title: Biological Age Acceleration and Colonic Polyps in Persons Under Age 50

city: Miami

first: Shria

last: Kumar

state: FL

address: 1120 NW 14th St

department: Gastroenterology

institute: University of Miami

summary: Epigenetic clocks can quantify DNA methylation by measuring the methylation levels at specific sites in the genome, which correlate with biological age (BA). Accelerated aging, where BA exceeds chronological age (CA), has been studied in relation to cancer development, but its utility in cancer prevention remains unclear. Accelerated aging holds promise as a tool to explain the rise in early onset colorectal cancer (EOCRC). We investigate the association of accelerated aging and the presence of pre-neoplastic polyps (PNP) in the colon, defined as tubular adenomas and sessile serrated adenomas. In this study of persons under age 50 undergoing colonoscopy, we used peripheral blood samples to determine BA and age acceleration metrics. Age acceleration was determined by interrogating DNA methylation (DNAm) at specific CpG sites across the genome, which has been shown to correlate with age. We then conducted logistic regression analyses to evaluate the association between age acceleration and PNPs. In total, 51 patient samples were evaluated. We found that that the odds of harboring a PNP are 17% higher with 1 year of accelerated aging, as measured by GrimAge. However, the strongest risk factor for PNPs remained male sex. This represents one of the first studies to explore accelerated aging and PNP in patients under the age of 50. A risk-stratified approach to EOCRC screening would minimize unnecessary colonoscopies and minimize healthcare burden while addressing the rise in EOCRC. Our findings suggest that BA calculations with peripheral blood collections could be an important component of such a risk model.

overall_design: Our study aims to better understand the potential role that biological age plays in explaining the rise in early onset colorectal cancers. We analyzed DNA methylation at CpG sites in the buffy coat of 51 patients using Illumina Infinium MethylationEPIC Bead Chip array. This information was then inputed into biological clock models and compared with same-day colonoscopy findings to evaluate the assocition between pre-neoplastic polyps and age acceleration.

first: Chloe

middle: M

last: Brown

first: Maria

middle: V

last: Yow


title: 4DNESV11RYSF - Replicate experiments of in situ Hi-C on CyT49 differentiated to definitive endoderm with MboI

status: Public on Dec 12 2024

city: Boston

last: DCIC

state: MA

address: 10 Shattuck St

country: USA

institute: 4D Nucleome - Data Coordination and Integration Center

summary: Replicates of Hi-C on CyT49 cells differentiated to definitive endoderm

overall_design:
**Data Use Guidelines:** This is a data set generated by the 4DN Network and made freely available to the scientific community. If you are intending to use these data for a publication, we ask that you please contact the data generating lab to discuss possible coordinated publication. In your manuscript, please cite the 4DN White Paper ([doi:10.1038/nature23884](https://doi.org/10.1038/nature23884)) and the 4DN Data Portal paper ([doi:10.1038/s41467-022-29697-4](https://doi.org/10.1038/s41467-022-29697-4)), and please acknowledge the 4DN lab which generated the data. Please direct any questions to the [Data Coordination and Integration Center](mailto:support@4dnucleome.org).
lab: Bing Ren, UCSD
award: 1U54DK107977-01
accession: 4DNESV11RYSF
condition: definitive endoderm
submitted_by: Bin Li
dataset_label: Hi-C on hESC differentiated to pancreatic endoderm
experiment_type: in situ Hi-C
url: https://data.4dnucleome.org/experiment-set-replicates/4DNESV11RYSF/
number_of_experiments: 2

experiment: 4DNEXVGPPF1H; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXLV2KQRB; replicate_number: Biorep 2, Techrep 1

Series supplementary files:
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/50ca456c-5fe8-484b-ba6a-1cd9e07fabfe/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFI4LG5248.pairs.gz, 4DNFIKZHGYEO.pairs.gz, 4DNFI823L812.txt
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-combined
file_format: pairs
file name: 4DNFI5YPTDEP.pairs.gz
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/50ca456c-5fe8-484b-ba6a-1cd9e07fabfe/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFI4LG5248.pairs.gz, 4DNFIKZHGYEO.pairs.gz, 4DNFI823L812.txt
description: This is an output file of the Hi-C processing pipeline
file_type: contact matrix
file_format: mcool
file name: 4DNFINXSKZ4F.mcool
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/96710a5c-4c2e-4616-939e-7f5be4dbd3cd/
genome_assembly: GRCh38
derived_from: 4DNFINXSKZ4F.mcool
description: Boundaries calls on Hi-C contact matrices
file_type: boundaries
file_format: bed
file name: 4DNFIJ8V3M13.bed.gz
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/96710a5c-4c2e-4616-939e-7f5be4dbd3cd/
genome_assembly: GRCh38
derived_from: 4DNFINXSKZ4F.mcool
description: Diamond insulation scores calls on Hi-C contact matrices
file_type: insulation score-diamond
file_format: bw
file name: 4DNFIQ3W2RN4.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/4994a1d5-96f1-4668-a48c-6eb20d609dd4/
genome_assembly: GRCh38
derived_from: 4DNFINXSKZ4F.mcool, 4DNFI7MCA4R6.bedGraph.gz
description: Compartments signals on Hi-C contact matrices
file_type: compartments
file_format: bw
file name: 4DNFI1R7X63K.bw


title: 4DNESOL9JVE2 - Replicate experiments of in situ Hi-C on CyT49 differentiated to endoderm of foregut with MboI

summary: Replicates of Hi-C on CyT49 cells differentiated to gut tube endoderm

overall_design:
**Data Use Guidelines:** This is a data set generated by the 4DN Network and made freely available to the scientific community. If you are intending to use these data for a publication, we ask that you please contact the data generating lab to discuss possible coordinated publication. In your manuscript, please cite the 4DN White Paper ([doi:10.1038/nature23884](https://doi.org/10.1038/nature23884)) and the 4DN Data Portal paper ([doi:10.1038/s41467-022-29697-4](https://doi.org/10.1038/s41467-022-29697-4)), and please acknowledge the 4DN lab which generated the data. Please direct any questions to the [Data Coordination and Integration Center](mailto:support@4dnucleome.org).
lab: Bing Ren, UCSD
award: 1U54DK107977-01
accession: 4DNESOL9JVE2
condition: gut endoderm
submitted_by: Bin Li
dataset_label: Hi-C on hESC differentiated to pancreatic endoderm
experiment_type: in situ Hi-C
url: https://data.4dnucleome.org/experiment-set-replicates/4DNESOL9JVE2/
number_of_experiments: 2

experiment: 4DNEX3JHGDNA; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXCVNMNQ1; replicate_number: Biorep 2, Techrep 1

Series supplementary files:
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/fb0c3978-1093-48c3-b1b8-ae67414fe86a/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFIZ1BMAHE.pairs.gz, 4DNFIZUV87TW.pairs.gz, 4DNFI823L812.txt
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-combined
file_format: pairs
file name: 4DNFI63M3S1S.pairs.gz
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/fb0c3978-1093-48c3-b1b8-ae67414fe86a/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFIZ1BMAHE.pairs.gz, 4DNFIZUV87TW.pairs.gz, 4DNFI823L812.txt
description: This is an output file of the Hi-C processing pipeline
file_type: contact matrix
file_format: mcool
file name: 4DNFI2VYSX9M.mcool
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/eef60573-c20a-440e-b947-5995e9bbe4f6/
genome_assembly: GRCh38
derived_from: 4DNFI2VYSX9M.mcool
description: Boundaries calls on Hi-C contact matrices
file_type: boundaries
file_format: bed
file name: 4DNFINWCQ7KA.bed.gz
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/eef60573-c20a-440e-b947-5995e9bbe4f6/
genome_assembly: GRCh38
derived_from: 4DNFI2VYSX9M.mcool
description: Diamond insulation scores calls on Hi-C contact matrices
file_type: insulation score-diamond
file_format: bw
file name: 4DNFI7IFRH31.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/540699e6-aadc-4a7d-bcb2-a164f9bd6ef2/
genome_assembly: GRCh38
derived_from: 4DNFI2VYSX9M.mcool, 4DNFI7MCA4R6.bedGraph.gz
description: Compartments signals on Hi-C contact matrices
file_type: compartments
file_format: bw
file name: 4DNFI4WZGW78.bw


title: Tumor cell heterogeneity drives spatial organization of the intratumoral immune response in squamous cell skin carcinoma

city: Houston

first: Kenneth

middle: H

last: Hu

state: Texas

address: 7455 Fannin Street

department: Immunology

institute: MD Anderson

type: Expression profiling by high throughput sequencing

summary: Intratumoral heterogeneity (ITH)—defined as genetic and cellular diversity within a tumor—is linked to a failure of immunotherapy in multiple cancer types and to an inferior anti-tumor immune response even in the absence of therapy. To determine how tumor heterogeneity shapes the immune microenvironment and impacts responses to therapy, we modeled heterogeneous tumors comprised of a pro-inflammatory (“hot”) and an immunosuppressive (“cold”) tumor population. This was done by mixing two squamous skin carcinoma cell lines that alone give rise to tumors with a reproducible immunologically “hot” or “cold” immune phenotype respectively, and labeling these with YFP or RFP fluorescent tags to enable precise spatial tracking. The resulting mixed-population tumors were made up of a patchwork of distinct regions that could be classified as being comprised of YFP+(“hot”) cells, RFP+(“cold”) cells, or a mixture of YFP+and RFP+cells. We find the spatial organization of tumor cells creates a blueprint for the spatial organization and functional activity of infiltrating immune cells, defining the architecture of both tumor-infiltrating T cell and myeloid cell compartments. Using a combination of microdissection techniques and single-cell spatial transcriptomics, we show that YFP regions harbor a higher frequency of Th1 cells and IFNψ+CD8 T cells compared to RFP regions, whereas immunosuppressive macrophages preferentially accumulate in RFP regions. Total CD4 T cells were also enriched in YFP regions, but by contrast, total CD8 T cells—despite their superior function in YFP regions—were of low abundance throughout the heterogeneous tumors. We identify the chemokine Cx3cl1, produced at higher levels by our “cold” tumors, as a mediator of intratumoral macrophage abundance, and show that overexpression of Cx3cl1 in pro-inflammatory (“hot”) tumor cells leads to an increase in immunosuppressive CD206Himacrophages. We further interrogated the impact of this spatial patterning of immune cells on the responses of heterogeneous tumors to checkpoint blockade. We find that combination of PD-1 blockade and CD40 agonist is able to increase the Th1 response in “cold” RFP regions, however the T cell response in “cold” regions remains inferior to “hot” regions and treatment achieves only a modest reduction in tumor growth. Collectively, our results demonstrate that the spatial organization of heterogeneous tumor cells has a profound impact on directing the spatial organization and function of tumor-infiltrating immune cells as well as on responses to immunotherapy.

overall_design: Subcutaneous tumors from mosaic tumors formed from coinjection of two squamous cell carcinoma lines (CIT6 YFP and CIT9 RFP) were harvested and sectioned. Using light based barcoding, we barcoded immune  cells coming from YFP+, RFP+ and mixed regions. Sections were then dissociated and barcoded immune cells sorted out and encapsulated using 10X to generate gene expression and spatial barcode libraries.

