title: Chronic Type I interferons signaling promotes lipid peroxidation-driven terminal CD8+T cell exhaustion and curtails anti-PD-1 treatment efficacy [ATAC-Seq]

last: Chen

overall_design: CD8+T cells were isolated using Human CD8+ T Cell Isolation Kit (Miltenyi Biotec) according to the manufacturers procedure. Purified CD8+T cells were then stimulated with anti-CD3/anti-CD28-coated microbeads (Dynabeads M-450 Epoxy, Invitrogen; bead to cell ratio of 1:1) in the presence of 10U/ml recombinant human IL-2 (PeproTech) in T cell medium (RPMI 1640 medium supplemented with 10% FBS, 50M -mercapteoethanol, 1M HEPES, 1X non-essential amino acids (NEAA), 100mM sodium pyruvate, and 1% penicillin-streptomycin). Surviving cells were passaged every 48 hours with fresh microbeads and IL-2 until day2 or day 8 to generate Teff or Tex cells. In these conditions, human universal Type I interferon (PBL Assay science) was added at 1000U/mL throughout the culture. 50,000 alive CD8+ T cells were sorted through FACs with Influx (BD Biosciences) for establishing ATAC-seq library.

first: Jia


title: Chronic Type I interferons signaling promotes lipid peroxidation-driven terminal CD8+T cell exhaustion and curtails anti-PD-1 treatment efficacy

status: Public on Nov 16 2022

city: Hong Kong

first: Weixin

address: 21 Sassoon Road

country: Hong Kong

institute: The University of Hong Kong

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Identifying signals that govern the differentiation of tumor-infiltrating CD8 + T cells (CD8 + TILs) towards exhaustion can improve current therapeutic approaches for cancer. Here, we show that type I interferons (IFN-Is) act as environmental cues enhancing terminal CD8 + T cell exhaustion in tumors. We found enrichment of IFNIs-stimulated genes (ISGs) within exhausted CD8 + T cells (Tex cells) in patients across various cancer types, with heightened ISG levels correlating with poor response to immune checkpoint blockade (ICB) therapy. In preclinical models, CD8 + TILs devoid of IFN-Is signaling developed less exhaustion features, provided better tumor control and showed greater response to ICB-mediated rejuvenation. Mechanistically, chronic IFN-Is stimulation perturbed lipid metabolism and redox balance in Tex cells, leading to aberrant lipid accumulation and elevated oxidative stress. Collectively, these defects promoted lipid peroxidation, which potentiated metabolic and functional exhaustion of Tex cells. Thus, cell intrinsic IFN-Is signaling regulates the extent of CD8+ TIL exhaustion, and has important implications for immunotherapy.

overall_design:
For RNA-seq, the peripheral blood CD8+ T cells purified from heathy donors were stimulated with a-CD3/a-CD28 conjugated microbeads in the presence of IFN-Is, and then the alive CD8+ T cells were harvested on the day 2. Their high-quality RNA were extracted to submit pair-end RNA sequencing.
For ATAC-seq, the peripheral blood CD8+ T cells purified from heathy donors were stimulated with a-CD3/a-CD28 conjugated microbeads, and 50,000 live CD8+ T cells were sorted by flow cytometry immediately before library generation at day2. ATAC-seq libraries were prepared for the paired-end sequencing using Omni-ATAC protocol (Corces et al. Nature Methods 2017)


title: First-in-human study of the novel fibroblast activation protein-targeted 4-1BB agonist RO7122290 in patients with advanced solid tumors

city: Basel

first: Chia-Huey

last: Ooi

address: Grenzacherstrasse 124

country: Switzerland

institute: F. Hoffmann-La Roche Ltd.

summary: This first-in-human (FIH) study evaluated RO7122290, a novel, bispecific fusion protein carrying a split trimeric 4-1BB (CD137) ligand and a fibroblast activation protein-α (FAP) binding site that effectively co-stimulates T cells for improved tumor cell killing in FAP-expressing tumors. Patients with advanced and/or metastatic solid tumors received escalating weekly intravenous doses of RO7122290 as a single agent (n = 65) or in combination with 120mg fixed dose of the anti-PD-L1 antibody atezolizumab given every 3 weeks (n = 50), across a tested RO7122290 dose range of 5 to 2000 mg and 45 to 2000 mg, respectively. Three dose-limiting toxicities (DLTs) were reported, two at different RO7122290 single-agent dose levels (grade 3 febrile neutropenia, grade 3 cytokine release syndrome) and one for the combination (grade 3 pneumonitis). No maximum tolerated dose (MTD) was identified. The pharmacokinetic (PK) profile of RO7122290 was typical of target-mediated drug disposition. The observed modulation of proximal and distal pharmacodynamic (PD) biomarkers is consistent with the postulated immune mode of action (MoA). Treatment-induced PD changes included an increase of proliferating and activated T cells in peripheral blood both in the single agent and combination arm. Furthermore, we observed an increased infiltration of intratumoral CD8+ and Ki67+CD8+ T cells for both treatment regimens, accompanied with the up-modulation of T cell activation genes and gene-signatures. Eleven patients experienced a complete or partial response, from which six were confirmed immune checkpoint inhibitor (CPI)-naive patients. Our results support continued evaluation of RO7122290 in combination with atezolizumab and other immuno-oncology agents.

overall_design: Gene expression profiling analysis of RNA-seq data from patient biopsies before and after treatment

first: Chiahuey

first: Tamara

last: Tanos


title: Transcriptome analysis between wild-type and DM1-affected fibroblast.

city: Shanghai

first: Min

last: Hu

state: Select a State or Province

address: 1800 Yuntai Road, Shanghai 200123, China

country: China

institute: Tongji University School of Medicine

summary: Human skin fibroblast cell lines from 3 normal individuals and 3 individuals with DM1 in one pedigree were obtained from the biobank of Shanghai East Hospital. Human skin fibroblast cells were grown in DMEM (Life Technologies), NaPyr, GlutaMAX, β-mercaptoethanol and 10% foetal bovine serum (FBS) supplemented medium as previously described (Richner et al. 2015). Cells were collected after 80% confluency with TRIzol reagent and stored at -80℃ for RNA-seq and RT-PCR.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wild-type and  DM1-affected fibroblast.

first: Bei

last: Zhang

first: Gang

last: Li


title: Mechanisms of caspase-8 suppression of the RIPK1-TBK1 axis in homeostatic type I interferon production and regulation

city: Memphis

first: Raghvendra

last: Mall

state: Tennessee

address: 262 Danny Thomas Place

department: Department of Immunology

country: USA

institute: St Jude Children's Research Hospital

summary: Type-I interferons (IFNs) are an essential component of the innate immune response that are upregulated in response to infection. However, a low level of basal, or tonic, IFN expression is also critical to maintain tissue homeostasis. While the regulation of type-I IFN production during infection is well studied, the mechanisms controlling this basal expression and its impacts on homeostasis remain enigmatic. Here, we report the role of caspase-8 as a negative regulator of type-I IFN production during homeostasis in vitro and in vivo. Caspase-8 deficiency led to hyperactivation of basal type-I IFN signaling across multiple cell types and tissues and provided naturally heightened resistance to viral infection with norovirus. Mechanistically, the absence of caspase-8 allowed for an interaction between RIPK1 and TBK1, leading to enhanced TBK1 activation and aberrant type-I IFN production under homeostatic conditions. Loss of RIPK1 in caspase-8–deficient cells normalized TBK1 phosphorylation, IFN production and IFN signaling, thereby sensitizing cells to viral infection-induced inflammasome activation and inflammatory cell death, PANoptosis. In vivo, the elevated type-I IFN signaling, as well as the previously established early onset lymphadenopathy at 8 weeks of age, in caspase-8–deficient mice were reduced upon deletion of RIPK1 or type-I IFN neutralization. Overall, our study identified a mechanism which constrains tonic type-I IFN production and signaling during homeostasis. These results advance our understanding of tissue homeostasis and IFN regulation in infectious, autoimmune and autoinflammatory diseases, providing new insights for the development of disease treatments.

