title: Exosomal STK39 is a Predictive Biomarker for Anti-VEGF Treatment Response in Neovascular Age-Related Macular Degeneration

city: Bursa

first: Ceyda

last: Colakoglu Bergel

address: Görükle Kampüsü, Nilüfer

country: Turkey

institute: Bursa Uludag University

summary: Background: Age-related macular degeneration (AMD) is the leading cause of blindness worldwide, predominantly affecting individuals over 60. AMD is classified into two clinical forms: dry (DAMD) and neovascular (NAMD). NAMD, characterized by choroidal neovascularization and increased vascular endothelial growth factor (VEGF) levels, is treated with anti-VEGF therapy, the gold standard for preventing vision loss. However, challenges including non-response to treatment, persistent disease activity, and unnecessary anti-VEGF administration necessitate the identification of predictive biomarkers to optimize therapy. Exosomes (exo) are extracellular vesicles known for their stability and role in cellular communication, carrying diverse molecular contents, including RNA. Although the role of exo-RNA in AMD pathogenesis is well known, their role in the response to anti-VEGF treatment has not yet been investigated. Current study aim to investigate the role of exo-RNAs as potential biomarkers for predicting anti-VEGF treatment response in NAMD patients. Methods: Plasma-derived exo-RNA were analyzed pre- and post-treatment to identify predictive biomarkers from 41 NAMD patients treated with intravitreal bevacizumab. Exo were isolated using exoRNAeasy midi kit and characterized by TEM, NTA, and Western blot. Then, RNA-seq was performed to profile exo-RNAs and key candidates were validated using RT-qPCR. Results: Following anti-VEGF therapy, 68.3% of NAMD patients (mean age: 70.8 ± 6.14), demonstrated anatomical success, while 53.7% achieved functional success. Based on RNA-seq comparative analysis between the two groups revealed that translation mechanisms were significantly regulated, particularly within the context of upregulated pathways. Genes associated with molecular functions such as insulin response, transport, angiogenesis, and oxygen transport were prominently implicated. Conversely, the evaluation of downregulated pathways indicated substantial alterations in RNA catabolic processes and the regulation of gene expression. RNA-seq revealed BMP6 and STK39 as key candidate genes, with post-treatment dysregulation in hsa-miR-4692 expression, a microRNA targeting STK39. Finally, RT-qPCR validation show that elevated pre-treatment exo-STK39 levels were significantly associated with anatomical success (*p=0.04).

overall_design: RNA-seq analysis was performed to evaluate the effect of anti-VEGF treatment on exo-RNA regulation in NAMD patients. For RNA-seq analysis, a cohort of 5 anti-VEGF(-) and 4 anti-VEGF(+) patients were selected to evaluate the treatment response at the exo-mRNA and exo-miRNA levels. Following treatment, one patient was excluded from the analysis due to suboptimal read quality, resulting in a final analysis of 5 anti-VEGF(-) and 4 anti-VEGF(+) patients. For the miRNA analysis, 3 anti-VEGF (-) and 3 anti-VEGF(+) patients were selected, based on the quality of small RNA sequencing data, ensuring comparable read quality across both groups. The most optimal exo- RNA candidate at the mRNA level was identified by analyzing the pathways, interactions, and external regulations associated with the obtained miRNA data. This approach allowed for the  determination of key biological processes and regulatory networks in which the miRNA- derived exo-RNAs were involved, thereby facilitating the identification of the most relevant candidate for further investigation. Total RNA isolation was performed using the QIAGEN exoRNeasy Midi kit (Qiagen, Hilden, Germany). RNA quality and concentrations were analyzed using Agilent Technologies 4200 TapeStation (Agilent Technologies, Santa Clara, California, USA). To perform RNA sequencing, mRNA and small RNA libraries were generated using the Illumina NextSeq 500 platform with the SMARTer smRNA-Seq Kit (Illumina, Takara Bio, Shiga, Japan) based on the manufacturer’s instructions. The libraries were gel-purified using the D1000 ScreenTape System (Agilent Technologies, Waldbronn, Germany). Then, RPKM-normalized count were used for analysis to identify differentially expressed genes and mature miRNAs between anti- VEGF (-) vs anti-VEGF (+). A p-value correction was performed using the false discovery rate (FDR) correction determined for each gene or miRNA. The cut- off value for the adjusted p- value was accepted at 0.05, Dysregulated genes/miRNAs were determined by fold changes.

first: Semih

last: Ozmen

first: Isil Ezgi

last: Eryilmaz

first: Bilge

last: Ariöz

first: Unal

last: Egeli

first: Duygu

last: Erdem

first: Guven

last: Ozkaya

first: Gulsah

last: Cecener

first: Selim

last: Doganay


title: Malignant transformed cells of bladder epithelium: control CdC12-V2 vs NSUN6-knockout Malignant transformed cells of bladder epithelium

status: Public on May 13 2025

city: Guangzhou

first: Ying

last: Xiaoling

address: 250 Changgang east road, Guangzhou

country: China

institute: The second affiliated Hospital of Guangzhou Medical University

summary: m5C-specific methylated small RNA immunoprecipitation microarray analysis in CdC12-V2 vs NSUN6-knockout Malignant transformed cells of bladder epithelium

overall_design: 1-5 μg of each total RNA sample was immunoprecipitated by 4 μg anti-5-methylcytosine antibody (Mab-006-500) with 1 mg DynabeadsTM M-280 Sheep Anti-Mouse IgG (Invitrogen, 11201D) in 500 μL RIP buffer. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”. The “IP” and “Sup” RNAs were enzymatically labeled with Cy5 and Cy3 respectively in separate reactions using Arraystar’s standard protocols. The labeled RNAs were combined together and hybridized onto Arraystar Human small RNA Modification Microarray (8x15K, Arraystar) and the array was scanned in two-color channels by an Agilent Scanner G2505C.

first: Xiaoling

last: Ying

first: Yapeng

last: Huang


title: RNA-seq analysis of grape-like organoids and others in iPSC derived Hepatocyte organoids (iHOs)

city: bunkyo-ku

first: Masato

last: Miyoshi

address: yushima

department: Gastroenterology

country: Japan

institute: Tokyo Medical and Dental University

type: Expression profiling by high throughput sequencing

summary: Under iHO conditions, distinctive grape-like organoids emerge. To evaluate the hepatocyte characteristics of grape-like organoids and other organoid forms, grape-like organoids were isolated under a microscope, and RNA-seq was performed.

overall_design: The iHOs around 14 days after passage were isolated from Matrigel in ice-cold PBS and grape-like organoids were visually collected under a microscope for RNA-Seq. Remaining organoids were collected as others.

first: Taro

last: Shimizu

first: Sei

last: Kakinuma


title: Bladder epithelial cells with different degrees of malignancy: SV1 vs SV1 Cdcl2 vs T24

summary: m5C-specific methylated small RNA immunoprecipitation microarray analysis in SV-HUC-1, Cd-SV-HUC-1 and T24 cells


title: Mismanagement of Cellular Iron Leads to Ferroptosis Susceptibility in Cancer Cells Surviving Chemotherapy

city: Baltimore

first: Sarah

middle: R

last: Amend

state: MD

address: 600 N Wolfe St

department: Brady Urological Institute

country: USA

institute: Johns Hopkins University

summary: Despite centuries of research, metastatic cancer remains incurable due to resistance against all conventional cancer therapeutics. Alternative strategies leveraging non-proliferative vulnerabilities in cancer are required to overcome cancer recurrence. Ferroptosis is an iron dependent cell death pathway that has shown promising pre-clinical activity in several contexts of therapeutic resistant cancer. However, ferroptosis sensitivity is highly variable across tissue types and cell state posing a challenge for clinical translation. We describe a convergent phenotype induced by chemotherapy where cells surviving chemotherapy have similar transcriptomic signatures and dysregulated iron homeostasis, regardless of initial cell type or chemotherapy used. Elevated labile iron levels are counteracted by NRF2 signaling that does not alleviate the amount of labile iron. Selectively inhibiting GPX4 leads to uniform susceptibility to ferroptosis in surviving cells, highlighting the common reliance on lipid peroxidation defenses. Cellular iron dysregulation is a vulnerability of chemoresistant cancer cells that can be leveraged by triggering ferroptosis

overall_design: MDA-MB-231 (breast cancer cell line) were treated with chemotherapy (cisplatin or docetaxel) and surviving cells were analyzed 1, 5 and 10 days following chemotherapy (DPT). SIngle cell RNA sequencing was performed on untreated cell lines and surviving cells 1, 5, and 10 DPT in biological triplicate. Parse Biosciences sequencing is done by combinatorial barcoding, whereby cells from every sample type is present in each sublibrary. Sublibraries are sequenced and individual cells called by barcode identifier.

first: Luke

middle: V

last: Loftus

first: Christopher

last: Cherry.

first: Michael

last: Patatanian


title: Multi-omics insights into the response of Aspergillus parasiticus to long-chain alkanes in relation to polyethylene modification

city: Athens

first: Romanos

last: Siaperas

address: 9 Iroon Polytechniou str.

department: School of Chemical Engineering

country: Greece

institute: National Technical University of Athens

summary: In this study, we employed a multi-omics approach to study the ability of Aspergillus parasiticus MM36, an isolate derived from Tenebrio molitor intestines, to metabolize long-chain alkanes (lcAlk) and secrete enzymes able to modify polyethylene (PE). Following genome sequencing, assembly, and annotation the fungus was grown with hexadecane (C16) or a mixture of long-chain alkanesl (C24 to C36) as carbon sources and secretomes were tested for their ability to modify PE to select timepoints for the multi-omics analysis. The selected conditions were lcAlk after days 2 and 3 and C16 after day 3. Transcriptomic analysis comparing lcAlk to C16 cultures highlighted the enrichment of oxidoreductase activities and carboxylic acid metabolism in both lcAlk days, with transmembrane transporters and transferases predominating on day 2 and biosynthetic processes on day 3. In C16 cultures, hydrolytic enzymes, including esterases, were upregulated alongside Baeyer-Villiger monooxygenases, suggesting a shift toward sub-terminal hydroxylation. Integrating transcriptomic and secretomic data, we propose a mechanism for lcAlk assimilation by A. parasiticus MM36, involving extracellular oxyfunctionalization, hydrocarbon uptake via surface-modifying proteins and channeling through membrane transporters for energy consumption and biosynthesic processes.

overall_design: Aspergillus parasiticus MM36 was grown in liquid cultures using mineral medium either supplemented with hexadecane (C16) or a mixture of long-chain alkanes (lcAlk), ranging from C24 to C36, dissolved in hexadecane. Three different conditions were chosen based on the ability of A. parasiticus MM36 secretomes to modify low density polyethylene structure over time. These conditions include hexadecane cultures after 3 days and lcAlk cultures after 2 and 3 days. We conducted RNA-seq at the three conditions in triplicates, however one hexadecane sample with a RIN value of 3.7 was discarded leaving this condition with two replicates.

first: George

last: Taxeidis

first: Anastasia

last: Gioti

first: Efstratios

last: Nikolaivits

first: Evangelos

last: Topakas


title: Transcriptome profiles of neonatal intestinal organoids under fibroblast coculture with or without LPS sitimulation and tryptophan metabolites intervention

city: Shanghai

first: Yihuang

address: No.399, Wanyuan Road, Minhang District

institute: Children's Hospital of Fudan University

summary: We performed RNA sequencing to identify the role of fibroblast in the effects of tryptphan metabolites on LPS-stimulated mouse neonatal intestinal organoids.