first: Miho

last: Tanaka

first: Lotus

last: Lum

first: Cecilia

last: Ledezma-Soto

first: Daphne

last: Superville

last: Ng

first: Zoe

last: Adams

first: Kelly

last: Kersten

first: Lawrence

last: Fong

first: Matthew

last: Krummel

first: Melissa

last: Reeves


title: Differential mRNA expression from oviduct and uterus between control Smad4 fx/fx and mutant Amhr2-cre; Smad4 fx/fx mice

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

summary:
In female mammals, the oviduct and uterus play an important role in successful pregnancy by affecting on gamete transport, fertilization, implantation and maintenance of pregnancy. In the mutant Amhr2-cre; Smad4 fx/fx mice, the reproductive functions of both the oviduct and uterus are impaired due to the development of oviductal diverticula and defective uterine vascularization and decidualization, respectively.
We used microarrays to decipher the gene expression changes responsible for this phenotype.

overall_design: Nine to eleven weeks old mutant and control mice were mated with wild-type male mice. Oviduct (8 weeks corresponds to the time of diverticula appearance) and uteri were collected at day 6 of gestation, when decidualization and vascularization develop after implantation. Collected tissues were subjected to RNA extraction. RNAs were used for hybridization on Affymetrix microarrays.

first: Fabrice

last: Petit

first: Soazik

last: Jamin

first: Bertrand

last: Evrard


title: 4DNESSSDVO27 - Replicate experiments of in situ Hi-C on CyT49 with MboI

summary: Replicates of Hi-C on undifferentiated CyT49 human embryonic stem cells

overall_design:
**Data Use Guidelines:** This is a data set generated by the 4DN Network and made freely available to the scientific community. If you are intending to use these data for a publication, we ask that you please contact the data generating lab to discuss possible coordinated publication. In your manuscript, please cite the 4DN White Paper ([doi:10.1038/nature23884](https://doi.org/10.1038/nature23884)) and the 4DN Data Portal paper ([doi:10.1038/s41467-022-29697-4](https://doi.org/10.1038/s41467-022-29697-4)), and please acknowledge the 4DN lab which generated the data. Please direct any questions to the [Data Coordination and Integration Center](mailto:support@4dnucleome.org).
lab: Bing Ren, UCSD
award: 1U54DK107977-01
accession: 4DNESSSDVO27
condition: undifferentiated
submitted_by: Bin Li
dataset_label: Hi-C on hESC differentiated to pancreatic endoderm
experiment_type: in situ Hi-C
url: https://data.4dnucleome.org/experiment-set-replicates/4DNESSSDVO27/
number_of_experiments: 2

experiment: 4DNEX94DX4XP; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXFRAFIWZ; replicate_number: Biorep 2, Techrep 1

Series supplementary files:
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/ffd4e6a8-1ad3-40d9-97fa-ad1bbfbdb94d/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFI9VR75SS.pairs.gz, 4DNFIKGQSUNZ.pairs.gz, 4DNFI823L812.txt
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-combined
file_format: pairs
file name: 4DNFI3WK3QYQ.pairs.gz
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/ffd4e6a8-1ad3-40d9-97fa-ad1bbfbdb94d/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFI9VR75SS.pairs.gz, 4DNFIKGQSUNZ.pairs.gz, 4DNFI823L812.txt
description: This is an output file of the Hi-C processing pipeline
file_type: contact matrix
file_format: mcool
file name: 4DNFIXOWKAM6.mcool
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/97a9ea35-ef5c-4c52-9ac0-11391794a02d/
genome_assembly: GRCh38
derived_from: 4DNFIXOWKAM6.mcool
description: Boundaries calls on Hi-C contact matrices
file_type: boundaries
file_format: bed
file name: 4DNFI23RGV8B.bed.gz
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/97a9ea35-ef5c-4c52-9ac0-11391794a02d/
genome_assembly: GRCh38
derived_from: 4DNFIXOWKAM6.mcool
description: Diamond insulation scores calls on Hi-C contact matrices
file_type: insulation score-diamond
file_format: bw
file name: 4DNFIKIGIIY4.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/a5ed29eb-493f-46ab-a599-416b15bc3a1f/
genome_assembly: GRCh38
derived_from: 4DNFIXOWKAM6.mcool, 4DNFI7MCA4R6.bedGraph.gz
description: Compartments signals on Hi-C contact matrices
file_type: compartments
file_format: bw
file name: 4DNFIN3O5SOJ.bw


title: Proliferative stress in hematopoietic stem cells partially drives their functional decline during aging by DNA methylation imprints

status: Public on Dec 11 2024

city: Baltimore

first: Bongsoo

last: Park

state: Maryland

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

summary: Aging of hematopoietic stem cells (HSCs) has been shown to drive many aging phenotypes including immune dysfunction, anemia, malignancies, and more. It has been proposed that HSC aging can be driven by their proliferation, however, the dynamics of this phenomenon and how it relates to stress induced proliferation are unclear. Therefore, we induced forced replications of HSCs in vivo by a cyclical treatment with low-dose fluorouracil (5FU) and examined the impact on HSC aging phenotypes. We find the blood profile of mice where HSCs were forced to proliferate develop some, but not all aging phenotypes. Initially, forced replication of HSCs can promote repair of DNA damage accrued with age, but continuous proliferative stress then drives accumulation of double strand breaks. We also find HSC functional potential is reduced prior to that damage accumulation in a manner that does not impact the HSC self-renewal capacity and is associated with an accumulation of CD150high HSCs. Lastly, we find that the DNA methylation profile, rather than mRNA expression, carries the replicative stress imprint. These DNA methylation changes include a global hypermethylation in non-coding regions, and a balanced hypo- and hyper-methylation of promoter regions that correlate to the observed functional changes. Specifically, we observed a differential methylation in promoter regions of genes that are targets of the PRC2 complex. Our results overall indicate that HSC proliferation can drive some, but not all, aging phenotypes, and that this is mediated primarily by epigenetic mechanisms including DNA methylation.

overall_design: RRBS analysis of 0x, 2x, 4x, 10x 5FU treated murine HSCs

first: Hagai

last: Yanai

first: Taylor

last: McNeely

first: Saipriya

last: Ayyar

first: Michael

last: Leone

first: Le

last: Zong

first: Isabel

last: Beerman


title: The genetic basis of worker reproduction in Bombus terrestris

city: Norwich

first: David

middle: C.

last: Prince

address: Norwich Research Park

country: United Kingdom

institute: University of East Anglia

summary: We examined the transcriptomic changes associated with worker reproduction in the brain, fat body, ovary and eggs of B. terrestris.

overall_design: RNA-Seq of four Bombus terrestris tissue types (brain, fat body, ovary and eggs) in two/one phenotypes of workers (ovary active and ovary inactive for brain, fat body and ovary, ovary active for eggs), with three biological and three technical replicates per tissue/phenotype combination (for brain, fat body and ovary) and two biological replicates for eggs.

first: Anders

last: Wirén

first: Tim

last: Huggins

first: Tamas

last: Dalmay

first: Andrew

last: Bourke


title: Changes in RNA Polymerase II distribution in stage 5 Drosophila embryos following either inhibition of DNA replication, or elimination of anterior-posterior patterning inputs.

city: Evanston

first: Shelby

middle: A

last: Blythe

state: IL

address: Northwestern University, Hogan Hall, 2205 Tech Drive

department: Molecular Biosciences

institute: Northwestern University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In an associated manuscript, we have formulated a stochastic model for transcription factor-nucleosome competition to account for how the homeodomain transcription factor Bicoid (Bcd) regulates its targets in a concentration-sensitive manner. This model has three central assumptions that we tested using ChIP-seq. First, we assume that, following mitotic exit, Bcd has the ability to compete with nucleosomes and bind to DNA independently of the completion of DNA replication. Second, we also assume that transcription becomes immediately detectable following the completion of both Bcd binding and DNA replication, and that therefore the recruitment of RNA Pol II to the promoter likely also occurs independently of these processes. Finally, we assumed that RNA Pol II initiates transcription at Bcd target genes independently of Bcd, whose function is to release initiated RNA Pol II into productive elongation. We did two experiments to test these assumptions. First, we measured binding of RNA Pol II and Bcd to chromatin in control and replication-inhibited embryos. Second, we measured RNA Pol II binding in control and bcd oskar torsolike triple-mutant embryos. We find that RNA Pol II initiates transcription under conditions of DNA replication arrest, but shows decreases within gene bodies, suggesting that entry into productive transcriptional elongation requires completion of DNA replication. We also find that Bcd binds chromatin independently of DNA replication. Finally, we find that in the absence of Bcd, Bcd target genes initiate transcription, but lack elongating RNA Pol II. These ChIP-seq measurements therefore support the assumptions made in our modeling approach.

overall_design: ChIP-seq of either RNA Pol II, Bcd, or a negative control (anti myc-tag) in stage 5 Drosophila embryos. Experiment 1: embryos were permeabilized and treated with hydroxyurea for 40 minutes prior to fixation, followed by hand-sorting for embryos staged at late nuclear cycle 13, and processing for ChIP-seq. Experiment 2: wild-type or bcd oskar torsolike mutant embryos were collected and fixed prior to hand-sorting for stage 5 morphology, followed by processing for ChIP-seq.

first: Eleanor

last: Degen

first: Corinne

last: Croslyn


title: Test case data for ChIC - ChIP-seq quality control pipeline

city: Milan

first: Chiara

last: Lanzuolo

address: Via Francesco Sforza 35

country: Italy

institute: CNR and Istituto Nazionale Genetica Molecolare

summary: Despite the widespread adoption of ChIP-seq there is still no consensus on quality assessment metrics. No single published metric can reliably discriminate the success or failure of an experiment, thus hampering objectivity and reproducibility of quality control. We introduce a new framework for ChIP-seq data quality assessment that overcomes the limitation of previous solutions. Our tool called "ChIC" incorporates a novel set of quality control metrics integrated into one single score summarizing the sample quality and a reference compendium with thousands of published ChIP-seq samples, for easier evaluation of new data. This test dataset contain an example of succesfull and non-succesfull ChIP-seq sample for mouse H3K27me3.

overall_design: We are testing our pipeline on a succesfull and non-succesfull ChIP-seq sample for mouse H3K27me3

first: Federica

last: Lucini

first: Andrea

last: Bianchi


title: RNA-seq analysis of bread wheat grown under hydroponic Fe deficient conditions

city: Parkville

first: Oscar

last: Fung

state: VIC

address: BioSciences 3

department: School of BioSciences

country: Australia

institute: The University of Melbourne

summary: Bread wheat (Triticum aestivum L., cv. Fielder) plants were grown under iron (Fe) deficient hydroponic conditions to analyise transcriptomic changes in leaf and root tissue.