overall_design: We used microarrays to investigate global expression profiles in bone marrow derived macrophages from WT, Casp8-/-Ripk3-/-, Ripk3-/- and Casp8-/-Ripk3-/-Ripk1-/-  mice

first: Yaqiu

last: Wang

first: Karki

last: Rajendra

first: Sharma

last: Bhesh Raj

first: Ravi

middle: C

last: Kalathur

first: SangJoon

last: Lee

first: Kancharana

last: Balabhaskararao

first: Matthew

last: So

first: Katie

middle: L

last: Combs

first: Kanneganti

last: Thirumala-Devi


title: Mcm2 promotes stem cell differentiation via its ability to bind H3-H4 (ChIP-Seq)

city: New York

first: zhiguo

last: zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

summary: Mcm2, a subunit of the Mcm2-7 helicase best known for its role in DNA replication, contains a histone binding motif that facilitates the transfer of parental histone following DNA replication. Here we show that Mcm2 is important for the differentiation of mouse embryonic stem (ES) cells. Mcm2-2A mutation defective in histone binding impairs differentiation and programmatic changes in gene expression and histone modifications during differentiation. Mcm2 localizes at the transcription starting sites and the binding of Mcm2 at gene promoters is disrupted in both Mcm2-2A ES cells and neuro-precursor cells (NPCs). Reduced Mcm2 binding in Mcm2-2A ES cells correlates with decreased chromatin accessibility at bivalent chromatin domains containing repressive H3K27me3 and active H3K4me3 modifications in NPCs. Together, our studies reveal a novel function of Mcm2 in ES differentiation, likely through manipulating chromatin landscape at bivalent chromatin domains.

overall_design: ChIP-seq for H3K4me3, H3K27me3,MCM2, EZH2 and ATAC-seq were performed in mouse ES and NPC cells.

first: Xiaowei

last: Xu

first: Xu

last: Hua

first: Zhiguo


title: Mcm2 promotes stem cell differentiation via its ability to bind H3-H4 (RNA-Seq)

overall_design: total RNA-Seq were performed in mouse ES and NPC cells.


title: Mcm2 promotes stem cell differentiation via its ability to bind H3-H4

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

overall_design: Refer to individual Series


title: Retinoid X receptor promotes hematopoietic stem cell fitness and quiescence by repressing MYC pathway activation [RXR_CnR]

city: Madrid

first: Mercedes

last: Ricote

address: Darwin 3

country: Spain

institute: CNB-CSIC

summary: Hematopoietic stem cells (HSCs) maintain homeostasis and fitness by balancing self-renewal and differentiation. Alterations to the symmetry of HSC divisions reduce quiescence and induce myeloid/megakaryocyte-biased hematopoiesis. Here, we show that HSC self-renewal, fitness, and function are preserved by the master transcription factor retinoid X receptor (RXR). We demonstrate that dual lack of hematopoietic RXRα and RXRβ induces HSC asymmetric cell division resulting in HSC exhaustion and age-associated myeloproliferative disease. Characterization of transcriptomic and epigenetic changes in RXR-deficient HSCs demonstrated chromatin opening, acquisition of a premature aging-like HSC signature, MYC pathway upregulation, and RNA intron retention. Myc haploinsufficiency completely prevents the loss of RXR-deficient HSC activity. Our study unveils the critical relevance of RXR for HSC homeostasis and fitness.

overall_design: Here, we performed cleavege under target and release using nuclease followed by library preparation and subsequent next generation sequecing (CUT&RUNseq). HSCs (Lin-cKit+Sca1+CD48-CD150+) and MPPs (Lin-cKit+Sca1+CD150-) were sorted, bound to Concanavalin A magnetic bead, permeabilized using digitonin. The Concanvalin A bound and digitonin permeabilized cells were treated with RXRa Ab followed by proteinA-MNase (pA-MNase) and targeted digestion in presence of CaCl2. The CUT&RUN released DNA fragments were extracted using QIAGEN MinElute Reaction Cleanup kits, and were used for library preparation prepared using NEBNext Ultra II DNA library preparation kit for Illumina and NEBNext multiplex Oligoes for Illumina. Libraries followed next generation paired end sequencing.

first: José

middle: A

last: Cancelas

first: M

middle: P

last: Menéndez-Gutiérrez

first: Jesús

last: Porcuna

first: Ramesh

last: Nayak


title: A novel histone deacetylases inhibitor exerts promising anti-breast cancer activity via triggering AIFM1-dependent programmed necrosis

city: Qingdao

first: Peipei

last: Shan

address: Dengzhou Rd 38

institute: Qingdao University

summary:
Breast cancer is one of the most lethal cancers in women, and its resistance to chemotherapy remains a challenging problem. Histone deacetylases inhibitors (HDACIs) are a promising therapeutic tool for breast cancer. Here, we screened a library of synthetic small molecules and identified a novel HDACi, YF349, which possessed promising anti-breast cancer ability both in vitro and in vivo. Molecular and biochemical studies demonstrated that YF349 significantly increased the mRNA level of apoptosis-inducing factor (AIFM1) by blocking the binding of HDAC1 to the AIFM1 promoter. Further study revealed that YF349 significantly induced nuclear translocation of AIFM1 and promoted the formation of the AIF-CypA-gH2Ax complex in the nuclei, finally inducing AIF-mediated necrosis. Our finding suggests that AIFM1 can be explored as a molecular target in breast cancer and that targeting the HDAC1-AIFM1-CypA-gH2Ax signaling axis by YF349 may be a promising therapeutic strategy for breast cancer.
We identified a novel compound for breast cancer therapy

overall_design: RNA  profiles of MDA-MB231 cells after treatment with YF349 for 24 h at 2 μmol/L

first: Feifei

last: Yang


title: Characterization of an Entner-Doudoroff pathway-activated Escherichia coli

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

summary: We obtained pfkAB-deleted E. coli K-12 MG1655 strain that can thrive on glucose minimal medium with adaptive laboratory evolution (pfk_ALE-1 strain). Functional analysis of the mutations detected in the pfk_ALE-1 strain was conducted to elucidate the molecular mechanisms underlying the effects of these mutations. We performed transcriptome analysis with RNA-seq to investigate the transcriptomic effects of mutations involved in the glycolytic pathway and global transcriptional regulation. Transcriptomic analysis revealed the expression levels of 4,497 genes on the chromosome of MG1655 and ALE-1 strains.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: [RNA-seq]: A total of four samples were analyzed. E.coli_WT and E.coli_ALE cells were cultured in glucose minimal medium with biological duplicates.

first: Ina

last: Bang

first: Kyung-Hyun

last: Cho

first: Sung-Kuk


title: Differential Multigenomic Effect of Soluble Epoxide Hydrolase Inhibition on the Hippocampal Brain Microvasculature of FeFemale Mice on Low and High Glycemic Diets.