overall_design: The neonatal intestinal organoids were passaged and seeded into 24-well plates. Concurrently, fibroblasts were passaged and seeded into 0.4 µm pore-size transwell inserts, which were then placed into the wells containing organoids. The co-cultures were treated with lipopolysaccharide (LPS, 200 µg/mL), ILA or IAA (each at 6 µM), and/or AhR antagonist CH223191 (1 µM), based on the experimental conditions.

first: Luyang

last: Hong

first: Shangyu

first: Yun

last: Cao


title: Benchmark of chromatin-protein interaction methods in haploid round spermatids

city: Nanjing

first: Peng

last: Hua

state: Jiangsu

address: 101 Longmiandadao

department: State Key Laboratory of Reproductive Medicine and Offspring Health

institute: Nanjing Medical University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Chromatin-protein interactions are fundamental for the regulation of gene transcription. While ChIP-seq has long been the standard method for mapping these interactions, emerging techniques such as CUT&RUN and CUT&Tag, which offer advantages including low input requirements and high signal-to-noise ratios, have garnered attention. However, these enzyme-based tagmentation approaches may introduce potential biases, and comparative assessment with ChIP-seq remain absent. This study aims to systematically evaluate and compare the performance of ChIP-seq, CUT&Tag, and CUT&RUN for profiling genome-wide transcription factors and histone modifications binding. This study provides a comprehensive evaluation of ChIP-seq, CUT&Tag, and CUT&RUN for detecting active and repressive histone modifications as well as transcription factor binding. Our results show that all three methods reliably detect histone modifications and transcription factor enrichment, with CUT&Tag demonstrating a relatively higher signal-to-noise ratio. Rigorous peak comparison analysis identified differential enrichment sites detected by the three methods. Additionally, we observed a notable correlation between CUT&Tag signal intensity and chromatin accessibility, suggesting the potential for CUT&Tag to detect regions of active chromatin.

overall_design: ATAC-seq, CUT&Tag and CUT&RUN of histone modification H3K4me3, H3K27me3 and CTCF in round spermatids.


title: Transcriptome profiles of neonatal mouse intestinal organoids with or without LPS sitimulation and tryptophan metabolites intervention

summary: We performed RNA sequencing to identify the effects of tryptphan metabolites on LPS-stimulated intestinal fibroblast.

overall_design: Neonatal mouse intestinal organoids were cultured from C57B/L6 mice on postnatal day 8 and were treated with lipopolysaccharide (LPS, 100 µg/mL), ILA or IAA (each at 6 µM), and/or CH223191 (1 µM), based on the experimental conditions for 48 hours.


title: Phenotypic and Transcriptomic Profiling of Induced Pluripotent Stem Cell (iPSC)-Derived NK Cells and Their Cytotoxicity against Cancers

city: Bangkok

first: Methichit

last: Wattanapanitch

state: Bangkok

address: 2 Prannok rd., Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkoknoi

department: Research Department

country: Thailand

institute: Mahidol University

summary: Pluripotent stem cell-derived Natural Killer cells (iNK) hold great promise for adoptive immunotherapy for cancer. However, current protocols rely on embryoid body cultures, which pose technical challenges and increase costs. We developed an alternative differentiation method using monolayer culture systems, allowing for cost-effectiveness and control over cellular differentiation. These iNK cells have the ability to perform cytotoxic functions, capable of combating tumor cells. Herein, we performed single-cell RNA sequencing of our iNK cells and NK-enriched samples from human peripheral blood mononuclear cells (PBMCs) to validate and interrogate NK cell identity.

overall_design: Induced pluripotent stem cells were cultured and differentiated into iNK cells using multiple-stage induction within the hematopoietic lineage.

first: Nontaphat

last: Thongsin

first: Punn

last: Augsornworawat


title: Extracellular vesicles from antler blastema progenitor cells improve age-related phenotypes in rodents and nonhuman primates

city: Xi'an

first: Beibei

last: Yu

address: No. 157, Xiwu Road, Xincheng District, Xi'an City, Shaanxi Province

institute: The Second Affiliated Hospital, Xi’an Jiaotong University

summary: Antler blastema progenitor cell (ABPC) is a novel type of skeletal stem cells with strong stemness and renewal ability. Here, we discovered that ABPC-derived extracellular vesicles (EVsABPCs) can strongly rejuvenate aging tissues in aged mice and rhesus macaques (Macaca mulattas). We identified a variety of rejuvenating signals in EVsABPCs, which exhibited a robust in vitro ability to rejuvenate senescent bone marrow stromal stem cells. In vivo, EVsABPCs increased bone mineral density in femur by 2.4-fold in mice, and 1.53-fold in rhesus macaques. Besides, intravenous EVsABPCs significantly outperformed fetal-EVsBMSCs in improving physical performance, reducing systemic inflammation and rejuvenating major tissues of aged mice, with no observed immunological side effects. Notably, EVsABPCs showed similar rejuvenating effects in old rhesus macaques as in elderly mice. These findings suggest that ABPC is a novel and practical source of EVs containing unique rejuvenating factors and has considerable translational value for anti-aging interventions, particularly rejuvenation of aging bones.

overall_design: Nine monkeys were randomly divided into three groups, with three monkeys in each group, namely the Vehicle group (injected with PBS); EVs FBMS group (injection of EVs FBMSC); EVs ABPC group (injection of EVs ABPC)

first: Jinghui

last: Huang


title: Transcriptome profiles of RAW264.7 cells under fibroblast coculture with or without LPS sitimulation and tryptophan metabolites intervention

summary: We performed RNA sequencing to identify the role of fibroblast in the effects of tryptphan metabolites on LPS-stimulated RAW264.7 cells.

overall_design: Intestinal fibroblasts were cultured and passaged into 24-well plates. Separately, RAW264.7 cells were passaged and seeded into 0.3 µm pore-size transwell inserts, which were then placed into the 24-well plates containing the fibroblasts.  The co-cultures were then exposed to lipopolysaccharide (LPS, 100 µg/mL), indole lactic acid (ILA) or indole acetic acid (IAA) (each at 6 µM), and/or CH223191 (1 µM), depending on the experimental group.


title: Adipose-derived Stem cll and Stronal Vascular Fraction response to inflammation sc RNA seq

city: Providence

first: Eric

last: Darling

state: RI

address: 171 Meeting St

institute: Brown University

summary: The therapeutic potential of mesenchymal stem/stromal cells (MSCs) relies on their ability to modulate immune responses in disease and wound contexts. In this study, we present an analytical pipeline using established algorithms to better characterize the response of adipose-derived stem/stromal cells (ASCs) to in vitro inflammatory stimuli, which in turn has therapeutic benefit in the context of MSC cell therapies. By integrating single-cell RNA sequencing and bulk proteomics data of ASCs derived from the stromal vascular fraction of adipose tissue, we present a detailed characterization of the ASC response to inflammation and additionally introduce a method of relating phenotypes observed in exogenously stimulated culture conditions to subpopulations of in vivo cells. Our pipeline involves multiple benchmarks to establish concordance between single-cell and bulk assays to more comprehensively characterize the ASC response to inflammation. This study is the introduction of a practical and efficient approach to identify functionally homogeneous and therapeutically relevant cell populations from heterogeneous mixtures using computational strategies and provides deeper insight into the ASC response to inflammation.

overall_design: Stromal vascular fraction derived from human adipose tissue, as welll as passaged control (ctrl) and cytokine-stimulated (Stim) ASCs from one of the SVF donors. Stim cells were cultured in IFNg and TNFa fro 48 hours. Samples were all run on the 10x genomics single cell RNA sequencing platform.

first: Darling

last: Eric

first: Parsons

last: Adrienne

first: Ahsan

last: Nagib


title: RNA-seq analysis of SHP inducible human iPSC derived Hepatocyte organoids (iHOs)

first: Masato

last: Miyoshi

summary: To investigate the function of small heterodimer partner (SHP) in hepatocytes, we established Dox-inducible SHP overexpression iPSC cell lines and differentiated hepatocytes and cultured iPS-hepatocyte organoids (iHO). A comprehensive RNA-seq analysis was conducted.  performed comparative gene expression analysis using data obtained from iHO vehicle and iHO dox.

overall_design: After differentiation into iPS-derived hepatocytes, the cells were dissociated and seeded in matrigel semi-sphere. These cells were treated with 0,1 ug/mL doxycycline or vehicle. After about 2weeks of cultivation, grown organoids were harvested. Then total RNA was purified by RNeasy Mini. Then a library was prepared by Illumina TruSeq Stranded mRNA Sample Prep Kit. The data was obtained by Illumina NovaSeq.  Comparison with two condition (Dox or Veh) were performed.

first: Taro

last: Shimizu

first: Sei

last: Kakinuma


title: scRNA-seq analysis of human iPSC derived Hepatocyte organoids (iHOs) [scRNA-seq]

summary: Liver has abundant regenerative capacity, but hepatocytes cannot be cultured long-term in vitro. Activation of FXR signaling induced iHOs with both hepatocyte traits and proliferative potential. To investigate the transcriptomic analysis of iHOs, we performed bulk RNA-seq analysis of organoids in different passages and single cell RNA-seq analysis of iHOs. Compared to 2D-iPS-Heps and organoids in other culture conditions, iHOs have expression profiles more similar to primary human hepatocytes and human fetal liver cells. Single cell RNA-seq revealed iHOs have a fraction that co-expresses hepatocyte markers and proliferation markers.

overall_design: iPSC-derived organoids cultured under iHO and FO conditions were dissociated into single cells, and scRNA-seq was performed.


title: Transcriptome Analysis in Human Breast Milk and Blood in a Randomized Trial after Inactivated or Attenuated Influenza Immunization

city: Rockville

first: Johannes

last: Goll

address: 401 N Washington St

department: Bioinformatics Service Group

institute: The Emmes Company

summary: Transcriptomic signatures were identified in human peripheral blood mononuclear cells (PBMCs) and breast milk lymphocyte (BML) cells induced by trivalent inactivated influenza vaccine (TIV) or live attenuated influenza vaccine (LAIV) administered after delivery. We performed an RNA-Seq analysis on blood and breast milk samples from a subset of subjects enrolled in a randomized, double-blind controlled study in breastfeeding women who received either intranasal LAIV and intramuscular placebo, or intramuscular TIV and intranasal placebo (LAIV, n=10 and TIV, n=6). Differentially expressed genes, gene clusters, and enriched pathways were identified. We observed increased innate immune signaling responses in BML but not in PBMC at Day 28 for the LAIV group. We hypothesize that breastfeeding extended the innate response to LAIV via mucosal immunity. An association between an increased IgG antibody response in TIV vs. LAIV identified in the parent study using ELISA corresponded to IGHG1 immunoglobulin gene expression in Day 28 PBMCs.

overall_design:
This study seeks to understand the immunologic mechanisms of breast milk mediated protection by analyzing mucosal immunity via sequencing of breast milk lymphocyte cell RNA when subjects are immunized postpartum with LAIV versus TIV.
The primary goal of this study was to identify transcriptomic signatures using RNA-Seq in human peripheral blood mononuclear cells (PBMCs) and breast milk lymphocyte cells (BMLs) in response to TIV or LAIV after delivery.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

first: Elizabeth

middle: P

last: Schlaudecker

first: Travis

middle: L

last: Jensen

first: Casey

middle: E

last: Gelber

first: Phillip

middle: J

last: Dexheimer

first: Mark

middle: C

last: Steinhoff

first: David

middle: I

last: Bernstein

middle: B


title: RNA Sequencing of Human iPSC-Derived Hepatocyte Organoids (iHOs)

