title: RNAseq analysis of Xenopus laevis wildtype and emi2 mutant multiciliated cells during and post differentiation

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

summary: Multiciliated cells (MCCs) form when progenitors massively expand centriole number, yielding the hundreds of basal bodies required to extend multiple motile cilia.  This organelle biogenesis is promoted transcriptionally by Multicilin acting in a complex with the E2F transcription factors, which activates the expression of genes known to be involved required to form centrioles during the cell cycle, but also requires a cell cycle state required for the centrosome cycle.  Multicilin also activates the expression of Emi2 (fbxo43) an inhibitor of the APC/C ubiquitin ligase. In Emi2 mutants, basal body formation during MCCl differentiation is blocked.  RNAseq analysis is used to show that gene expression associated with MCC differentiation is upregulated normally in Emi2 mutants, but surprisingly is not downregulated when MCC differentiation is complete.  Emi2 is required to promote the centrosomal cycle during MCC differentiation, but then also acts to turn off gene expression associated with centriole biogenesis in differentiated cells.

overall_design: An inducible form of multicilin was used to promote MCC differentiation in Xenopus skin progenitors from both wildtype and emi2 mutant embryos, and analyzed by RNAseq at both stage 17 (mid-differentiation) and stage 26 (when differentiation is complete)

first: Chris

last: Kintner

first: Seongjae

last: Kim

first: Yuan-Hung

last: Chein


title: Mutant p53 dysregulates gene transcription in hematopoietic stem and progenitor cells [RNA-seq 2]

status: Public on Mar 19 2024

city: Chicago

first: Yan

last: Liu

state: IL

address: 303 E. Superior Street, Lurie 5-107, Northwestern University

department: Department of Medicine

country: USA

institute: Northwestern University

type: Expression profiling by high throughput sequencing

summary: We found that mutant p53 dysregulates gene transcription in hematopoietic stem and progenitor cells duirng aging.

overall_design: Aged mice to 13to 15 months. Sorted LSKs from the bone marrow of wild type and p53 mutant mice. We then performed paired-RNA sequencing.


title: Mutant p53 alters chromatin accessibility in hematopoietic stem and progenitor cells [ATAC-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To investigate how mutant p53 regulates gene transcription in HSPCs, we performed ATAC-seq assays in LSKs to identify differential regions of chromatin accessibility. We obsreved approximately 600 peaks significantly increased chromatin accessibility in mutant p53 LSKs compared to wild type p53 LSKs.

overall_design: To elucidate the mechanism of how mutant p53 regulates gene transcription in hematopoietic stem an dprogenitor cells (HSPCs), we sorted Lin-Sca1+Kit+ cells LSKs) from the bone marrow of p53+/+ and p53R248W/+  mice and then perfromed ATAC-seq assays.

first: Sisi

last: Chen


title: PLPP1-deficiency-mediated ferroptosis induced by PD-1 signaling impairs antitumor activity of intratumoral CD8+ T cells II

city: Zhengzhou

first: Jiqi

last: Shan

state: Henan

address: 1 Jianshe East Road, Erqi District, Zhengzhou City, Henan Province

country: China

institute: The First Affiliated Hospital of Zhengzhou University, Zhengzhou,

summary: Metabolic programming plays a crucial role in T-cell activation. Herein, we describe how phospholipid metabolism regulates CD8+ T-cell function in patients with cancer. We found that phosphatidylcholine (PC) and phosphatidyl ethanolamine (PE) levels were lower in intratumoral CD8+ T cells than in circulating CD8+ T cells. The expression of phospholipid phosphatase 1 (PLPP1), an enzyme that catalyzes PE and PC synthesis, was also downregulated in CD8+ T cells upon infiltrating tumors. Moreover, unsaturated fatty acid-mediated ferroptosis was a major factor impairing the antitumor function of PLPP1-deficient CD8+ T cells infiltrated in tumors, accompanied by enhanced reactive oxygen species production and lipid peroxidation. The activation of programmed cell death 1 (PD-1) signaling in CD8+ T cells suppressed the PLPP1 expression by increasing GATA1 binding to the promoter region of PLPP1. PLPP1 expression was upregulated after anti-PD-1 therapy. Our findings revealed therapeutic potential of enhancing PLPP1 levels to restore CD8+ T-cell function.

overall_design: Female PLPP1fl/fl and Lckcre-PLPP1fl/fl mice were subcutaneously implanted with 5×105 B16 cells into the right flank. Intratumoral CD8+ T cells were sorted on day 14 using mouse CD8a microbeads. RNA-seq and data analyses were conducted by SeqHealth Technology Co., Ltd. (Wuhan, China).

first: Yu

last: Ping


title: Immune response to RSV in preterm and term infants

status: Public on Mar 20 2024

city: Melbourne

first: Jeremy

last: Anderson

state: Victoria

address: 50 Flemington Rd, Parkville

department: Infection and Immunity

country: Australia

institute: Murdoch Children's Research Institute

summary: This study measured the cytokine, cellular and transcriptomic response to RSV and compared these between preterm and term infants CBMC responses

overall_design: Comparison of the immune response to RSV stimulation in CBMCs from infants born preterm or term

first: Lien

last: Anh Ha Do

first: Paul

middle: V

last: Licciardi


title: Critical gene filtration for the caviar yield of hybrid sturgeon

city: Changchun

first: Yutao

last: Li

address: Jingyue Street

institute: Northeast Normal University

summary: Hybrid sturgeon, an ancient fish, has great economic and nutritional value as a source of caviar. Although significant differences exist in the female reproductive capacity under artificial breeding conditions, differential gene expression associated to domesticated female reproductive capacity have never been investigated. In this study, we conducted reference genome-based transcriptome sequencing of 16 individuals from high-yield (H) and low-yield (L) populations, respectively.

overall_design: Two sturgeon populations located in the Hulan Farming Base, Chinese Academy of Aquatic Sciences (Harbin, China) were selected in the present experiment. One is ranked to high yield group (H) ,  the other is ranked to the low yield group (L).Only eight female adult individuals in each group were euthanized and removed the ovary tissue quickly.


title: TDG orchestrates ATF4-dependent gene transcription during retinoic acid-induced cell lineage committment

city: Rennes

first: Gilles

last: Salbert

address: 263 Av. Gal. Leclerc

department: IGDR UMR6290

country: France

institute: University Rennes 1

summary: Cell differentiation during development is associated to large-scale modifications in the methylome that require the engagement of an active DNA demethylation machinery including Ten-Eleven-Translocation enzymes for oxidation of 5-methylcytosine and the T:G mismatch DNA glycosylase (TDG) for removal of the oxidized bases. Despite this well-defined molecular function, the biological output of TDG activity remains elusive. Here we combined transcriptomic and epigenomic approaches in TDG knock-out embryonal carcinoma cells, an epiblast stem-like cell model, to decipher TDG function in pluripotent cells and their retinoic acid-induced differentiated progeny. We determined that TDG activity is balancing differentiation in favor of a neural fate at the expense of a cardiac mesoderm fate. This process is associated with a sustained activity of a large set of ATF4-dependent genes in relation with TDG engagement at the Atf4 gene promoter and in conjunction with a TDG-dependent regulation of the mammalian target of rapamycin complex 1. These observations highlight the central role of TDG in cell differentiation and support a model linking metabolic reprogramming to cell fate acquisition.

overall_design: To investigate the role of TDG during cell differentiation, we invalidated the Tdg gene by CRISPR-Cas9 in P19 embryonal carcinoma cells. wt and Tdg-null cells were then grown as monolayers in the presence or not of 1 micromolar retinoic acid. MNase-seq was then applied to the different samples in order to establish genome-wide maps of nucleosome occupancy in these different conditions..

first: Stéphane

last: Avner


title: Adhesion GPCR ADGRE2 maintains proteostasis to promote progression in acute myeloid leukemia

city: Hangzhou

first: lu

last: huan

address: 866 Yuhangtang Road

institute: Zhejiang University medical center

summary: Acute myeloid leukemia (AML) is an aggressive and heterogenous hematological malignancy. In elderly patients, AML incidence is high and has a poor prognosis due to a lack of effective therapies. G-protein coupled receptors (GPCRs) play integral roles in physiological processes and human diseases. Particularly, one-third of adhesion GPCRs, the second largest group of GPCRs, are highly expressed in hematopoietic stem and progenitor cells or lineage cells. Therefore, we investigated the role of adhesion GPCRs in AML and whether they could be harnessed as anti-leukemia targets. Systematic screening of the impact of adhesion GPCRs on AML functionality by combined bioinformatic and functional analyses revealed high expression of ADGRE2 in AML, particularly in leukemic stem cells (LSCs), which was associated with poor patient outcomes. Silencing ADGRE2 not only exerted anti-leukemia effects in AML cell lines and AML patient-derived cells in vitro but also delayed AML progression in xenograft models in vivo. Mechanistically, ADGRE2 activated PLC-β/PKC/MEK/ERK signaling to enhance expression of AP-1 and transcriptionally drive expression of DUSP1, a protein phosphatase. DUSP1 de-phosphorylated Ser16 in the J-domain of the co-chaperone DNAJB1, which facilitated DNAJB1-HSP70 interaction and maintenance of proteostasis in AML. Finally, combined inhibition of MEK, AP-1, and DUSP1 exhibited robust therapeutic efficacy in AML xenograft mouse models. Collectively, this study deciphers the roles and mechanisms of ADGRE2 in AML and provides a promising therapeutic strategy for treating AML.

overall_design: To investigate the function of adhesion G-protein coupled receptor ADGRE2 in promoting the growth of AML cells and AML progression in vivo, we established the OCI-AML2 cell line in which ADGRE2 has been knocked down by shRNA. We then performed gene expression profiling analysis using data obtained from RNA-Seq of OCI-AML2 cells with control shRNA or shRNA targeting ADGRE2.

first: Deyu

last: Huang

first: Zebin

last: Yu

first: Huan

last: Lu

first: Penglei

last: Jiang

first: Xinyue

last: Qian

first: Yingli

last: Han

first: Pengxu


title: Effects of fasting on gene expression from livers with or without Mcl1 genetic deletion

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

summary:
MCL-1 is an essential pro-survival molecule of the BCL-2 family of proteins. Recent data, however, suggest it may play an as-yet unclarified role in mitochondrial metabolism.
Liver-specific deletion of MCL-1 followed by dietary stress leads to alteration of multiple genetic programs including fatty acid metabolic processes.

overall_design: We used Affymetrix arrays to investigate the transcriptional changes that occur upon fasting in animals wherein MCL-1 has been deleted specifically in the liver.

first: Meghan

middle: E

last: Turnis

first: Joseph

middle: T

last: Opferman


title: Mutant p53 dysregulates gene transcription in hematopoietic stem and progenitor cells [RNA-seq 1]

first: Yan

last: Liu

summary: We found that p53 mutant hematopoietic stem and progenitor cells are resistant to iL-1ϐ treatment through altering inflammatory response.

overall_design: To determine the mechanism by which mutant p53 HSPCs are resistant to IL-1β, we performed RNA-seq in wild type and mutant p53 LSKs treated with 10 ng/ml of IL-1β or PBS in vitro.


title: Chromatin remodeller Chd7 is developmentally regulated in the neural crest by tissue - specific transcription factors

city: Oxford

first: Tatjana

last: Sauka-Spengler

state: Oxfordshire

address: Radcliffe Department of Medicine

department: University of Oxford

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine

summary: Neurocristopathies such as CHARGE syndrome result from aberrant neural crest development. A large proportion of CHARGE cases are attributed topathogenic variantsin the gene encoding CHD7, chromodomain helicase DNA binding protein 7, which remodels chromatin. While the role for CHD743in neural crest development is well documented,how this factor is specifically upregulated in neural crest cells is not understood. Here, we use epigenomic profiling of chick and human neural crest to identify a cohort of enhancers regulating Chd7 expression in neural crest cells and other tissues. We functionally validate upstream transcription factor binding at candidate enhancers, revealing novel epistatic relationships between neural crest master regulators and Chd7, showing tissue-specific regulation of a globally-acting chromatin remodeller for the first time. Furthermore, we find conserved enhancer features in human embryonic epigenomic data and validate the activity of the human equivalent CHD7 enhancers in the chick embryo. Our findings embed Chd7 in the neural crest gene regulatory network and offer potentially clinically relevant elements for interpreting CHARGE syndrome cases without causative allocation.

overall_design: Transcription-factor binding determined by biotin ChIP-seq and Cut and Run for SOX10 and PAX7, respectively, in chick embryos.

first: Ruth

middle: M

last: Williams

first: Ivan

last: Candido-Ferreira

first: Daniel

last: Fountain


title: Mutant p53 alters chromatin accessibility in hematopoietic stem and progenitor cells.