city: Davis

first: Saivageethi

last: Nuthikattu

state: CA

address: 550 Hutchison Dr

department: Internal Medicine, Cardiovascular division

institute: University of California Davis

summary:
Microvascular dysfunction is central to the development of dementia.  The effect of high glycemic diet (HGD), independent from dietary fat, on brain microvasculature is crucial, yet an understudied research topic, especially in feFemales. Our study aimed to determine the transcriptomic changes in feFemale brain hippocampal microvasculature induced by a HGD and characterize the response to soluble epoxide hydrolase inhibitor (sEHI).
We demonstrated for the first time in feFemales that the HGD had an opposite gene expression profile compared to the LGD and differentially expressed 506 genes, primarily downregulated, with functions related to cell signaling, cell adhesion, cellular metabolism, and neurodegenerative diseases.  Surprisingly, the sEHI modified the transcriptome of feFemale mice consuming the LGD more than the HGD, by modulating genes involved in metabolic pathways that synthesize neuroprotective epoxyeicosatrienoic acids (EETs) and associated with a higher EETs/ dihydroxyeicosatrienoic acids (DHETs) ratio.

overall_design: Wild type feFemale mice were fed a low glycemic diet (LGD, 12% sucrose/weight) or a HGD (34% sucrose/weight) with/without the sEHI, trans-4-[4-(3-adamantan-1-yl-ureido)-cyclohexyloxy]-benzoic acid (t-AUCB), for 12 wks. Brain hippocampal microvascular gene expression was assessed by microarray and data analyzed using a multiomic approach for differential expression of protein and non-protein coding genes, functional pathways, and transcription factors.

first: Dragan

last: Milenkovic

first: Jennifer

last: Norman

first: John

last: Rutledge

first: Amparo

last: Villablanca


title: Retinoid X receptor promotes hematopoietic stem cell fitness and quiescence by repressing MYC pathway activation [RXR_ATACSeq]

overall_design: The chromatin accessibility profiles of LT-HSCs and MPPs were generated using sorted bone marrow cells from WT and RXR-KO mice. Transposition was performed using Tn5 enzyme. (Illumina), applying size selection. Sequencing was performed  in duplicate using 2×50 HiSeq 3000 (Illumina) and with an average of 25 million paired-end reads per sample.Here, we performed a low input bulk RNAseq experiment. LT-HSCs and MPPs were sorted and total RNA was extracted using Arcturus PicoPure kit. Then, RNA samples (5ng) were used for library preparation. Libraries followed next generation paired end sequencing.


title: Retinoid X receptor promotes hematopoietic stem cell fitness and quiescence and preserves hematopoietic homeostasis


title: HiTIMED: hierarchical tumor immune microenvironment epigenetic deconvolution for accurate cell type resolution in the tumor microenvironment using tumor‑type‑specific DNA methylation data

city: Boston

first: Ze

last: Zhang

state: MA

address: 375 Longwood Ave

department: Medical Oncology & Population Sciences

institute: Harvard Medical School

summary: The solid tumor microenvironment is heterogeneous and varies in composition by tumor type. High-resolution profiling of the cell composition in tumor microenvironments is crucial to understanding its biological role and function in clinical outcomes. Previously, gene expression and DNA methylation-based deconvolution approaches for tumor microenvironment have succeeded in deconvolving major cell types. However, existing methods lack accuracy and specificity to tumor type and include a limited amount of cell types. We developed a novel DNA methylation-based algorithm, HiTIMED, to estimate cell proportions in tumor microenvironments with a high resolution. HiTIMED employs a tumor-site-specific hierarchical model to enhance the accuracy of the predictions. Seventeen cell types, three major tumor microenvironment components (tumor, immune, angiogenic), and twenty carcinoma types can be profiled by HiTIMED. We demonstrated prognostic significance of HiTIMED cell types that other methods in the tumor microenvironment deconvolution were not capturing. The high resolution of HiTIMED deconvolution provides additional opportunities to study the impact of the tumor microenvironment on clinically significant outcomes like immunotherapy response.

overall_design: Bisulphite converted DNA from five isolated dendritic cell samples were hybridised to the Illumina Infinium HumanMethylationEPIC Beadchip v1.0_B4

first: Lucas

last: Salas

first: Karl

middle: T

last: Kelsey

first: Brock

last: Christensen

middle: K

last: Wiencke

first: Devin

last: Koestler


title: Circadian lncRNA ADIRF-AS1 binds PBAF and regulates renal clear cell tumorigenesis

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: We identified ADIRF-AS1 as a BMAL1-CLOCK regulated circadian lncRNA. Loss of ADIRF-AS1 in U2OS cells altered rhythmicity of clock-controlled genes and expression of genes associated with cell adhesion and the extracellular matrix (ECM) but did not affect neighboring genes in cis. Affinity based enrichment of U2OS ADIRF-AS1-interacting proteins identified all components of the tumor suppressive PBAF (PBRM1/BRG1) complex. Because PBRM1 is a tumor suppressor mutated in 40% of clear cell renal carcinoma (ccRCC) cases, we studied ccRCC 786O cells and also found PBRM1 bound to ADIRF-AS1. Reducing ADIRF-AS1 expression in 786O and A498 ccRCC cells decreased expression of PBAF-suppressed genes, consistent with ADIRF-AS1 acting to antagonize the function of PBAF. Loss of PBRM1, however, rescued PBAF responsive cell cycle genes in ADIRF-AS1 KO 786O ccRCC cells. Importantly, ADIRF-AS1 expression correlates with survival in human ccRCC, particularly in PBRM1 wild-type, but not mutant PBRM1 tumors. In this regard, loss of ADIRF-AS1 did not affect in vitro 786O cell growth, but strikingly eliminated in vivo tumorigenesis, which was partially rescued by concurrent loss of PBRM1. This rescue, however, requires Matrigel, suggesting a PBRM1-independent function of ADIRF-AS1 in regulating the ECM. Collectively, our findings suggest that ADIRF-AS1 functions partly to antagonize the tumor suppressive effect of the PBAF complex and behaves as an unforeseen BMAL1-regulated, oncogenic lncRNA.

overall_design:
RNA-seq experiment in U2OS and 786O in control and ADIRF-AS1 or/and PBRM1 knockout conditions.
ChIP-seq experiment in empty vector or ADIRF-AS1 KO cells.

first: Rebehak

last: Brooks

first: Chi

last: Dang


title: Transcriptional signatures to AS01-adjuvanted tuberculosis vaccine in naïve and primed participants

city: Rixensart

first: Margherita

last: Coccia

address: Rue de l'Institut 89

country: Belgium

institute: GSK Vaccines

summary: In this exploratory post-hoc analysis of clinical trial samples (clinicalTrials.gov: NCT01424501), we compared gene expression patterns elicited by two immunizations with the candidate tuberculosis (TB) vaccine M72/AS01, between three groups of individuals with different levels of memory responses to TB antigens before vaccination

overall_design: There were a total of 239 samples from 64 subjects across 3 time points (D0, D7, D37). Subjects were distributed in 3 groups, TB disease naïve PPD negative (TBDN -NEG), TB disease naïve PPD positive (TBDN -POS), and  TB experienced individuals (TB-TRT). A third, incompletely recruited cohort of subjects receiving treatment for active TB was not analyzed due to its small sample size (ACTIVETB_TRT). Per-protocol immunization was at Day (D)0 and D30, and all but three of these participants received two vaccine doses.