overall_design: Grain harvested from cv. Fielder plants were stratified at 4°C for two days and then surface sterilised with VitaVax 200FF (Hewitt & Whitty, Geelong, Victoria, Australia) and placed on sterile moist filter paper at 20°C for two days. Germinated seedlings were transferred to hydroponic boxes containing a nutrient replete solution: 2 mM NH4NO3, 5 mM KNO3, 2 mM Ca(NO3)2·4H2O, 2mM MgSO4·7H2O, 0.1 mM KH2PO4, 10 µM H3BO3, 5 µM MnCl2·4H2O, 5 µM ZnSO4·7H2O, 0.5 µM CuSO4·5H2O, 0.1 µM Na2MoO4·2H2O, and 50 µM NaFe3+EDTA. Following 12 days of nutrient replete growth, the solution was replaced with an Fe deficient solution (0 µM NaFe3+EDTA) and grown for a further 11 days. The nutrient solution was replaced every four days. Leaf tissues were harvested at days 0 (1st leaf), 1 (1st leaf), 7 (3rd leaf) and 11 (3rd, 4th, 5th leaves) of Fe deficiency and root tissues were harvested at day 11 of Fe deficiency. All tissues were immediately snap frozen in liquid nitrogen following sampling. Approximately 50 mg of tissue in TRI Reagent® (Merck, Darmstadt, Germany) was homogenised with stainless steel beads and a TissueLyser II (Qiagen, Hilden, Germany). Three plants were used  (105_, 106_ and 112_).

last: Carey-Fung

first: Alexander

last: Johnson


title: Lysine-targeting, covalent inhibitors of bromodomain BD1 of BET proteins in live cells and animals

city: JiNan

first: Tao

last: Li

address: No.44, West Wenhua Road

country: China

institute: Shandong University

summary: Bromodomain (BRD) is an epigenetic reader of acetylated lysine. It has emerged as a therapeutic target for cancer and other diseases. Current nonselective BRD inhibitors (BRDis) face several adverse events (i.e. gastrointestinal toxicity and thrombocytopenia), making the development of target covalent inhibitor (TCI) for BD1/2 as a fresh avenue to overcome safety challenges. We report herein a set of activity-based probes (ABPs; P3-P7) based on various lysine-reactive covalent warheads capable of global profiling of ligandable lysine within BRDs in live cells and animals. Chemoproteomic experiments with P7 by utilizing 2-ethynylbenzaldehyde (EBA) identified 16 endogenous BRDs, thus giving a global landscape of ligandable lysines in BRDs. By further introducing EBA and salicylaldehyde into PLX51107 (a non-covalent BRDi), we generated novel irreversible (BDS1-4) and reversible (BDS5-6) lysine-reactive TCIs. Mass spectrometry and X-ray crystallography confirmed the successful covalent engagement between the covalent warhead and lysine near Kac binding site. BDS4 showed 104-fold selectivity for BD1 over BD2 with prolonged anti-cancer effect than non-covalent BRDi. Importantly, BDS4 retained robust activity against fibrosis in cells and animals in comparison to the marginal effect of BD2 inhibitor RVX-208. Our work serves as a useful tool to delineate the distinct function of BD1 and BD2.

overall_design: 3 × 105 LX-2 cells were evenly distributed into 6-well plates and incubated overnight at 37 °C in 5% CO2. Upon starvation for 24 h in DMEM containing 0.5% FBS, the cells were treated only with TGF-β (20 ng/mL, HZ-1011, Proteintech) or cotreated with TGF-β (20 ng/mL) and indicated compounds (5 μM) for 24 h. After incubation, the cells were collected for RNA sequencing carried out by Sinotech Genomics Co., Ltd. (Shanghai, China) at a cost, and the details are presented below.     RNA of cells was isolated by using AG RNAex Pro Reagent (AG21102，Accurate Biology). RNA concentration and quality were determined with the Qubit®3.0 Fluorometer (Life Technologies, USA) and the Nanodrop One spectrophotometer (Thermo Fisher Scientific Inc., USA). Integrity of total RNA was assessed by using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., USA). One microgram of RNA was used as input material for the RNA sample preparations. Paired-end libraries were synthesized by using the Stranded mRNA-seq Lib Prep Kit for lllumina (RK20349, ABclonal) following Preparation Guide. Purified libraries were quantified by Qubit® 3.0 Fluorometer and validated by Agilent 2100 bioanalyzer to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA). FPKM values for known gene models were generated by Stringtie (version: 1.3.0).

first: Xiaotong

last: Ze

first: Yiqing

last: Wang

first: Wenjie

last: Zhang

first: Fengfei

last: Miao

first: Peng

last: Chen

first: Guanghui

last: Tang

first: Jing

last: Xiang

first: Guangyu

last: Xu

first: Jiaqian

last: Yan

first: Miaomiao

first: Min

last: Liu

first: Xiaojie

first: Wei

first: Fan

last: Yi

first: Zhi-Min

first: Rui

first: Shao Q

last: Yao

first: Yusheng

last: Xie


title: Agonism of the glutamate receptor GluK2 suppresses dermal mast cell activation and cutaneous inflammation

city: PITTSBURGH

first: Jishnu

last: Das

state: PA

address: 5051 CENTRE AVE

department: Department of Immunology

institute: University of Pittsburgh

summary: Activation of dermal mast cells through the Mas-related G-protein-coupled receptor B2 receptor (MrgprB2; MrgprX2 in humans) is a key component of numerous inflammatory skin diseases including dermatitis and rosacea. Sensory neurons actively suppress mast cell activation through the regulated release of glutamate resulting in reduced expression of Mrgprb2 and genes associated with proteins found in granules. To determine whether exogenous glutamate receptor agonism could suppress mast cell function, we determined that mast cells have relatively selective expression of the glutamate receptor GluK2.  A GluK2-specific agonist, SYM2081, effectively inhibited mast cell degranulation in response to MrgprB2 agonism in vitro in murine mast cells and human skin explants as well as in vivo, following both intradermal and topical administration in mice. Analyses of transcriptomic datasets from SYM2081 treated mast cells using standard differential expression approaches as well as a novel interpretable machine learning technique revealed a previously unrecognized cellular program coordinately regulated by GluK2 agonism.  Notably, GluK2 agonism suppressed the expression of Mrgprb2 and genes associated with proliferation. Suppression of mast cell proliferation by SYM2081 exposure was confirmed based on reduced Ki-67 expression and BrdU incorporation in vitro and in vivo. Finally, pretreatment with SYM2081 significantly reduced skin inflammation in murine dermatitis and rosacea models.  Thus, agonism of GluK2 represents a promising approach to suppress mast cell activation and may prove beneficial as therapy for inflammatory diseases in which mast cell activation is pathogenic.

overall_design:
The goal of this study was to determine the glutamate receptor expression on mast cells, and if glutamate receptor agonism could modulate mast cell activation and skin inflammation
To characterize the transcriptomic changes within MC following GluK2 modulation, we performed bulk RNA sequencing on PCMC treated with vehicle, glutamate, and SYM2081 as well as sorted dermal MCs from MrgprDDTR mice.

first: Daniel

last: Kaplan

first: Youran

middle: R

first: Swapnil

last: Keshari


title: Analysis of the quadruple lsu mutant reveals molecular determinants of the role of LSU proteins in sulfur assimilation in Arabidopsis

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

summary: Because plants are immobile, they have developed intricate mechanisms to sense and absorb nutrients, adjusting their growth and development accordingly. Sulfur is an essential macroelement, but our understanding of its metabolism and homeostasis is limited. LSU (RESPONSE TO LOW SULFUR) proteins are plant-specific proteins with unknown molecular functions and were first identified during transcriptomic studies on sulfur deficiency in Arabidopsis. These proteins are crucial hubs that integrate environmental signals and are involved in the response to various stressors. Herein, we report the direct involvement of LSU proteins in primary sulfur metabolism for the first time. Our findings revealed that the quadruple lsu mutant, q-lsu-KO, which was grown under nonlimiting sulfate conditions, exhibited a molecular response resembling that of sulfur-deficient wild-type plants. This led us to explore the interactions of LSU proteins with sulfate reduction pathway enzymes. We found that all LSU proteins interact with ATPS1 and ATPS3 isoforms of ATP sulfurylase, all three isoforms of adenosine 5´phosphosulfate reductase (APR), and sulfite reductase (SiR). Additionally, in vitro assays revealed that LSU1 enhances the enzymatic activity of SiR. These results highlight the supportive role of LSU proteins in the sulfate reduction pathway.

overall_design: To dissect the role of LSU proteins in plant metabolism, we investigated the impact of knocking out all four LSU genes on the plant global transcriptome under both normal and sulfur deficiency conditions using 3’RNA-seq. Libraries were generated from total RNA extracted from either the shoots or roots of 15-day-old q-lsu-KO mutant and Col-0 (wild-type) plants. The plants were grown under normal sulfur or sulfur deficiency conditions.

first: Justyna

last: Piotrowska

first: Anna

last: Wawrzyńska

first: Marcin

last: Olszak

first: Agnieszka

last: Sirko


title: RNA-Seq analysis SIRT6 knockdown effect on vascular smooth muscle cells

city: Jinan, Shandong

first: Shuai

last: Leng

address: 105 Jiefang Road

institute: Central Hospital Affiliated to Shandong First Medical University

summary: Vascular smooth muscle cells (VSMCs) phenotype switch has been thought to be critical to the development of thoracic aneurysm/dissection. To investigate the function SIRT6 in the regulation of VSMCs phenotype switch, we established mouse vascular smooth muscle cells in which each target gene has been knocked down by siRNA.

overall_design: VSMCs isolated and cultured from mouse aorta were siSirt6 or control (n=3 for each group) for 48 hours. Total RNA was isolated using Trizol reagent (Invitrogen, USA). Agilent 2100 Bioanalyzer (Agilent Technologies, USA) was used to evaluate the RNA quality.

first: Wenqian

last: Yu


title: Genome-wide mapping of the Galleria mellonella larvae transcription start sites during infection with the madurella mycetomatis pathogen

city: Yokohama

first: Imad

last: Abugessaisa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: IMS

country: Japan

institute: RIKEN

summary: Using Low Quantity single strand CAGE (LQ-ssCAGE) we mapped the transcription start sites (TSS) and annotated the 5' end of the invertebrate Galleria mellonella which is upcoming and booming in the last years as an experimental model in infection disease and immunology research. The current genome annotation of this model lacks the annotation of the 5' end and TSS information. To map TSS under healthy and infection conditions, the G. mellonella larva was infected with the fungal pathogen Madurella mycetomatis  After 4, 30 and 52 hours of the infection, larvae were treated with itraconazole or ravuconazole. RNA-seq and LQ-ssCAGE libraries prepared and sequenced. The LQ-ssCAGE data was processed to identify CAGE transcription start site (CTSS), uni- and bi-directional clusters. LQ-ssCAGE enabled us to precisely identify (39,410) TSS and (249) active enhancers. We assigned genomic features to the resulting TSSs and enhancers. The majority of the TSS peaks are annotated as promoter regions while the enhancers were annotated as intergenic and genic. Furthermore, we confirmed the quality of TSS by promoter shapes and GC bias.  We identified a set of super-enhancers and predicted de-novo motifs. In this study we reported the first atlas of TSS and active enhancers of the G. mellonella.

overall_design: To map and annotate the transcription start sits of the invertebrate Galleria mellonella larvae we prepared and sequenced LQ-ssCAGE (low quantity single strand CAGE) libraries (n=72). The resulting sequence tags are mapped against the reference genome for the Galleria mellonella. The CAGE tags are called using the mapped reads. Using statistical and clustering methods, TSS and active enhancers are identified and annotated again genomics regions.