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Expression data from T-cell Acute Lymphoblastic Leukemia (T-ALL) patient-derived xenograft treated with anti-CD3 mAb

city: Orsay

first: Sabine

last: Druillennec

address: Bat 110 centre universitaire

institute: Institut Curie

summary: T-cell acute lymphoblastic leukemia is a hematological malignancy treated by chemotherapy, with a poor prognosis. We have demonstrated that activation of the T cell receptor (TCR) by anti-CD3 antibodies has a potent anti-leukemic effect in patient-derived xenograft models (PDX) of T-ALL. Therefore, with this experiment, we aim to identify the molecular mechanisms underlying the anti-leukemic properties of the OKT3 anti-CD3 mAb in T-ALL PDX.

overall_design: T-ALL PDX were treated with the isotype control antibody IgG2a or OKT3 mAb. After 6 hours of treatment, T-ALL cells were extracted and isolated from mouse cells by FACS sorting (hCD45+, hCD7+) for RNA collection. RNA-sequencing data were used to compare gene expression profiles upon OKT3 mAb treatment.

first: Andrea

last: Avila Avila

first: Benedeta

last: Zaniboni

first: Jacques

last: Ghysdael

first: Christine

last: Tran Quang


title: Gene regulatory networks underlying intrinsic properties in human hematopoietic stem cell ontogeny

city: Guangzhou

first: Fei

last: Li

address: 190 Kai Yuan Avenue,Science Park

institute: Guangzhou Institutes of Biomedicine and Health

summary: Human hematopoiesis starts at early yolk sac and undergoes site- and stage-specific changes over development. However, the gene regulatory networks (GRN) that drive the developmental changes in naive hematopoietic stem/progenitor cells (HSPCs) remain poorly understood. Here, we analyzed single-cell transcriptome of human naive HSPCs in different developmental stages, including yolk-sac (YS), AGM, fetal liver (FL), umbilical cord blood (UCB) and adult peripheral blood (PB) mobilized HSPCs. These stage-specific HSPCs display differential intrinsic properties, such as metabolism, self-renewal, differentiating potentialities etc. We generated highly co-related GRN modules underlying the differential HSC key properties. Particularly, we identified GRNs and key regulators controlling lymphoid potentiality, self-renewal and aerobic respiration in human HSCs. Introducing selected regulators promotes establishing key HSC functions in HSPCs derived from human pluripotent stem cells. Therefore, GRNs underlying key intrinsic properties of human HSCs provide a valuable guide to generate fully functional HSCs in vitro.

overall_design: 10X Single-cell RNASeq of FACS-sorted Lin-CD34+CD38- HSPCs mobilized in human umbilical cord blood (CB-HSPCs).

first: Yanling

last: Zhu

first: Tianyu

first: Guangjin

last: Pan


title: Co-expression analysis reveals gene cluster associated with methylation of enhancers and chromosomal instability under TP63 and TRIM29 regulation [methylation]

city: Moscow

first: Rinat

middle: I

last: Sultanov

address: Malaya Pirogovskaya, 1a

country: Russia

institute: FRCC of Physical Chemical Medicine of the FMBA of the Russian Federation

type: Methylation profiling by genome tiling array

summary: Prostate adenocarcinoma (PRAD) is the second most common cause of cancer-related deaths in men. In PRAD, high variability in DNA methylation and a high rate of large genomic rearrangements is often observed. To elucidate the reasons behind such high variance, we integrated DNA methylation, RNA-seq, and copy number alterations datasets from The Cancer Genome Atlas (TCGA) focusing on PRAD and subsequently employed weighted gene co-expression network analysis (WGCNA). Our results show that only a single cluster of co-expressed genes is associated with genomic and epigenomic instability. Within this cluster, TP63 and TRIM29 are key transcription regulators and are downregulated in PRAD. We revealed that TP63 regulates the level of enhancer methylation in prostate basal epithelium cells. TRIM29 forms a complex with TP63 and together regulate the expression of genes specific to the prostate basal epithelium. Moreover, TRIM29 binds DNA repair proteins and prevents formation of the TMPRSS2:ERG gene fusion typically observed in PRAD. Therefore, the study shows that TRIM29 and TP63 are important regulators maintaining the identity of the basal epithelium under physiological conditions. Finally, we uncover the role of TRIM29 in PRAD development.

overall_design: DNA methylation analysis of cell line PC3 with TP63 or GFP overexpression

first: Georgij

middle: P

last: Arapidi


title: Fetal Sex Does Not Influence Rates of Gastrulation-Stage Alcohol-Induced Craniofacial Malformations in C57BL/6J Mice

city: Chapel Hill

first: Austin

middle: J

last: Hepperla

state: NC

address: 7018B Mary Ellen Jones Building

department: Genetics

institute: University of North Carolina at Chapel Hill

summary: Prenatal alcohol exposure during mouse gastrulation (embryonic day [E] 7 in mice, corresponding to ~3rd week of human pregnancy) impairs eye, facial, and cortical development, recapitulating birth defects characteristic of Fetal Alcohol Syndrome (FAS). However, the impact of sex on the prevalence or severity of craniofacial features associated with FAS is currently unknown. The current study administered either alcohol (2.9g/kg, two i.p. doses, four hours apart) or vehicle control to pregnant C57BL/6J females on E7 and assessed fetal morphology at E17. Whereas sex did not affect fetal size in vehicle-treated litters, alcohol-exposed females were smaller than both control females and alcohol-treated males. Alcohol exposure increased the incidence of eye defects to a similar degree in males and females. Together, this suggests that females might be more sensitive to the general developmental effects of alcohol, but not to the effects of alcohol specifically on the craniofacies. We also established a developmental transcriptional baseline via whole transcriptomic analysis of untreated E7 embryos, and found 214 differentially expressed genes in females vs. males, including those in pathways related to cilia and mitochondria structure and function, histone demethylase activity, and pluripotency.

overall_design: RNA-seq between embryonic day 7.0 (E7.0) male and female embryos in C57BL/6J mice

first: Karen

last: Boschen

first: Constance

last: Dragicevich

first: Eric

middle: W

last: Fish

first: Jeremy

last: Simon

first: Scott

last: Parnell


title: ASOs are an effective treatment for disease-associated oligodendrocyte signatures in premanifest and symptomatic SCA3 mice

city: SAN FRANCISCO

first: Hanrui

last: Zhang

address: 148 Locksley Ave Apt2

institute: University of Michigan

summary: Spinocerebellar ataxia type 3 (SCA3) is the most common dominantly inherited ataxia. Currently, no preventative or disease-modifying treatments exist for this progressive neurodegenerative disorder, although efforts using gene silencing approaches are under clinical trial investigation. The disease is caused by a CAG repeat expansion in the mutant gene, ATXN3, producing an enlarged polyglutamine tract in the mutant protein. Similar to other paradigmatic neurodegenerative diseases, studies evaluating the pathogenic mechanism focus primarily on neuronal implications. Consequently, therapeutic interventions often overlook non-neuronal contributions to disease. Our lab recently reported that oligodendrocytes display some of the earliest and most progressive dysfunction in SCA3 mice. Evidence of disease-associated oligodendrocyte signatures has also been reported in other neurodegenerative diseases, including Alzheimer's disease, Amyotrophic Lateral Sclerosis, Parkinson's disease, and Huntington's disease. Here, we assess the effects of anti-ATXN3 antisense oligonucleotide (ASO) treatment on oligodendrocyte dysfunction in premanifest and symptomatic SCA3 mice. We report a severe, but modifiable, deficit in oligodendrocyte maturation caused by the toxic gain-of-function of mutant ATXN3 early in SCA3 disease that is transcriptionally, biochemically, and functionally rescued with anti-ATXN3 ASO. Our results highlight the promising use of an ASO therapy across neurodegenerative diseases that requires glial targeting in addition to affected neuronal populations.

overall_design: RNA was extracted from PBS-perfused, flash-frozen BS/Dien, spinal cord, and cerebellum samples from the left hemisphere. Using the Next Advance Bullet Blender, samples were homogenized in radioimmunoprecipitation assay (RIPA, by Sigma, St. Louis, MO) buffer (750 µL for BS/Dien and 500 µL for cerebellum and spinal cord samples) with added proteinase inhibitor (BioRad, Hercules, CA). A 250 µL aliquot of this lysate was reserved for Western blot Journal Pre-proof19 analysis and the remaining sample was used for RNA extraction. RNA extraction was conducted using the QIAshredder (Qiagen Hilden, Germany), RNeasy Mini Kit (Qiagen, Hilden, Germany), and DNase I kit (Qiagen, Hilden, Germany), then eluted in RNase-free water, according to manufacturer’s instructions. RNA samples were assessed by nanodrop to determine concentration and sample purity. For library preparation, 1 μg of total BS/Dien RNA was submitted to the University of Michigan Sequencing Core for Illumina HiSeq library preparation, quality control, and RNA sequencing. WT and Q84 RNA samples were chosen for RNA sequencing based on RIN number (>7 RIN) and, if applicable, CAG repeat expansion size (>average 72Q) as determined by Laragen, Inc. (Culver City, CA).

first: Kristen

middle: H

last: Schuster

first: Annie

last: Zalon

first: Danielle

last: DiFranco

first: Alexandra

middle: F

last: Putka

first: Nicholas

middle: R

last: Stec

first: Sabrina

last: Jarrah

first: Arsal

last: Naeem

first: Zaid

last: Haque

first: Yuanfang

last: Guan

first: Hayley

middle: S

last: McLoughlin


title: ADGRB1 contributes to astrocyte-mediated phagocytosis of excitatory synapses

city: Atlanta

first: Fu Hung

last: Shiu

email: fshiu@emory.edu, fshiu@mgh.harvard.edu

state: GA

address: 615 Michael Street Suite 361

institute: Emory

summary: The phagocytic activity of astrocytes plays an important role in synapse refinement through the elimination of excess synapses during brain development. The adhesion G protein-coupled receptor BAI1/ADGRB1 contributes to phagocytosis in various tissues, including the clearance of apoptotic myoblasts in skeletal muscle and epithelial cells in the intestine. However, the phagocytic function of ADGRB1 in the brain has not been thoroughly investigated. Given that Adgrb1 is highly expressed in astrocytes but not in microglia, we examined changes in astrocyte gene expression resulting from the loss of ADGRB1. RNA-seq analysis revealed that astrocytes lacking ADGRB1 exhibit altered expression of genes associated with cytoskeleton organization and chemotaxis, processes that are required for phagocytosis. Using cultured astrocytes from mice lacking full-length ADGRB1 (Adgrb1exon2-/-) and wildtype (WT) littermates, we found that Adgrb1exon2-/- astrocytes exhibit significantly reduced phagocytic capacity when compared to similarly prepared astrocytes from WT littermates. Immunostaining of astrocytes and pre-synaptic markers showed less engulfed pre-synaptic elements in astrocytes from Adgrb1exon2-/- mutants. Finally, immunostaining of pre-synaptic and post synaptic markers revealed a significantly higher density of excitatory synapses in Adgrb1exon2-/- mutants. These findings highlight the importance of ADGRB1 in synaptic remodeling and raise the possibility that reduced astrocyte-mediated phagocytosis might underlie the behavioral alterations previously observed in Adgrb1exon2-/- mutants, including increased seizure susceptibility and deficits in social memory.