first: Wivine

last: Burny

first: Marie-Ange

last: Demoitié

first: Paul

last: Gillard

first: Robert

last: van den Berg

first: Robbert

last: van der Most


title: A conserved Bacteroidetes antigen induces anti-inflammatory intestinal T lymphocytes

first: Tiago

last: Castro

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

summary: The microbiome contributes to the development and maturation of the immune system. In response to commensal bacteria, intestinal CD4+ T lymphocytes differentiate into functional subtypes with regulatory or effector functions. Whereas the development of small intestine intraepithelial lymphocytes that express CD4 and CD8aa homodimers (CD4IELs) depends on the microbiota, the identity of the microbial antigens recognized by CD4+ T cells that can differentiate into CD4IELs remains unknown. We identified B-hexosaminidase, a conserved enzyme across commensals of the Bacteroidetes phylum, as a driver of CD4IEL differentiation.  In a mouse model of colitis, B-hexosaminidase-specific lymphocytes protected against intestinal inflammation. Thus, T cells of a single specificity can recognize a variety of abundant commensals and elicit a regulatory immune response at the intestinal mucosa.

overall_design: mRNA profile of 175 IELs tetramer-positive or negative for P. goldsteinii  B-N-acetylhexosaminidase (B-hex)

first: Djenet

last: Bousbaine

first: Laura

middle: I

last: Fisch

first: Mariya

last: London

first: Preksha

last: Bhagchandani

middle: B

first: Mark

last: Mimee

first: Scott

last: Olesen

first: David

last: VanInsberghe

first: Bernardo

last: Reis

first: Juliana

last: Bortolatto

first: Mathilde

last: Poyet

first: Ross

middle: W

last: Cheloha

last: Sidney

first: Jingjing

last: Ling

first: Aaron

last: Gupta

first: Timothy

last: Lu

first: Alessandro

last: Sette

first: Eric

last: Alm

first: James

last: Moon

first: Gabriel

middle: D

last: Victora

first: Daniel

last: Mucida

first: Hidde

last: Ploegh

first: Angelina

middle: M

last: Bilate


title: NAT10-mediated N4-Acetylcytidine is Required for Spermatogenesis and Male Fertility

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

summary: RNA modifications are rapidly emerging as critical post-transcriptional regulators which play a key role in various biological processes. N4-acetylcysteine (ac4C) is one of the “epi-transcriptome” that is present on tRNA, rRNA, mRNA and is also highly conserved in all species. However, cytidine acetylation's in vivo physiological functions remain poorly understood particularly in mammals. Here we demonstrate only known ac4C “writer”—N-acetyltransferase 10 (NAT10) plays essential roles in male reproduction. NAT10 protein and the ac4C modification have different patterns in different organs and there are dynamic changes during spermatogenesis. Germ cell-specific ablation of NAT10 severely inhibited meiotic entry and defects in synapse the homologous chromosomes, repair of DNA double-strand breaks (DSBs) during prophase of the first meiotic division. ac4C RIP-qPCR reveals genes functioning in meiotic prophase I show a decrease in Nat10fl/-; Stra8 GFP-Cre mouse testes. These findings highlight the crucial physiological functions of mRNA ac4C modification in male spermatogenesis and expand our understanding of mRNA ac4C modification in the regulation of specific physiological processes in vivo.

overall_design: Examination of WT and Nat10-SKO transcriptome: A total of 17 samples were analyzed in this study, including WT and Nat10-SKO spermatogenic cells from 3 stages,  spermatogonia, preleptotene and leptotene/zygotene stage.

first: Lu

last: Chen

first: Wen-Jing

last: Wang

first: Yu-Ke

last: Wu

first: Heng-Yu


title: Glucocorticoids Unmask Silent Non-Coding Genetic Risk Variants for Common Diseases [HiChIP]

city: Rochester

first: Thanh Thanh

middle: Le

last: Nguyen

state: Minnesota

address: 200 1st St. SW

institute: Mayo Clinic

summary: 30 B-lymphoblastoid cell lines (LCLs) with genome-wide genotype data were treated with hydrocortisone (GR agonist) and CORT108297 (GR modulator), followed by RNA-seq to identify PGx-eQTLs. We then integrated GR chromatin immunoprecipitation-sequencing (ChIP-seq) to characterize the epigenetic function of PGx-eQTLs that interfere with GR response elements. We also applied a high-throughput enhancer assay (STARR-seq) using PGx-eQTL loci DNA sequences to “scan” for drug-dependent SNPs.

overall_design: H3K27ac HiChIP of LCL CA61 before and after Cortisol treatment

first: Jeong-Heon

last: Lee

first: Geng-xian

last: Shi

first: Tamas

last: Ordog

first: Richard

last: Weinshilboum


title: Single-cell transcriptional and functional analysis of human dopamine neurons in 3D fetal ventral midbrain organoid like cultures

city: Lund

first: Petter

last: Storm

address: Sölvegatan 19, BMC A11

department: Developmental and Regenerative Neurobiology

country: Sweden

institute: Lund University

summary: Significant efforts are ongoing to develop refined differentiation protocols to generate midbrain DA neurons from pluripotent stem cells (PSCs) for application in disease modeling, diagnostics, drug screening, and cell-based therapies for Parkinson’s Disease. An increased understanding of the timing and molecular mechanisms promoting the generation of distinct subtypes of midbrain DA during normal development will be essential for guiding future efforts to precisely generate molecularly defined and subtype-specific DA neurons from pluripotent stem cells. In this study, we used droplet-based single-cell RNA sequencing (scRNA-seq) to transcriptionally profile fetal DA neurons from human embryos at different stages of ventral midbrain (VM) development (6, 8, and 11 weeks post-conception) and primary fetal 3D cultures thereof that allowed differentiation and functional maturation of human DA neurons. This approach allowed us to define the molecular identities of distinct human DA progenitors and neurons at single-cell resolution and construct developmental trajectories of cell types in the developing fetal VM. Overall, these findings provide a unique transcriptional profile of developing human fetal VM and functionally mature human DA neurons, which can be used to guide stem cell-based therapies and disease modeling approaches in PD.

overall_design:
Single-cell RNA-seq of human fetal midbrain and midbrain derived organoids
>>> Submitter states that raw data are unavailable due to patient privacy concerns <<<

first: Marcella

last: Birtele

first: Malin

last: Parmar


title: To identify differentially expressed gene in the atrium tissues between wildtype control and the Dnajb6 heterozygous knockout mouse

city: Baltimore

first: Yuji

last: Zhang

state: MD

address: 660 W. Redwood Street

institute: University of Maryland

summary: To seek molecular mechanisms underlying the sick sinu syndrome phenotypes observed in Dnajb6 heterozygous knockout mice, we performed whole transcriptome RNA-sequencing experiments using right atrial tissues isolated from Dnajb6 heterozygous knockout mic and WT control mice at 1 year of age.

overall_design: Total RNA was extracted from the right atrium (RA) tissues of 1-year-old Dnajb6+/- heterozygous mutant hearts and WT sibling controls. Six total samples (3 biological replicates for each genotype) were submitted for RNA sequencing (Azenta Life Science, NJ). Genes were considered to be differentially expressed between the two groups if they exhibited a greater than 2-fold change and an False Discovery Rate (FDR) of less than 0.05 according to the DESeq approach.