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

overall_design: Refer to individual Series


title: The methyltransferases METTL7A and METTL7B confer resistance of cancer cells to thiol-based histone deacetylate inhibitors (ATAC-Seq)

city: Bethesda

first: Pedro

last: Batista

address: 37 Convent Street Bldg 37

department: National Cancer Institute

institute: National Institutes of Health

summary:
Histone deacetylase inhibitors (HDI) are among the growing class of epigenetic therapies used for the treatment of cancer. Although histone deacetylase inhibitors (HDIs) are effective in the treatment of T-cell lymphomas, solid tumors are largely resistant, and few mechanisms of resistance have been described. Overexpression of the multi-drug resistance gene ABCB1 that encodes P-glycoprotein (P-gp) is known to confer resistance to the HDI romidepsin, yet it is not associated with resistance in patients, suggesting other mechanisms of resistance arise in patients. To identify alternative romidepsin resistance mechanisms, we selected MCF-7 breast cancer cells with romidepsin in the presence of verapamil to reduce the chance of P-gp over-expression developing as a resistance mechanism. The resulting subline, MCF-7 DpVp300, does not express P-gp and was found to be selectively resistant to romidpesin but not other HDIs such as belinostat, panobinostat, or vorinostat. RNA sequencing analysis demonstrated upregulation of the putative methyltransferase, METTL7A, a paralog of which, METTL7B, was found to methylate thiol groups on hydrogen sulfide and captopril. We hypothesized that METTL7A could methylate and inactivate romidepsin as well as other HDIs with a thiol as the zinc binding group.
Here we show that expression of METTL7A is necessary for thiol-based HDI resistance in the MCF-7 DpVp300 cell line, and that expression of METTL7A or METTL7B in sensitive cells confers resistance to thiol based HDIs. We thus propose that METTL7A and METTL7B confer resistance to thiol-based HDIs by methylating and inactivating the zinc-binding thiol.

overall_design: ATAC-seq with 20,000 cells per sample using Corces et al,

first: Robert

middle: W

last: Robey

first: Christina

middle: M

last: Fitzsimmons

first: Wilfried

last: Guiblet

first: William

last: Frye

first: Jose

last: Gonzalez Dalmasy

first: Li

last: Wang

first: Lyn

last: Huff

first: Fatima

last: Ali-Rahmani

first: Crystal

last: Lipsey

first: Heidi

last: Wade

first: Allison

last: Mitchell

first: Siddhardha

middle: S

last: Maligireddy

first: Lisa

last: Jenkins

first: Tatiana

last: Nikitina

first: Victor

last: Zhurkin

first: Anthony

middle: D

last: Piscopio

first: James

last: Winkler

first: Susan

last: Bates

first: H

last: Arda

first: Michael

last: Gottesman


title: The methyltransferases METTL7A and METTL7B confer resistance of cancer cells to thiol-based histone deacetylate inhibitors (Mnase-Seq)

first: Pedro

last: Batista

overall_design: Mnase-Seq

first: Robert

last: Robey

first: Christina

last: Fitzsimmons

first: Wilfried

last: Guiblet

first: William

last: Frye


title: The methyltransferases METTL7A and METTL7B confer resistance of cancer cells to thiol-based histone deacetylate inhibitors (RNA-Seq)

overall_design: RNAseq of Total RNA from drug resistant and parental cell lines, triplicate data

first: Jose

last: Gonzalez Dalmasy

first: Li

last: Wang

first: Lyn

last: Huff

first: Fatima

last: Ali-Rahmani

first: Crystal

last: Lipsey


title: Targeting AURKA to induce synthetic lethality in CREBBP-deficient DLBCL via attenuation of MYC expression

first: Jianfeng

last: Chen

state: Shanghai

address: 270 Dong'an Road

institute: Fudan University Shanghai Cancer Center

summary: Loss-of-function mutations in CREBBP, which encodes for a histone acetyltransferase, occur frequently in diffuse large B-cell lymphoma (DLBCL), highlighting CREBBP deficiency as an attractive therapeutic target. Using established isogenic DLBCL cell models, we demonstrated that CREBBP deficient cells are selectively vulnerable to AURKA inhibition. Mechanistically, we found that co-targeting CREBBP and AURKA suppressed MYC transcriptionally and post-translationally induce replication stress and apoptosis. Inhibition of AURKA dramatically decreased MYC protein level in CREBBP-deficient cells, implying a dependency on AURKA to sustain MYC stability. Furthermore, in vivo studies showed that pharmacological inhibition of AURKA was efficacious in delaying tumor progression in CREBBP-deficient cells and was synergistic with CREBBP inhibitors in CREBBP-proficient cells. Our study sheds light on a novel synthetic lethal interaction between CREBBP and AURKA, indicating that targeting AURKA represents a potential therapeutic strategy for high-risk DLBCL harboring CREBBP inactivating mutations.

overall_design: RNA-seq for  SC1 treated with DMSO, alisertib, SGC-CBP30 and combination was performed (duplicate).

first: Yichen

last: Sun

first: Rong

last: Xiao

first: Choon

middle: K

last: Ong

first: Jing

last: Tan


title: Multi-modal skin atlas associates a multicellular immune-stromal community with altered cornification and T cell expansion in atopic dermatitis [scATAC-seq]

city: Cambridge

first: Evgenij

last: Fiskin

state: MA

address: 415 Main St

institute: Broad Institute of MIT and Harvard, Massachusetts General Hospital

summary: In healthy skin, a cutaneous immune system maintains balance between tolerance towards innocuous environmental antigens and immune responses against pathological agents, but in atopic dermatitis (AD), barrier and immune dysfunction result in chronic tissue inflammation. Our understanding of the skin tissue ecosystem in AD remains incomplete, including pathological barrier formation, and cellular state and clonal composition of disease-promoting cells. Here, we generated a multi-modal cell census of 310,691 cells from 86 cell subsets from whole skin tissue of 19 adult individuals, including non-lesional and lesional skin from 11 AD patients, and integrated it with 396,321 cells from 4 studies into a comprehensive atlas. Lesional skin comprised a unique immune and stromal multicellular community that included populations of MMP12+ DCs, mature migratory DCs, cycling ILCs, NK cells, inflammatory CCL19+ IL4I1+ fibroblasts, and clonally expanded IL13+IL22+IL26+ T cells with overlapping type 2 and type 17 characteristics, connected by multiple inter-cellular positive feedback loops. Reconstruction of human keratinocyte differentiation from basal to cornified layers revealed a disrupted cornification trajectory in AD associated with signals from the disease-associated immune compartment. AD GWAS gene expression was enriched in cornified keratinocytes, IL13+IL22+IL26+ T cells, and ILCs, suggesting that epithelial or immune dysfunction can initiate and then converge towards AD. Our work highlights specific, disease-associated cell subsets and interactions as potential targets in progression and resolution of chronic inflammation.

overall_design:
3mm patient biopsies from healthy donors, non-lesional and lesional biopsies from atopic dermatitis patients or scleroderma patients were enzymatically dissociated and analyzed using 10x Genomics 3' scRNA-seq platform using Chromium 3’- v3 chemistry or 10x Genomics scATAC-seq platform using Chromium ATAC- v1.1 chemistry or 10x Genomics 5' scRNA-seq and VDJ platform using Chromium 5’- v1.1 chemistry. Murine samples were processed the same, but constituted dorsal skin that was either treated with MC903 to induce AD-like skin inflammation or left untreated as control.
***Please note that raw data is to be made available through dbGaP (controlled access) due to human subject privacy concerns***

first: Gokcen

last: Eraslan


title: Multi-modal skin atlas associates a multicellular immune-stromal community with altered cornification and T cell expansion in atopic dermatitis [scRNAseq_VDJ]


title: RNA-seq analysis of human iPSC derived Hepatocyte organoids (iHOs), 2D-iPS-Heps, iPS-HPCs, iPSCs, and other iPSC derived organoids cultured in woBA medium and fetal organoid medium

first: Masato

last: Miyoshi

overall_design: Comparative gene expression profiling analysis of RNA-seq data for iHOs, organoids in other culture conditions, 2D-iPS-Heps, iPS-HPCs, and iPSCs. RNAs of iHOs and other organoids were extracted in different passages.

first: Taro

last: Shimizu

first: Sei

last: Kakinuma


title: Multi-modal skin atlas associates a multicellular immune-stromal community with altered cornification and T cell expansion in atopic dermatitis [scRNA-seq]

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Multi-modal skin atlas associates a multicellular immune-stromal community with altered cornification and T cell expansion in atopic dermatitis.


title: Genome-wide binding profile of PfSIP2 in Plasmodium falciparum

status: Public on May 12 2025

city: Nijmegen

first: Martijn

last: Broek

address: Geert Grooteplein 24, route 846

department: Molecular Biology

country: Netherlands

institute: Radboud university - RIMLS Science

summary: This dataset provides information regarding the genome-wide binding of the ApiAP2-type transcription factor PfSIP2 in the malaria parasite Plasmodium falciparum

overall_design: Genome-wide binding profile was assessed by Chromatin Immunoprecipitation seqenencing (ChIP-seq) using a 3D7 parasite line in which the endogenous PfSIP2 is tagged with GFP. This experiment was performed in a single replicate and hence the two different files represent sequencing the same libraries twice.

first: Igor

last: Niederwieser

first: Nicole

last: Bertschi

first: Till

last: Voss

first: Richard

last: Bartfai


title: The transcriptomics of phenotypic nonspecificity in Drosophila melanogaster

city: London

first: Gabriella

middle: Alves

last: Sidhu

state: Ontario

address: The Laurene O. Paterson Building, Western Science Centre

department: Biology

country: Canada

institute: Western University

summary: Transcription factor (TF) function is redundant as TF phenotypes are frequently rescued by TFs not resident to the TF locus, a phenomenon termed phenotypic nonspecificity.  Phenotypic nonspecificity is not dependent on the DNA binding specificity of the TFs and generally due to genetic complementation.  Two TF phenotypes (doublesex [dsx] and apterous [ap]) are rescued by multiple TFs, and the rescue and non-rescue by resident and non-resident TFs of these two phenotypes were used to distinguish between three possible outcomes of the comparison of the TF dependent mRNA accumulation in these two systems: first the sets of TF dependent mRNAs are independent and non-overlapping; second the sets of TF dependent mRNAs are independent and overlapping; and third the sets of TF dependent mRNAs are constrained and have extensive overlap.  The transcriptomes associated with rescue and non-rescue by resident and non-resident TFs of the two TF phenotypes (dsx and ap) provided many examples of extensive overlap indicating regulation of constrained sets of genes.  However, the strength of correlation of transcript accumulation observed between the resident and non-resident TFs was not a strong predictor of the ability of the TFs to rescue the phenotype.  The regulation of a constrained set of genes supports the hypothetical assembly of TFs into wolfpacks, and not the hypothetical limited specificity of TF function, as a potential explanation of phenotypic nonspecificity.

overall_design:
Transcription factors DSXF, BAB1, ANTP, EY, ODD, FOXO, and SQZ were expressed in Drosophila melanogaster pupal abomens lacking expression of DSX using the UAS-GAL4 expression system. RNA sequencing of abdomens, including those from wildtype (OreR) and mutant (w; dsx1/dsxGAL4) lines, was performed to determine differential gene expression.
Transcription factors AP, CAD, MYB, TTK, and SISA were expressed in Drosophila melanogaster wing imaginal discs lacking expression of AP using the UAS-GAL4 expression system. RNA sequencing of wing discs, including those from wildtype (y w) and mutant (y w; apnull/apGAL4) lines, was performed to determine differential gene expression.