overall_design: Total of 3 WT and  3 ADGRB1 KO astrocytes. To examine the gene expression changes in astrocytes due to the loss of ADGRB1


title: Co-expression analysis reveals gene cluster associated with methylation of enhancers and chromosomal instability under TP63 and TRIM29 regulation.

first: Rinat

last: Sultanov


title: Co-expression analysis reveals gene cluster associated with methylation of enhancers and chromosomal instability under TP63 and TRIM29 regulation [ChIP-seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for TP63 in RWPE-1 and PC3 with overexpression TP63 cell lines

first: Georgij

last: Arapidi


title: Transcriptomes of WT and ClSnRK2.3-OE lines during watermelon fruit development and ripening

city: Beijing

first: Jinfang

last: Wang

address: No.50 Zhanghua Road, Haidian District

institute: Beijing Academy of Agricultural and Forestry Sciences

summary: Analysis of gene expression level. The hypothesis tested in the present study that ClSnRK2.3 negatively regulated watermelon fruit development and ripening.

overall_design: mRNA profiles of  wild type (WT) and ClSnRK2.3-OE lines (OE1 and OE2) at 10 DAP and 18 DAP were generated by deep sequencing, in triplicate, using Illumina Novaseq 6000 (Citrullus lanalus).

first: Yong

last: Xu


title: Integrative multi-omics analyses to identify the genetic and functional mechanisms underlying ovarian cancer risk regions [H3K4me3]

status: Public on Mar 18 2024

city: Los Angeles

first: Michelle

middle: Renee

last: Jones

state: CA

address: 8720 Alden Dv

department: Biomedical Sciences

institute: Cedars-Sinai Medical Center

summary: In the current study we performed characterization of 18 different in vitro models of  high-grade serous (HGSOC), low-grade serous (LGSOC), mucinous (MOC), endometrioid (ENOC) and clear cell (CCOC) carcinoma. This study seeks to fill in this gap by generating an integrative Ovarian Cancer Regulatory Atlas (OCRA) of 18 ovarian normal and cancer cells profiled for epigenomic, transcriptomic, chromatin state and chromatin looping signatures.

overall_design:
Chromatin Immuno Precipitation DNA Sequencing (ChIP-Seq) for histone modifications H3K4me3 was performed in 18 cell lines.
Please note that each processed data file was generated from *ChIP and *input samples together and is linked to the corresponding ChIP (or *A, if replicates) sample records.

first: Simon

last: Gayther


title: Pro-cachectic factors link experimental and human chronic kidney disease to skeletal muscle wasting programs

city: Hamburg

first: Nicola

last: Wanner

address: Martinistr

country: Germany

institute: UKE Hamburg-Eppendorf

summary:
Skeletal muscle wasting is commonly associated with chronic kidney disease (CKD), resulting in increased morbidity and mortality. However, the link between kidney and muscle function remains poorly understood. Here, we took a complementary interorgan approach to investigate skeletal muscle wasting in CKD. We identified an increased production and elevated blood levels of soluble pro-cachectic factor Activin A, directly linking experimental and human CKD to skeletal muscle wasting programs.
Systemic pharmacological blockade of Activin A using soluble activin receptor type IIB ligand trap prevented muscle wasting in a mouse model of experimental CKD.

overall_design: Microarray was performed on muscle and kidney from 6 weeks old WT and Kif3aΔTub mice with or without systemic pharmacological blockade of Activin A using soluble activin receptor type IIB ligand trap.

first: Francesca

last: Solagna

first: Caterina

last: Tezze

first: Maja

last: Lindenmeyer

first: Shun

last: Lu

first: Guochao

last: Wu

first: Shuya

last: Liu

first: Yu

last: Zhao

first: Robert

last: Mitchell

first: Charlotte

last: Mayer

first: Saleh

last: Omairi

first: Temel

last: Kilic

first: Andrea

last: Paolini

first: Olli

last: Ritvos

first: Arja

last: Pasternack

first: Antonios

last: Matsakas

first: Dominik

last: Kylies

first: Julian

last: Schulze zur Wiesch

first: Jan-Eric

last: Turner

first: Viji

last: Nair

first: Felix

last: Eichinger

first: Rajasree

last: Menon

first: Ina

last: Martin

first: Barbara

last: Klinkhammer

first: Elion

last: Hoxha

first: Clemens

middle: D

last: Cohen

first: Pierre-Louis

last: Tharaux

first: Peter

last: Boor

first: Tammo

last: Ostendorf

first: Matthias

last: Kretzler

first: Marco

last: Sandri

first: Oliver

last: Kretz

first: Victor

middle: G

last: Puelles

first: Ketan

last: Patel

first: Tobias

middle: B

last: Huber


title: Investigating Immune Escape of Chronic Myeloid Leukemia in Blast Crisis by Comparing T cells from miR-142 KO BCR-ABL versus miR-142 WT BCR-ABL mice

city: Duarte

first: Hsun

middle: Teresa

last: Ku

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope


title: Expression data from T-cell Acute Lymphoblastic Leukemia (T-ALL) patient-derived xenograft treated with anti-CD3 mAbs.

first: Sabine

last: Druillennec

summary:
T-cell acute lymphoblastic leukemia is an aggressive hematological malignancy treated with chemotherapy and has a poor prognosis. In previous studies, we demonstrated that T cell receptor (TCR)-induced negative selection is highly effective in combating T-ALL in mouse models. Moreover, targeting the TCR of diagnostic T-ALL-derived PDX with anti-hCD3 (aCD3) mAb OKT3 or the clinically relevant aCD3 mAb Teplizumab resulted in leukemic cell death, regression of leukemia, and improved host survival. The objective of the present experiment is to uncover the molecular mechanisms responsible for the anti-leukemic properties of the anti-CD3 mAbs OKT3 and Teplizumab in a T-ALL PDX model.
We compare the transcriptomic profiles of FACS-sorted T-ALL cells extracted from T-ALL patient-derived xenograft (PDX) treated  for 6h with  isotype control antibody IgG2a or OKT3 mAb or Teplizumab mAb.

overall_design: The transcriptome of 9 T-cell Acute Lymphoblastic Leukemia (T-ALL) patient-derived xenograft models were analyzed using Affymetrix GeneChip Human Gene 2.0 ST arrays.

first: Andrea

last: Avila Avila

first: Benedeta

last: Zaniboni

first: Jacques

last: Ghysdael

first: Christine

last: Tran Quang


title: Co-expression analysis reveals gene cluster associated with methylation of enhancers and chromosomal instability under TP63 and TRIM29 regulation [RNA-seq]

first: Rinat

last: Sultanov

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 2 different cell lines with knockdown and overexpression TP63 and TRIM29

first: Georgij

last: Arapidi


title: 3M-Brazzein, a Natural Sugar Substitute, can Suppress Metabolic Disorders, NAFLD, and Depression-like Behaviors in Diabetic Mice

city: seoul

first: sungguan

last: hong

address: 84, Heukseok-ro, Dongjak-gu, Seoul, 104-407

department: Chemistry

country: South Korea

institute: Chung-Ang

summary: The increasing consumption of sugar-sweetened beverages (SSBs) in modern society has enhanced the epidemic of obesity, metabolic disorders, and mental illnesses. Therefore, the current study investigated the potential of 3M-Brazzein as a promising natural sugar substitute.  4-weeks-old leptin receptor knockout mice (db/db) were supplied with water, 10% sucrose solution, or a 3M-Brazzein solution respectively for 16 weeks. Chronic consumption of 3M-Brazzein did not cause any degeneration of adipogenesis, insulin resistance, hepatic lipogenesis, and depression-like behaviors. However, 10% sucrose consumed mice exhibited completely different outcomes. Furthermore, the mRNA expression levels of GLUT2, SREBF-1, and PPARγ in liver were significantly increased in knockout mice supplied with the 10% sucrose solution, thereby the excessive sucrose consumption induced severe obesity, impairment of glucose homeostasis, non-alcoholic fatty liver disease (NAFLD), and major depressive disorder in them. Consequently, the present study demonstrated the positive effects of 3M-Brazzein on various health problems prevalent in the modern world, and suggests some genetic clues related to the pathogenesis of NAFLD and major depressive disorder.

overall_design: A study was performed to examine the effects on brain and liver health following the consumption of 3M-Brazzein and sucrose in a leptin receptor knockout model (db/db)

first: Seungwoo

last: Hong

first: Kwang-Hoon

last: Kong

first: Sungguan


title: Androgen receptor-negative prostate cancer is vulnerable to SWI/SNF-targeting degrader molecules

city: San Fransisco

first: Xiaosai

last: Yao

address: 1 DNA Way

department: Oncology Bioinformatics

institute: Roche/Genentech

summary: The switch/sucrose non-fermentable (SWI/SNF) chromatin remodeling complex becomes frequently deregulated in advanced castration-resistant prostate cancer (CRPC). SWI/SNF ATPase degrader molecules, also known as Proteolysis targeting chimera (PROTAC), offer a novel approach to tackle resistance to androgen receptor (AR) antagonists in AR-dependent CRPC (CRPC-AR). However, the frequent emergence of AR-negative CRPC remains a major clinical hurdle. We investigated SWI/SNF ATPase targeting agents in AR-negative CRPC. SWI/SNF targeting PROTAC treatment reduced the viability of both CRPC-AR and WNT-signaling dependent CRPC (CRPC-WNT), which accounts for about 10% of all clinical CRPC cases. In CRPC-WNT, we characterized that SWI/SNF ATPase SMARCA4 depletion interfered with WNT signaling via the master transcriptional regulator TCF7L2 (TCF4).  Functionally, TCF7L2 maintains proliferation via the AP-1/MAPK signaling axis in this subtype of CRPC.

overall_design:
We performed a ChIP-seq experiment using 2 biological replicates of WCM1078 treated with A858 or A947 (1µM) for 24h.
A947, is a novel PROTAC degrader that co-binds the bromodomain in SMARCA2/SMARCA4/PBRM1 and the von Hippel-Lindau (VHL) ubiquitin ligase12.
A858 is A947's inactive epimer control (SMARCA-binder control).
Both molecules were synthesized at Genentech.