first: Yonghe

last: Ding

first: Xiaolei

last: Xu


title: Time-point analysis to characterize the molecular evolution for gemcitabine-resistant T24 cell

city: Yuseong-gu

first: Seung Woo

last: Baek

state: Daejeon

address: Gwahak-ro 125

institute: Korea Research Institute Biology & Biotechnology

summary: transcriptomic data for T24 were generated to observe the process of acquiring Gemcitabine resistance in time-point changes.

overall_design: To gain new insights into chemotherapy resistance and bladder cancer recurrence, in this study, we first established stepwise gemcitabine-resistant bladder cancer cell lines to understand the molecular evolution of drug resistance.

first: Seung-Woo

first: Sun-Hee

last: Leem


title: Transcriptome analysis of human DMD-K2957fs and CRISPR-corrected (CORR-K2957fs ) myogenic cultures during secondary myogenic differentiation.

city: Cambridge

first: Rob

last: Moccia

address: 610 Main Street

department: Rare Disease Research Unit

institute: Pfizer Inc

summary: To investigate transcriptomes of skeletal muscle cells in health and Duchene muscular dystrophy (DMD), we performed RNA sequencing of DMD-K2957fs and CRISPR-corrected (CORR-K2957fs ) myogenic cultures during secondary differentiation at 5 time points.

overall_design: RNA sequencing was performed on DMD-K2957fs and CRISPR-corrected (CORR-K2957fs ) myogenic cultures during secondary differentiation at 5 time points (day -1, 0, 2 ,5 and 7). Four biological replicates were performed per condition.

first: Cristina

last: Morera

first: Jihee

last: Kim

first: Amaia

last: Paredes-Redondo

first: Seth

last: Garren

first: Muriel

last: Nobles

first: Denis

last: Rybin

first: Anna

last: Kowala

first: Jinhong

last: Meng

first: Pentao

last: Liu

first: Jennifer

middle: E

last: Morgan

first: Francesco

last: Muntoni

first: Nicolas

last: Christoforou

first: Jane

last: Owens

first: Andrew

last: Tinker

first: Yung-Yao

last: Lin


title: Effect of IBSP on patient-delived gliomasphere culture [microarray]

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

summary: We aim to examine gene expression changes on patient-derived gliomasphere by IBSP treatment

overall_design: Patient-derived gliomasphere was cultured for 4D in the presence and absence of IBSP

first: Yasmin

last: Ghochani

first: Alireza

last: Sohrabi

first: Sree

last: Muthukrishnan

first: Michael

last: Condro

first: Soniya

last: Bastola

first: Fuying

last: Gao

first: Yue

last: Qin

first: Jack

last: Mottahedeh

first: M

last: Iruela-Arispe

first: Nagesh

last: Rao

first: Dan

middle: R

last: Laks

first: Linda

last: Liau

first: Gary

last: Mathern

first: Steven

last: Goldman

first: Thomas

last: Carmichael

first: Ichiro

last: Nakano

first: Giovanni

last: Coppola

first: Stephanie

last: Seidlits

first: Harley

last: Kornblum


title: Transcriptomic characterization of GBM tumor and vascular cells

first: Riki

last: Kawaguchi

summary: We aim to profile transcrional regulation of GBP tumor and vascular cells by RNA sequencing

overall_design: Tumor and vasucular cells are isolated by FACS-sorting dissociated GBM

first: Yasmin

last: Ghochani

first: Alireza

last: Sohrabi

first: Sree

last: Muthukrishnan

first: M.


title: Transcriptomic characterization of GBM tumor and vascular cells and IBSP on patient-delived gliomasphere culture

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

overall_design: Refer to individual Series


title: Retinoid X receptor promotes hematopoietic stem cell fitness and quiescence by repressing MYC pathway activation [HISTONE_CnR]

first: Mercedes

last: Ricote

summary: Hematopoietic stem cells (HSCs) maintain homeostasis and fitness by balancing self-renewal and differentiation. Alterations to the symmetry of HSC divisions reduce quiescence and induce myeloid/megakaryocyte-biased hematopoiesis. Here, we show that HSC self-renewal, fitness, and function are preserved by the master transcription factor retinoid X receptor (RXR). We demonstrate that dual lack of hematopoietic RXRα and RXRβ induces HSC asymmetric cell division resulting in HSC exhaustion and age-associated myeloproliferative disease. Characterization of transcriptomic and epigenetic changes in RXR-deficient HSCs demonstrated chromatin opening, acquisition of a premature aging-like HSC signature, MYC pathway upregulation, and RNA intron retention. Myc haploinsufficiency completely prevents the loss of RXR-deficient HSC activity. Our study unveils the critical relevance of RXR for HSC homeostasis and fitness.

overall_design: Here, we performed cleavege under target and release using nuclease followed by library preparation and subsequent next generation sequecing (CUT&RUNseq) for global mapping of histone marks (H3K4me1, H3K4me3, and H3K27Ac) in Rxrabfl/fl (WT) and VaviCre+Rxrabfl/fl (RXRKO) hematopoietic stem cells (HSCs). HSCs (Lin-cKit+Sca1+CD48-CD150+) were sorted, bound to Concanavalin A (Con-A) magnetic bead, permeabilized using digitonin. The Con-A bound and digitonin permeabilized cells were treated with antibodies against H3K4me1, H3K4me3, or H3K27Ac followed by protein A-MNase (pA-MNase) binding and targeted digestion in presence of CaCl2. The CUT&RUN released DNA fragments were extracted using QIAGEN MinElute Reaction Cleanup kits, and were used for library preparation prepared using NEBNext Ultra II DNA library preparation kit for Illumina and NEBNext multiplex Oligoes for Illumina. Libraries followed next generation paired end sequencing.

first: José

last: Cancelas

last: Menéndez-Gutiérrez

first: Jesús

last: Porcuna

first: Ramesh

last: Nayak

first: Nathan

last: Salomonis


title: A molecular switch between mammalian MLL complexes dictates response to Menin-MLL inhibition

first: Douglas

last: Barrows

address: 1230 York Ave

institute: Rockefeller University

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: A molecular switch between mammalian MLL complexes dictates response to Menin-MLL inhibition [ChIP-seq]

summary: The chromatin adaptor Menin interacts with oncogenic fusion proteins encoded by MLL1-rearrangements (MLL1-r), and small molecules that disrupt these associations are currently in clinical trials for the treatment of leukemia. Here, we delineate a molecular switch between the MLL1-Menin and MLL3/4-UTX chromatin modifying complexes that dictates response to Menin-MLL inhibitors. We show that Menin safeguards leukemia cell fitness by impeding binding of the histone demethylase UTX at a subset of non-canonical target gene promoters. Disrupting the interaction between Menin and MLL1 leads to UTX-dependent transcriptional activation of genes with tumor suppressive function. We show that this epigenetic mechanism is operative in murine and human models of AML, and clinical responses to Menin-MLL inhibition in primary human leukemia are accompanied by induction of tumor suppressive gene expression at Menin-UTX targets. These findings shed light on the context-dependent and often antagonistic roles that chromatin regulators exhibit in development and disease and provide mechanistic insight for rational design of targeted epigenetic therapies.

overall_design: ChIP-Seq for Menin, UTX, MLL1, MLL3/4 and various histone post-translational modifications in mouse and human leukemia cells and fibroblasts.

