various time points required to establish mature NMJs.

first: Neha Jadhav

last: Giridhar

first: Bita

last: Hambrecht

first: Thorsten

last: Bischler

first: Michael

last: Briese


title: Divergent functions of master TFs in LUSC [RNA-seq]

first: Yihui

last: Zhang

summary: To examine the essential role of these four TFs particularly the two novel ones KLF5 and GRHL2, we depleted individual factors with siRNA in a human LUSC cell line HCC95. The results consistently showed that cells deficient of any of these 4 factors except SOX2 were revealed with most prominent deficiency in epidermal cell development which is important features of LUSC development . Note that SOX2 is known also to play a primary role in neuron development, and the depletion indeed caused disturbance in regulation of nervous system development. The pathways involved in epidermal cell development involving regulating keratinization and epithelial-mesenchymal transition influencing tumor behavior, aggressiveness, and response to treatment.

overall_design: RNA-seq of TP63/SOX2/KLF5/GRHL2-targeting siRNA (siTP63, siSOX2, siKLF5, siGRHL2) compared to negative control siRNA (siNC) in HCC95 cells.

first: Yongqiang

last: Ning

first: Jie

last: Wang


title: Master TFs bind SOEs to drive tumorigenesis in LUSC cells [ChIP-seq]

summary: These SOEs were highly enriched for  H3K27ac signals in H520/HCC95 cells. Binding of key TFs, also known as mater regulators, is usually enriched in cell fate determinant or disease-specific cis-regulatory elements, such as super-enhancers.To find out which TFs were essential for the tumorigenesis of LUSC, sequence motif enrichment analysis was performed in SOE using all CDE as background. As expected, the well-established master TFs of LUSC, i.e., SOX2 and TP63, exhibited the highest enrichment of binding sites among all tested TFs .To confirm their binding in SOEs, we performed ChIP-seq for these factors, including p63, SOX2, GRHL2 and KLF5, all of which exhibited significant and specific binding to most SOEs, compared to other non-SOE genomic regions.

overall_design: ChIP-seq of the H3K27ac in BEAS-2B, H520, HCC95, H226 cells and TP63, SOX2, GRHL2 and KLF5 in HCC95 cells.


title: Master TFs in LUSC


title: The molecular signature and regulatory network of human umbilical cord mesenchymal stromal cells as a niche for hematopoietic stem and progenitors

city: Klong Luang

first: Pornprapa

last: Srimorkun

state: Pathumthani

country: Thailand

institute: Thammasat University

summary: UC-MSCs have been classified as an alternative niche for expanding HSPCs. However, inconsistent outcomes in hematopoietic recovery and the shift toward specific lineage differentiation were observed following co-cultures. Moreover, the underlying molecular mechanisms and regulatory roles of UC-MSCs during hematopoiesis have not been fully understood. The co-cultures of UC-MSCs UCB-CD34+ cells were established. Integrative transcriptomic analysis of UC-MSCs collected on day 3 of co-cultures has highlighted the molecular signature and comprehensive regulatory networks. The lncRNA-RNA binding protein interaction network and lncRNA cis- and trans-regulation networks were evident. The 3 gene modules and 10 hub genes were identified in the protein-protein interaction (PPI) network, including RPS16, CD74, RPL35, COX7C, RPL38, RPS28, RPS27, RPS10, TARDBP, and TOMM7. These have shed light on niche activity of UC-MSCs in regulation of cell differentiation, genomic stability, and hematopoietic supportive during co-culture with HSPCs.

overall_design: RNA-seq profiles of human UC-MSCs co-culture with UCB-CD34+ cells on day 3 and human UC-MSCs culture in medium alone.