>>>Submitter states that raw data are not available due to patient privacy concerns.<<<

first: Phillip

last: Thienger

first: Philip

last: Rubin

first: Andrej

last: Benjak

first: Sagar

last: Shah

first: Alden

middle: K

last: Leung

first: Simone

last: de Brot

first: Alina

last: Naveed

first: Joanna

last: Triscott

first: Giada

last: Cassanmagnago

first: Marco

last: Bolis

first: Lia

last: Mela

first: Himisha

last: Beltran

first: Yu

middle: C

last: Salvatore Piscuoglio

first: Julien

last: Tremblay

first: Haiyuan

last: Yu

first: Charlotte

last: Ng

first: Robert

last: Yauch

first: Mark

middle: A


title: Modulation of HDAC activity directly reprogramme embryonic stem cell to trophoblast stem cell

first: Man

last: Zhang

state: Guangdong

address: No.9, XingDaoHuanBei Road, Guangzhou International Bio-island, Haizhu District

department: Department of Basic Research

institute: Guangzhou Laboratory


title: microRNA profiling in PBMCs of patients at risk for mood disorders

city: Zürich

first: Gerhard

last: Schratt

address: Winterthurerstrasse 190

department: D-HEST

country: Switzerland

institute: ETH Zürich

type: Non-coding RNA profiling by high throughput sequencing

summary: microRNAs are a large class of small regulatory non-coding RNAs that play important roles in nervous system development and plasticity. Differential microRNA expression in peripheral blood mononuclear cells (PBMCs) has been observed in different neurological disorders and could potentially be used for diagnostic purposes and disease classification.

overall_design: This project aims to identify miRNAs that are differentially expressed between three different subgroups (control group, genetic risk group, environmental risk group) of patients form a large cohort (n>2000) Recruited in a longitudinal study for affective disorders (MACS). The identified miRNA profiles could be useful for assessing the risk for developing affective disorders, biotyping and treatment response.

first: Helena

last: Martins

first: Carlotta

last: Gilardi

first: Pierre-Luc

last: Germain


title: Structural basis of MALAT1 RNA maturation and mascRNA biogenesis

city: Bethesda

first: Markus

last: Hafner

state: MD

address: 50 South Drive

department: NIAMS

institute: NIH

summary: MALAT1 lncRNA plays key roles in regulating transcription, splicing, and tumorigenesis. Its maturation and stabilization require precise processing by RNase P, which simultaneously initiates the biogenesis of a 3′ cytoplasmic mascRNA. mascRNA was proposed to fold into a tRNA-like secondary structure, but lacks eight conserved linking residues required by the canonical tRNA fold.  Here, we report crystal structures of human mascRNA before and after processing, which reveal an ultracompact, quasi-tRNA-like structure. Despite lacking all linker residues, mascRNA faithfully recreates the characteristic “elbow” feature of tRNAs to recruit RNase P and ELAC2 for processing, which exhibit distinct substrate specificities. Rotation and repositioning of the D-stem and anticodon regions preclude mascRNA from aminoacylation, avoiding interference with translation. Therefore, a class of metazoan lncRNAs employ a previously unrecognized, unusually streamlined quasi-tRNA architecture to recruit select tRNA-processing enzymes while excluding others, to drive bespoke RNA biogenesis, processing, and maturation.

overall_design: We performed sequencing to examine the processing of WT and mutant pre-mascRNAs in Flp-In 293 cells expressed from transfected plasmids

first: Ilias

last: Skeparnias

first: Dimitrios

last: Anastasakis

first: Jinwei


title: Transcription factor C/EBP⍺ is required for the development of Ly6Chi monocytes but not Ly6Clo monocytes

city: Saint Louis

first: Sunkyung

last: KIM

state: MO

address: 660 S. Euclid Ave.

department: Pathology and Immunology

institute: Washington University in Saint Louis

summary: Monocytes comprise two major subsets, Ly6Chi classical monocytes and Ly6Clo non-classical monocytes. Notch2 signaling in Ly6Chi monocytes triggers transition to Ly6Clo monocytes, which require Nr4a1, Bcl6, Irf2 and Cebpb. By comparison, less is known about transcriptional requirements for Ly6Chi monocytes. We find transcription factor CCAAT/enhancer-binding protein alpha (C/EBPα) is highly expressed in Ly6Chi monocytes, but down-regulated in Ly6Clo monocytes. A few previous studies described the requirement of C/EBPα in the development of neutrophils and eosinophils. However, role of C/EBPα for in vivo monocyte development has not been understood. We deleted the Cebpa +37 kb enhancer in mice, eliminating hematopoietic expression of C/EBPα, reproducing the expected neutrophil defect. Surprisingly, we also discovered a severe and selective loss of Ly6Chi monocytes, while preserving Ly6Clo monocytes. We find that BM progenitors from Cebpa +37–/– mice rapidly progress through the cMoP stage to develop directly into Ly6Clo monocytes even in the absence of Notch2 signaling. These results identify a previously unrecognized role for C/EBPα in maintaining Ly6Chi monocyte identity.

overall_design: mRNA profiles of splenic Ly6Chi monocytes and/or Ly6Clo monocytes isolated from the WT and Cebpa +37–/– mice

last: Kim

first: Jing

last: Chen

first: Kenneth

middle: M

last: Murphy


title: Single-nucleus RNA diverse brain regions after electrical brain stimulation (EBS)

city: Shenzhen

first: Yan

last: WANG

address: 1068 Xueyuan Ave

institute: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences

summary: Electrical brain stimulation (EBS) has gained popularity for laboratory and clinical applications. However, comprehensive characterization of the cellular diversity and cell type-specific gene expression changes induced by EBS remains limited, particularly with respect to specific brain regions and stimulation sites. In this study, we present the first single-nucleus RNA sequencing (snRNA-seq) profiles of rat cortex, hippocampus, and thalamus subjected to alternating current electrical stimulation (ACES) at 40 Hz.

overall_design: snRNA-seq was employed to profile rats brain.

last: Wang

first: Qian

last: Liu


title: Effect of Romidepsin treatment on patient-derived liver cancer cells

status: Public on Mar 17 2024

city: GUANGZHOU

first: LEI

last: SUN

state: GUANGDONG

address: XIAOGUWEI STREET

department: School of Pharmacy 619

institute: Sun Yat-sen University

summary: Romidepsin displayed potent antitumor activity in our lenvatinib-resistant PDCs, we wanted to investigate the underlying mechanism of how romidepsin initiated susceptibility to conquer lenvatinib resistance in liver cancer.

overall_design: PDCs were treated with two doses of romidepsin (1μM and 2 μM) for 48h.

first: Lei

last: Sun

first: Guohui

last: Wan


title: Stress-regulated miR-708-5p affects recognition memory and manic-like behavior through Neuronatin downregulation.

last: Schratt

summary: microRNAs are posttranscriptional regulators that bind to target mRNAs. We tested the regulatory effect of miR-708-5p, a miRNA associated with Bipolar Disorder, in the mouse hippocampus. To unveil molecular mechanisms downstream of miR-708-5p, we stereotactically injected a virus overexpressing miR-708-5p for target discovery.

overall_design: We injected a miR-708-5p overexpressing virus or a control virus in the dorsal and ventral hippocampus of male wild type C57BL/6JRj  mice, 7/8 weeks old. Four weeks post-surgery, we dissected the hippocampi and extracted RNA.


title: Primary osteoarthritis chondrocyte map of chromatin conformation (Hi-C)

city: Munich

first: Norbert

last: Bittner

address: Ingolstädter Landstraße 1

department: Computational Health

institute: Helmholtz Munich

summary: Osteoarthritis is a complex disease with a huge public health burden. Genome-wide association studies (GWAS) have identified hundreds of osteoarthritis-associated sequence variants, but the effector genes underpinning these signals remain largely elusive. Understanding chromosome organization in 3D space is essential for identifying long-range contacts between distant genomic features (e.g., between genes and regulatory elements), in a tissue-specific manner. Here, we generate the first whole genome chromosome conformation analysis (Hi-C) map of primary osteoarthritis chondrocytes.

overall_design: Human knee cartilage samples were collected during routine joint replacement surgery. Healthy cartilage was defined according to the International Cartilage Repair Society macroscopic grading system (Grade 0-1).

first: Chenfu

last: Shi

first: Danyun

last: Zhao

first: James

last: Ding

first: Lorraine

last: Southam

first: Diane

last: Swift

first: Peter

last: Kreitmaier

first: Mauro

last: Tutino

first: Odysseas

last: Stergiou

first: Jackson

middle: T

last: Cheung

first: Georgia

last: Katsoula

first: Jenny

last: Hankinson

first: J

last: Wilkinson

first: Gisela

last: Orozco

first: Eleftheria

last: Zeggini


title: single-cell RNA-seq of OVCAR3 and CCL218 cancer cells with evolved hydroxychloroquine resistance

city: Charleston

first: Joe

last: Delaney

state: SC

address: 173 Ashley Avenue

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

summary: OVCAR3 and CCL218 cells were passaged in the presence or absence of hydroxychloroquine. Drug pulse chases were used, with 48h of drug exposure followed by replacement of fresh media. Cells were allowed to grow to near confluence and then another drug pulse-chase was performed. After 15 hydroxychloroquine pulse-chases, cells were allowed to proliferate for 7 days in drug-free media so that transient drug effects were no longer present.

overall_design: Cells were then pelleted and cell pellets were processed for concomitant bulk RNA-seq, whole-exome-sequencing, and single-cell RNA-seq. This project represents the single-cell transcriptomic sequencing and analysis.


title: Genome-scale CRISPR-Cas9 screen of OVCAR3 and CCL218 cancer cells with or without hydroxychloroquine

summary: A Brunello CRISPR-Cas9 library screen was performed with OVCAR3 and CCL218 cells in the presence or absence of hydroxychloroquine. Drug pulse chases were used, with 48h of drug exposure followed by replacement of fresh media. Cells were allowed to grow to near confluence and then another drug pulse-chase was performed. After each pulse-chase, a pool of cells were collected for sgRNA quantitation. Three pulse chases were performed. Cell pellets were processed for genomic DNA and sgRNA sequences amplified by PCR for NGS-based quantitation. Once quantified by NGS analysis, MAGeCK MLE analysis was performed to determine which sgRNAs were most associated with resistance or sensitization to hydroxychloroquine.


title: ASH2L mediates epidermal differentiation and hair follicle morphogenesis via the regulation of the Notch signaling pathway activity [RNA-Seq]

city: Shanghai

first: Qirui

last: Wang

state: Shanghai

address: 639 Zhi Zao Ju Road

department: Department of Plastic and Reconstructive Surgery

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

summary: To elucidate the role of H3K4 methylation in epidermal development, we conditionally knocked out the core subunit ASH2L of the COMPASS complex in mouse epidermal progenitor cells (eps). Then, we performed RNA-seq analysis on FACS-classified integrin α6 positive epidermal progenitor cells from P0 control mice (K14Cre,Ash2lF/+) and cKO mice (K14Cre,Ash2lF/ F).

overall_design: We performed RNA-seq analysis on FACS-classified integrin α6 positive epidermal progenitor cells from P0 control mice (K14Cre,Ash2lF/+) and cKO mice (K14Cre,Ash2lF/ F).

first: Siyi

last: Zeng

first: Yimin

last: Liang

first: Renpeng

last: Zhou

first: Danru


title: RNA-seq of OVCAR3 and CCL218 cancer cells with evolved hydroxychloroquine resistance

summary: OVCAR3 and CCL218 cells were passaged in the presence or absence of hydroxychloroquine. Drug pulse chases were used, with 48h of drug exposure followed by replacement of fresh media. Cells were allowed to grow to near confluence and then another drug pulse-chase was performed. After 15 hydroxychloroquine pulse-chases, cells were allowed to proliferate for 7 days in drug-free media so that transient drug effects were no longer present. Cells were then pelleted and cell pellets were processed for concomitant bulk RNA-seq, whole-exome-sequencing, and single-cell RNA-seq. This project represents the bulk transcriptomic sequencing and analysis.