middle: A

first: Anthony

last: Percival-Smith


title: Mitochondrial oxidative transport is inhibited by NDUFA4L2 to promote primary tumor escape [ATAC-Seq]

city: Nashville

first: w. Kimryn

middle: N.

last: Rathmell

state: TN

address: 1161 21st Avenue South

institute: Vanderbilt University Medical Center

summary: Metastases cause most cancer deaths and reflect cellular transitions from epithelial to mesenchymal states (EMT) that enable primary tumor escape to seeding and growth at metastatic sites. Rare cancer-driving mutations that disrupt mitochondrial oxidative metabolism (OxPhos) can promote EMT, yet molecular mechanisms that more broadly link metabolism to metastases are uncertain. Analyses of clear cell renal cell carcinoma (RCC) cells identified the hypoxia-induced mitochondrial electron transport inhibitor, NDUFA4L2, as highly enriched in cancer cells with EMT signatures. NDUFA4L2 suppressed OxPhos, altering levels of metabolites that govern chromatin accessibility of EMT-related loci. NDUFA4L2 specifically promoted cell escape from primary orthotopic RCC rather than colonization to drive lung metastasis. These results demonstrate OxPhos inhibition by NDUFA4L2 is essential for RCC cells undergoing EMT to escape primary tumors.

overall_design: ATAC-seq of murine renal cell carcinoma cell line (RENCA) with empty vector (EVP), NDUFA4L2 knocked out using CRISPR/CAS9 (KO), and NDUFA4L2 stably re-expressed in the knockout cell line (RES). 3 replicates were sequenced per cell line (except the KO, which only had two replicates).

first: Emily

last: Arner

first: W. Kimryn

first: Jeff


title: Mitochondrial oxidative transport is inhibited by NDUFA4L2 to promote primary tumor escape [RNA-Seq]

overall_design: RNA-seq of murine renal cell carcinoma cell line (RENCA) with empty vector (EVP), NDUFA4L2 knocked out using CRISPR/CAS9 (KO), and NDUFA4L2 stably re-expressed in the knockout cell line (RES). 3 replicates were sequenced per cell line (except the KO, which only had two replicates).


title: Raw RNA-sequencing data for deriving BCR sequences from the NIH U01 project: Finding the optimal balance of immunotherapy efficacy and toxicity.

city: Dallas

first: David

last: Gerber

state: Texas

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: IrAEs convey substantial morbidity, incur considerable costs, and in some cases may preclude further use of immune checkpoint blockades. Recent studies indicate that (1) up to 80% of individuals on ICIs experience some form of irAEs; (2) ~35% of patients require corticosteroid treatments to mitigate these events; and (3) up to 20% terminate their therapy due to irAEs. As immunotherapy use extends from major centers to smaller, isolated, and less experienced community sites, predicting the development of irAEs and incorporation of this prediction into ICI treatment considerations becomes extremely valuable. Despite the substantial efforts invested in machine learning models for predicting ICI treatment responses, few studies have focused on predictive modeling for irAEs. We address this unmet need by leveraging the unique patient resources collected at UTSW and developing a BCR-based biomarker for irAEs. Moreover, irAEs can happen as short as a few weeks or as long as a few years after ICI treatment. We deployed our model longitudinally to track if the evolution of autoreactive BCRs align with the timings of irAEs.

overall_design: The dataset contains RNA sequencing profiles from peripheral blood samples of patients receiving immune checkpoint inhibitor (ICI) treatments at UT Southwestern Medical Center. Blood was collected at three points: baseline, during immune-related adverse events (irAEs), and at scheduled intervals throughout treatment. A total of 256 samples were gathered from 113 patients who received anti-PD1, anti-PDL1, and/or anti-CTLA4 therapies, either as single agents or in combination. The research examines B cell receptor (BCR) repertoire changes during ICI therapy and their relationship to clinical outcomes, with special attention to irAE development. The Illumina TruSeq® Stranded mRNA Library preparation protocol was used for RNA sequencing, with samples sequenced on the Illumina NovaSeq 6000 platform using PE-150 sequencing protocol. The processed data files contain BCR sequences extracted from RNA-seq data using MiXCR, including heavy chain sequences from each patient sample, clonotype information (groups of similar BCR sequences from the same B cell lineage), and clonal expansion data (abundance of each BCR clonotype). These receptor files were utilized to: calculate BCR binding scores toward various antigens using the Cmai model, monitor BCR repertoire changes during treatment, explore relationships between BCR binding patterns and irAEs, and develop an irAE risk score based on predicted autoantibody binding.

first: Yang

last: Xie


title: Polycomb repressive complex 2 regulates sexual development in Neurospora crassa

first: Zachary

last: Lewis

state: GA

address: 120 E. Green St.

department: Microbiology

institute: University of Georiga

summary: In most branches of the fungal kingdom  sexual development marks a dramatic shift from simple multicellular hyphae to complex fruiting bodies composed of multiple tissues and cell types. It is essential to tightly regulate development to prevent unnecessary energy investment into building these structures. Polycomb Repressive Complex 2 (PRC2) is a highly conserved regulator of development in multicellular organisms. In plants  animals  and some fungi  PRC2 represses genes by depositing histone H3 lysine 27 tri-methylation (H3K27me3) in promoters and gene bodies of conditionally activated genes. In Neurospora crassa  H3K27me3-associated genes are poorly conserved and stably repressed in most RNA-seq datasets. Through analysis of publicly available RNA-seq experiments  we found that PRC2-methylated genes are broadly and uniquely activated during sexual development. PRC2-methylated genes comprise a distinct subset of developmentally induced genes (DIGs) characterized by an exceptionally high degree of cell-type specificity. Loss of PRC2 activity results in the precocious formation of perithecia-like structures (dubbed false perithecia)  even in the absence of a compatible mating-type partner. These structures show a unique gene expression profile with activation of both PRC2-methylated and unmethylated DIGs  showing evidence of a transcriptional reprogramming event. Together  these data suggest that PRC2 is part of a developmental checkpoint that restricts fruiting body development to the appropriate conditions.

overall_design: isogenic siblings were isolated from a backcross between FGSC11182 (set-7) and wild-type N. crassa. Individual wild-type and set-7 progeny were inoculated on plates containing SCM agar overlain with cellophane and grown at room temperature in constant darkness for 12 days. Tissue was harvested from the cellophane surface and then snap frozen and ground in liquid nitrogen. RNA was isolated using TRIzol reagent  using methods optimized for solid fungal tissue.

first: Abigail

last: Deaven

middle: R

last: Ameri


title: The cell wall controls stem cell fate in the Arabidopsis shoot apical meristem

city: Tübingen

first: Sebastian

last: Wolf

state: Baden-Württemberg

address: Auf der Morgenstelle 32, ZMBP, ZMBP

country: Germany

institute: ZMBP, Universität Tübingen

summary: At the basis of plant developmental plasticity are continuously active pluripotent stem cells, which fuel the life-long post-embryonic formation of new organs. Since plant cells are encased in cell walls and thus immotile, their individual fate-specification program is dependent on the relative position within the organism. It is assumed that the cell wall and its mechanical properties are under surveillance linking cell wall state to intracellular gene-regulatory networks. However, the role of these cell wall signalling pathways in plant development and the contribution of cell wall properties to cell behaviour and cell identity are unclear. Here, we show that control of cell wall properties is essential for the perpetuation of stem cell populations and pattering in the shoot apical meristems. The expression of pectin methylesterases (PMEs), which modify homogalacturonan methylesterification and thereby modulate cell wall mechanics is maintained at low levels in stem cells by the stem cell specifying transcription factor WUS. Low PME expression is required for stemness, auxin patterning and stem cell-specific mechanical properties. Conversely, WUS depletion reduces wall stiffness in the meristem centre, reinforcing its role in maintaining mechanical homeostasis. Together, our findings establish that WUS-mediated control of cell wall-modifying enzymes is essential for sustaining stem cell identity and SAM organization. These results point to a scenario in which the plant cell wall is not only involved in cell differentiation, but also feeds back on developmental transitions, paving the way to study how the immediate physical environment is able to guide cell fate decisions in plants.

overall_design: To study meristem-wide effects of cell wall changes in stem cells, we performed RNA-seq experiments on dissected meristems 72 hours after stem cell-specific PME expression in pCLV3>>VGD1 lines

first: Zerin

last: Tasnim

first: Ruiz-Duarte

last: Paola

first: Wolf

last: Sebastian


title: CircRNA expression profiling in plasma of early-stage lung adenocarcinoma patients and healthy controls

city: Shaanxi

first: Peini

last: Xue

address: Department of Pulmonary and Critical Care Medicine, Tangdu Hospital,

institute: Fourth Military Medical University

summary: This study aimed to explore circRNA expression profiles in the plasma of patients with early-stage lung adenocarcinoma compared to healthy controls. Using Agilent microarray technology, we profiled total RNA extracted from plasma samples of 4 patients with early-stage lung adenocarcinoma (stages IA–IIA) and 4 healthy individuals. All subjects provided peripheral blood samples, and cell-free RNA was isolated from plasma. The objective was to identify potential circRNA biomarkers that could distinguish lung cancer patients from healthy individuals at early stages.

overall_design: Total RNA was extracted from plasma samples of 8 individuals, including 4 early-stage lung adenocarcinoma patients (stage IA or IIA) and 4 age- and gender-matched healthy controls. CircRNA expression profiling was performed using Agilent-072363 microarray platform. Comparative expression analysis was conducted to identify circRNAs that were differentially expressed between cancer and control groups. All samples were processed under the same protocol to minimize technical variation.


title: Age-associated changes in the shell gland transcriptomics and eggshell quality of broiler breeder hens

city: Honolulu

first: Birendra

last: Mishra

state: HI

address: 1955 East west road

department: Department of Human Nutrition Food and Animal Sciences

institute: University of Hawaii at Manoa

summary: The egg production cycle of broiler breeder hens is comparatively shorter than laying hens, and as they age, their egg production and eggshell quality decline. The eggshell formation occurs in the shell glands, which are influenced by several factors, including aging. The objectives of the study were to 1) identify differentially expressed genes (DEGs) and biological pathways in the shell glands (young vs aged) and 2) determine the age-associated changes in eggshell quality. The shell glands tissues were collected from broiler breeder hens at peak-lay (35 weeks of age; termed as “young”) and late-lay phases (50 weeks of age; termed as “aged”) (n=30/group) at 10-15 hours post-ovulation (unclassified egg present in the shell glands). To delineate the genes and biological pathways associated with eggshell biomineralization, total RNAs extracted from the shell glands of young and aged hens (n=6/group) were analyzed using RNA sequencing and validated using real-time PCR. The ultrastructure quality of eggshells (n=10 eggs/group) was analyzed using a Scanning Electron Microscope (SEM), and the elemental composition of eggshells was measured using SEM-Energy Dispersive Spectrometry, and their variability was confirmed by t-test in RStudio. Eggshell strength, thickness, palisade layer, and mammillary width were significantly higher in the young, while mammillary knobs were wider in aged hens (p<0.05). The sulfur and potassium levels in eggshells were higher in young hens than aged ones. Although the young group had a higher calcium concentration in the eggshells, the difference was statistically insignificant (p>0.05). RNA-Seq data identified highly upregulated genes specific to eggshell biomineralization, such as SPP1 (binds to hydroxyapatite), OTOP2 (maintains high conc. of cytosolic Ca2+), PKD2 (helps in releasing Ca2+), SLC22A15 (transports organic ions), and STAB2 (binds to gram-positive and gram-negative bacteria). The DEGs showed significant enrichment for biological pathways (SLC6A6, KCNK7, UCP3, SCNN1A, PKD2, OTOP2) associated with the transport of monoatomic and inorganic cations across the cell membrane, molecular functions related to the transport of potassium ions and the activity of monoatomic cation channels (KCNK7, PKD2, OTOP2),  and the cellular components involved in the luminal side of the endoplasmic reticulum membrane (CALR, PKD2).  These findings suggest that the aging process downregulates the transcriptomes of the shell glands, negatively impacting the transportation of ions required for eggshell formation, resulting in poor eggshell quality.