first: Kittisak

last: Suanpan

first: Oytip

last: Nathalang

first: Suradej

last: Hongeng

first: Sawang

last: Petvises

first: Usanarat

last: Anurathapan


title: Loss-of-function mutations in the melanocortin-2-receptor (mc2r) lead to skin hyperpigmentation in teleost fish

city: Vigo

first: Laura

middle: Guerrero

last: Peña

state: Pontevedra

address: Eduardo Cabello, 8

department: Aquaculture and Biotecnology

institute: CSIC

summary: Melanocortins regulate pigmentation via melanocortin receptors (MCRs), which exhibit high conservation across zebrafish and humans. MC2R is distinctive among melanocortin receptors in that it is activated exclusively by ACTH and requires Mrap1 for optimal functionality, in contrast to other receptors that possess the capacity to bind diverse ligands. Although the melanocortin 1 receptor (MC1R) is well characterised for its role in pigmentation, the function of MC2R remains largely unknown. This study examines the influence of MC2R on pigmentation by generating MC2R knockout zebrafish using the CRISPR/Cas9 system. The results demonstrated that the mc2rKO mutants exhibited pronounced hyperpigmentation, characterised by an elevated number of melanophores and xanthophores, while preserving the distinctive striped pattern and dorsoventral countershading. Gene expression analyses show an increase in the expression of genes involved in melanosome synthesis and melanin production, contributing to a darker phenotype, as well as genes associated with lipid metabolism and carotenoid accumulation, which result in enhanced yellow coloration. These results suggest that mc2r plays a role in modulating the development, distribution and metabolic activity of pigment cells.

overall_design: RNA-seq profiling of wild-type and mc2r gene knockout zebrafish

first: Elisa

last: Barreiro-Docío

last: Guerrero-Peña

first: Pryanka

last: Soni

first: Luis

last: Méndez-Martínez

first: Carolina

last: Costas-Prado

first: José

middle: A

last: Vázquez

last: Cerdá-Reverter

first: Josep

last: Rotllant


title: Supplement and refinement the standard and analysis of primary human hepatocytes.

first: Xinyang

last: Jia

address: haike street 501

institute: Shanghai Institute of Materia Medica

summary: We use high-throughout single-cell RNA sequencing technology to analyze primary human hepatocytes, combining with LC-MS/MS for drug-metabolizing function research. We measure the enzymatic metabolic function of PHH and perform a correlation analysis with the values documented in the quality inspection report. Furthermore, we assess functions beyond cellular metabolism as specified in the PHH standards. These additional functions include bile secretion, albumin (ALB) secretion, and cell purity, which are not addressed in the quality inspection report. Additionally, we examine the impact of donor characteristics such as body weight, age, underlying health conditions, and lifestyle habits (including smoking and alcohol consumption) on cellular function. We aim to conduct a comprehensive analysis of the factors that influence cellular function. This research not only seeks to supplement and refine the standards of PHH but also aspires to provide a crucial reference for the application of PHH in the domains of disease research and drug development in the future.

overall_design: scRNA-seq of six donors of primary human hepatocytes to profile gene expression and facilitate the verification of cell purity and asses differences in drug-metabolizing enzyme function.

first: Zhaoliang

last: Peng


title: Cellular and molecular evolutionary mechanisms of retinal cells governing color vision perception

city: guagnzhou

first: Zhibin

last: Li

address: tianhe

institute: The Third Affiliated Hospital of Sun Yat-Sen University

summary: Insights into the cellular and molecular evolutionary mechanisms of retinal cells that govern color vision perception across various species are limited. In this study, we established a single-cell prediction (scPred) model to construct an atlas of single-cell retinas from multiple species and subsequently analyzed interspecies variations in the retinal cells of 24 different species. We identified conserved compositions and expression profiles of retinal cells, with photoreceptor cells, including rods, showing dynamic changes from lower to higher species. Moreover, we observed marked interspecies variations in opsin expression patterns and core transcriptional programs that regulate color vision in rods and cones. We also identified distinct cell metabolism patterns and key transcription factors influencing the cell functional difference of different cone types. Notably, our findings indicated an association between fatty acid biosynthesis and OPN1SW+ cones and OPN1MW+ cones, as well as an association between FOXO3 and OPN1LW+ cones across species.

sample_organism:
Oreochromis
Anas platyrhynchos
Gallus gallus
Felis catus
Melopsittacus undulatus
Channa argus

overall_design: Supplementary six Retinas samples were freshly dissociated and analyzed using scRNA-seq

first: Wei

middle: I

last: Qiu


title: Eosinophils are mediators of adipose tissue angiogenesis

city: Sydney

first: Kate

last: Quinlan

state: NSW

address: Room 3102, Level 3, Biosciences South Building (E26)