overall_design: Cells were pooled, representing one-third of each 96-well plate, pelleted, and processed by Genewiz for RNA-seq and whole-exome sequencing (WES). Qiagen AllPrep DNA/RNA kits were used to isolate RNA and DNA from the same sample. Agilent SureSelect Human All Exon V8 kits were used and polyA selection performed for transcriptomes.


title: Effect of sirt6 deficiency on gene expression in zebrafish at 3 dpf

city: Guangzhou

first: Luping

address: East Wai-huan Road, Guangzhou 510006, Guangdong, China.

institute: South China University of Technology

summary: To investigate the underlying  mechanisms of sirt6  in the regulation of HSCs and neutrophils lineage  expansion in zebrafish.

overall_design: We generated a sirt6 mutant zebrafish line using CRISPR/Cas9 methods

first: Wenqing

last: Zhang


title: ASH2L mediates epidermal differentiation and hair follicle morphogenesis via the regulation of the Notch signaling pathway activity [CUT&Tag]

summary: To elucidate the role of H3K4 methylation in epidermal development, we conditionally knocked out ASH2L, the core subunit of the COMPASS complex, in mouse epidermal progenitor (EP) cells. Then, we performed  H3K4me3 modification profiling of FACS-sorted integrin α6-positive epidermal progenitor cells in P0 control mice (K14Cre,Ash2lF/+) by CUT&Tag-seq.

overall_design: We performed  H3K4me3 modification profiling of FACS-sorted integrin α6-positive EP cells in P0 control mice (K14Cre,Ash2lF/+) by CUT&Tag-seq.


title: Mettl3-mediated m6A Methylation Determines the Size of Endocrine Progenitor Pool and Postnatal Islet Mass [scRNA-seq]

first: Jiajun

last: Sun

state: Shanghai City

address: 197 Rui Jing Er Rd

institute: Shanghai Jiao Tong University Medical School Affiliated Ruijin Hospital

summary: To investigate the role of RNA methyltransferase-like 3 (Mettl3)-mediated m6A modification in pancreatic endocrine differentiation in early embryonic period. We then performed single cell RNA-seq at E15.5 Mettl3pKO  pancreas group and E15.5 WT pancreas group

overall_design: We generated transgenic mice lacking Mettl3 specifically in Pdx1+ pancreatic progenitor cells(Mettl3pKO) and  dissect E15.5 Mettl3pKO and WT pancreata for single cell RNA-seq.


title: A novel model of binge ethanol exposure reveals enhanced neurodegeneration with advanced age

city: Aurora

first: paige

last: Anton

state: COLORADO

address: 12850 E Monteview Blvd, School of Pharmacy V20-3470D

institute: University of Colorado Anschutz

summary: Binge drinking is rising among aged adults (>65 years of age). The distinct effects of binge ethanol exposure on neurodegeneration in the aged brain are not well described. Using our model of intermittent binge ethanol exposure in young and aged mice, we investigated how binge ethanol expoure may promote neurodegenerative diease development. Spatial transcriptomics revealed that binge ethanol exposure enriched neurodegenerative disease pathways in the aged hippocampus, including tau hyperphosphorylation and neuronal death. These data suggest binge drinking during advanced aging may promote neurodegenerative disease development.

overall_design: Young (3-4 month old) and aged wild type (18-20 month old) female C57BL/6 mice were given intragastric gavages of ethanol (3g/kg) or vehicle every other day for 18 days, totaling 10 exposures. Hippocampal tissue was harvested 18 hours after final gavage for spatial transcriptomics.

first: Paige

middle: E

first: Michael

last: Kaufman

first: Rebecca

middle: L

last: McCullough


title: Transcriptional reprogramming by SPI1 (PU.1) modulates Alzheimer’s disease phenotypes in mouse models

city: Indianapolis

first: Luke

middle: Child

last: Dabin

state: Indiana

department: Medical and Molecular Genetics

institute: Indiana University

summary: SPI1 (PU.1) was recently reported as a genetic risk factor of Alzheimer’s disease (AD) in large-scale genome-wide association studies (GWAS). However, it is unknown whether PU.1 should be downregulated or increased to have therapeutic benefits. This is a critical question that must be answered before initiating any drug discovery project. To investigate the effect of modulating PU.1 level on AD pathology, we performed biochemical, histological, transcriptomic, and proteomic analyses using PU.1-knockdown and overexpression mouse models. PU.1-knockdown markedly increased amyloid-b (Ab) levels, amyloid plaque deposition, and gliosis. Conversely, PU.1-overexpression significantly decreased Ab levels, amyloid plaque deposition, gliosis, and dystrophic neurites. Furthermore, we identified several biological pathways, such as immune response pathways and complement system, regulated by the altered PU.1 expression through the analyses of proteomics as well as bulk and single-cell transcriptomics data. Our data provide crucial in vivo data to guide future therapeutic strategies for AD.

overall_design: Three Pu.1Tg/0;5XFAD mice were compared with three 5XFAD mouse as controls. Similarly, three Pu.1+/-;APP/PS1 mice were compared with Pu.1+/+;APP/PS1 mice as controls

first: Byungwook

last: Kim

first: Mason

last: Tate

first: Hande

last: Karahan

first: Ahmad

last: Sharify

first: Huan

first: Md

last: Al-Amin

first: Stéphanie

last: Philtjens

first: Daniel

last: Smith

first: Dom

middle: J

last: Acri

first: Younghye

last: Moon

first: Mathias

last: Jucker

first: Junmin

last: Peng

first: Jungsu


title: MicroRNA-494 augments fibroproliferation in human retinal pigment epithelial cells and targets p27 with cell-type specificity

city: Palo Alto

first: Theodore

last: Leng

address: 2452 Watson Ct

department: Ophthalmology

institute: Stanford University

summary: Epiretinal membranes (ERMs) are the result of fibro-cellular proliferation that cause distortion and impairment of central vision. We hypothesized that select microRNAs (miRs) regulate retinal fibroproliferation and ERM formation. Following IRB approval, a pilot study was performed in patients presenting for retina surgery with and without clinical ERMs. Total RNA was isolated from ERM tissue and controls from non-ERM vitreous and subjected to miR profiling via microarray analysis. MiR-494 was identified as the only miR selectively expressed at significantly greater levels, and in silico analysis identified p27 as a putative fibroproliferative gene target of miR-494. In vitro testing of miR-494 and p27 in fibroproliferation was assessed in spontaneously immortalized human retinal pigment epithelial (RPE) and human Müller cell lines, stimulated to transform into a fibroproliferative state via transforming growth factor beta (TGFb). Fibroproliferative transformation was characterized by de novo cellular expression of alpha smooth muscle actin (aSMA). In both RPE and Müller cells, both TGFb and miR-494 mimic decreased p27 expression. In parallel experiments, transfection with p27 siRNA augmented TGFb-induced aSMA expression, while only in RPE cells did co-transfection with miR-494 inhibitor decrease aSMA levels. These results demonstrate that miR-494 augments fibroproliferation in both Müller cells and RPEs, however only in RPEs does miR-494 mediate fibroproliferation via p27. As p27 is known to regulate cellular proliferation and differentiation, future studies should extend clinical testing of miR-494 and/or p27 as a potential novel non-surgical therapy for ERMs, as well as identify relevant miR-494 targets in Müller cells.

overall_design: Total RNA was isolated from 5 ERM tissue and 2 controls from non-ERM vitreous and subjected to miR profiling via microarray analysis.

first: Georgia

last: Kamboj

first: Creed

last: Stary


title: Modulation of HDAC activity directly reprogramme embryonic stem cell to trophoblast stem cell [ChIP-Seq]

first: Man

last: Zhang

summary: Embryonic stem cells (ESCs) can differentiate into all cell types of each of the embryonic germ layers. ESCs can also generate totipotent 2C-like cells and trophectodermal cells. However, these latter transitions occur at low frequency due to epigenetic barriers, the nature of which are not fully understood. Here, we show that mouse ESCs treated with sodium butyrate, an HDAC inhibitor, have a greatly increased 2C-like cell population and can transdifferentiate into trophoblast stem cells (TSCs). Interestingly, this ESC to TSC transition is a direct reprogramming event that does not require transition through a 2C-like state. Mechanistically, butyrate inhibits Class I histone deacetylases activities in LSD1-HDAC1/2 corepressor complex, increasing acetylation levels in the regulatory regions of 2C and TSC specific genes. Importantly, butyrate treated cells acquire the capacity to generate blastocyst-like structures that can develop beyond the implantation stage in vitro and induce decidualization in vivo. These results uncover how epigenetic changes can expand the potency of ESCs.

overall_design: Mouse ESCs (Day -2) were treated with 0.5 mM NaB for 2 days in ESC medium and followed by culturing in TSC medium for 2 days (Day 2). Histone marks H3K27ac and H3K9ac were profiled on cells from day -2 and day 2 using ChIP-seq.

first: Boyan

last: Huang

first: Jie

last: Hu

first: Xing


title: Modulation of HDAC activity directly reprogramme embryonic stem cell to trophoblast stem cell [bulk RNA-Seq]

overall_design: Mouse ESCs were treated with 0.5 mM NaB for 2 days in ESC medium. Gene expression profiling using RNA-seq was performed on mESCs (GFP negative) and 2C-like cells (GFP positive). Gene expression of mouse TSCs (NaB induced or blastocyst-derived) were also profiled.


title: Influence of the pqs genes on Pseudomonas quorum sensing

city: Seattle

first: Nicole

last: Smalley

state: Washington

address: 1705 NE Pacific St Health Sci Bldg  K-359

department: Pulmonary, Critical Care and Sleep Medicine

institute: University of Washington

summary: The opportunistic pathogen Pseudomonas aeruginosa has complex quorum sensing (QS) circuitry, which involves two acylhomoserine lactone (AHL) systems, the LasI AHL synthase and LasR AHL-dependent transcriptional activator system and the RhlI AHL synthase-RhlR AHL-responsive transcriptional activator. There is also a quinoline signaling system (the Pseudomonas quinolone signal, PQS, system). Although there is a core set of genes regulated by the AHL circuits, there is substantial strain-to-strain variation in the non-core QS regulated genes. Reductive evolution of the QS regulon, and variation in specific genes activated by QS occurs in laboratory evolution experiments with the model strain PAO1. We used a transcriptomics approach to test the hypothesis that reductive evolution in the PAO1 QS regulon can in large part be explained by a simple null mutation in pqsR, the gene encoding the transcriptional activator of the pqs operon. We found that PqsR had very little influence on the AHL QS regulon. This was a surprising finding because the last gene in the PqsR-dependent pqs operon, pqsE, codes for a protein, which physically interacts with RhlR and this interaction is required for full RhlR-dependent activation of some genes. We used comparative transcriptomics to examine the influence of a pqsE mutation on the QS regulon and identified only three transcripts, which were strictly dependent on PqsE. By using reporter constructs we showed that the PqsE influence on other genes was dependent on experimental conditions and we have gained some insight about those conditions. This work adds to our understanding of the plasticity of the P. aeruginosa QS regulon and to the role PqsE plays in RhlR-dependent gene activation.