first: Mickey

last: Konings

first: Takeya

last: Kasukawa

first: Wendy

middle: W

last: Sande


title: Regulatory T cells promote decidual vascular remodeling by modulating uterine natural killer cells to support pregnancy in mice

city: Adelaide

first: Ha

middle: Manh

last: Tran

state: SA

address: 4 North Terrace

institute: University of Adelaide

summary: Regulatory T (Treg) cells are essential for maternal immune tolerance of the fetus and placenta. In preeclampsia, aberrant Treg cell tolerance is implicated, but whether and how Treg cells affect the uterine vascular dysfunction thought to precede placental impairment and maternal vasculopathy is unclear. We utilized Foxp3 DTR mice to test the hypothesis that Treg cells are essential regulators of decidual spiral artery adaptation to pregnancy. Transient Treg cell depletion during early placental morphogenesis caused impaired remodeling of decidual spiral arteries and altered uterine artery function, resulting in late gestation fetal loss and fetal growth restriction. Treg cell depletion impaired acquisition of the activation receptor NKp46 on uterine natural killer (uNK cells) and was associated with reduced decidual synthesis of Treg cell-derived cytokines Il35, Il10 and Tgfb implicated in modulating uNK cell phenotype. When Treg cells were replaced, the adverse impact on uNK cell abundance and phenotype, decidual spiral artery remodeling, uterine artery function, and fetal loss was mitigated. These data implicate Treg cells as essential upstream drivers of uterine vascular adaptation to pregnancy through regulation of uNK cell recruitment and activation. The findings provide a mechanism linking impaired adaptive immune tolerance and altered spiral artery remodeling, two hallmark features of preeclampsia.

overall_design: To characterize the decidual transcriptome following Treg cell depletion, and assess the degree of normalization by infusion of wild-type Treg cells, we performed RNA sequencing on decidual tissue collected at GD10.5 from vehicle, DT-treated Foxp3DTR, or DT-treated Foxp3DTR mice given wild-type Treg cells (n = 5-6 samples per group).

first: Shanna

middle: L

last: Hosking

first: Lachlan

last: Moldenhauer

first: Hon

middle: Y

last: Chan

first: Holly

last: Groome

first: Evangeline

last: Lovell

first: Ella

middle: S

last: Green

first: Stephanie

middle: E

last: O'Hara

first: Claire

middle: T

last: Roberts

first: Kerrie

last: Foyle

first: Sandra

last: Davidge

first: Sarah

last: Robertson

first: Alison

last: Care


title: Early Age Efferocytosis Directs Macrophage Arachidonic Acid Metabolism for Tissue Regeneration

city: Chicago

first: Connor

last: Lantz

address: 303 E. Chicago Ave. Ward 4-075

summary: In response to organ injury in adults, macrophages often promote scarring, yet during early life are required for tissue regeneration. To elucidate mechanisms underlying age-associated regeneration, we compared the macrophage injury response in newborns versus adult hearts. Single cell analysis revealed an accumulation of tissue-resident macrophages in neonates that were selectively polarized for apoptotic cell recognition and uptake (efferocytosis). Ablation of the apoptotic cell recognition receptor Mertk in newborns prevented cardiac regeneration. These findings could be attributed to reprogramming of macrophage gene expression that was required for biosynthesis of the eicosanoid Thromboxane A2, which unexpectedly activated parenchymal cell proliferation. Markers of Thromboxane A2 production were suppressed in adult macrophages after efferocytosis. Moreover, macrophage-neighboring neonatal cardiomyocytes expressed the Thromboxane A2 receptor, whose activation induced a metabolic shift supporting cellular proliferation. Our data reveal a fundamental age-defined macrophage response in which lipid mitogens produced during efferocytosis support receptor-mediated tissue regeneration.

overall_design:
Single cell mRNA sequencing. Single cell suspensions were isolated as described in the method section “Flow Cytometry” by Collagenase Type II and DNase digestion of hearts. After RBC lysis, samples underwent dead cell removal (StemCell Technologies) by Annexin V staining. Next, samples underwent a CD45-positive selection (StemCell Technologies) to enrich cardiac leukocytes. Enriched cells and flow-through cells were both counted and recombined at a ratio of 2 CD45+ cells for every 1 non-CD45+ cell. Combined single cell suspensions were diluted to target a recovery of 5,000 cells per sample. The single cell RNA-sequencing libraries were prepared using the 10X Genomics Single Cell 3’ Gene Expression (v3 or v3.1 chemistry) pipeline. The prepared libraries were run on an Agilent Bioanalyzer High Sensitivity Chip and Kapa Biosystems Library Quantification Kit for Illumina platforms for quality control before sequencing. All libraries were sequenced on the Illumina NovaSeq 6000 platform with the following parameters: Read 1—26 cycles; i7 Index—8 cycles; Read 2—98 cycles.

Processing and analysis of scRNA-seq data.
Raw Sequencing Data Processing (Alignment, Barcode Assignment, and UMI Counting). The raw FASTQ files were first aligned to the murine transcriptome (GRCm38; mm10) using CellRanger (10X Genomics, v4.0.0). Aligned reads were then filtered for valid barcodes and UMIs to generate gene-cell matrices used for downstream analysis.

first: Edward

middle: B

last: Thorp


title: Mesocricetus auratus transcriptome and UPR genes expression analysis.

city: New York

first: Arturo

last: Marin Alguacil

state: New York

address: One Gustave L. Levy Place

department: Microbiology

institute: Icahn School of Medicine at Mount Sinai

summary: To investigate the relationship between the expression of the UPR (unfolded protein response) genes, and the SARS-CoV-2 infection, a study was carried out based on the infection of hamster, Mesocricetus auratus. UPR gene levels were compared between infected and uninfected hamsters at different temporal points.

overall_design: Comparative gene expresion analysis of RNA-seq from hamster uninfected and infected with SARS-CoV-2. Four replicates for each time point and condition.

last: Marin


title: Upregulation of FGF13 promotes type 2 diabetic nephropathy by modulating glomerular endothelial mitochondrial homeostasis

city: wenzhou

first: jia

last: sun

address: wenzhou medical university

institute: wenzhou medical university

summary: Studies of diabetic glomerular injury raise the possibility of developing useful early biomarkers and therapeutic approaches for the treatment of type 2 diabetic nephropathy (T2DN). In this study, it is found that FGF13 expression is induced in glomerular endothelial cells (GECs) during T2DN progression, and endothelial-specific deletion of Fgf13 potentially alleviates T2DN damage. Fgf13 deficiency restores the expression of Parkin both in the cytosolic, mitochondrial, and nuclear fractions under diabetic conditions, resulting in improved mitochondrial homeostasis and endothelial barrier integrity due to promotion of mitophagy and inhibition of apoptosis. Additionally, it is confirmed that the beneficial effects of Fgf13 deficiency on T2DN are abolished by endothelial-specific double deletion of Fgf13 and Prkn. The effects of Fgf13 deficiency on mitophagy and apoptosis via Parkin-dependent regulation may be distinct and separable events under diabetic conditions. These data show that the bifunctional role of Fgf13 deficiency in promoting mitophagy and inhibiting apoptosis through Parkin can shape mitochondrial homeostasis regulation in GECs and T2DN progression. Acting as a potential biomarker and therapeutic target for prevention and control of T2DN, mechanistically understanding of the biofunction of FGF13 may also be of relevance to the pathogenesis of other FGF13- and Parkin-associated diseases.

overall_design: To explore the transcriptional profiles of HRGEC treated with HG-PA alone or together with L-shFgf13, or with L-shFgf13+siPrkn.

first: Weitao

last: Cong


title: The chromatin accessibility landscape of T-Cell Acute Lymphoblastic Leukemia

first: Junfei Zhao

last: Zhao

state: NY

address: 1130 St. Nicholas Ave

institute: Columbia University

summary: We investigated the chromatin accessibility landscape of normal T cells and T-Cell Acute Lymphoblastic Leukemia to define the thymocyte development using chromatin accessibility profiles and map the aberrant leukemia-associated accessibility sites in T-ALL.

overall_design: We performed ATAC-seq on 14 normal T cell samples and 35 Leukemia samples including 14 pairs (Diagnosis & Relapse) and another 7 Leukemia daignosis samples. 31 of the leukemia samples also have RNAseq data.

first: Junfei

first: Adolfo

last: Ferrando


title: Sox15 is a novel retinal developmental gene that promotes cone photoreceptor differentiation through inhibition of alternative rod photoreceptor fates

status: Public on Dec 10 2024

city: Toronto

first: Derek

last: van der Kooy

state: Ontario

address: 160 College Street

department: Molecular Genetics

country: Canada

institute: University of Toronto

summary: The type of cell fate decisions a progenitor can make in the developing nervous system are dependent on a combination of cell intrinsic gene expression programs and cell extrinsic signaling molecules that influence expression programs. Moreover, both the progenitor’s spatial location in the tissue and time at which it exists during development can, to varying degrees, influence the competency of differentiation. Here, we use the developing mouse retina to understand how signaling factors in the retinal niche can influence a progenitor to become unipotentially restricted to differentiate into cone photoreceptors, and how this competency changes over the course of retinal development. We show that the secreted inhibitory protein COCO causes progenitors to become cone restricted, and that the competency for this restricted differentiation is maintained throughout retinal development. Using RNA-sequencing, we identify the transcription factor Sox15 as a potential novel marker of restricted progenitors in the developing retina, and that it acts in response to COCO’s effects. Knockdown experiments indicate that this novel retinal transcription factor is involved in the survival of retinal progenitors and promotes cone differentiation by inhibiting differentiation into alternative photoreceptor types.

overall_design: Bulk RNA-seq profiling of in vitro mouse neural retinal progenitors cells undergoing rod or cone photoreceptor directed differentiation conditions. Cells were profiled at day 0, 5, 12, 21, and 35.

first: Justin

middle: J

last: Belair-Hickey

first: Saeed

last: Khalili

first: Brenda

last: Coles

first: Brian

middle: G

last: Ballios

first: Jeff

middle: C

last: Liu

first: Gary

middle: D

last: Bader


title: Skeletal dysplasia-causing mutations in TRPV4 alter the chondrocyte’s transcriptomic response to mechanical loading

city: Saint Louis

first: Farshid

last: Guilak

state: MO

address: 660 S Euclid Ave, Campus Box 8233

department: Dept of Orthopedics

institute: Washington University in St. Louis

summary: Transient receptor potential vanilloid 4 (TRPV4) is a mechanosensitive ion channel highly expressed in chondrocytes that maintains cartilage homeostasis during development and throughout aging. Mutations in the channel cause a wide range of developmental disorders including skeletal dysplasias. The gain-of-function mutations V620I and T89I have been identified to lead to brachyolmia and metatropic dysplasia, respectively. Although it is known these mutations suppress hypertrophic differentiation, the mechanisms by which they alter chondrocyte response to mechanical loading remain to be elucidated. To determine the effect of these mutations on chondrocyte mechanotransduction, tissue-engineered cartilage was derived from differentiated CRISPR-edited human induced pluripotent stem cells harboring the moderate V620I or severe T89I TRPV4 mutations. Tissue-engineered hiPSC-derived cartilage was then subjected compressive mechanical loading at physiological levels, and RNA-sequencing was used to assess the transcriptomic signatures of wildtype and mutant tissue-engineered cartilage. Our results demonstrate that the V620I and T89I mutations lead to reduced mechanoresponsiveness, characterized by a lower number of differentially expressed genes and diminished activation of genes downstream of TRPV4 signaling and contributing towards the process of endochondral ossification. Changes in extracellular matrix production and organization were found to contribute towards the phenotype in V620I chondrocytes, whereas dysregulated retinoic acid signaling was linked to T89I, and disrupted proliferation was common to both. Our findings suggest that dysfunctional mechanotransduction arising due to the V620I and T89I mutations contribute to the developmental phenotypes observed in their respective skeletal dysplasias, introducing potential pharmacologic targets for these conditions.