overall_design: RNA sequencing of the broiler breeder shell gland to compare between peak (35 weeks) and declining (50 weeks) production to see the traanscriptomic variation of the shell gland with the shell qualit changes.

first: Prem

last: Mahato

first: Vedbar

last: Khadka

first: Prafulla

last: Regmi

first: Ken

last: Macklin

first: Rajesh

last: Jha


title: Deciphering ESR1-driven transcription in human endometrial stromal cells via transcriptome, cistrome, and integration with chromatin landscape [ESR1_HiChIP]

city: Durham

first: Skylar

middle: Grace

last: Montage Redecke

state: North Carolina

address: 111 TW Alexander Dr, 101/C416

department: Reproductive and Developmental Biology Laboratory

institute: National Institute of Environmental Health Sciences

summary: Estrogen (E2) acting through the estrogen receptor alpha (ESR1) is a critical regulator of endometrial growth, differentiation and disease. The endometrial stromal cell (ESC) is a key target of ESR1 action and plays a crucial role in regulating paracrine communication to control uterine function. A mechanistic understanding of the role of ESR1 in ESCs is limited by low levels of expression of ESC lines.   Here we engineered telomerase-immortalized hESC (THESC) to express the CRISPR activation system to activate ESR1. Among six tested guide RNAs, the ESR1-3 gRNA induced robust ESR1 activation, restoring E2 responsiveness in THESC. Bulk RNA-seq revealed ESR1-mediated E2-dependent and E2-independent transcriptional programs, regulating pathways involved in inflammation, proliferation, extracellular matrix organization, and cancer. Notably, 72% of differentially expressed genes (DEGs) overlapped with genes active in human endometrial tissue during the proliferative E2 dominant phase, supporting their physiological relevance. Cut&Run-seq identified genome-wide ESR1 binding sites, with most located at distal regulatory elements. To associate distal ESR1 binding sites with genes, we integrated H3K27ac HiChIP chromatin loops in hESC to identify distal ESR1 binding sites that loop to gene promoters. We identified genes regulated by ESR1/E2 through long-range chromatin looping that are involved in stromal cell decidualization, including FOXO1 and IL6R. Additionally, we identified genes implicated in endometrial cancer, including ERRFI1, NRIP1, and EPAS1, suggesting a role for stromal ESR1 driven endometrial pathologies. Functional assays confirmed that ESR1 promotes cell viability and, in the presence of E2, enhances migration. In this study, we reveal novel insights into ESR1-dependent transcriptional regulation using a newly developed cell culture model that restores ESR1 expression in hESCs to overcome their limited E2 responsiveness. Additionally, we demonstrate the utility of integrating HiChIP chromatin looping data with cistromic data to associate distal ESR1 binding sites to gene promoters.

overall_design: Primary endometrial stroma cells (hESCs) were isolated from endometrial biopsies collected under the human subject protocol number H-13062 approved by the institutional review board of Baylor College of Medicine. The biopsies were obtained from two healthy, reproductive-aged volunteers with regular menstrual cycles and no history of gynecological malignancies. hESC were treated with 0.2% ethanol (vehicle) or a mixture of 10 nM 17β-estradiol (Sigma-Aldrich, St. Louis, MO, USA), 1 µM medroxyprogesterone acetate (Sigma-Aldrich, St. Louis, MO, USA) and 100 µM dibutyral cyclic AMP (Sigma-Aldrich, St. Louis, MO, USA), termed EPC, for 3 days. H3K27ac HiChIP libraries were prepared by Arima Genomics.

middle: G

last: Montague Redecke

first: Austin

last: Bell-Hensley

first: Shuyun

last: Li

first: MyeongJin

last: Yi

first: Akshadha

last: Jain

first: Abdull

last: Massri

first: Francesco

last: DeMayo


title: Tumor microenvironment modulation by SERPINE1 increases radioimmunotherapy in murine model of gastric cancer

city: SEOUL

first: JIN SU

last: KIM

address: 75 Nowon-ro, Nowon-gu, Seoul, 01812, Republic of Korea

country: South Korea

institute: Korea Institute of Radiological & Medical Sciences

summary: An elevated extracellular matrix (ECM) and interstitial fluid pressure (IFP) in gastric cancer limits the targeting of HER2-expressing GC cells when radioimmunotherapy (RIT) with Cu-64 trastuzumab (Cu-64 TRZ) is utilized. Here, we used Losartan (LOS) to downregulate ECM and IFP in gastric cancer mice model. In our study we treated the gastric cancer mice model with a dose of 40 mg/kg of LOS. We found that the LOS treatment increases a 2-fold higher Alexa-647-TRZ accumulation which significantly enhanced Cu-64 TRZ. We determined that the LOS-treated samples exhibited reduced mRNA and protein expression of SERPINE1, a gene associated with the ECM degradation. Additionally, LOS treatment resulted in the downregulated mRNA expression of the TGF-β1 and COL13A1, the genes involved in ECM deposition and an upregulated RNA expression of MMP2, a gene associated with the ECM degradation. There were no significant changes in metastatic markers of N-Cadherin and E-Cadherin. Moreover, our study demonstrates that silencing SERPINE1 increases the activity of the MMP2 and decreases COL13A1 with no effect on the N-cadherin and E-cadherin were observed. Our novel combinational therapy of using Cu-64 TRZ with LOS is attributed to the downregulation of SERPINE1 targeting ECM and IFP is highly effective for treatment of gastric cancer.

overall_design: Effect of Losartan (40 mg/kg) on ECM and interstitial fluid pressure in a gastric cancer mouse model by assessing its impact on Alexa-647-TRZ and Cu-64 trastuzumab accumulation, SERPINE1, TGF-β1, COL13A1, and MMP2 expression, as well as metastatic markers (N-Cadherin and E-Cadherin), using both LOS-treated and untreated groups, along with SERPINE1-silenced samples to evaluate ECM modulation and radioimmunotherapy efficacy.

first: Javeria

last: Zaheer

first: Joycie

last: Shanmugiah

first: Seungyoun

last: Kim

first: Hyeongi

first: Jin Su


title: Deciphering ESR1-driven transcription in human endometrial stromal cells via transcriptome, cistrome, and integration with chromatin landscape [ESR1_Cut_Run]

overall_design: Immortalized human endometrial stroma cells (THESC) were engineered with the CRISPR activation system to activate the Estrogen Receptor Alpha gene. ESR1 activated THESC were then treated with 10nM E2 or vehicle (0.01% ethanol) for 1, 3 or 6 hours and Cut&Run was conducted with an ESR1 Antibody in biological duplicates.


title: Oxford Nanopore Technology (ONT) long-read data of NCIH2170 cell line

city: Chapel Hill

first: Elizabeth

last: Brunk

state: NC

address: 250 Bell Tower Dr.  4352 Genome Sciences Bldg.

department: Pharmacology, Lineberger Comprehensive Cancer Center, UNC School of Medicine

institute: University of North Carolina at Chapel Hill

summary: The ONT long-read data of NCIH2170 focusing on chr17 and chr8

overall_design: ONT long-read sequencing with adaptive sampling was performed on NCIH2170 cells. Chr17 and chr8 regions were especially focused in the sequencing. Both the ligation-based and rapid sequencing approaches were performed according to the ONT protocol.

first: Yue

last: Wang


title: 10X sc-multiome data of NCIH2170 cell line

summary: NCIH2170 is a lung cancer cell line harboring a large amount of extrachromosomal DNA (ecDNA) with high cell-to-cell variation. We performed 10X sc-multiome sequencing on this cell line to study the pattern of gene expression and chromatin accessibility with the existence of ecDNA.

overall_design: 10X sc-multiome sequencing was performed on NCIH2170 cell line


title: Deciphering ESR1-driven transcription in human endometrial stromal cells via transcriptome, cistrome, and integration with chromatin landscape [ESR1_RNAseq]

overall_design: Immortalized human endometrial stroma cells (THESC) were engineered with the CRISPR activation system to activate the Estrogen Receptor Alpha gene. ESR1 activated THESC or control THESC were then treated with 10nM E2 or vehicle (0.01% ethanol) for 24 hours and RNA was collected for RNAseq.


title: Deciphering ESR1-driven transcription in human endometrial stromal cells via transcriptome, cistrome, and integration with chromatin landscape

city: Research Triangle Park

middle: John

address: 111 T W Alexander Dr

department: DIR

institute: NIEHS

overall_design: Refer to individual Series


title: Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish

city: Bronx

first: Teresa

last: Bowman

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: Innate Lymphoid cells (ILCs) are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis, hematopoietic stem cells (HSCs) and HSC-independent Progenitor Cells (HPCs) form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs, we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC-like cells are derived from the definitive hematopoietic wave, we did lineage tracing and scRNA-seq experiment in runx1W84X mutants and illustrated that all ILC-like clusters are Runx1-dependent. We confirmed that the transcriptionally detected larval ILC-like cells are Rag-independent and Il2rg-dependent. Lastly, embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function.

overall_design: Experiment (1): for lineage tracing experiment, HSPCs were labled with mCherry at 3 timepoints in development: either at 1, 2, or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one-day-post labelling, 6 dpf, and 10 dpf. Experiment (2): for Runx1 mutants experiment, early-HSPCs (1dpf) derived mCherry cells were isolated from sibling controls or homozygous runx1(W84X) mutants at 6 dpf from whole zebrafish. Experiment (3): for rag1/R848 experiment, mCherry cells derived from early-HSPCs (1dpf) were isolated at 8 dpf from slc24a5 crispant controls, rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.

first: Anastasia

last: Nizhnik

first: Bianca

last: Ulloa

first: Kevyn

last: Jackson

first: Deyou

last: Zheng


title: Gene expression profile of CD8+ T cells in glioblastoma after ex vivo treatment of anti-PD-1 and/or galunisertib.

city: Daejeon

first: Seung Hyuck

last: Jeon

address: 291 Daehak-ro, Yuseong-gu

institute: Korea Advanced Institute of Science and Technology

summary: We aimed to analyze the effects of anti-PD-1 and/or galunisertib on tumor-infiltrating CD8+ T cells in glioblastoma.

overall_design: Anti-CD3 with anti-PD-1 and/or galunisertib was treated to single cell suspension of glioblastoma. Then, live CD8+ T cells were sorted and processed into bulk RNA sequencing.

first: A-Reum

first: Junsik

last: Park

first: Eui-Soon

first: Minsuk

last: Kwon

first: Jihwan

last: Yoo

first: Seok-Gu

last: Kang

first: Su-Hyung

first: Jong Hee

last: Chang

first: Eui-Cheol

last: Shin


title: Gene expression profile of CD8+ T cells sorted from single cell suspensions of tumors and peripheral blood of glioblastoma patients.