overall_design:
We used comparative transcriptomics to contrast the quorum sensing (QS) regulons of the lab strain PAO1, PAO1 ∆pqsR and PAO1 ∆pqsE grown in buffered LB to better understand the effect of PqsE on acylhomoserine lactone (AHL) QS-regulated genes.
The AHL-degrading enzyme AiiA lactonase (100 ug/ml) was added (or not)  to our growth medium to prevent activation of the LasR/I and RhlR/I circuits by their respective signals, 3OC12-HSL and C4-HSL. Lactonase does not degrade the third QS signal, pseudomonas quinolone signal (PQS), the activator of the pqs circuit. Using RNAseq we compared the transcripts from cells collected at OD 2.0 with and without AHL QS-activation to determine the core genes under QS control in each strain. We then compared the QS regulons of the wildtype, PqsR and PqsE mutants.

first: Martin

middle: P

last: Soto-Aceves

first: Amy

last: Schaefer

first: E

last: Greenberg


title: In the aftermath of stroke or myocardial infarction, neutrophil extracellular traps disrupt systemic immunoglobulin production

city: Essen

first: Vikramjeet

last: Singh

state: Nordrhein-Westfalen

address: Universitätsstr. 2

department: Institute for Experimental Immunology and Imaging

institute: University Duisburg-Essen

summary: Post-injury dysfunction of humoral immunity accounts for infections and poor outcome in cardiovascular diseases. Immunoglobulin A (IgA), the most abundant mucosal antibody is produced by plasma B cells in intestinal Peyer’s patches (PP) and lamina propria. Here, we show that stroke and myocardial ischemia (MI) patients had strongly reduced IgA blood levels. This was phenocopied in experimental mouse models where decreased plasma and fecal IgA were accompanied by rapid and macroscopic shrinkage of PP caused by substantial B cell loss. Stroke/MI triggered neutrophils to release neutrophil extracellular traps (NETs). Depletion of neutrophils, NET-degradation, or blockade of NET-release inhibited PP shrinkage and loss of B cells and IgA in stroke mice. Also, stroke and MI patients had higher amounts of circulating NETs, correlating with reduced IgA levels. Strikingly, stroke patients treated with DNase-I had reduced circulating NETs and stable IgA levels. Our results unveil how tissue-injury-triggered systemic NET release disrupts physiological IgA secretion and how this can be inhibited in patients.

overall_design: 12 C57BL/6JHsd wild-type male mice were randomly divided into two groups that underwent either sham surgery or ischemic brain injury. Gene expression profiling analysis was performed on data obtained by high-throughput total-RNA sequencing on isolated B cells from the Peyer's Patches of the mice intestines.

first: Ali

last: Tuz

first: Susmita

last: Ghosh

first: Markus

last: Gallert

first: Dimitris

last: Ttoouli


title: Alternative splicing decouples local from global PRC2 activity

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

summary: PRC2 mediates epigenetic maintenance of gene silencing in eukaryotes via methylation of H3K27. This complex interacts with sets of accessory factors forming two distinct subtypes (PRC2.1 and PRC2.2) that differ in their action and chromatin targeting mechanisms.  However, the underlying molecular mechanisms orchestrating PRC2 assembly are not yet understood. Here, we report the identification of an alternative splicing event involving  that alternative splicing of the PRC2 core component SUZ12 exon 4 which generates two isoforms coexisting in the same cell in virtually all tissues and developmental stages. Skipping this exon generates a previously uncharacterized isoform (SUZ12S) that forces the formation of the PRC2.1 subtype and favors PRC2 dimerization. Our results suggest that while SUZ12L is needed for maintenance of global H3K27 methylation levels, While SUZ12S is necessary and sufficient to ensure correct repression of Polycomb target genes via promoter-proximal H3K27me3 deposition, the full-length SUZ12L isoform is needed for maintenance of global H3K27 methylation levels. Lastly, we show that mouse embryonic stem cells lacking either of the two isoforms display impaired exit from pluripotency upon differentiation stimulus. Our findings thus reveal evidence for the existence of a physiological mechanism regulating PRC2 assembly and higher order interactions, with an impact on H3K27 methylation and gene repression.

overall_design: 18+37 ChIP-seq + 14+18 RNA-seq (WT means wild-type, CSex4 means WT with constitutive exon 4, Deltaex4 means Suz12 KO deleting exon4, KO means Suz12 full knock-out, KO-L means Suz12 full knock-out + long isoform rescue, and KO-S means Suz12 full knock-out + short isoform rescue). L3D and S3D stand, respectively, for Suz12 KO cells rescued with either the SUZ12-L or SUZ12-S (in the Rosa26 locus) where each isoform specific rescue contained the 3D mutation at position 196 (downstream of exon4).

first: Ivano

last: Mocavini

first: Niccolo

last: Arecco

first: Cecilia

last: Ballare

first: Luciano

last: Di Croce


title: RNA-seq Data of Liver Tissue and Tumors

city: Trento

first: Fulvio

last: Chiacchiera

address: Via Sommarive  9

department: Department of Cellular, Computational and Integrative Biology (CIBIO)

country: Italy

institute: University of Trento

summary: Oncogenic mutations accumulating in many chromatin-associated proteins have been identified in different tumor types. With a mutation rate from 10 to 57%, ARID1A has been widely considered a tumor suppressor gene. However, whether this role is mainly due to its transcriptional-related activities or its ability to preserve genome integrity is still a matter of intense debate. Here, we show that ARID1A is largely dispensable for preserving enhancer-dependent transcriptional regulation, being ARID1B sufficient and required to compensate for ARID1A loss. We provide in vivo evidence that ARID1A is mainly required to preserve genomic integrity in adult tissues. ARID1A loss primarily results in DNA damage accumulation, interferon type I response activation, and chronic inflammation leading to tumor formation. Our data suggest that in healthy tissues, the increased genomic instability that follows ARID1A mutations and the selective pressure imposed by the microenvironment might result in the emergence of aggressive, possibly immune-resistant, tumors.

overall_design: RNA was extracted from whole liver tissue and isolated tumors. The genotypes of the study are the follow: WT, Arid1a KO, Arid1a/b DKO mice, Arid1a KO/BcatEXON (liver tumor samples). Mouse liver samples were collected at two different time points (at 9 days and 30 days from Tamoxifen injection). A set of mice were also injected with an NR1L3 agonist (referred as TC in the file names). 2 biological replicates per condition.

first: Alessandro

last: D'Ambrosio

first: Davide

last: Bressan

first: Elisa

last: Ferracci


title: ChIP-Seq Data of purified hepatocytes

overall_design: ChIP-Seq data of purified hepatocytes extracted from WT, Arid1a KO, and Arid1a/b DKO mice (30 days from Tamoxifen injection). Two histone modifications were profiled in all three conditions and in duplicate: H3K27Ac and H3K4me1. The input is also included for each condition.


title: MOUSE peritoneal macrophages treated with LUP or Vehicle

city: Qingdao

first: Zhihua

last: Wu

address: Yushan 5rd

institute: Ocean university of China

summary: Mouse peritoneal macrophages were isolated and treated with vehicle or LUP (0.5 mg/ml) for 24 h.

overall_design: Mouse peritoneal macrophages were isolated and treated with vehicle (complete medium)  or LUP (0.5 mg/ml) for 24 h.

first: Qiaoling

last: Song

first: Chenyang

last: Zhao

first: Peng

last: Wang


title: Modulation of HDAC activity directly reprogramme embryonic stem cell to trophoblast stem cell [scRNA-Seq]

first: Man

last: Zhang

address: No.9, XingDaoHuanBei Road, Guangzhou International Bio-island, Haizhu District

institute: Guangzhou Laboratory

first: Boyan

last: Huang

first: Jie

last: Hu

first: Xing

last: Peng


title: Effect of low-level Er:YAG laser irradiation on proliferation and gene expression changes of primary gingival fibroblasts isolated from mouse maxilla.

city: Bunkyo City

first: Hiromi

last: Niimi

state: Tokyo

address: Yushima 1-5-45

department: Periodontology

country: Japan

institute: Tokyo Medical and Dental University

summary: This study aimed to explore the effects of low-level Er:YAG laser irradiation on the proliferation of gingival fibroblasts without the photothermal effect.

overall_design: Comprehensive gene expression analysis (RNA-seq) was performed in this research to reveal the early influence of laser irradiation on gingival fibroblasts.

first: Peiya

last: Lin

first: Tomomitsu

last: Hirota

first: Yujin

last: Ohsugi

first: Tsuyoshi

last: Shimohira

first: Keita

last: Toyoshima

first: Sayaka

last: Katagiri

first: Takanori

last: Iwata

first: Akira

last: Aoki


title: Translational and Transcriptional control of gene expression during serum stimulation on human RPE-1 cells

city: Salt Lake City

first: Bruce

last: Edgar

state: UT

address: 2000 Cir of Hope Dr.

department: Department of Oncological Sciences

institute: University of Utah

summary: In animal cells, growth factor signaling promotes both cell cycle progression and cell growth. To understand how the cell cycle is coupled to growth, we examined translational activities in human Retinal Pigment Epithelial cells by whole-transcriptome ribosome profiling.

overall_design: We performed Ribo-Seq and RNA-Seq on human RPE-1 cells that are serum starved for 18h, then serum stimulated for 5h, 10h, and 15h with 4 biological replicates each.

first: Yiqin

last: Ma

first: Stephen

last: Pronovost


title: A scalable and cost-efficient rRNA depletion approach to enrich RNAs for molecular biology investigations

city: West haven

first: Antariksh

last: Tyagi

state: CT

address: 830 West Campus Dr

institute: Yale University

summary: Transcriptomics analyses play pivotal roles in understanding the complex regulatory networks that govern cellular processes. The abundance of rRNAs, which account for 80-90% of total RNA in eukaryotes, limits the detection and investigation of other transcripts. While mRNAs and long non-coding RNAs have polyA(+) tails that are often used for positive selection, investigations of polyA(-) RNAs, such as circular RNAs, histone mRNAs, and small RNAs, typically require the removal of the abundant rRNAs for enrichment. Current approaches to deplete rRNAs for downstream molecular biology investigations are hampered by restrictive RNA input masses and high cost. To address these challenges, we developed rRNA Removal by RNase H (rRRR), a method to efficiently deplete rRNA from a wide range of human, mouse, and rat RNA inputs and qualities at a cost 10-20-fold cheaper than other approaches. We employed probe-based hybridization and enzymatic digestion to selectively target and remove rRNA molecules while preserving the integrity of non-rRNA transcripts. Comparison between rRRR to two commercially available approaches found that they had similar efficiencies at depleting rRNAs and comparable off-target effects. Our developed method provides researchers with a valuable tool for investigating gene expression and regulatory mechanisms across a wide range of biological systems at an affordable price that increases the accessibility for researchers to enter the field, ultimately advancing our understanding of cellular processes.

overall_design: 1 ug of total RNA was treated with rRRR (Our Method) and NEBNext Kit. rRNA levels were measured for both the methods. Transcriptome levels were also analyzed for off target effects if any. PolyA RNA was used as a negative control for certain analyses.

first: Amrita

last: Singh

first: Grace

last: Chen


title: Effect of epithelial depletion of Wnt10a on gene expression alteration during tooth root furcation development

status: Public on Mar 16 2024

city: Beijing

first: Kai

last: Sun

address: No.22 Zhongguancun South Avenue

institute: Peking university

summary:
In our previous study,  the knockout of Wnt10a in dental epithelium resulted in the occurrence of taurodontism and root furcation defects, suggesting that epithelial Wnt10a was a pivotal signal to guide root furcation patterning. Nevertheless, the exact mechanisms within dental epithelium leading root furcation development remained to be deeply elucidated.
To explore the downstream molecular alterations caused by epithelial Wnt10a ablation, we conducted RNA-Seq of molar epithelium tissue from furcation region.