overall_design: To understand how the V620I and T89I skeletal-dysplasia causing mutations in TRPV4 impact chondrocyte mechanotransduction, CRISPR-Cas9 gene-edited hiPSCs with these mutations or unedited Wildtype cells were differentiated into chondrocytes. WT, V620I, and T89I chondrocytes were then embedded in an agarose hydrogel to form tissue-engineered hiPSC-derived cartilage, cultured for 14 days, and mechanically loaded with cyclic, unconfined compressive loading (10% stain, 1 Hz) over 3 hours or left unloaded as free-swelling controls. Mechanically loaded samples were collected at two points (immediately at 0 hours or after  24 hours). Constructs were also treated with the TRPV4 antagonist GSK205 (10 uM) under these same conditions.

first: Zainab

last: Harissa

first: Yuseon

last: Kim

first: Amanda

last: Dicks

first: Nancy

last: Steward


title: Erianin abrogates vasculogenic mimicry through targeting m5C methylase NSUN2

city: Shanghai

first: Sipeng

last: Zuo

state: Shanghai

address: No. 12, Lane 833, Zhizaoju Road, Huangpu District

institute: Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

summary: Purpose: The precise temporal and spatial regulation of N5-methylcytosine (m5C) RNA modification plays essential roles in RNA metabolism. Targeting m5C regulation in cancer cells may be a potential strategy for cancer therapy. Erianin is a natural product isolated from Dendrobium chrysotoxum Lindl. Howbeit, the in‐depth understanding of interaction between erianin and m5C modification remains indistinct. Methods: Natural product library screening was used to explore the effects of natural product monomers on uveal melanoma (UM) cells. Intraocular xenografts model was established to examine the effect of erianin. Immunoprecipitation mass spectrometry (IP-MS) and molecular docking analyses were performed to identify NSUN2 as the target of erianin. m5C-meRIP-seq and m5C-meRIP-qPCR analyses were performed to identify the functional target of NSUN2. Tube formation assay and CD31-PAS double staining were used to detect vasculogenic mimicry (VM) in UM. Results: Herein, we report the discovery of erianin as an effective inhibitor of uveal melanoma. Mechanistically, the targeted inhibition of NSUN2 function by erianin results in a decrease in the m5C modification and expression levels of CHAC1 in UM, thereby curtailing the formation of VM. Conclusions: Collectively, our data suggested that erianin significantly inhibited UM progression in vitro and in vivo. Our study unveils a novel therapeutic strategy for combating UM.

overall_design: merip-m5C-seq and RNA-seq  upon erianin treatment in human uveal melanoma cells


title: Single-nucleus transcriptome sequencing reveals a specific neuronal subtype in the arcuate nucleus.

city: Beijing

first: Yaxin

last: Wang

address: No. 2, No. 1, Beichen West Road, Olympic Village Subdistrict

department: Institute of Genetics and Developmental Biology

institute: Chinese Academy of Sciences

summary: Over recent decades, research has established the hypothalamus, particularly the arcuate nucleus, as a central hub for the homeostatic control of energy balance. The hypothalamic arcuate nucleus is a pivotal regulator of energy balance, containing anorexic proopiomelanocortin (POMC) neurons and orexigenic agouti-related peptide (AgRP) neurons, which exert opposing effects on energy homeostasis. However, the molecular identity of “non-AgRP, non-POMC” neurons remains unclear. We identified a distinct neuronal subtype characterized by the absence of Agrp and Pomc expressions, while exhibiting robust Crabp1 expression.

overall_design: The hypothalamic arcuate nucleus of adult mice was microdissected for single-nucleus RNA sequencing.

first: Ting

first: Qingfeng

last: Wu


title: Comparison of the translatome of follicle cells during developmental phagoptosis and starvation-induced apoptotic death of nurse cells in Drosophila melanogaster oogenesis.

city: Boston

first: Kimberly

last: McCall

state: Massachusetts

address: 24 Cummington Mall

department: Biology

institute: Boston University

summary: The death and clearance of nurse cells is a consequential milestone in Drosophila melanogaster oogenesis. In preparation for oviposition, the germline-derived nurse cells bequeath to the developing oocyte all their cytoplasmic contents and undergo programmed cell death. The death of the nurse cells is controlled non-autonomously and is precipitated by epithelial follicle cells of somatic origin acquiring a squamous morphology and acidifying the nurse cells externally. Alternatively, stressors such as starvation can induce the death of nurse cells earlier in mid-oogenesis, manifesting apoptosis signatures, followed by their engulfment by epithelial follicle cells. To identify and contrast the molecular pathways underlying these morphologically and genetically distinct cell death paradigms, both mediated by follicle cells, we compared their genome-wide translational profiles before and after differentiating to acquire a phagocytic capability, as well as during well-fed and nutrient-deprived conditions. By coupling the GAL4-UAS system to Translating Ribosome Affinity Purification (TRAP-seq) we performed high-throughput screens to identify pathways selectively activated or repressed by follicle cells to employ nurse cell-clearance routines contextually and preferentially. Our analyses and in vivo follow-up studies identified several key genes and pathways that play vital roles during the making of a healthy egg, such as maintaining the oocyte reserve, ensuring structural integrity of the egg chamber, and regulating metabolic and signaling pathways.

overall_design: To capture the translatome or the set of all mRNAs undergoing translation in follicle cells, we performed TRAP-seq by expressing GFP-tagged large ribosomal subunit 10a using the GAL4/UAS system. We then performed immunoprecipitation to capture ribosome-bound mRNAs and subsequently performed single-end RNA-sequencing of the transcripts. We used the GR1-Gal4 strain to express RpL10a-GFP in Main Body Follicle Cells (GR1>RpL10a-GFP) and PG150-Gal4 strain to express RpL10a-GFP in Stretch Follicle Cells (PG150>RpL10a-GFP). Flies were either fed or starved to obtain the profiles of follicle cells during developmental phagoptosis and starvation-induced apoptotic death of nurse cells.

first: Diane

middle: P

last: Lebo

first: Shruthi

last: Bandyadka


title: Gene expression profiles in the lung following intratracheal instillation of cellulose nanofibrils and multi-walled carbon nanotubes in a murine COPD model

city: Tsukuba

first: Katsuhide

last: Fujita

address: 16-1 Onogawa

department: Research Institute of Science for Safety and Sustainability

institute: National Institute of Advanced Industrial Science and Technology

summary: To evaluate the transcriptional-level biological effects of manufactured nanomaterials, a whole-genome microarray analysis was performed on the lungs of a murine chronic obstructive pulmonary disease (COPD) model. Mice were intratracheally instilled with cellulose nanofibrils (CNFs) or multi-walled carbon nanotubes (MWCNTs).

overall_design: Mice were intratracheally instilled with CNFs, MWCNTs (80µg/mouse), or vehicle solutions (Control). Lungs were excised 28 days post-instillation for microarray analysis.

first: Sawae

last: Obara


title: scRNA-seq analysis for CD11c+ cells recruited to the MLNs in colitis induced in mice supplied with PBS or lysine

city: Tianjin, China

first: Tang

last: Qiang

address: 22 Qixiangtai Road, Heping District 300070, Tianjin, China

institute: Tianjin medical university

summary: L-lysine (Lysine) is an indispensable amino acid that cannot be synthesized by the human body. Lysine effects on DCs in colitis is unkonwn. We investigated whether whether lysine could alter DC differentiation trajectories in colitis. We sorted CD11c+ cells recruited to the MLNs in colitis induced in mice by DSS and profiled the cells by single-cell RNA sequencing.

overall_design: To go insight into lysine effects on DCs in colitis, we sorted CD11c+ cells recruited to the MLNs in colitis induced in mice by DSS on day 7. The mice were treatment with 100mg/kg lysine or PBS daily after 2 days of  DSS treatment


title: Metformin enhances human oligodendrocyte function by altering metabolism

city: Edinburgh

first: Nadine

last: Bestard-Cuche

address: 5 Little France Drive

institute: University of Edinburgh

summary: Metformin rejuvenates adult rat oligodendrocyte progenitor cells (OPCs) allowing more efficient differentiation into oligodendrocytes and improved remyelination of CNS axons and therefore is of interest as a possible therapeutic in demyelinating diseases such as multiple sclerosis (MS). We set out to test whether metformin had a similar effect in human stem cell derived-OPCs. We assessed the suitability of human monoculture, organoid and transplantation into immunodeficient mice (chimera model) culture systems in simulating in vivo adult human oligodendrocytes, finding most close resemblance in the chimera model. Metformin increased myelin proteins and/or sheaths in all models even when human cells had fetal signatures. In the chimera model, metformin led to a marked increase in mitochondrial area both in the human transplanted cells and in the mouse axons with associated increase in transcripts related to mitochondrial function and metabolism. Human oligodendrocytes from MS brain donors treated pre-mortem with metformin also expressed similar transcripts suggesting that metformin’s brain effect is not cell-specific, altering metabolism in both oligodendrocytes and axons leading to more myelin production, in part through mitochondrial changes.  This bodes well for ongoing clinical trials testing metformin for neuroprotection.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Human embryonic stem cell-derived (hESC) oligodendroglia were generated and processed for single-cell RNA sequencing (scRNAseq) using the 10X Genomics pipeline across three model systems: monolayers, organoids, and chimeric animals. In the monolayer model, oligodendroglia were grown in vitro and then prepared for sequencing. For the organoid model, cortical brain organoids containing oligodendroglial cells were cultures in vitro, with ten organoids pooled together per sample for scRNAseq. In the chimeric model, chimeric human-mouse animals were created by injecting GFP+ hESC-derived oligodendrocyte progenitor cells (OPCs) into the rostral and caudal corpus callosum of myelin-deficient and immunodeficient Shi/Shi x Rag2-/- mice. A total of 500,000 cells were distributed between both hemispheres. Following transplantation, chimeric animals were treated daily with 10mg/ml metformin or vehicle (ddH2O) by oral gavage for 21 days, between days 42-63 post transplantation. At day 70 post transplantation, the corpus callosum region of each animal was processed for scRNAseq, with sorted live cells pooled from two animals per sample.

first: Nina Lydia

last: Kazakou

first: Anna

last: Williams


title: RNA sequencing analysis of  Bone Marrow-Derived Dendritic Cells (BMDCs) supplied with PBS or lysine

summary: L-lysine (Lysine) is an indispensable amino acid that cannot be synthesized by the human body.We investigated whether lysine is involved in the remission of ulcerative colitis (UC) through dendritic cells.We performed RNA sequencing analysis in   Bone Marrow-Derived Dendritic Cells (BMDCs) supplied with PBS or lysine to study the molecular mechanisms through which lysine regulates BMDCs gene expression.

overall_design: Gene expression profiles of BMDCs supplied with PBS or 18 mM lysine for 6 h were generated by deep sequencing, using Illumina NovaSeq 6000.To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM)method. RSEM was used to quantify gene abundances.