summary: We aimed to analyze the characteristics of tumor-infiltrating and peripheral blood CD8+ T cells in glioblastoma.

overall_design: Live CD8+ T cells were sorted from single cell suspensions of tumors and peripheral blood of glioblastoma patients.. The sorted cells were processed into single cell RNA sequencing.


title: Gene expression RNAseq profiles of TNKS/PARP-inhibitor Regulated Naïve (TIRN) cells with or without transgenic inducible DUX4 (iDUX4) activation.

city: Baltimore

first: Ludovic

last: Zimmerlin

email: lzimme14@jhmi.edu, ludovicz@gmail.com

address: 733 N. Broadway

department: Pediatric Oncology

institute: Johns Hopkins University

summary:
Proteogenomic Reprogramming to a Functional Human Blastomere-like Stem Cell State via a PARP-DUX4 Regulatory Axis; Zimmerlin et al, 2024.
PARP1 (ARTD1) and Tankyrases (TNKS1/TNKS2; PARP5a/5b) are poly-ADP-ribose polymerases (PARPs) with catalytic and non-catalytic functions that regulate both the genome and proteome during zygotic genome activation (ZGA), totipotent, and pluripotent embryonic stages. Here, we show that primed, conventional human pluripotent stem cells (hPSC) cultured continuously under non-specific TNKS1/TNKS2/PARP1-inhibited chemical naïve reversion conditions underwent epigenetic reprogramming to clonal blastomere-like stem cells. TIRN stem cells concurrently expressed hundreds of gene targets of the ZGA-priming pioneer factor DUX4, as well as a panoply of four-cell (4C)-specific (e.g., TPRXL, HOX clusters), eight-cell (8C)-specific (e.g., DUXA, GSC, GATA6), primitive endoderm-specific (e.g., GATA4, SOX17), trophectoderm-specific (e.g., CDX2, TFAP2C), and naïve epiblast-specific (e.g., DNMT3L, NANOG, POU5F1(OCT4)) factors; all in a hybrid, combinatorial single-cell manner. Mapping of proteomic and single-cell expressions of TIRN cells against human preimplantation embryo references identified them as relatively homogenous 4C-8C stage populations. The bulk RNA-seq and proteomics analyses of TIRN cells (+/- iDUX4) revealed acquisition of pre-lineage embryonic transcriptional programs. To determine if TIRN +/- iDUX4 cells were mixed populations or clonal blastomere-like cells, single cell (sc)RNA-seq was performed to investigate transcriptional heterogeneity at a single cell level. Overall, single, unmodified TIRN cells shared high transcriptional identity with single TIRN+iDUX4 cells, and single primed hPSC and TIRN +/- iDUX4 cells expressed comparable and uniformly homogenous levels of core pluripotency factors (e.g., NANOG, POU5F1 (OCT4), SOX2, KLF4, CMYC). However, single TIRN and TIRN+iDUX4 populations homogenously co-expressed not only higher levels of naïve ICM-specific genes (e.g., DNMT3L, SP5, ERVH48-1, GDF3, and IFITM1) (Park et al., 2020; Zimmerlin et al., 2016), but also hundreds of diverse and antagonistic lineage-specifying genes (e.g., HOX-PRD, T-BOX, FOX, GATA families) that are co-expressed simultaneously only during 4C-to-morula human embryonic stages (Petropoulos et al., 2016; Zou et al., 2022). Transcript levels of 4C-specific (i.e., TPRXL, HOXA1, EBF2), 8C-specific (i.e., GATA6, FOXB1), trophectoderm lineage-specific (i.e., CDX2, TFAP2C), and endoderm lineage-specific (i.e., GATA4, SOX17) pioneer factors were co-expressed in the same single cell populations; with expressions that were further augmented following iDUX4 activation.

overall_design: TIRN cells were originally reported as possessing a naive epiblast-like pluripotent stem cell molecular phenotype. We  used RNAseq to examine expression of transcriptional factors and a transcriptional program defining the human cleavage embryonic stage in primed and TIRN hESC, with or without transgenic activation of the pioneer factor DUX4. The hESC line RUES02 was cultured in parallel in primed (E8) or TIRN (LIF-3i) condition. RUES02 with transgenic doxycycline-inducible DUX4 expression (pCW57.1-DUX4-CA) were cultured in primed (E8 + 24 hours 2ug/mL doxycycline) or TIRN (LIF-3i + 24 hours 2ug/mL doxycycline).

first: Elias

middle: T

last: Zambidis


title: Gene expression profiles at the single cell level of TNKS/PARP-inhibitor Regulated Naïve (TIRN) cells with or without transgenic inducible DUX4 (iDUX4) activation.

overall_design: TIRN cells were originally reported as possessing a naive epiblast-like pluripotent stem cell molecular phenotype, but also simultaneously expressed cohorts of transcriptional factors and a transcriptional program defining the human cleavage embryonic stage.  We used single cell RNA sequencing (scRNA-seq) to examine cellular heterogeneity in TIRN cells, with or without transgenic activation of the pioneer factor DUX4. The hESC line RUES02 was cultured in parallel in primed (E8) or TIRN (LIF-3i) condition. RUES02 with transgenic doxycycline-inducible DUX4 expression (pCW57.1-DUX4-CA) were cultured in TIRN (LIF-3i + 24 hours 2ug/mL doxycycline). Viable cells were enriched and processed for single cell analysis.


title: Differential Localization of β-catenin Protein in CTNNB1 mutant Endometrial Cancers Results in Distinct Transcriptional Profiles

first: Andrew

last: Gladden

address: 160 N. Medical Drive

department: Pathology & Laboratory Medicine

institute: The University of North Carolina at Chapel Hill

summary: CTNNB1 exon 3 mutation is a well-established driver of nearly 30% of endometrioid endometrial cancers (EEC), and this is associated with worse patient survival.  The purpose of this study was to determine downstream gene expression in these cancers with nuclear or membrane/cytoplasmic mutant b-catenin protein localization. We determined that EECs with exon 3 CTNNB1 mutations have variable b-catenin localization, and this is associated with profoundly distinct foci of gene expression within the same cancer.

overall_design: Sixteen formalin-fixed paraffin embedded tumors with exon 3 CTNNB1 mutations and heterogenous localization of b-catenin (nuclear or non-nuclear) were analyzed with spatial transcriptomics. Six regions of interest were selected per tumor, 3 with nuclear mutant b-catenin and 3 with non-nuclear mutant b-catenin.

first: Molly

middle: L

last: Parrish

first: Macy

last: Osborne-Frazier

first: Russell

last: Broaddus


title: Genome-binding/occupancy profiling of TNKS/PARP-inhibitor Regulated Naïve (TIRN) cells.

summary: Proteogenomic Reprogramming to a Functional Human Blastomere-like Stem Cell State via a PARP-DUX4 Regulatory Axis; Zimmerlin et al, 2024.                                                                                PARP1 (ARTD1) and Tankyrases (TNKS1/TNKS2; PARP5a/5b) are poly-ADP-ribose polymerases (PARPs) with catalytic and non-catalytic functions that regulate both the genome and proteome during zygotic genome activation (ZGA) and pluripotent embryonic stages. Here, we show that primed, conventional human pluripotent stem cells (hPSC) cultured continuously under non-specific TNKS1/TNKS2/PARP1-inhibited chemical naïve reversion conditions underwent proteogenomic reprogramming to a functional blastomere-like state. Tankyrase-PARP1 inhibitor-regulated naïve stem cells (TIRN-SC) concurrently expressed hundreds of gene targets of the ZGA-priming pioneer factor DUX4, as well as two- to eight-cell (2C-8C) (e.g., TPRXL, HOX clusters, EOMES, DUXA, GATA6), pre-lineage morula (e.g., GATA4, SOX17, FOXA2), and naïve epiblast (e.g., LEFTY2, DNMT3L, NANOG) lineage-specifying pioneer factors; all in a hybrid, single-cell manner. Mapping of the single-cell transcriptome of TIRN-SC to human embryo references identified populations expressing hybrid transcriptional programs that not only spanned 2C-4C (pre-ZGA) and morula-ICM stages, but that were also augmented following brief induction of DUX4 expression (iDUX4).  Here, we performed ChIP-Seq profiling of PARP1, the core pluripotency factors NANOG, SOX2 and OCT4, phosphorylated-STAT3, BRD4 and modified histones H3K4me3, H3K27me3, H3K27ac. Co-binding analyses of core NANOG-SOX2-OCT4 (NSO) pluripotency factors with PARP1 (NSOP) identified genome-wide reprogramming of novel NSOP sites to DUX4-accessible distal and cis-regulatory enhancer regions in TIRN-SC. Gained NSOP enhancer regions possessed co-binding motifs for hundreds of the same 2C-8C-ICM-specific embryonic, and extraembryonic lineage-specifying pioneer factors (e.g., HOX, FOX, GATA, SOX, TBX families) that were concurrently co-expressed in TIRN-SC; suggesting that PARP1 and DUX4 chromatin co-binding cooperated with NSO core factors to regulate ZGA-associated lineage plasticity.

overall_design: TIRN cells were originally reported as possessing a naive epiblast-like pluripotent stem cell molecular phenotype. We  used ChIP-Seq to examine the chromatin state  and the occupancy of PARP1, NANOG, SOX2 and OCT4 in TIRN stem cells. The hESC line RUES02 was cultured in parallel in primed (E8) or TIRN (LIF-3i) condition.


title: Impact of microgravity on a three-dimensional microphysiologic culture of the human kidney proximal tubule epithelium: cell response to serum and vitamin D

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: The microgravity environment aboard the International Space Station (ISS) provides a unique stressor that can help understand underlying cellular and molecular drivers of pathological changes observed in astronauts with the ultimate goals of developing strategies to enable longterm spaceflight and better treatment of diseases on Earth. We used this unique environment to evaluate the effects of microgravity on kidney proximal tubule epithelial cell (PTEC) response to serum exposure and vitamin D biotransformation capacity. To test if microgravity alters the pathologic response of the proximal tubule to serum exposure, we treated PTECs cultured in a microphysiological system (PT-MPS) with human serum and measured biomarkers of toxicity and inflammation (KIM-1 and IL-6) and conducted global transcriptomics via RNAseq on cells undergoing flight (microgravity) and respective controls (ground). We also treated 3D cultured PTECs with 25(OH)D3 (vitamin D) and monitored vitamin D metabolite formation, conducted global transcriptomics via RNAseq, and evaluated transcript expression of CYP27B1, CYP24A1, or CYP3A5 in PTECs undergoing flight (microgravity) and respective ground controls. We demonstrated that microgravity neither altered PTEC metabolism of vitamin D nor did it induce a unique response of PTECs to human serum, suggesting that these fundamental biochemical pathways in the kidney proximal tubule are not significantly altered by short-term 3 exposure to microgravity. Given the prospect of extended spaceflight, more study is needed to determine if these responses are consistent with extended (>6 month) exposure to microgravity.

overall_design: Kidney proximal tubule epithelium cells in a 3D microfluidic chamber were treated with either culture medium (control), human serum, or vitamin D in either full gravity or microgravity to assess differences due to the combination of treatment and gravity environment.