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: UNSW Sydney

summary: Adipose eosinophils confer protection against obesity and metabolic disease, yet the mechanism by which adipose eosinophils mediate this process is incompletely understood. Here we found that transgenic elevation of adipose eosinophil number results in increased adipose tissue levels of vascular endothelial growth factor A (VEGFA), with resulting elevation in adipose tissue vascularisation and production of thermogenic beige fat. We found that this process is directly regulated by Activator Protein 1 (AP-1) family member activating transcription factor 3 (ATF3), with eosinophil-specific deletion of ATF3 both in vitro and in vivo resulting in decreased adipose tissue VEGFA, reduced adipose tissue vascularisation, and decreased thermogenic beige fat. We thus propose a novel mechanism by which eosinophils promote metabolic homeostasis and highlight ATF3 as a key driver of adipose eosinophil tissue specialisation.

overall_design: RNA-seq profiling of wild type EoL-1 cell and their knockdown derivative (ATF3)

first: Annalise

last: Psaila

first: Tsz Ho

first: Nadia

last: Iannarella

first: Rhys

last: Allan

first: Jennifer

last: Felton

first: Julie

last: Caldwell

first: Marc

last: Rothenberg


title: JUN and JUN/ATF3 knockout EoL-1 RNA-seq

summary: To study the effect of knocking out transcription factor JUN or both JUN and ATF3 in EoL-1 cells

overall_design: RNA-seq profiling of JUN and JUN/ATF3 knockout EoL-1 cells


title: CEBPA repression by MECOM blocks differentiation to drive aggressive leukemias [PRO-Seq]

city: Boston

first: Travis

last: Fleming

state: MA

address: 1 Blackfan St

department: Hematology/Oncology

institute: Boston Children's Hospital

summary: Acute myeloid leukemias (AMLs) have an overall poor prognosis and many high-risk cases co-opt stem cell gene regulatory programs, yet the mechanisms through which this occurs remain poorly understood. Increased expression of the stem cell transcription factor, MECOM, underlies one key driver mechanism in largely incurable AMLs. How MECOM results in such aggressive AML phenotypes remains unknown. To address existing experimental limitations, we engineered and applied targeted protein degradation with functional genomic readouts to demonstrate that MECOM promotes malignant stem cell-like states by directly repressing pro-differentiation gene regulatory programs. Remarkably and unexpectedly, a single node in this network, a MECOM-interacting regulatory element located 42 kb downstream of the myeloid differentiation regulator CEBPA is both necessary and sufficient for MECOM-driven leukemogenesis. Importantly, targeted activation of this regulatory element promotes differentiation of these aggressive AMLs and reduces leukemia burden in vivo, suggesting a broadly applicable differentiation-based approach for improving therapy.

overall_design: Nascent RNA-seq (PRO-seq) profiling of a MECOM-FKBP12F36V cell line (MUTZ-3) treated with 500nM dTAGV-1 or DMSO for 1-4 hrs during in vitro culture.

first: Vijay

last: Sankaran


title: OpenTn5: Open-Source Resource for Robust and Scalable Tn5 Transposase Purification and Characterization [sciATAC-Seq]

city: New York

first: Viviana

middle: I.

last: Risca

state: NY

address: 1230 York Ave, Box 176

department: Laboratory of Genome Architecture and Dynamics

institute: The Rockefeller University

summary: Tagmentation is an efficient approach for sequencing library preparation, which combines DNA fragmentation by transposition of sequencing adapters, using the bacterial cut-and-paste transposase Tn5. Here we present an open-source protocol for the generation of multi-purpose hyperactive Tn5 transposase, including its benchmarking in CUT&Tag, bulk and single-cell ATAC-seq. The OpenTn5 protocol yields multi-milligram quantities of pG-Tn5E54K, L372P protein per liter of E. coli culture, sufficient for thousands of tagmentation reactions and the enzyme retains activity in storage for more than a year.