first: Quan

first: Qiang

last: Tang


title: ChIP-seq analysis for H3K79me2 in Bone Marrow-Derived Dendritic Cells (BMDCs) supplied with PBS or lysine

summary: L-lysine (Lysine) is an indispensable amino acid that cannot be synthesized by the human body. Lysine catabolites can influence the cellular chromatin landscape. We investigated whether lysine supplementation could alter the epigenetic landscape of BMDCs by reprogramming their metabolism. We performed ChIP-seq analysis for H3K79me2 to study the molecular mechanisms through which lysine regulates epigenetic of BMDCs.

overall_design: ChIP-seq analysis for H3K79me2 in BMDCs supplied with PBS or 18 mM lysine for 6 h.The ChIP and input DNA fragments were processed for end repair and A-tailing using the NEBNext End Repair/dA-Tailing Module (E7442, NEB)


title: Integrative biology of patients acutely infected with yellow fever virus

city: Oxford

first: Andre

last: Goncalves

address: Old Road Campus, Roosevelt Dr, Headington

department: Department of Paediatrics

institute: University of Oxford

summary: Yellow fever (YF) is a life-threatening mosquito-borne disease prevalent in South America and Africa, accounting for up to 60,000 annual deaths. Between December 2016 and May 2018, Brazil reported its worst YF outbreak this century with a fatality rate of 33.6%. While YF vaccines have shown protective capabilities, the genetic profile of those infected with the wild-type YF virus (YFV) remains uncharacterized. Building on recent findings by Kallas et al. (2019), which discerned clinical and immunological determinants of YF mortality, we conducted a comprehensive transcriptional profiling of blood samples from YFV-infected patients. Our investigation integrated omics data with clinical and immunological metrics, contrasting the wild-type YFV acute infection signature against the response triggered by the YF17D vaccine strain and the signature linked to severe COVID-19. Our analyses revealed key molecular mechanisms of YFV infection and determinants of disease severity. Notably, a comparative assessment elucidated distinct gene expression patterns between wild-type YFV infections, YF17D vaccination, and severe COVID-19. This study offers pivotal insights into the molecular underpinnings of YFV infection and its severity, potentially enhancing our comprehension of viral infections at large.

overall_design: RNA from PBMCs was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany), quantified using Nanodrop ND-1000 Spectrophotometer (Thermo Fisher Scientific), and integrity checked in a 2200 TapeStation system using RNA ScreenTape (Agilent Technologies, Santa Clara, CA). The cDNA libraries were constructed using the QuantSeq 3' mRNA-Seq Library Prep Kit for Illumina FWD (Lexogen GmbH, Austria), following the manufacturer's protocol. The concentration and the median size of the libraries were assessed by 2200 TapeStation with a DNA1000 ScreenTape (Agilent). The final pool of libraries was quantified by qPCR using the Kapa Sybr Green qPCR Kit (Roche Diagnostics, Mannheim, Germany) and subjected to a single-end sequencing (75 bp) in a NextSeq 500 Sequencing with NextSeq 500/550 High Output Kit v2.5 (Illumina, San Diego, CA). Raw single-end reads were preprocessed for quality control. Sequencing quality was assessed before and after adapter trimming using the program FastQC (Andrews 2010). The Trimmomatic software version 0.39 (Bolger, Lohse, and Usadel 2014) was used to remove adapters sequence trimming the 5, and 3 ends with a mean quality score below 25 (Phred+33) and discard reads shorter than 36 bp after trimming. We used the parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36. After preprocessing, the high-quality reads were mapped into the reference genome Homo sapiens (version GRCh38) with the bowtie2 program (version 2.2.5) (Langmead and Salzberg 2012). To quantify the gene abundance of the mapped reads in each sample, we used the featureCounts tool from the R/Bioconductor package Rsubread (Liao, Smyth, and Shi 2019) with the following parameters: GTF.featureType = gene, GTF.attrType = gene_id, isPairedEnd = FALSE, minOverlap = value 1, allowMultiOverlap = FALSE, countMultiMappingReads = FALSE. Normalization of the gene counts was performed with counts per million normalization (CPM) and quantile normalization, which accounts for differences in library size.

first: Helder

last: Nakaya


title: Robust messenger RNA (mRNA) markers in blood for lung cancer diagnosis

city: Trondheim

first: Pål

last: Sætrom

address: Erling Skjalgsons gate 1

department: Clinical and Molecular Medicine

country: Norway

institute: Norwegian University of Science and Technology, NTNU

summary:
Background: Lung cancer (LC) is the leading cause of cancer deaths worldwide with more than 1.7 million deaths each year. Early detection of LC may be crucial to achieve efficient treatment and to increase survival. However, there are limitations to current methods for early detection of LC as they are too invasive and represent potential health hazards, necessitating improved tools to detect LC at an early stage. Blood-based gene expression profiling is an alternative, or additional tool for diagnostic purposes as blood samples are easily available, essentially non-invasive, and can be collected at a low cost. However, as the blood collection method can affect measured gene expression, the aim of this study was to identify mRNAs that are robust biomarkers for LC in blood.
How: We sampled blood from 123 LC patients at the St. Olavs university hospital, and 180 controls from two different biobanks sampled on two different blood tubes (PAXgene and Tempus) and used Illumina (HT-12 v4) microarrays to measure whole blood gene expression. We did three analyses: (i) finding relevant gene expression differences between cases and controls, (ii) finding a robust set of genes to be used as a panel to identify presence of LC in blood, and (iii) identifying differences between patients with different pathological traits such as stage and histology. We collected phenotype data from questionnaires and hospital medical records, and evaluated the potential effects of CRP, tumour size, gender, and smoking habits.
Results: By comparing cases and controls sampled on the same RNA sampling system (training set), we identified 355 significant genes (Bonferroni adjusted p < 0.05) with biological relevance. When evaluating these on our test set comprising of the same cases as used in the training set but analysed against controls from a different biobank sampled on a different RNA sampling system (test set), we found 50 genes that were robust as they were unaffected by either technical issues in sampling systems, biobank differences, gender, or pathological traits such as LC subtype or stadium. These findings were confirmed in three validation sets and the robust list’s diagnostic potential was validated on RNA sequencing data from a new cohort. By analysing the cases separately, we found seven genes distinguishing squamous cell carcinoma (SCC) from other LC subtypes, and six genes distinguishing early from late-stage LC patients. Pathway analyses and a literature survey indicated that the identified genes show biological relevance for cancer development and lung related diseases.

overall_design:
Number of samples: 303 (123 lung cancer patients, 180 controls).

The idat files are not available.

first: Anne

middle: H

last: Skogholt

first: Espen

last: Jensen

first: Einar

last: Ryeng

first: Bjørn

last: Grønberg

first: Frank

last: Skorpen

first: Svanhild

last: Schønberg


title: ETV2/ER71 regulates hematovascular lineage generation and vascularization through an H3K9 demethylase, KDM4A

city: Jeonju-si

first: Donghyun

last: Shin

state: Jeollabuk-do

address: 567 Baekje-daero, Deokjin-gu

department: Agricultural Convergence Technology

country: South Korea

institute: Jeonbuk National University

summary: ETV2/ER71, an ETS transcription factor, is critical for hematopoiesis and vascular development. However, knowledge on the molecular mechanisms behind ETV2-mediated gene transcription is limited. Here, we show that ETV2 together with KDM4A, an H3K9 demethylase, regulates hematopoietic and endothelial genes. Etv2-/- mouse embryonic stem cells (mESCs), which fail to generate hematopoietic and endothelial cells, showed enhanced levels of H3K9me3 on hematopoietic and endothelial genes. ETV2 interacts with KDM4A and the ETV2-mediated transcriptional activation of hematopoietic and endothelial genes is dependent on KDM4A histone demethylase activity. ETV2 and KDM4A co-occupy the transcription regulatory regions of genes whose expression is directly regulated by ETV2. Mice lacking Kdm4a and Etv2 in endothelial cells (Cdh5Cre;Kdm4af/f;Etv2f/f) displayed a more severe defect in perfusion recovery and neovascularization compared with Cdh5Cre;Kdm4af/f, Cdh5Cre;Etv2f/f mice and controls. Collectively, we demonstrated that ETV2 interacts with KDM4A and that this interaction is critical for FLK1+ cell generation, differentiation into the downstream lineages, and vascular regeneration.

overall_design:
Experiment 1. Transcriptome analysis of DOX treatment of mouse embryonic stem cells (confirmation of ETV2 expression after treatment).
Experiment 2. Transcriptome analysis of mouse embryonic stem cell DOX treatment (confirmation of ETV2 and KDM4A expression after treatment).
Experiment 3. Transcriptome analysis of KDM4A/4C double knock [DKO] ESCs.
Experiment 4. Epigenetic analysis for DOX treatment.

first: Changwon

last: Park


title: Tubular Foxp2 promotes kidney fibrosis by regulating epithelial-mesenchymal transition and cell cycle arrest

city: Hong Kong

first: YIXIN

last: ZOU

state: State...

address: PB301, 3/F, Professorial Block, No.102, Pokfulam Road, Queen Mary Hospital

department: Department of Medicine

institute: the University of Hong Kong

summary: Kidney fibrosis results in progressive loss of function, ultimately leading to kidney failure, for which there are limited effective therapeutic strategies. The transcription factor, Forkhead box P2 (Foxp2), has been implicated in organ development and tumorigenesis through its association with the epithelial-to-mesenchymal transition (EMT) process. In this study, we uncovered a novel role of Foxp2 in kidney fibrosis. Expression of Foxp2 was upregulated in kidney tubules from both human chronic glomerulonephritides and animal models of chronic kidney disease. In vitro, Foxp2 was induced in tubular epithelial cells via TGF-β/Smad3 signaling while knockdown of Foxp2 suppressed TGF-β-induced EMT and accumulation of extracellular matrix proteins. In vivo, tubule-specific deletion of Foxp2 attenuated kidney inflammation and tubulointerstitial fibrosis in murine unilateral ureteral obstruction and unilateral ischemic-reperfusion models of progressive CKD, which were accompanied by reduction in cell cycle arrest. Mechanistically, overexpression of Foxp2 inhibited tubular cell proliferation with induction of G2/M cell cycle arrest. Using chromatin-immunoprecipitation sequencing, we identified Foxp2 target genes that are enriched in PI3K/Akt and TGF-β signaling pathways, and further revealed that Foxp2 directly regulated the transcriptional activities of collagen-1, E-cadherin and p21 that are involved in EMT and cell cycle arrest, thereby promoting the profibrotic process. Collectively, our findings provide novel evidence that Foxp2 regulates TGF-β-induced EMT and cell cycle arrest, the key signaling pathways of kidney fibrosis, and suggest that Foxp2 may be a potential therapeutic target for kidney fibrosis.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Foxp2 in Foxp2 overexpressing murine tubular epithelial cell line (C1.1). Input samples collected before immunoprecipitation were used as control for analysis.