first: Yadira

last: Soto-Feliciano

first: Francisco

last: Sánchez-Rivera

first: Florian

last: Perner

first: Scott

last: Armstrong

last: Lowe

first: C

last: Allis


title: A molecular switch between mammalian MLL complexes dictates response to Menin-MLL inhibition [RNA-seq]

overall_design: Using RNA-Seq followed by gene expression analyses we determined genes that change in expression upon treatment with Menin-MLL inhibitors in leukemia cell lines (days 0 and 4 post treatment) in triplicates of samples.


title: Glucocorticoids Unmask Silent Non-Coding Genetic Risk Variants for Common Diseases [ChIP-seq]

first: Thanh Thanh

last: Nguyen

overall_design: GR-targeted ChIP-sequencing of LCL CA61 before and after Cortisol or C297 treatment

first: Duan

last: Liu

first: Zhenqing

last: Ye

first: Jeong-Heon

last: Lee

first: Tamas

last: Ordog

first: Richard

last: Weinshilboum


title: Glucocorticoids Unmask Silent Non-Coding Genetic Risk Variants for Common Diseases


title: Translational regulation in response to sulfur in Sorghum bicolor

city: Tokyo

first: Naoyuki

last: Sotta

address: 1-1-1 Yayoi, Bunkyo-ku

department: Department of Applied Biological Chemistry

country: Japan

institute: Graduate School of Agricultural and Life Sciences, The University of Tokyo

summary: Sorghum is a C4 cereal important not only as food, but also as forage and a bioenergy resource. Its resistance to harsh environments has made it an agriculturally important research subject. Recent accumulation of genomic and transcriptomic information has facilitated genetic studies. Yet genome-wide translational profiles in sorghum are still missing, although increasing evidence has demonstrated that translation is an important regulatory step, and the transcriptome does not necessarily reflect the profile of functional protein production in some organisms. Deep sequencing of ribosome-protected mRNA fragments (ribosome profiling, or Ribo-seq) has enabled genome-wide analysis of translation. In this study, we took advantage of Ribo-seq and identified actively translated reading frames throughout the genome. We detected translation of 7,304 main ORFs annotated in the sorghum reference genome version 3.1 and revealed a number of unannotated translational events. A comparison of the transcriptome and translatome between sorghums grown under normal and sulfur-deficient conditions revealed that gene expression is modulated independently at transcript levels and translation levels. Our study revealed the translational landscape of sorghum’s response to sulfur and provides datasets that could serve as a fundamental resource to extend research on sorghum, including translational studies.

overall_design: Whole shoot tissues of 13-day-after-sowing Sorghum bicolor grown under Control and sulfur deficiency conditions (Ctrl, 500 µM; Sminus, 0 µM). 3 biological replicates.

first: Yukako

last: Chiba

first: Haruka

last: Aoyama

first: Seidai

last: Takamatsu

first: Takamasa

last: Suzuki

first: Kyoko

last: Miwa

first: Yui

last: Yamashita

first: Satoshi

last: Naito

first: Toru

last: Fujiwara


title: Tet2 negatively regulates memory fidelity

city: Lewiston

first: Andrew

middle: John

last: Kennedy

state: ME

address: 5 Andrews Rd, Dana 322

department: Chemistry

institute: Bates College

type: Methylation profiling by high throughput sequencing

summary: Tet2 functions in the CA1 as a negative regulator of long-term memory, and its haploinsufficiency in glutamatergic neurons or knockdown across the CA1 in mice is sufficient to enhance the fidelity of hippocampal-dependent spatial and associative memory.

overall_design: Changes in DNA methylation was determined using whole genome bisulfite sequencing from glutamatergic Tet2 haploinsufficient CA1 tissue from mice.


title: Zfp503/Nlz2 is Required for RPE Differentiation and Optic Fissure Closure

city: Bethesda

first: David

last: McGaughey

address: 10 Center Dr

department: NEI

institute: NIH

summary: Uveal coloboma is a congenital eye malformation caused by failure of the optic fissure to close in early human development.  Despite significant progress in identifying genes whose regulation is important for executing this closure, mutations are detected in a minority of cases using known gene panels, implying additional genetic complexity.  We show that the mouse Zfp503/Nlz2 gene is dynamically regulated in developing mouse eyes and that loss of its expression results in uveal coloboma. KO embryos exhibit altered expression patterns of several key transcription factors involved in eye development, including Otx2, Mitf, Pax6, Pax2, Vax1 and Vax2, resulting in reduced melanin pigmentation in the presumptive retinal pigment epithelium and its differentiation into a neural-retina-like lineage.  From a large cohort of patients with exome sequencing records, only one patient with clinical diagnosis of retinal degeneration was identified carrying a pPresumed loss-of-function variants in the human ortholog, ZNF503. Although no disease-causing association was demonstrated, because of the retinal degeneration rather than of uveal coloboma phenotype, are rare and may be associated with retinal degeneration, rather than a uveal coloboma phenotype, suggesting it is tempting to speculate that a pleiotropic role of ZNF503 might have a pleiotropic role in ocular development and physiology

overall_design: RPE mRNA profiles of Wild Type and Zfp503 knockout mice

first: Brian

last: Brooks

first: Elangovan

last: Boobalan


title: Glucocorticoids Unmask Silent Non-Coding Genetic Risk Variants for Common Diseases [RNA-seq]

first: Thanh Thanh

last: Nguyen

overall_design: RNA-sequencing of 30 LCLs before and after Cortisol or C297 treatment

first: Huanyao

last: Gao

first: Duan

last: Liu

first: Liewei

last: Wang


title: RNA sequencing analysis of HEK293T cells infected with a lentivirus coding the BRCT domain from Leishmania major Pes protein

city: Pamplona

first: Esther

last: Larrea

state: Navarra

address: CIMA Avda. Pio XII 55

institute: Institute of Tropical Health of Universidad de Navarra

summary: Given the prevalence of leishmaniasis and cancer, the co-existence of these two diseases may be merely coincidental. However, a number of epidemiological studies suggest that an association between these two entities does exist. Mammalian PES protein has been reported to be involved in different cellular processes such as cell cycle regulation. Its BRCT domain has been identified as a key factor in DNA damage-responsive checkpoints. We aimed to elucidate the hypothetical oncogenic character of this BRCT domain from Leishmania major PES protein (LmPES) on the host cells. For this purpose, we generated a lentivirus carrying this BRCT domain sequence (lentiBRCT) and a lentivirus expressing the lucifarese protein (lentiLuc), as control. Then, HEK293T mammal cells were infected with these lentivirus. Gene expression profiling analysis revealed that BRCT domain from LmPES protein altered the expression of proliferation, survival and chemoresistance related genes. In addition, RNA sequencing study showed a down-regulation of mitochondrial genes in the BRCT domain expressing cells triggering a mitochondrial dysfunction. Altogether, our results reinforce the idea that in eukaryotes, horizontal gene transfer may be also achieved by parasitism like Leishmania infection driving therefore to some crucial biological changes such as proliferation and drug resistance.