first: Kevin

last: Lidberg

first: Kendan

last: Jones-Isaac

first: Jade

last: Yang

first: Jacelyn

last: Bain

first: Lu

last: Wang

first: Theo

last: Bammler

first: Justina

last: Calamia

first: Kenneth

middle: E

last: Thummel

first: Catherine

last: Yeung

first: Stefanie

last: Countryman

first: Paul

last: Koenig

first: Jonathan

last: Himmelfarb

first: Edward

middle: J

last: Kelly


title: Anti-CD25 Treg targeting antibodies sparing IL-2 signaling promote regression of established glioblastoma tumors and innate cell activation.

first: Gordon

last: Beattie

address: Gower Street

country: United Kingdom

institute: UCL

summary: Treg depletion in mouse GBM using the anti-CD25 antibody, led to tumor regression and improved survival. We performed single cell RNA sequencing on tumor, lymphoid and myeloid samples from treated and untreated samples

overall_design: Myeloid, lymphoid and tumor/stroma cells were isolated using fluorescence-activated cell sorting based on the expression of CD45 and CD11b

first: Felipe

last: Galvez-Cancino

first: Mariela

middle: N

last: Sanchez

first: Sergio

last: Quezada


title: Dysregulated cell states revealed by single-cell multiomics in mild malformations of cortical development with oligodendroglial hyperplasia in epilepsy

city: Campinas

first: Diogo

middle: Fernando Troggian

last: Veiga

state: SP

address: Rua Vital Brasil, 80

department: Department of Translational Medicine

country: Brazil

institute: Universidade Estadual de Campinas

summary: Mild malformations of cortical development with oligodendroglial hyperplasia in epilepsy (MOGHE) is a distinct form of focal epilepsy characterized by oligodendroglial clusters, heterotopic neurons, and hypomyelination in the white matter. While previous studies have implicated somatic mutations in the SLC35A2 gene, the cellular and molecular mechanisms underlying MOGHE pathogenesis remain largely unknown. In this study, we utilized multiomic single-nuclei sequencing to profile the gene expression and chromatin accessibility of MOGHE lesions at cellular resolution. Analysis of grey and white matter regions from two MOGHE patients revealed significant alterations in cellular composition, highlighting an expansion of oligodendrocytes and the presence of heterotopic neurons within the subcortical white matter. We identified a population of MOGHE-associated oligodendrocytes, which were enriched in genes involved in immune response, myelination disruption, and epilepsy-related pathways, and shared transcriptional similarities with pathological oligodendrocytes identified in other neurological disorders. Further analysis of heterotopic neurons in MOGHE revealed the upregulation of genes associated with neuronal migration and the Wnt signaling pathway, suggesting a potential mechanism underlying their atypical localization. Altogether, this high-resolution cellular characterization of MOGHE unveils the neuronal and glial subpopulations affected in the disease and provide novel insights into the pathophysiological mechanisms of MOGHE.

overall_design: We obtained frozen cortical tissue specimens from two donors aged 22 and 57 years with a confirmed pathological diagnosis of MOGHE after epilepsy surgery. We isolated nuclei from the MOGHE grey matter (MOGHE-GM, n=2) and white matter regions (MOGHE-WM, n=2), and performed paired snRNA-seq and snATAC-seq on each nucleus using the Multiome ATAC + Gene Expression kit (10X Genomics) to measure chromatin accessibility and gene expression at nuclei resolution.

first: Isabella

middle: C

last: Galvão

first: Manuela

last: Lemoine

first: Ludmyla

last: Kandratavicius

first: Clarissa

last: Yasuda

first: Marina

middle: M

last: Alvim

first: Enrico

last: Ghizoni

first: Helder

last: Tedeschi

first: Ingmar

last: Blümcke

first: Fernando

last: Cendes

first: Fabio

last: Rogerio

first: Iscia

last: Lopes-Cendes


title: NONO preferentially binds to exon-intron boundary and regulates alternative splicing in Rat Cardiac Fibroblasts

city: Urumuqi

first: chao

last: peng

state: Xinjiang

address: tianchi road 91

institute: people's hospital of xinjiang uygur autonomous region

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


title: Inducible intestinal epithelial knockout of PRMT1 in mouse model

city: Bethesda

first: Zhaoyi

last: Peng

state: maryland

address: 49 CONVENT DR

department: National Institutes of Health

institute: Eunice Kennedy Shriver National Institute of Child Health and Human Development

summary: Many studies investigated the mechanisms that control enteroendocrine cell (EEC) fate determination; however, regulation of EEC development and function are still unclear. Here, We performed RNA-Sequencing analyses on the small intestinal crypts of tamoxifen-inducible intestinal epithelium-specific knockout of PRMT1 and wildtype mice.  Our finding for the first time revealed that the epigenetic enzyme PRMT1 controls mouse enteroendocrine cell differentiation, which probably via inhibition of Neurogenin 3-mediated commitment to the EEC lineage.

overall_design: To provide insight into the mechanisms underlying PRMT1 function in the adult intestine, we performed RNA-Sequencing (RNA-Seq) of the small intestinal crypts in tamoxifen-induced intestinal epithelial cell-specific deletion of PRMT1 adult mice and littermates as control at different doses or time point after the first tamoxifen injection.


title: The polyploidy of the scion and the rootstock in citrus is shaping the better tolerance to water deficit

city: Petit-bourg

first: Leny

last: Calvez

address: Station de Roujol

country: France

institute: CIRAD

summary: Citrus, one of the world’s most important crops is facing considerable challenges due to drought events. Previous studies have demonstrated that tetraploid rootstocks exhibit greater tolerance to abiotic stresses than their diploid counterparts. The effects of combining tetraploid rootstock with a triploid scion under water deficit treatment have not been thoroughly explored. A water deficit experiment was conducted in pot using four citrus scion/rootstock combinations: diploid and tetraploid Swingle citrumelo rootstocks grafted with diploid Mexican Lime and triploid Persian lime. Physiological, biochemical, and transcriptomic analyses revealed that scions grafted onto tetraploid rootstocks had significantly better drought tolerance, especially when combined with triploid Persian lime. This improved resilience was linked to enhanced water regulation, higher photosynthesis, increased stomatal conductance and transpiration during water stress. Elevated abscisic acid levels and stronger antioxidant activity in polyploid rootstocks further contributed to stress response. Transcriptomic data showed notable gene expression changes, providing insights into drought tolerance mechanisms. These findings underscore ploidy’s role at both the rootstock and scion levels in shaping the plant’s response to water deficit, revealing useful interactions between rootstock and scion influencing drought resilience. This study highlights the potential for leveraging polyploid rootstocks and scions to improve drought tolerance in citrus cultivation.

sample_organism:
Citrus sinensis
Citrus x aurantiifolia
Citrus x latifolia

overall_design: In the present study, we investigated the response of four scion/rootstock combinations with different ploidy levels under water deficit conditions. Diploid Swingle citrumelo seedlings and their homologous 4x were grafted with 3x Persian Lime (C. latifolia) and 2x Mexican Lime (C. aurantiifolia (Christm.) Swing.). The objective of this study was to test whether 4x rootstock and/or 3x scion could improve tree adaptation to water deficit compared to the usual 2x scion/rootstock combinations. For that purpose, trait tolerance were investigated using phenotypes, physiological, biochemical, electrochemical and transcriptomic analyses allowing deciphering the impact of the polyploidy through the scion/rootstock interactions. In total, 28 trees were split in two group treatments as follow: (i) control plant set with 3 trees per combination under regular irrigation and (ii) and a drought stress set with 4 trees per combination subjected to water deficit condition by stopping the irrigation for nine days. At the end of the experimentation leaves and roots from each trees were colected to perfomed analysis.

first: Benedicte

last: Favreau

first: Alexis

last: Dereeper

first: Gary

last: Sivager

first: Barbara

last: Hufnagel

first: Pierre

last: Mournet

first: Saturnin

last: Bruyere

first: Marie

last: Bonnin

first: Hélène

last: Vignes

first: Guillaume

last: Marti

first: Gerardo

last: Cebrian-Torrejon

first: Antonio

last: Doménech-Carbó

first: Patrick

last: Ollitrault

first: Raphaël

last: Morillon


title: Effect of splenectomy on liver regeneration after 70% resection in a mouse model.

city: Moscow

first: Polina

last: Vishnyakova

address: Oparina 4

country: Russia

institute: National Medical Research Center for Obstetrics, Gynecology and Perinatology

summary: In this work, the effect of splenectomy on liver regeneration was studied. For this purpose in  the animals were reproduced splenectomy, and after 7 days 70% liver resection was performed. Animals in which the spleen was intact and only 70% liver resection was performed served as a comparison group. Animals in which only the spleen was removed also served as controls. The animals were removed from the experiment after 24 hours, 3 and 7 days. Macrophages were isolated from the livers of control animals as well as from the liver after 70% resection by magnetic sorting using the F4/80 marker. RNA was isolated from the obtained macrophages and used for transcriptome analysis. Macrophages in the regenerating liver were transcriptomically enriched for signaling pathways associated with monocyte migration, cell adhesion and cell death.

overall_design: In the first series of experiments, liver resection was performed in intact animals (n=25); in the second series of experiments the animals were splenectomized 7 days before the resection (n=25). Intact animals (n=6) and splenectomized animals with preserved liver (n=6) were used as respective controls. The animals were withdrawn from the experiment 24 hours, 72 hours and 7 days post-resection using a CO2 chamber. Macrophages were isolated from the liver using magnetic sorting for F4/80 and their gene expression profiles were analyzed using Clariom™ S Assay, mouse.

first: Andrey

last: Elchaninov


title: RNA-seq of mouse tissue samples from animal model : Effects of GSK3 on gene expression

city: Kaifeng

first: Zhu

last: Renkai

state: Henan

address: Dongjing avenue

institute: Henan  university

summary: In the present study, RNA-seq technique were performed To explore biological significance of GSK3 in the neuro-cutaneous signaling network of chronic itch.Five repetitive mRNAs were deeply sequenced using MGISEQ-2000 to generate an mRNA profiles. We found that when using GSK3's inhibitor SB415286 AD mouse model or non  GSK3's inhibitor SB415286 AD mouse model for high-throughput sequencing, using GSK3's inhibitor SB415286 ACD mouse model or non  GSK3's inhibitor SB415286 ACD mouse model for high-throughput sequencing，SB415286 affected the expression of a variety of itching factors and skin inflammatory factors related to the skin pathology of human chronic dermatitis. These changes may indicate that GSK3 is closely related to inflammation and pruritus. This finding might help us to better understand the immune-neuro-modulatory mechanism in itch circuits.

overall_design: Mouse ear tissue were from SB415286-injected AD model mice (0.7mg/kg/mice iintraperitoneal injection) or vehicle control，mouse ear tissue were from SB415286-injected ACD model mice (2mg/kg/mice iintraperitoneal injection) or vehicle control，The gene expression of these cells were investigated utilizing MGISEQ-2000.

first: Renkai

last: Zhu

first: Jianghui

last: Meng

first: Ruizhen

last: Wang


title: NONO preferentially binds to exon-intron boundary and regulates alternative splicing in Rat Cardiac Fibroblasts [RIP-seq]

first: chao

last: peng

summary: Myocardial fibrosis occurs in a variety of cardiac diseases. As one of the markers of cardiac activated-myofibroblast protein, NONO may be involved in this process while the underlying mechanisms have not been explored. NONO, assumed to hold a role in the regulation of global transcriptome profile in cardiac fibrotic, was silenced in rat cardiomyocytes. RNA-seq and improved RNA immunoprecipitation and sequencing (iRIP-seq) were used to analyze the dysregulated transcriptome by NONO, as well as the NONO-bound RNAs in the control and siNONO group. Quantitative PCR and western blotting were applied to determine NONO-regulated mRNA and protein expression levels in rat cardiomyocytes. RNA-seq and iRIP-seq were successfully performed, and NONO-bound RNAs were characterized.