first: Yixin

first: WaiHan

last: Yiu

first: C


title: Transcriptome of erythroid cells derived from human CD34+ cells edited at the BCL11A erythroid enahncer or at the HBG1 and HBG2 promoters using CRISPR-Cas9

city: Cambridge

first: KaiHsin

last: Chang

address: 11 Hurley St

institute: Editas Medicine

summary: BCL11A represses gamma globin expression by binding to the gamma globin gene (HBG1 and HBG2) promoters. Genome editing of the BCL11A erythroid enhancer in the intron 2 of BCL11A gene or the BCL11A binding site at the HBG1/2 promoters disrupts this pathway and leads to gamma globin induction. Transcriptomic profiling of erythroid cells derived from human CD34+ cells edited at either target site using CRISPR-Cas9 revealed broader transcriptome perturbation when edited at the BCL11A erythroid enhancer.

overall_design: Human CD34+ cells were electroporated with CRISPR-Cas9 RNP targeting either the BCL11A erythroid enhancer or the HBG1/2 promoter BCL11A binding site. Unedited CD34+ cells were included as a control. CD34+ cells were placed in erythroid culture conditions for 11 days and their erythroid progenies were subjected to RNA-seq to evaluate transcriptome changes induced by editing at the either target site.


title: Diethylene Glycol Oligomer Squalene Derivative Improves Hepatic Metabolism and Attenuates Obesity-Related Dysmetabolism via Sirt-AMPK axis Activation

city: Ibaraki, Tsukuba

first: Yu

last: Cheng

address: Amakubo

institute: University of Tsukuba

summary:
Transcriptomic analysis comprehensively revealed the metabolic improvement effects of di-SQ on the liver and white adipose tissue in ob/ob mice.
Di-SQ demonstrated effects in improving inflammation and lipid metabolism in both the liver and white adipose tissue of ob/ob mice and restored the expression of genes and GO terms associated with mitochondrial respiration and glucose metabolism. The metabolic disorder observed in untreated ob/ob mice was reversed by a 42-day-di-SQ treatment, the di-SQ treated ob/ob mice showed a gene expression pattern in key metabolic pathways and processes that more closely resembles that of wild-type mice.

overall_design: RNA was extracted using Isogen (Nippon Gene Co. Ltd., Toyama, Japan). The integrity of RNA was quantified using NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). Clariom S assay system (Thermo Fisher, Japan) was used on duplicate RNA samples of each group. In accordance with the user manual, complementary DNA (cDNA) for microarray was generated using the GeneChip WT Plus Reagent kit (Thermo Fisher Science, Japan). Samples were hybridized using Clariom S GeneChip microarray kit (Thermo Fisher Science, Japan). After washing and staining, images were captured, and then CEL data were generated using the GeneChip Scanner 3000 (Thermo Fisher Science, Japan). The raw CEL data were normalized using the transcriptome analysis console (TAC) software ver.4.0.1 following the SST-robust multichip average (SST-RMA) algorithm (Thermo Fisher Scientific, Japan).


title: Transcriptome sequencing data of sgControl and sgHcar1 MC38 cells incubated with or without lactate

first: Jiacheng

last: He

address: 500 Dongchuan Road

institute: East China Normal University

summary: To explore the downstream effector and pathway of lactate/HCAR1 axis, We performed a RNA-seq on gene expression profiles of sgControl and sgHcar1 MC38 cells incubated with or without lactate.

overall_design: mRNA profiles of sgControl MC38 cells (n = 3) (control / lactate), sgHcar1 MC38 cells (n = 3) (control / lactate).

first: Weiqiang

last: Lu


title: Dual specific STAT3/5 degraders effectively block acute myeloid leukemia and natural killer/T cell lymphoma

city: Vienna

first: Thomas

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

country: Austria

institute: University of Veterinary Medicine, Vienna

summary: The transcription factors STAT3, STAT5A and STAT5B steer hematopoiesis and immunity, but their enhanced expression and activation promotes acute myeloid leukemia (AML) or natural killer/T cell lymphoma (NKCL). Current therapeutic strategies focus on blocking upstream tyrosine kinases to inhibit STAT3/5, but these kinase blockers are not selective against STAT3/5 activation and frequent resistance causes relapse, emphasizing the need for STAT3/5 targeted therapy. We evaluated JPX‑0700 and JPX-0750 efficacy as dual STAT3/5 binding inhibitors promoting protein degradation. JPX‑0700/-0750 decreased the mRNA and protein levels of STAT3/5 targets involved in cancer survival, metabolism and cell cycle progression, exhibiting nanomolar to low micromolar efficacy. They induced cell death and growth arrest in both AML/NKCL cell lines and primary AML patient blasts. We found that both AML/NKCL cells hijack STAT3/5 signaling through either upstream activating mutations in kinases, activating mutations in STAT3, mutational loss of negative STAT regulators, or genetic gains in survival, proliferative or epigenetic-modifier STAT3/5 targets. This emphasizes a vicious cycle for proliferation and survival through STAT3/5. Both JPX-0700/-0750 treatment reduced leukemic cell growth in human AML or NKCL xenograft mouse models significantly, being well tolerated in mice. Synergistic cell death was induced upon combinatorial use with approved chemotherapeutics in AML/NKCL cells.

overall_design: Cells were incubated for 24 h with compounds and washed twice with PBS. RNA extraction followed the standard protocol employing the RNeasy Mini Kit (QIAGEN). Subsequently, sequencing libraries were created utilizing the QUANT seq 3’ mRNA-Seq Library Prep Kit (Lexogen). The combined libraries underwent processing at the Vienna Biocenter Next Generation Sequencing Facility in Vienna, Austria, and were then subjected to sequencing through single-read 70-bp chemistry on a NextSeq550 instrument (Illumina).

first: Daniel

last: Pölöske

first: Helena

last: Sorger

first: Anna

last: Schönbichler

first: Elvin

last: de Araujo

first: Heidi

last: Neubauer

last: Orlova

first: Sanna

last: Timonen

first: Diaaeldin

middle: I

last: Abdallah

first: Aleksandr

last: Ianevski

first: Heikki

last: Kuusanmäki

first: Marta

last: Surbek

first: Elisabeth

last: Heyes

first: Christina

last: Wagner

first: Tobias

last: Suske

first: Martin

last: Metzelder

first: Michael

last: Bergmann

first: Maik

last: Dahlhoff

first: Florian

last: Grebien

first: Roman

last: Fleck

first: Christine

last: Pirker

first: Walter

last: Berger

first: Emir

last: Hadzijusufovic

first: Wolfgang

last: Sperr

first: Lukas

last: Kenner

first: Peter

last: Valent

first: Tero

last: Aittokallio

first: Marco

last: Herling

first: Satu

last: Mustjoki

first: Patrick

last: Gunning

first: Richard

last: Moriggl


title: Epigenome-wide DNA methylation profiling in CBMCs

city: Tucson

first: Donata

last: Vercelli

state: Arizona

address: 1657 E. Helen St.

institute: University of Arizona

type: Methylation profiling by genome tiling array

summary: To identify epigenetic mechanisms present at birth that underpin asthma development during childhood. Note - the Infant Immune Study cohort was only consented for asthma-related research.

overall_design: Differential methylation analysis related to maternal prenatal immune status

first: Avery

last: DeVries


title: Chronic viral mimicry induction following p53 loss promotes immune evasion [CUTandRUN]

first: Sajid

middle: A

last: Marhon

state: ON

address: 101 College Street

institute: Princess Margaret Cancer Centre

summary: Epigenetic therapies that alter DNA- and/or histone modifications facilitate transcription of immunogenic repetitive elements that cull cancer cells through ‘viral mimicry’ responses. Paradoxically, cancer-initiating events that include functional inactivation of canonical tumor suppressor proteins also facilitate transcription of repetitive elements. Contributions of repetitive element transcription towards cancer initiation, and the mechanisms by which cancer cells evade lethal viral mimicry responses during tumor initiation remain poorly understood. In this report, we characterize patient-derived premalignant lesions of the fallopian tube along with syngeneic mouse models of epithelial ovarian cancer to explore the earliest events of tumorigenesis following loss of the p53 tumor suppressor protein. We report that p53 loss disrupts constitutive heterochromatin to permit transcription of immunogenic repetitive elements capable of activating viral mimicry responses. While acute viral mimicry activation diminishes cell fitness, chronic viral mimicry activation following p53 loss promotes epigenetic reprogramming that increases tolerance of cytosolic nucleic acids and diminishes cellular immunogenicity as a pro-survival adaptation. This selection process we describe as ‘viral mimicry conditioning’ can be partially attenuated by the reverse transcriptase inhibitor 3TC to delay spontaneous tumorigenesis. Altogether, these results reveal that viral mimicry conditioning following p53 loss selects for diminished cell immunogenicity to promote immune evasion upon cancer initiation. Disruption of viral mimicry conditioning during cancer initiation may represent a pharmacological target for early cancer interception.

overall_design: CUTandRUN

first: Charles

last: Ishak

first: Daniel

last: De Carvalho


title: Human FcgRIIa mediates attenuation of IFN-I response in human monocytes

city: SUZHOU

first: Xiao-Ming

last: Gao

state: JiangSu

address: No. 199, Ren'ai Road

department: Institute of Biology and Medical Sciences, School of Biology and Basic Medical Sciences

institute: Soochow University

summary: It is generally believed that there is continued cross-regulation between adaptive humoral immunity and Type I interferon (IFN-I) response during viral infections, but the question how antibodies (Abs), and/or Ab-antigen immunocomplexes (ICs), regulate IFN-I production and/or signaling in immune cells remains unanswered. Here we report that plate-coated IgG (cIgG), a mimic IC without antigen restriction, could dampen IFN-I signaling in monocytes through FcgRIIa.

overall_design: Freshly isolated CD14+ monocytes from peripheral blood of 3 unrelated healthy donors  were cultured for 24 hrs in RPMI-10 medium or  IVIG(10 μg/ml) for preparation, then half of these cultures were washed and given a 12 hrs IFN-alpha or IFN-beta (10 ng/mL) stimulation,respectively.

first: S

last: Hua

first: F

last: Gong

first: X

last: Dai


title: Chronic viral mimicry induction following p53 loss promotes immune evasion [scRNASeq]

city: Toronto

overall_design: scRNASeq


title: GSTM1 null genotype underpins recurrence of NF2 meningiomas

status: Public on Dec 09 2024

city: Oklahoma City

first: Anthony

last: Johnson

state: OK

address: 1122 NE 13th St, O'Donoghue Research Building 332

department: Neurosurgey

institute: University of Oklahoma Health Sciences

summary: Introduction: Meningiomas are the most common primary central nervous system (CNS) tumor in adults, comprising one-third of all primary adult CNS tumors. Although several recent publications have identified molecular alterations in meningioma including characteristic mutations, copy number alterations, and gene expression signatures, our understanding of the drivers of meningioma recurrence is limited. Objective: To identify gene expression signatures of 1p-22q-NF2- meningioma recurrence, with concurrent biallelic inactivation of NF2 and loss of chr1p that are heterogenous but enriched for recurrent meningiomas. Methods: Transcriptomic alterations present in recurrent versus primary 1p-22q-NF2- meningiomas were identified using RNA sequencing (RNA-seq) data in a clinically annotated cohort. Results: Recurrent 1p-22q-NF2- meningiomas were enriched for a newly identified GSTM1 null genotype compared to primary meningiomas that showed variable GSTM1 expression and independent external validation was performed. Conclusions: The GSTM1 null genotype is a novel biomarker of 1p-22q-NF2- meningioma recurrence that resolves heterogeneity in existing meningioma subtypes and may be used to guide future clinical management decisions on extent of treatment to improve patient outcomes.