overall_design: To study the effect of  BRCT domain from Leishmania major Pes protein expression in mammal cells

first: Paul

last: Nguewa

first: Celia

last: Fernández-Rubio


title: Hsa-miR-1-2/miR-133a-1 cluster expression silencing by DNA hypermethylation triggers oncogenes contributing to prostate cancer aggressiveness

city: Ciudad Autónoma de Buenos Aires

first: Cintia

middle: Lorena

last: Massillo

state: Buenos Aires

address: Vuelta de Obligado 2490

country: Argentina

institute: Instituto de Biología y Medicina Experimental

summary:
We developed a metabolic syndrome (MeS)-like disease model using C57BL/6J mice chronically fed with high fat diet (HFD) that were inoculated with TRAMP-C1 prostate cancer (PCa) cells to investigate the effect of a HFD on the expression of cancer-related miRNAs.
In this dataset, we include the expression data obtained from TRAMP-C1 tumors developed in control diet (CD) versus high fat diet (HFD) C57BL/6J male mice.  For differential expression analysis we used the Rank Product Method for two class unpaired data and a fold discovery rate (FDR) < 0.05 .

overall_design: C57BL/6J male mice were fed with a high fat diet (HFD) for 15 weeks, then injected s.c with TRAMP-C1 murine prostate cancer cells. Animals were sacrificed in the 27th week and tumor samples were processed, total RNA was obtained and hybridized with GeneChip® miRNA 4.0 Array (Affymetrix)


title: Next Generation Sequencing Analysis Identifies Genes Whose Expression is Regulated by SIRT1 and IGF2BP2

city: Ithaca

first: Elena

last: Panizza

address: 930 Campus Rd

department: Molecular Medicine

institute: Cornell University

summary: This study shows how cells that are depleted of sirtuin1 (SIRT1) regulate IGF2BP2 to promote the degradation of the transcript that encodes ATP6V1A, a major catalytic subunit of the v-ATPase. IGF2BP2 and SIRT1 actions lead to altered gene expression by determining epigenetic modifications and by modulating RNA stability. This raises the question of whether the regulation of IGF2BP2 impacts additional transcripts, similarly to what we found for the transcript encoding ATP6V1A. The purpose of this RNA sequencing analysis is to identify genes whose expression is regulated similarly to ATP6V1A.

overall_design: RNA-seq analysis was performed on control, SIRT1 KD, IGF2BP2 KD, and SIRT1/IGF2BP2 double KD MDA-MB-231 cells.  Each condition was analyzed 3 independent times.

first: Fangyu

first: Marc

last: Antonyak

first: Richard

last: Cerione


title: Expression data from  Minoxdil, Keratin and microsphere keratin in vivo

status: Public on Nov 15 2022

city: Tsukuba,

first: Meriem

last: Bejaoui

state: Ibaraki

address: 1 Chome-1-1 Tennodai

institute: University of Tsukuba

summary:
Gene expression profiling reveals a potential  effect of microsphere keratin in stimulating hair growth in vivo
Mice back was depilated and then treated with 1% milliQ, 1% minoxidil, 1% keratin, 1% microsphere keratin for 20 days. Then the skin was collected and RNA was extracted from thetreatd skin as explained in the following section. The microarray was conducted for two biological replicates

overall_design: Expression data from skin treated with Minoxdil, Keratin and microsphere keratin in vivo


title: LncRNA and mRNA profiles of human milk-derived exosomes

city: Nanjing

first: Xiangyun

last: Yan

address: 123rd Tian Fei Xiang, Mo Chou Road, Nanjing 210004

institute: Women’s Hospital of Nanjing Medical University,  Nanjing Maternity and Child Health Care Hospital

summary: To further explore the underlying mechanisms of the protection functions of human milk exosmes, high throughput sequencings were used to identify differentially expressed lncRNA and mRNA profiles between human milk exosomes form term human breast milk (Term-Exos) and preterm human breast milk (Pre-Exos).

overall_design: Comparative  expression profiling analysis of differentially expressed lncRNA and mRNA between Term-Exos and Pre-Exos.

first: Linjie


title: The clock protein FREQUENCY (BcFRQ1) in Botrytis cinerea is required for normal mitochondrial function and has an extra-circadian role in  nitrogen metabolism

city: Valdivia

first: Javier

last: Canales

state: Los Ríos

address: Campus Isla Teja s/n

department: Instituto de Bioquimica y Microbiologia

country: Chile

institute: Universidad Austral de Chile

summary: A functional circadian clock was previously characterized in Botrytis cinerea and demonstrated the crucial role of BcFRQ, the ortholog of core clock component FREQUENCY from Neurospora crassa. It was previously shown that the corresponding knockout mutant Δbcfrq displayed an abnormal developmental phenotype (always-sclerotia) when grown on potato dextrose agar. In the present study, we demonstrate that this phenotype can be reversed back to macroconidia production by adding primary nitrogen sources, suggesting an extra-circadian role for BcFRQ in nitrogen metabolism. We performed an RNAseq study of wildtype and knockout mutant Δbcfrq under varying nutritional and light conditions, to identify the genes involved in 1) perturbed nitrogen metabolism in the mutant Δbcfrq and 2) additional extra-circadian functions of BcFRQ.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Botrytis cinerea strains (B05.10 and DeltaBcFRQ1) on CM media without nitrogen sources and complemented with Glutamine 0.1M as a primary source of Nitrogen. Samples were treated with constant light (LL), constant darkness (DD) or a light pulse (LP, 4 hours) and harvested at 48 hours.

first: Aldo

last: Seguel

first: Rebecca

last: Spanner

first: Consuelo

last: Olivares-Yañez

first: Marlene

last: Henriquez-Urrutia

first: Rodrigo

last: Pérez-Lara

first: Hanna

last: Müller-Esparza

first: Luis

middle: F

last: Larrondo


title: Adenosine signaling in T cell activation favors development of IL-17 positive cells with suppressive properties

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary:
It is assumed that the anti-inflammatory nucleoside adenosine can shape immune responses by shifting the Treg/Th17 balance in favor of Tregs. This assumption is based on in vivo and vitro studies mostly performed in murine models and warrants confirmation in human models.
In the study underlying these microarray data, we demonstrate that the pan-adenosine agonist 5'-N-ethylcarboxamidoadenosine (NECA) skews human CD3+ T cell responses towards non-inflammatory Th17 cells. We used microarrays to confirm transcriptome changes consistent with genetic signatures of non-pathogenic Th17 cells and to explore relevant metabolic pathways potentially contributing to this development.

overall_design: CD3+ T cells collected from healthy human donors (n= 3) were stimulated with anti-CD3/anti-CD28-streptamer premix (iba Lifesciences, Göttingen) and cultured with (positive) and without (negative) the addition of 50 uM NECA for three days. Cells were then harvested and prepared for RNA extraction and hybridization on Affymetrix microarrays. Cells cultured without NECA (negative) served as reference samples.

first: Lisa

last: Leikeim

first: Hui

last: Li

first: Jan

last: Leipe

first: Bernhard

last: Krämer

first: Benito

last: Yard

first: Anna-Isabelle

last: Kälsch


title: The transcriptomic landscape in the hypothalamus, brown adipose tissue and liver of chow- and AIN93G-fed mice before and after influenza virus infection

city: Darlington

first: Tracy

last: Chew

state: NSW

address: Merewether Building (H04) City Rd & Butlin Ave

department: Sydney Informatics Hub

country: Australia

institute: University of Sydney

summary: AIN93G-fed mice display increased mortality to influenza, which is associated with an inability to restore physiological homeostasis. To investigate the underlying mechanisms of the heightened susceptibility, we performed RNA-seq in organs critical for energy metabolism during IAV infection in chow- and AIN93G-fed mice.