overall_design: Three pairs of biological replicates (pooling dental epithelium from 4 first mandibular molars as 1 sample) of the RNA samples were collected from K14-Cre;Wnt10aflox/flox and Wnt10aflox/flox mice at PN2.5.

first: Miao

last: Yu


title: Gene exprssion at single cell level in patients broncoalveolar lavage (BAL) cells stimulated ex vivo with bacterial lysate OM-85

city: Bellinzona

first: Greta

last: Guarda

address: Via Francesco Chiesa 5

institute: Institute for Research in Biomedicine (IRB)

summary: OM-85 is a bacterial lysate used in clinical practice to reduce duration and frequency of recurrent respiratory tract infections. Whereas knowledge on its regulatory effects in vivo has substantially advanced, the mechanisms of OM-85 sensing remain inadequately addressed.The purpose of this study was to investigate the transptomic profile of human airway immune cells in the BAL after ex vivo stimulation with OM-85 at the single cell level and determine to what extent OM-85-induced gene signature in different myeloid cell subsets is dependent on TLR2/TLR4 expression.

overall_design: To this aim we harvested  Bronchoalveolar lavage fluid (BALF) cells from four subjects including two COPD (patients 1 and 3), one pulmonary silicosis (patient 4), and a patient with healthy lung (patient 2). BAL cells were stimulated or not with isotype control antibody (mIgG1k) or a combination of Anti-hTLR2 and Anti-hTLR4 (10ug/ml each) for 90 min, followed by stimulation with bacterial lysate OM-85 (150ug/ml) for 3hr. sc-RNA-seq was performed on these samples to assesss the gene expression profiles of various myeloid cell subsets.


title: Transcriptional Dynamics of Hepatic Sinusoid-Associated Cells After Liver Injury [bulk RNA-seq]

city: Odense M

first: Kim

last: Ravnskjaer

address: Campusvej 55

country: Denmark

institute: University of Southern Denmark

summary: Here we profile the transcripts of app. 35.000 single cells isolated from livers of healthy and diseased mice. We show the transcriptomic change associated with fibrosis induction in the non-parenchymal cell types (hepatic stellate cells, liver endothelial cells and macrophages). We reveal a hitherto unknown feature of the HSCs otherwise functionally attributed to the LECs.

overall_design: Bulk RNA-seq of Lrat-cre/mCherry-RPL10A treated with chow diet for 4 weeks, CLL4 for 2 and 4 weeks.

first: M

last: Terkelsen

first: K


title: Comprehensive analysis of lipid metabolism-related enzymes including ceramide in skin of psoriasis patients

city: Sakado

first: Madoka

last: Kage

address: 1-1 Keyakidai

institute: Josai University

summary: Ceramide is an important lipid in skin barrier function. Psoriasis is a chronic inflammatory skin disease, and the skin barrier function has disturbed. Furthermore, the balance of each ceramide species in stratum corneum is disrupted in psoriatic skin. However, it involved remains unclear what detailed mechanism ceramide species changed in psoriatic skin lesion. We comprehensively investigated lipid metabolism including ceramide in skin of psoriasis patients by DNA microarray analysis. The expression level of PNPLA1 gene involved in acylceramide synthesis which is epidermis-specific ceramide species essential for skin barrier function was decreased in psoriatic skin. In contrast, the expression level of lipid metabolism-related enzymes gene including ceramide were increased in psoriatic skin. Consequently, the acylceramide synthesis was decreased in skin of psoriasis patients, suggesting that increased biosynthesis of other sphingolipids to supplement the function of acylceramide may cause the pathology of psoriasis.

overall_design: Psoriasis vs. healthy control


title: Absence of chromosome axis proteins recruitment prevents meiotic recombination chromosome-wide in the budding yeast Lachancea kluyveri

city: Marseille

first: Sylvain

middle: Quentin

last: Legrand

address: 27 Bd Lei Roure

institute: CNRS

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

overall_design: Refer to individual Series


title: Epigenome analysis  of early gastric cancer(EGC) with and without  lymphovascular invasion(LVI)

status: Public on Mar 15 2024

city: Jinan

first: chuanxin

last: wang

address: 247 Beiyuan Street, Jinan 250033, Shandong, China,

institute: The Second Hospital of Shandong University

summary:
Genome wide DNA methylation profiling of EGC with and without LVI. The Illumina Infinium 850k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 820,000 CpGs in FFPE slides.
Samples included 10 EGC patients with LVI and 10 negative controls.

overall_design: Bisulphite converted DNA from the 20 samples were hybridised to the Illumina Infinium 850k Human Methylation Beadchip.

first: Yinghui

last: Zhao

first: Lutao

last: Du


title: Transcriptional dynamics of hepatic sinusoid-associated cells after liver injury super

department: Department of Biochemistry and Molecular Biology


title: Multi-Omics Characterization of Colon Mucosa and Submucosa/Wall from Crohn's Disease Patients

city: Worcester

first: Jing

last: Wang

state: MA

address: 100 Research Drive

institute: AbbVie

summary: Crohn’s disease (CD) is a subtype of inflammatory bowel disease (IBD) characterized by transmural disease. The concept of transmural healing (TH) has been proposed as an indicator of deep clinical remission of CD and as a predictor of favorable treatment endpoints. Understanding the pathophysiology involved in transmural disease is critical to achieving these endpoints. However, most studies have focused on the intestinal mucosa, overlooking the contribution of the intestinal wall in Crohn’s disease. Multi-omics approaches have provided new avenues for exploring the pathogenesis of Crohn’s disease and identifying potential biomarkers. .   We aimed to use transcriptomic and proteomic technologies to compare immune and mesenchymal cell profiles and pathways in the mucosal and submucosa/wall compartments to better understand chronic refractory disease elements to achieve transmural healing. The results revealed similarities and differences in gene and protein expression profiles, metabolic mechanisms, and immune and non-immune pathways between these two compartments. Additionally, the identification of protein isoforms highlights the complex molecular mechanisms underlying this disease, such as decreased RTN4 isoforms (RTN4B2 and RTN4C) in the submucosa/wall which may be related to the dysregulation of enteric neural processes. These findings have the potential to inform the development of novel therapeutic strategies to achieve TH

overall_design: Human colon resection tissues  were collected at surgery and dissected into regional compartments of mucosa and submucosa/wall for this study . Ulceration of some mucosal samples prevented their inclusion in this study, and sever-al samples were excluded from analysis due to poor sample or data quality. Mucosa samples (N = 25) consist 8 CD inflamed, 9 CD non-inflamed, and 8 normal (non-IBD control patients (cancerwith cancer or diverticular disease), and submucosa/wall samples (N = 27) consist 10 CD inflamed, 8 CD non-inflamed, and 9 normal (non-IBD control patients (cancerwith cancer or diverticular disease)

first: Liang

last: Jin

first: Michael

last: Macoritto

first: Yingtao

last: Bi

first: Fei

first: Abel

last: Suarez-Fueyo

first: Jesus

last: Paez-Cortez

first: Chenqi

last: Hu

first: Heather

last: Knight

first: Ivan

last: Mascanfroni

first: Matthew

last: Staron

first: Annette

last: Schwartz Sterman

first: Susan

last: Westmoreland

first: Yu

last: Tian


title: Vaccine based on immune evasion mutations integrated RBD protein have broad protection against SARS-CoV-2 [BCR-seq]

city: 昆明市

first: 然

last: 安

state: 云南省

address: 茭菱路935号医学生物学研究所

department: Institute of Medical Biology

institute: Peking Union Medical College

summary: Variants of SARS-CoV-2 continue to emerge and evade immunity, resulting in breakthrough infections in vaccinated populations. Continued vaccination with vaccines based on the antigens of newly emerged variants does not necessarily result in long-lasting protection. Thus, there is an urgent need for the development of vaccines with a broad spectrum of protective effects. In this study, we selected hotspot mutations in the receptor binding domain (RBD) based on immune escape properties and integrated them into the original RBD protein to obtain a complexed RBD protein (cRBD). We designed a total of three cRBD (cRBD1-3) and thoroughly evaluated their immunological properties. Compared with the BA.1 RBD protein, the cRBDs induced higher levels and broader spectrum of neutralizing antibodies, with cRBD3 being the best performer. In vivo protective capacity of cRBDs was further validated in Balb/c mice attacked by live virus. In order to investigate the reason for the broad protective efficacy of cRBD, whole blood from mice that had completed the immunization process was subjected to BCR sequencing. BCR transcriptome analysis found differences in the use of VJ pairs in IGH among the groups.

overall_design: BCR sequencing for blood collected from Balb/c mice completed immunization process.

first: Hongyu

last: Chen

first: Shuaiyao

last: Lu

first: Ran

last: An

first: Junbing


title: Role of SMN Protein in regulating the transcription and alternative splicing of Pulmonary Vascular Remodeling-Related Genes in HPASMCs

city: Wuhan

first: muqing

last: yu

address: 1095 Jiefang Avenue

department: Department of Respiratory and Critical Care Medicine, Tongji Hospital

institute: Huazhong University of Science and Technology

summary: To explore the effect of SMN protein on alternative splicing of multiple genes in human pulmonary artery smooth muscle cells (HPASMCs), we used shRNA specifically against the SMN to knock down the expression of SMN protein.Human primary pulmonary artery smooth muscle cells (hPASMCs) of donors were obtained from China Center for Type Culture Collection (Wuhan, Hubei, China).

overall_design:
We then performed gene expression profiling analysis using data obtained from RNA-seq of control cells and SMN knock-down cells (each group for three biological replicates).
Differentially expressed genes analysis and alternative splicing analysis of control cells and SMN knock-down cells.

first: Muqing

last: Yu

first: Lu

last: Wang

first: Lichen

last: Ouyang


title: YTHDF1-CLOCK axis contributes to pathogenesis of allergic airway inflammation through LLPS [m6A-seq]

city: Shanghai

first: Jing

state: Select...

address: huangpu Distinc, Ruijin Hospital

institute: 瑞金医院

type: Methylation profiling by high throughput sequencing

summary: N6-methyladenosine (m6A) modification has been implicated in many cell processes and diseases. YTHDF1, a translation-facilitating m6A reader, is not previously shown to be related to allergic airway inflammation. Here, we report that YTHDF1 is highly expressed in allergic airway epithelial cells (AECs) and asthmatic patients, and influences proinflammatory responses. CLOCK, a subunit of the circadian clock pathway, is the direct target of YTHDF1. YTHDF1 augments CLOCK translation in an m6A-dependent manner. Allergens enhance the liquid‒liquid phase separation (LLPS) of YTHDF1 and drive the formation of a complex comprising dimeric YTHDF1 and CLOCK mRNA, which is distributed to stress granules (SGs). Moreover, YTHDF1 strongly activates NLRP3 inflammasome production and IL-1β secretion, leading to airway inflammatory responses, but these phenotypes are abolished by deleting CLOCK. These findings demonstrate that YTHDF1 is an important regulator of asthmatic airway inflammation, suggesting a potential therapeutic target for allergic airway inflammation.

overall_design: we assessed the impact of YTHDF1 on allergic airway inflammation; explored the mechanism by which YTHDF1 regulated the target gene CLOCK, and further inferred the clinical significance of its action in human subjects.