overall_design: RNA-seq profiling of human (male and female) primary and recurrent meningioma tumors.

first: Erdyni

middle: N

last: Tsitsikov

first: Khanh

last: Phan

first: Jeffrey

last: Zuccato

first: Andrew

middle: M

last: Bauer

first: Christopher

last: Graffeo

first: Sanaa

last: Hameed

first: Tressie

last: Stephens

first: Yufeng

last: Liu

first: Gavin

last: Dunn

first: Alla

middle: V

last: Tsytsykova

first: Pamela

last: Jones

first: Ian

middle: F


title: Transcriptomic sterol response in the HepG2 human hepatoma cell line

city: Oakland

first: Marisa

last: Medina

state: CA

address: 5700 Martin Luther King Jr. Way

department: Pediatrics

institute: UCSF

summary: Statins are cholesterol lowering drugs that inhibit cholesterol synthesis and reduce intracellular sterol levels, stimulating a transcriptional response. We sought to identify genes that were statin responsive in the HepG2 human hepatoma cell line and determine which of those genes were sterol responsive using sterol addback conditions. Though the vast majority of statin responsive genes are sterol responsive, we identified a subset of statin responsive genes whose gene expression changes are not reversed upon sterol addback.

overall_design: Up to 10 biological replicates of 7 different conditions: control (FBS), statin treatement/sterol depletion, or sterol addback

middle: W

first: Elizabeth

last: Theusch

first: Kristen

last: Stevens


title: GP IIb/IIIa-ICAM-1 Mediated Platelet-Endothelial Adhesion Exacerbates Pulmonary Hypertension

city: Guangzhou

first: Qianwen

last: Bai

state: GuangDong

address: Dongfeng Road 195

institute: the First Affiliated Hospital of Guangzhou Medical University

summary: Pulmonary hypertension (PH) patients typically present with a diminished platelet count, but the role of platelets in the development and progression of PH remains unclear.Transcriptomic analysis revealed that platelets from PH patients exhibited an upregulation of genes associated with cellular adhesion, platelet activation, and adhesion. Notably, the hub genes, glycoprotein IIb/IIIa (GP IIb/IIIa), were implicated in mediating platelet-endothelium adhesion through their interaction with intercellular adhesion molecule-1 (ICAM-1) on pulmonary artery endothelial cells, triggering platelet activation and the subsequent release of platelet-derived growth factor BB (PDGF-BB).

overall_design: To elucidate the role of platelets in  pulmonary hypertension (PH), we performed RNA sequencing (RNA-seq) on platelets from 8 patients with idiopathic pulmonary arterial hypertension (iPAH) and 5 healthy controls. Our objective was to identify unique transcriptional signatures associated with PH. There were 2920 differentially expressed genes (DEG) in platelets from iPAH patients when compared to healthy controls, with significant changes indicated by |Log2Fold change| > 1 and a false discovery rate < 0.05 . Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses using gene set enrichment analysis (GSEA) highlighted the biological relevance of these DEGs. The most enriched GO and KEGG terms were associated with cellular adhesion, platelet activation, and extracellular matrix remodeling, suggesting heightened platelet adhesion and activation in PH.

first: Tao

last: Wang

first: Lingdan

last: Chen

first: Ruidi

last: Tang


title: Bulk RNA sequencing data of intact and digested rice root for Single-cell RNA-seq protoplasting induced gene filtering

city: Los Angeles

first: Rachel

last: Shahan

state: California

address: 610 Charles E. Young Dr. S

institute: University of California, Los Angeles

summary: We report raw bulk RNA sequencing data of intact rice roots and digested rice roots

overall_design: Intacted roots (directly harvested from gel grown conditions) and digested roots (protoplasts + undigested chunks) were havested. Samples were frozen in liquid nitrogen and RNA was isolated using the Zymo MagBead RNA Isolation kit. RNA was used as input into the Lexogen QuantSeq 3′ FWD RNA-Seq library preparation procedure. Libraries were indexed and pooled on an Illumina NextSeq. Reads were aligned to Michigan State University Rice genome v7 counted with HTSeq-Count.

first: Mingyuan

last: Zhu

first: Che-Wei

last: Hsu

first: Ogorek

last: Lucas

first: Isaiah

last: Taylor

first: Medhavinee

last: Mijar

first: Trevor

last: Nolan

first: Ari

last: Sadanandom

first: Malcolm

last: Bennett

first: Philip

last: Benfey

first: Bipin

middle: K

last: Pandey


title: Chronic viral mimicry induction following p53 loss promotes immune evasion [STIC RNASeq]

first: Sajid

last: Marhon

overall_design:
STIC RNASeq
*** Submitter declares raw data will be uploaded to a repository that can be controlled for the confidentiality of the patients. ***

first: Charles

last: Ishak

first: Daniel

last: De Carvalho


title: Targeting a key disulfide linkage to regulate RIG-I condensation and cytosolic RNA-sensing

city: Hangzhou

first: Bin

last: Wang

state: Zhejiang

address: 浙江省杭州市浙江大学紫金港校区纳米楼575

institute: Zhejiang University

summary: Maintaining innate immune homeostasis is critical for preventing infections and autoimmune diseases, but the effective interventions are lacking. Here, we identified Cys864-Cys869-mediated intermolecular disulfide-linkage formation as a critical step for human RIG-I activation that can be bidirectionally regulated to control innate immune homeostasis. The viral-stimulated Cys864-Cys869 disulfide-linkage mediates conjugation of an SDS-resistant RIG-I oligomer, which prevents RIG-I degradation by E3 ubiquitin-ligase MIB2 and is necessary for RIG-I to perform liquid-liquid phase separation to compartmentalize downstream signalsome, thereby stimulating IFN-I signaling. The corresponding C865S ‘knock-in’ caused defect of oligomerization and LLPS in mouse RIG-I, which inhibited innate immunity, resulting in increased viral load and mortality in mice. Through generating covalent Cys864-Cys869 linkage by unnatural amino-acid and developing interfering peptide to block Cys864-Cys869 residues, we bidirectionally regulate RIG-I activities in human diseases. These findings provide novel and in-depth insights on mechanism of RIG-I activation, develop methodologies that hold promising implications in clinics

overall_design: RNA-seq profiling of Rig-IWT/WT and Rig-IC865S/C865S MEFs was performed followed by SeV or PBS infection for 12 hours

first: Jing

last: Zou

first: Long

last: Zhang


title: Apolipoprotein C3 Involved in Diabetic Retinopathy by Promoting Retinal Angiogenesis via Activation of the MYC Pathway

first: guanrong

last: Wu

address: 106 Zhongshan Er Road

institute: Guangdong Provincial People's Hospital

summary: Purpose: To investigate the expression and function of apolipoprotein C3 (APOC3) in diabetic retinopathy (DR). Methods: The quantitative expression of APOC3 in aqueous humor of patients with DR was detected using our proteomic datasets (PXD046630 and PXD053634). A multiplex immunoassay was used to examine the level of APOC3 in serum of patients with DR. Western blot, immunohistochemistry and enzyme-linked immunosorbent assays were used to measure APOC3 expression in liver, duodenum, retina and serum of db/db mice and oxygen induced retinopathy (OIR) mice, and in the human retinal microvascular endothelial cells (hRMECs) exposed to high glucose, hypoxia or both of them. Cell proliferation, migration and tube formation assays were used to assessed the phenotypic characteristics of hRMECs treated with recombinant APOC3 (r-APOC3), hypoxia and both of them. RNA sequence analysis and inhibition assay were conducted to explore the pathway in r-APOC3 and hypoxia stimulation. Results: APOC3 expression were significantly increased in aqueous humor and serum of patients with DR, as well as in liver, duodenum, serum, and retina of db/db mice and OIR mice, while did not markedly change in both hRMECs and their conditioned medium when exposed to high glucose, hypoxia or both of them. r-APOC3 combined with hypoxia significantly enhanced the proliferation, migration and tube formation of hRMECs, and promoted the upregulation of MYC, VEGF and IL6. Inhibition of MYC expression alleviated the phenotypic changes in hRMECs treated with r-APOC3 combined with hypoxia. Purpose: To investigate the expression and function of apolipoprotein C3 (APOC3) in diabetic retinopathy (DR). Methods: The quantitative expression of APOC3 in aqueous humor of patients with DR was detected using our proteomic datasets (PXD046630 and PXD053634). A multiplex immunoassay was used to examine the level of APOC3 in serum of patients with DR. Western blot, immunohistochemistry and enzyme-linked immunosorbent assays were used to measure APOC3 expression in liver, duodenum, retina and serum of db/db mice and oxygen induced retinopathy (OIR) mice, and in the human retinal microvascular endothelial cells (hRMECs) exposed to high glucose, hypoxia or both of them. Cell proliferation, migration and tube formation assays were used to assessed the phenotypic characteristics of hRMECs treated with recombinant APOC3 (r-APOC3), hypoxia and both of them. RNA sequence analysis and inhibition assay were conducted to explore the pathway in r-APOC3 and hypoxia stimulation. Results: APOC3 expression were significantly increased in aqueous humor and serum of patients with DR, as well as in liver, duodenum, serum, and retina of db/db mice and OIR mice, while did not markedly change in both hRMECs and their conditioned medium when exposed to high glucose, hypoxia or both of them. r-APOC3 combined with hypoxia significantly enhanced the proliferation, migration and tube formation of hRMECs, and promoted the upregulation of MYC, VEGF and IL6. Inhibition of MYC expression alleviated the phenotypic changes in hRMECs treated with r-APOC3 combined with hypoxia.

overall_design: RNA-seq profiling of hRMECs treated with r-APOC3, hypoxia and both of them for 24h.

first: Xinyu

last: Chen

first: Guanrong

first: Xiyu

first: Yeanqi

last: Jin

first: Haoxian

first: Junbin

last: Liu

first: Mengya

first: Shuoxin

last: Liao

first: Fangfang

last: Li

first: Xiang

last: Fang

first: Qianli

last: Meng


title: Gene expression in mouse uterus during pre-implantation period after intrauterine administration treatment

city: Kyoto

first: Yoshimi

last: Kitawaki

state: Kyoto

address: 54 Shogoin-kawahara-cho, Sakyo-ku

department: Gynecology and Obstetrics

institute: Kyoto University Graduate School of Medicine

summary: Intrauterine peripheral blood mononuclear cells (PBMC) therapy for recurrent implantation failure (RIF) has been reported to improve embryo implantation by acting on the endometrium. However, the exact mode of action of PBMC on the endometrium and the differences in the therapeutic effects of PBMC therapy with and without human chorionic gonadotropin (hCG) are unknown. In this study, we investigated the changes in the endometrium during the implantation phase induced by PBMC administration and the differences in the efficacy of this therapy with and without hCG using a mouse model of implantation failure (IF).

overall_design: IF model was established by the subcutaneous administration of low-dose RU486. Pregnant mice were randomly divided into four groups: control, IF, PBMC, and PBMC-hCG (the latter two groups were IF model mice with intrauterine administration). Uteri from the preimplantation phase (evening of day 3.5) were collected and analyzed using RNA-sequencing.

last: Kiawaki

first: Akihito

last: Horie