overall_design: To determine if the performance of in-house pG-Tn5 is comparable to commercial pAG-Tn5 from Epicypher (SKU: 15-1017), we performed CUT&Tag using both enzymes to profile the distribution of H3K27me3 and H3K27ac histone modifications in MCF7 cells. To compare the performance of pG-Tn5 with commercially available Tn5 (Illumina TDE1, CAT: #20034198), we conducted ATAC-seq experiments in MCF7 and K562 human cell lines with matched enzyme volumes. We also performed an in-house pG-Tn5 transposome titration in K562 cells to understand how varying pG-Tn5 enzyme concentration influences ATAC-seq signal globally. We also demonstrated pG-Tn5 can be readily applied to sensitive emerging applications that require custom adapter loading, such as EasySci-ATAC, which was performed in MCF7 cells.

first: Jan

last: Soroczynski

first: Lauren

last: Anderson

first: Joanna

last: Yeung

first: Justin

last: Rendleman

first: Deena

last: Oren

first: Hide

last: Konishi


title: CEBPA repression by MECOM blocks differentiation to drive aggressive leukemias [ChIP-Seq]

overall_design: ChIP-seq profiling of MECOM and H3K27ac chromatin occupancy in a MECOM-FKBP12F36V cell line (MUTZ-3) treated with 500nM dTAGV-1 or DMSO for 6 hrs during in vitro culture.


title: Untreated Rat Cardiac Ventricular tissue Age

city: Liverpool

first: Richard

last: Barrett-Jolley

address: 6 West Derby Street

institute: University of Liverpool

summary: The objective of this study was to investigate changes in rat cardiac ventricle transcriptome with age.  It was run along similar with other tissues to look for common ageing signatures. Particular interest would be cardiomyocytes, but this is bulk RNA-sequencing.

overall_design: 3 Young adult rats compared with 3 old adult rats. Only males were available.

first: Fiona

last: O'Brien

first: Caroline

last: Staunton


title: Distinct hepatocyte adaptations during gestation and lactation [pregnant_liver_mm10_10x]

first: Cheng-ran

last: Xu

summary: The liver undergoes adaptive changes during pregnancy and lactation to meet specific physiological demands, but the precise processes, regulatory mechanisms, and functions remain unclear. Using high-resolution single-cell RNA sequencing (scRNA-seq), we comprehensively analyzed hepatocyte adaptations in mice throughout these periods. Our findings revealed a circular trajectory, termed the “pregnancy clock”, during gestation and non-lactating postpartum phases, reverting to the pre-gestation state after recovery. In contrast, lactation induced a distinct branching pathway, characterized by increased fatty acid synthesis and lipid accumulation. Deletion of Gp130 in the JAK/STAT pathway disrupted gestation transitions, leading to delayed embryonic development, while ACSS2 ablation impaired postpartum lipid metabolism, affecting milk quality and offspring growth. Comparative analysis with sheep demonstrated conserved hepatocyte adaptation pathways despite species-specific genetic regulatory networks. These insights offer potential targets for therapeutic interventions to optimize maternal and fetal health and enhance lactation efficiency, with broad implications for reproductive biology and livestock management.

overall_design: 10x Genomics scRNA-seq of mouse liver at gestational stages G0 and G14.5.

first: Li

last: Yang

first: Yu

last: Zhang

first: XinXin

last: Yu

first: YuHeng

last: Zhou

first: Shuang

last: He

first: Liu

first: TongYun

last: Mao

first: JunGe

first: Ying

last: Wu

first: QiQi

last: Zheng

first: ChengRan


title: Distinct hepatocyte adaptations during gestation and lactation [pregnant_liver_mm10_CUT_RUN]

overall_design: STAT3 CUT&RUN in G14.5 Il6st WT and KO hepatocytes, and H3K27ac CUT&RUN in P4-L Acss2 WT and KO hepatocytes.


title: CEBPA repression by MECOM blocks differentiation to drive aggressive leukemias [ATAC-Seq]

first: Travis

last: Fleming

overall_design: ATAC-seq profiling of MECOM-FKBP12F36V cell lines (MUTZ-3, UCSD-AML1, HNT-34, and OCI-AML4) treated with 500nM dTAGV-1 or DMSO during in vitro culture.

first: Vijay

last: Sankaran


title: OpenTn5: Open-Source Resource for Robust and Scalable Tn5 Transposase Purification and Characterization [ATAC-Seq]

first: Viviana

last: Risca

first: Jan

last: Soroczynski

first: Lauren

last: Anderson

first: Joanna

last: Yeung

first: Justin

last: Rendleman

first: Deena

first: Hide


title: Single-cell sequencing data on decidua and chorionic villi in the human placenta

first: Zehua

last: Zeng

state: State...