title: Vaccine based on immune evasion mutations integrated RBD protein have broad protection against SARS-CoV-2 [mRNA-seq]

address: 茭菱路935号医学生物学研究所

summary: Variants of SARS-CoV-2 continue to emerge and evade immunity, resulting in breakthrough infections in vaccinated populations. Continued vaccination with vaccines based on the antigens of newly emerged variants does not necessarily result in long-lasting protection. Thus, there is an urgent need for the development of vaccines with a broad spectrum of protective effects. In this study, we selected hotspot mutations in the receptor binding domain (RBD) based on immune escape properties and integrated them into the original RBD protein to obtain a complexed RBD protein (cRBD). We designed a total of three cRBD (cRBD1-3) and thoroughly evaluated their immunological properties. Compared with the BA.1 RBD protein, the cRBDs induced higher levels and broader spectrum of neutralizing antibodies, with cRBD3 being the best performer. In vivo protective capacity of cRBDs was further validated in Balb/c mice attacked by live virus. In order to investigate the reason for the broad protective efficacy of cRBD, whole blood from mice that had completed the immunization process was subjected to RNA sequencing. Transcriptome analysis revealed that the vaccine was able to stimulate an immune response.

overall_design: RNA sequencing for blood collected from Balb/c mice completed immunization process.


title: YTHDF1-CLOCK axis contributes to pathogenesis of allergic airway inflammation through LLPS [mRNA-seq]


title: On- and off-target effects of paired CRISPR-Cas nickase in primary human cells [Amplicon]

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary: Undesired on- and off-target effects of CRISPR-Cas nucleases remain a challenge in genome editing. While the use of Cas9 nickases has been shown to minimize off-target mutagenesis, their use in therapeutic genome editing has been hampered by a lack of efficacy. To overcome this limitation, we and others have developed double nickase-based strategies to generate staggered DNA double-strand breaks to mediate gene disruption or gene correction with high efficiency. However, the impact of paired single-strand nicks on genome integrity has remained largely unexplored. Here, we developed a novel CAST-Seq pipeline, D-CAST, to characterize chromosomal aberrations induced by paired CRISPR-Cas9 nickases at three different loci in primary keratinocytes derived from epidermolysis bullosa patients. While targeting COL7A1, COL17A1, or LAMA3 with Cas9 nucleases caused previously undescribed chromosomal rearrangements, no chromosomal translocations were detected following paired nickase editing. While the double nicking strategy induced large deletions/inversions within a 10 kb region surrounding the target sites at all three loci, similar to the nucleases, the chromosomal on-target aberrations were qualitatively different and included a high proportion of insertions. Taken together, our data indicate that double-nickase approaches combine efficient editing with greatly reduced off-target effects, but still leave substantial chromosomal aberrations at on-target sites.

overall_design: Primary patient-derived keratinocytes were treated with Cas9 nucleases and single- and double-nickases, with the addition of an ssODN. Amplicon sequencing was performed to determine on-target indel formation and correction efficiency.

first: Julia

last: Klermund

first: Melanie

last: Boerries

first: Toni

last: Cathomen


title: On- and off-target effects of paired CRISPR-Cas nickase in primary human cells - long read

summary: Undesired on- and off-target effects of CRISPR-Cas nucleases remain a challenge in therapeutic genome editing. While the use of Cas9 nickases has been shown to minimize off-target mutagenesis, their use in therapeutic genome editing has been hampered by a lack of efficacy. To overcome this limitation, we and others have developed double nickase-based strategies to generate staggered DNA double breaks to mediate gene disruption or gene correction with high efficiency. However, the impact of paired single-strand nicks on genome integrity has remained largely unexplored. Here, we developed a novel CAST-Seq pipeline, D-CAST, to characterize chromosomal rearrangements induced by paired CRISPR-Cas9 nickases at three different loci in primary keratinocytes derived from epidermolysis bullosa patients. While targeting COL7A1, COL17A1, or LAMA3 with Cas9 nucleases caused previously undescribed chromosomal rearrangements, no chromosomal translocations were detected following single or paired Cas9-based nickase editing. Conversely, whereas single nickase applications did not result in gross genomic aberrations, the double nicking strategy induced large deletions/inversions within a 10 kb region surrounding the target sites at all three loci, similar to the nucleases. Taken together, our data indicate that double-nickase approaches combine efficient editing with greatly reduced off-target effects, but still leave substantial chromosomal rearrangements at on-target sites.

overall_design: Primary patient-derived keratinocytes were treated with Cas9 nucleases and single- and double-nickases. On-target effects were assessed using long-read (LR) sequencing.


title: On- and off-target effects of paired CRISPR-Cas nickase in primary human cells - long-read


title: On- and off-target effects of paired CRISPR-Cas nickase in primary human cells - Illumina

overall_design: Primary patient-derived keratinocytes were treated with Cas9 nucleases and single- and double-nickases. Genotoxicity was assesed via CAST-Seq.


title: Mitochondrial perturbations in immune cells enhance cell-mediated innate immunity in Drosophila

city: Tampere

first: Laura

last: Vesala

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

summary: Mitochondria participate in various cellular processes including energy metabolism, apoptosis, autophagy, ROS production, stress responses, inflammation and immunity. We investigated the effects of immune tissue specific mitochondrial perturbations on immune responses at the organismal level. Drosophila melanogaster model was utilized to knockdown genes from oxidative phosphorylation (OXPHOS) complexes cI-V, by targeting the two main immune tissues of Drosophila, the fat body and the immune cells (hemocytes). While fat body targeted OXPHOS perturbations caused detrimental effects on the viability and immunity, hemocyte specific perturbations led to enhanced immunocompetence of the host. This was accompanied by the formation of melanized hemocyte aggregates (melanotic nodules), a sign of activated cell-mediated innate immunity. Furthermore, hemocyte specific OXPHOS perturbations caused proliferation and immune activation of the hemocytes, resulting to a similar hemocyte profile as seen upon infection, and the animals ultimately had an enhanced immune response when infected with a parasitoid. Our data shows that hemocyte targeted OXPHOS perturbations cause mitochondrial membrane depolarization and upregulation of genes associated with mitochondrial unfolded protein response, including aerobic glycolysis and reactive oxygen species. Overall, we show that while the effects of mitochondrial perturbations on immune responses are highly tissue specific, mild mitochondrial dysfunction can be beneficial in immune-challenged individuals and is causing variation in infection outcomes between individuals.

overall_design: The GAL4-UAS system was utilized to silence OXPHOS complex I gene UQCR-C1 specifically in hemocytes. We used the combination of two hemocyte GAL4 lines (He-GAL4 and Hml[delta]-GAL4, HH-GAL4 for short) to drive the expression of shRNA for UQCR-C1 (UAS-UQCR-C1) in hemocytes. As a control, the w1118 line was crossed to the HH-GAL4 line. We collected the hemocyte samples at two timepoints: early (90 hours post egg lay) and late (120 hours post egg lay). In addition, we included wasp-infected (Leptopilina boulardi) late timepoint samples. For the infections, larvae were kept with parasitoid wasps for two hours. The hemocyte samples were collected 48 h after infection start. Hemocytes were also collected from uninfected, age-matched larvae.

first: Yuliya

last: Basikhina

first: Tea

last: Tuomela

first: Anssi

last: Nurminen

first: Emilia

last: Siukola

first: Pedro

middle: F

last: Vale

first: Tiina

middle: S

last: Salminen


title: Flotillin-1 palmitoylation is essential for its stability and subsequent tumor promoting capabilities.

city: Austin

first: Bryan

last: McClellan

state: TX

address: 1601B Trinity St, Hdb 6.302

institute: University of Texas at Austin

summary: Flotillin-1 contributes to invasion and metastasis in triple negative breast cancer (TNBC).  Palmitoylation, the process of conjugating palmitoyl-CoA to proteins, plays an essential role in protein stability and trafficking.  Flotillin-1 is modified by palmitoylation, however, the role of its palmitoylation in the context of metastasis has not been explored. Using palmitoylation defective flotillin-1 constructs, we have demonstrated that flotillin-1 palmitoylation contributes to its stability and metastatic capabilities in vivo. Further investigation led to the identification of zDHHC5 as the main palmitoyl acyl transferase responsible for palmitoylating flotillin-1, which also contributed to its stability by preventing its poly-ubiquitylation. To assess the ability to target flotillin-1 palmitoylation therapeutically, we designed a competitive peptide, which displayed efficacy in blocking flotillin-1 palmitoylation in vitro without altering palmitoylation of other zDHHC5 substrates, highlighting its specificity. Additionally, multiple TNBC tumor models expressing a doxycycline inducible flotillin-1 palmitoylation inhibiting peptide construct displayed attenuated tumor growth and lung metastasis.  The current study has demonstrated the palmitoylation of flotillin-1, a known metastasis inducing protein, to be essential for its protein stability. The demonstrated methods in blocking its palmitoylation through the delivery of a competitive peptide provide proof-of-concept data for further development as a potential targeted therapeutic in TNBC.

overall_design: To evaluate the effects of flotillin-1 palmitoylation, MDA-MB-231 cells were engineered to express flotillin-1 WT or palmitoylation defective (C34A). WT flotillin-1 cells were labelled with a GFP reporter and C34A cells with a dTomato reporter. GFP-WT and dTomato-C34A cells were implanted bilaterally into mice in their #4 mammary fat  and allowed to form tumors for 8 weeks. Tumors were digested into single cell supsensions and flow sorted based on GFP or dTomato reporters. Gene expression was then compared between GFP-flotillin-1-WT and dTomato-flotillin-1-C34A MDA-MB-231 cells from xenograft  tumors.

first: Linda

last: deGraffenried


title: On- and off-target effects of paired CRISPR-Cas nickase in primary human cells - Amplicon sequencing


title: On- and off-target effects of paired CRISPR-Cas nickase in primary human cells


title: Increased genomic instability and reshaping of tissue microenvironment underlie oncogenic properties of Arid1a mutations

city: Trento

first: Fulvio

last: Chiacchiera

address: Via Sommarive  9

institute: University of Trento


title: Atf4 promotes erythroid differentiation by regulating ribosome biogenesis via RPS19BP1

city: Tianjin

first: chao

last: tang

state: Tianjin

address: 288 Nanjing Road

institute: Institute of Hematology and Blood Diseases Hospital

summary: To elucidate the mechanisms underlying the role of Atf4 deficiency in erythropoiesis, we performed 10X Genomics single-cell RNA sequencing on Lin-cKit+ cells from Atf4 hematopoietic cell-specific conditional knockout mice (KO) and Atf4 floxed mice (WT) at steady state (referred to KO_BM and WT_BM) and after secondary transplantation (referred to cKO_t and WT_t). Furthermore, we also sorted CMP cells from Atf4 hematopoietic cell-specific conditional knockout mice (KO) and ATF4 floxed mice (WT) for 10X Genomics scRNA-seq.

overall_design: We performed 10X Genomics scRNA-seq of fluorescence-activated cell sorter (FACS)-sorted bone marrow (BM) Lin-cKit+ cells from Atf4 floxed mice (WT) and Mx1cre; Atf4fl/fl (KO) mice at 4 weeks post-deletion. We also enriched Lin-cKit+ cells from the BM of secondary recipient mice for an additional scRNA-seq analysis. In total, we captured 33,237 cells, of which 29,026 passed quality control. To further determine the transcriptional profiles in CMP cells, we performed 10x Genomics scRNA-seq of FACS-sorted CMP cells from WT and KO mice at 4 weeks post-deletion. And 19,706 of 21,914 sequenced CMP cells were kept after quality control.

first: Tao

last: Cheng

first: Hui

first: Zhaofeng

last: Zheng

first: Shangda

last: Yang