overall_design: Transcrptional profile of  rat cardiac fibroblasts cells with/without GENE_NONO Knockdown were generated

first: Peng

last: Chao

first: Jie

last: Li

last: Ren

first: Xueqin

last: Zhang


title: NONO preferentially binds to exon-intron boundary and regulates alternative splicing in Rat Cardiac Fibroblasts [RNA-seq]


title: CXCR4-LASP1-G9a-SNAIL Axis Drives NEPC Transdifferentiation via Induction of EMT and Downregulation of REST

status: Public on May 11 2025

city: Vancouver

first: Yen-Yi

last: Lin

state: British Columbia

address: 2660 Oak St

institute: University of British Columbia


title: CXCR4-LASP1-G9a-SNAIL Axis Drives NEPC Transdifferentiation via Induction of EMT and Downregulation of REST [331R]

summary: Neuroendocrine prostate cancer (NEPC) is a lethal subtype of prostate cancer that can develop from prostate cancer following aggressive hormonal therapy. Unfortunately, there are few treatment options available and new therapeutic targets and more effective treatments are urgently needed to improve management of the disease. There is now little doubt that the majority of NEPC is derived from prostatic adenocarcinoma cells via “NE transdifferentiation” that is driven at least in part by AR-axis interference and lineage plasticity. We have developed a first-in-field patient-derived xenograft model of a prostatic adenocarcinoma (LTL331) that undergoes a complete transdifferentiation to NEPC (LTL331R) upon host castration. Using this unique, high-fidelity, patient-derived prostate cancer xenograft models and powerful genomic and transcriptomic analyses, we have obtained evidence that therapy induced development of NEPC may result from epigenetic alterations which drives lineage plasticity of dormancy-capable cancer cells and functional evaluation of key regulators.   These findings may lead to more suitable targets and better therapeutic strategies for prevention and treatment of NEPC.

overall_design: ChIP-seq profiling of 331R

first: Yuzhuo


title: Development of a closed culture system for the production of autologous clinical iPS cells using dental pulp cells

city: Kyoto

first: Yoshiki

last: Nakashima

state: Kyoto

address: Kyoto Research Park KISTIC Building Room 501, 5th floor, KISTIC building,  134 Chudoji Minami-cho, Shimogyo-ku

department: Research and Development Center

institute: Kyoto University Center for iPS Cell Research and Application Foundation (CiRA Foundation)

summary:
PluriTest score was 27.4 for iPSCs cultured on SSCW®. n = 1.
KaryoStat assays revealed no genetic or karyotypic mutations in iPSCs cultured on SSCW®. n = 1.

overall_design: SSCW® (n = 1). Non_iPSC data are stored in the PluriTest analysis service database provided by Life Technologies Corporation (Carlsbad, CA, USA).

first: Masayoshi

last: Tsukahara


title: Differential analysis of transcriptome of different Trichophyton mentagrophytes strains II

city: hangzhou

first: xiao

middle: chen

last: wen

address: desheng_road NO.298

institute: Zhejiang Academy of Agricultural Sciences

overall_design: The CDR1 gene of Magnaporthe grisea was knocked out and replenished by ATMT technology. The effect of CDR1 gene on the gene expression profile of Magnaporthe grisea was studied by high-throughput sequencing,all the strains were cultured on SDA  plates with  10 days. Then collect the colonies and store them in liquid nitrogen. Perform the next step of high-throughput sequencing.

first: Chenwen

last: Xiao

first: Siyuan

last: Liang

first: Jiaoyu

first: Fucheng


title: Reactivating cGAS-STING Signaling by Targeting SOS1 Enhances Antitumor Immunity in NRAS-Mutant Tumors

city: Guangzhou

first: Jia-Lu

last: Shan

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

summary: NRAS is commonly mutated in several different types of human cancer. NRAS-mutant tumors are aggressive and associated with poor outcomes. Although the development of targeted therapies as well as immune checkpoint inhibitors has led to a substantial improvement in the overall survival of patients with NRAS wild-type tumors, current therapies for NRAS-mutant cancers are limited. Here, analysis of RNA-sequencing data revealed a downregulation of the type I interferon response in NRAS-mutant tumors compared with NRAS wild-type tumors, which was associated with poor prognosis in NRAS-mutant melanoma. Knockdown of mutant NRAS, but not wild-type NRAS, enhanced the activation of cGAS-STING signaling. The formation of a trimeric complex between TBK1, STING, and IRF3, which is required for the activation and nuclear translocation, was blocked in NRAS-mutant tumor cells. Inactivation of innate immune signaling by mutant NRAS altered cytokine production, resulting in cell autonomous and non-cell autonomous signaling to prevent tumor cell death and in evasion of tumor immune surveillance. Screening of drugs for the ability to stimulate the release of CXCL10 revealed that SOS1 inhibitors reactivated cGAS-STING signaling in NRAS-mutant tumor cells. Importantly, combining SOS1 inhibitors with STING agonists maximized the activation of cGAS-STING signaling and elicited an increased antitumor immune response in vitro and in vivo. Overall, this study provides insights into the regulation of anti-tumor immunity by mutant NRAS and uncovers a potential strategy for treating NRAS-mutant cancer.

overall_design: To assess the interferon alpha response in NRAS-mutant tumors, we performed RNA-seq in HT1080 cells with knockdown of mutant NRAS as indicated. GSEA revealed that the interferon alpha response was significantly positively enriched with the knockdown of mutant NRAS and ranked first when stimulated with poly(dA:dT)

first: Kai-Ming

first: Wen-Qing

last: Zhong

first: Xiao-Yu

last: Yang

first: Zhi-Ling

first: Yun

last: Huang

first: Tian

last: Du

first: Dong

first: Jia-Hong

last: Tang

first: Yu-Hong

last: Chen

first: Hai-Liang

first: Xiao-Feng

first: Rong

last: Deng


title: Microglial cGAS Deletion Preserves Intercellular Communication and Alleviates Amyloid-β-Induced Pathogenesis of Alzheimer's Disease

city: SAN ANTONIO

first: Sijia

last: He

address: 7703 Floyd Curl Dr.

institute: uthealth sa

summary: This study investigates the impact of microglial cGAS deficiency on gene expression in the 5xFAD mouse cerebrum tissues, using the NanoString Neuroinflammation panel. The relevent publication is PMID: 39908354

overall_design: The measurment set contains 12 samples, 6 for each sex, composed of 2 genotypes (cGAS Loxp/5xFAD, and cGAS mKO/5xFAD) in triplicates. Note that mKO indicate mice with microglial cGAS deficiency.

first: Feng

last: Liu

first: Xianlin

last: Han


title: Transcriptional effects of rhizosphere microorganisms on shoot and roots of Arabidopsis thaliana under different light conditions

city: Shanghai

first: Chuanwei

address: 2005 Songhu Road, Yangpu District

department: school of life sciences

institute: Fudan university

summary: For shade-intolerant species, shade light indicates the close proximity of neighboring plants and triggers the shade avoidance syndrome (SAS), which causes exaggerated growth and reduced crop yield. We report that microbiotal root commensals(Pseudomonas fluorescens and Root918) alleviate the shade avoidance responses in Arabidopsis. To identify the functions of Pseudomonas fluorescens and Root918 during SAS, we performed RNA-seq to search for differentially expressed genes (DEGs) in different tissues by comparing the transcript levels of shoot and root parts of col0 in germ-free, Pseudomonas fluorescens and Root918 during white light and shade conditions.

overall_design: Wild type Arabidopsis seedlings were cultured under white light for 5 days, then inoculated with Pseudomonas fluorescens and Root918 under white light for 4 days, and finally treated under white light and shade for 4 hours to extract RNA from shoot and root samples, respectively.

first: Lin

last: Li

first: Huanhuan

last: Lu


title: Wnt5a-induced exosomes from bone marrow mesenchymal stem cells regulates immune cells via the NF-KB pathway, influencing neural stem cell proliferation and differentiation to promote spinal cord injury repair.

city: guangzhou

first: Dan

last: Luo

address: dade road Num.111

institute: The Second Affiliated Hospital of Guangzhou University of Chinese Medicine

summary: Spinal cord injury (SCI) remains a devastating neurological disorder with limited treatment options. Among emerging therapeutic strategies, the transplantation of mesenchymal stem cell-derived exosomes (MSC-Exos) has shown great promise owing to their functional consistency with donor cells, low immunogenicity, and suitability for various delivery routes. Wnt5a, a non-canonical Wnt ligand, has been reported to promote neuronal differentiation and spinal cord regeneration. However, its mechanistic role when delivered via exosomes (Exos) remains unclear. In the present study, the function and underlying mechanism of Wnt5a in promoting neuronal differentiation and spinal cord repair were investigated using bone marrow mesenchymal stem cell-derived exosomes (BMSC-Exos) in both in vitro and in vivo models. Our results demonstrated that Wnt5a-enriched BMSC-Exos significantly enhanced the proliferation and neuronal differentiation of neural stem cells, while suppressing astrocyte formation. High-throughput RNA sequencing revealed an association between Wnt5a and the nuclear factor-kB (NF-kB) signaling pathway. Intervention with lipopolysaccharide confirmed that Wnt5a exerts a suppressive effect on this pathway. In vivo, the transplantation of Wnt5a-modified BMSC-Exos facilitated the polarization of microglia toward an anti-inflammatory M2 phenotype, promoted neurogenesis, reduced astrocyte accumulation, improved spinal cord tissue architecture, and led to better motor function recovery. Collectively, these findings indicate that Wnt5a enhances the neuroregenerative potential of BMSC-Exos by modulating immune responses and suppressing neuroinflammation, likely through inhibiting the NF-kB signaling pathway. This strategy may offer a promising avenue for treating SCI

overall_design: Exploring the potential targets of Wnt5a on NSC differentiation through transcriptome sequencing research


title: Impact of Tissue-Resident Macrophages on the postnatal neuronal and vascular development in the eardrum

city: Portland

first: Xiaorui

last: Shi

state: OR

address: 3181 SW Sam Jackson Park Road, NRC04

department: Oregon Hearing Research Center

institute: Oregon Health & Science University

summary: We have employed a single cell sequencing approach using 10x Genomics scRNAseq to study postnatal eardrum tissue resident macrophages (TRMs) and pericytes. TRMs are essential components of the innate immune system, exhibiting diverse phenotypes and functional specialization across nearly all tissues and organs, including the eardrum. The vascular network in the eardrum is rich in pericytes, which are crucial for the proper development, stability, and maturation of blood vessels. This study represents the first transcriptome analysis of eardrum TRMs and pericytes and provides new insights into the role of TRMs during eardrum development postnatally.

overall_design: TRMs and pericytes from the eardrums of CX3CR1EGFP; NG2DsRed mice at P15 were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNA-seq.

first: Yunpei

last: Zhang

first: Kushal

last: Karma

first: Pingting

last: Wang


title: CXCR4-LASP1-G9a-SNAIL Axis Drives NEPC Transdifferentiation via Induction of EMT and Downregulation of REST [331R-2D]

first: Yen-Yi

last: Lin

overall_design: RNA-seq profiling of 331R-2D

first: Yuzhuo