address: 49 Huayuan North Road, Haidian District, Beijing

department: Department of Obstetrics and Gynecology

institute: Peking University Third Hospital

summary: The human placenta (the extra-embryonic organ in which the fetus is made) is essential for conception and protection of the fetus during pregnancy. Extravillous trophoblasts (EVT) from placental villi infiltrate the decidua and convert maternal arteries into high-conductance vessels. Defects in trophoblast invasion and arterial conversion in early pregnancy are at the root of common pregnancy disorders such as preeclampsia. Here, we generated ecdysone and chorionic monocytic profiles across different gestational weeks spanning the 22-45 year age range, which allowed us to resolve the differentiation trajectory of trophoblast cells at implantation and its relationship with maternal age. We used this age atlas to identify age nodes of placental implantation change, revealing patterns of EVT implantation in advanced versus normal maternal age. Our data provide a comprehensive analysis of post-bedding trophoblast cell differentiation and may inform the design of experimental models of the placenta in early human pregnancy.

overall_design: To investigate the interaction between meconium and chorionic villi in the placenta during early pregnancy, we performed scRNA-seq on meconium and chorionic villi, respectively, in 22-42 year old pregnant women spanning 6-10 weeks.

first: Guanlin

last: Li

first: Ping

first: Yang


title: OpenTn5: Open-Source Resource for Robust and Scalable Tn5 Transposase Purification and Characterization [CUT&Tag]

last: Oren

last: Konishi


title: Distinct hepatocyte adaptations during gestation and lactation [sheep_SmartSeq3]

first: Cheng-ran

last: Xu

overall_design: scRNA-seq of sheep hepatocytes during gestation and puerperium days.

first: Li

last: Yang

first: Yu

last: Zhang

first: XinXin

last: Yu

first: YuHeng

first: Shuang

first: Liu

first: TongYun

first: JunGe


city: guangzhou

first: Zhibin

address: tianhe road 600

sample_organism:
Ctenopharyngodon idella
Oreochromis mossambicus
Ambystoma mexicanum
Anas platyrhynchos
Gallus gallus
Serinus canaria
Macaca fascicularis
Homo sapiens
Canis lupus familiaris
Mustela putorius furo
Felis catus
Sus scrofa
Mesocricetus auratus
Meriones unguiculatus
Mus musculus
Rattus norvegicus
Cavia porcellus
Melopsittacus undulatus
Atelerix algirus
Trachemys scripta elegans
Tamias sibiricus
Pantherophis guttatus
Pogona vitticeps
Channa argus

overall_design: 25 Retinas samples from 24 species were freshly dissociated and analyzed using scRNA-seq

first: Wei

last: Qiu


title: CRISPRa screen with SARS-CoV-2 authentic virus in HEK293-ACE2

city: Camperdown

first: G.

middle: Greg

last: Neely

address: Charles Perkins Centre, D17.

institute: University of Sydney

summary: These studies used CRISPR-activation in order to identify genes that could confer increased survival to SARS-CoV-2. To do this, a clonal cell line expressing ACE2 and CRISPR-activation (Suntag) machinery was engineered. Then the Weismann library of activating guides was used to infect these populations at a ~2000 coverage. Diversity and experimental controls were used for analysis

overall_design: HEK293-ACE2 cells were infected using the Weissman CRISPRa sgRNA library. Two experiments per condition were set up. Controls show the diversity, while experimentals were collected from surviving cells exposed to a 50% lethal dose of SARS-CoV-2 (wuhan)

first: Cesar

last: Moreno

first: Felicity

last: Chung

first: Alberto

middle: O

last: Stella

first: Graham


title: CEBPA repression by MECOM blocks differentiation to drive aggressive leukemias [RNA-Seq]

first: Travis

last: Fleming

overall_design: RNA-seq profiling of MECOM-FKBP12F36V cell lines (MUTZ-3, UCSD-AML1, HNT-34, and OCI-AML4) treated with 500nM dTAGV-1 or DMSO for 6-24 hrs during in vitro culture.

first: Vijay

last: Sankaran