overall_design: Female C57BL6 mice were fed on chow or AIN93G for 3 weeks ad libitum. Some were left uninfected, others were infected with influenza A virus. The hypothalamus, brown adipose tissue and liver were collected in uninfected and day 7 infected mice in both diet groups.

first: Carl

middle: G

last: Feng

first: Taylor

last: Cootes


title: Structure of Escherichia coli heat shock protein Hsp15 in complex with ribosomal 50S sununits bearing peptidyl-tRNA

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

institute: Universitaet Hamburg

summary: In Escherichia coli, the heat shock protein 15 (Hsp15) is part of the cellular response to elevated temperature. Hsp15 interacts with peptidyl-tRNA-50S complexes that arise upon dissociation of   translating 70S ribosomes, and is proposed to facilitate their rescue and recycling. A previous structure  of E. coli Hsp15 in complex with peptidyl-tRNA-50S complex reported a binding site located at the  central protuberance of the 50S subunit. By contrast, recent structures of RqcP, the Hsp15 homolog in  Bacillus subtilis, in complex with peptidyl-tRNA-50S complexes have revealed a distinct site positioned  between the anticodon-stem-loop (ASL) of the P-site tRNA and H69 of the 23S rRNA. Here we  demonstrate that exposure of E. coli cells to heat shock leads to dissociation of 70S ribosomes and  accumulation of 50S subunits, thus identifying a natural substrate for Hsp15 binding. Additionally, we  have determined a cryo-EM reconstruction of the Hsp15-50S-peptidyl-tRNA complex isolated from  heat shocked E. coli cells, revealing that Hsp15 binds to the 50S-peptidyl-tRNA complex analogously to  its B. subtilis homolog RqcP. Collectively, our findings support a model where Hsp15 promotes access  to the A-site for putative rescue factors to release the aberrant nascent polypeptide chain.

overall_design: E. coli cell lysate and Hsp15-bound (i.e. immunopreciptated, Hsp15-IP) tRNAs used for tRNA microarrays to measure tRNA abundance - 4 biological replicates in total; 3 - Hsp15-IP and 1 - total tRNA (lysate)

first: Haaris

last: Safdari

first: Christine

last: Polte

first: Daniel

last: Wilson


title: Effect of depletion of OsSPT5-1 on gene expression in shoot and root tissues during vegetative growth

city: nanjing

first: Jiajun

last: Liu

address: Weigang no.1, Xuanwu District, Nanjing City, Jiangsu Province

institute: Nanjing Agricultural University

summary: To explore the molecular mechanisms of shoot and root development mediated by OsSPT5-1, we established osspt5-1#12 mutant line, and then examined the gene expression profiles in vegetative shoot and root tissues of WT and osspt5-1#12.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Nipponbare (WT) and osspt5-1#12 mutant line.

first: Wanrong

last: Jie

first: Xi'an

last: Shi

first: Chengqiang

last: Ding


title: Effect of P7C3-A20 treatment on gene expression after intracerebral hemorrhage injury

city: Xi’an

first: Yang

last: Wu

state: Shaanxi

address: 569 Xinsi Road

department: Department of Neurosurgery

institute: Tangdu Hospital, Air Force Medical University,

summary: To investigate the effect of P7C3-A20 on gene expression after intracerebral hemorrhage injury, we employed RNA sequencing (RNA-seq) to profile the mRNA expression ensuing P7C3-A20 treatment after ICH. Different gene distribution could be clearly seen on the volcano plot between diferent comparisions among Sham, ICH, and ICH+P7C3-A20 group. Finally, we showed that 1047 shared genes overlapping between those differentially expressed genes, which was reversed by P7C3-A20 treatment

overall_design: Experimental mice were randomly and equally divided into three groups: sham group, ICH group, ICH + P7C3-A20 group. At 3 days  after diferent treatments,  3 mice were randomly selected from each group and used to perform RNA sequencing.

first: Xun

first: Qing

last: Hu

first: Guo

last: Gao


title: E-cadherin expression distinguishes mouse from human hematopoiesis in the basophil and erythroid lineages

city: Amsterdam

first: micha

last: nethe

state: State

address: plesmanlaan 125

country: Netherlands

institute: Sanquin Bloedvoorziening

summary: E-cadherin is a key regulator of epithelial cell-cell adhesion, which loss accelerates tumor growth and invasion. Aside epithelia, E-cadherin is also expressed in hematopoietic cells. The function of hematopoietic E-cadherin is however mostly elusive. In this study, we validated mouse models for functional investigation of hematopoietic E-cadherin in human hematopoiesis. We generated a hematopoietic specific E-cadherin knockout mouse model. In mice, hematopoietic E-cadherin is predominantly expressed within the basophil lineage, which expression is dispensable for the generation of basophils. Remarkably, E-cadherin mRNA or protein were not detected in human basophils. In contrast, human hematopoietic E-cadherin marks the erythroid lineage. E-cadherin expression in hematopoiesis thereby revealed striking evolutionary differences within the basophil and erythroid cell lineage between human and mouse. This is remarkable as E-cadherin expression in epithelia is highly conserved among vertebrates including human and mouse. Our study therefore revealed that the mouse does not represent a suitable model to study the function of E-cadherin in human hematopoiesis. Mouse models can be used to define the role of E-cadherin in basophils, which regulation however may not be conserved in human basophils. Overall, our study underscores the need to develop alternative means to study the role of E-cadherin in human erythropoiesis.

overall_design: E-cadherin+;cKIT+ and Ecadherin+;cKIT- isolated from mouse (FVB) bone marrow were sorted and used at a 2x single cell suspension at final conc. 1000 cells/µl in 1xPBS containing 0.04% weight/volume BSA (400 µg/ml). Cells were loaded into a 10X Genomics_Chromium_Controller for capture and barcoding following the 10X Genomics Protocol (Chromium Single Cell 3’ Reagent Kits v3, CG000183 Rev A), as described by the manufacturer (10X Genomics).

first: Rosa

middle: A

last: Krimpenfort

first: Felix

last: Behr

first: Marja

last: Nieuwland

first: Iris

last: de Rink

first: Ron

last: Kerkhoven

first: Marieke

last: Von Lindern

first: Micha

last: Nethe


title: A Parathyroid Hormone/Salt-Inducible Kinase Signaling Axis Controls Renal Vitamin D Activation and Organismal Calcium Homeostasis

city: Cambridge

first: Anna

last: Greka

address: 415 Main St

department: Kidney Disease Initiative

institute: Broad Institute of MIT and Harvard

summary:
The underling mechanism used by PTH to promote 1,25-vitamin D synthesis remains unknown. Here, we demonstrate that Salt Inducible Kinases (SIK) inhibitors drive renal 1,25-vitamin D production, as PTH inhibits SIK cellular activity by cAMP-dependent PKA phosphorylation.
Although there are some evidence that PTH increases Cyp27b1 in proximal tubule epithelial cells, this has not been explored/confirmed using next generation sequencing. Thus, we are interested in identifying cell populations that are responsible for PTH- or SIK-inhibition induced Cyp27b1 increase.

overall_design: 8 week old C57BL6 male mice were treated with a single IP injection of either the vehicle, PTH (1-34) or SK-124 (n=3 per treatment group). After euthanasia, kidneys were immediately prepared for single cell suspensions.

first: Sung-Hee

last: Yoon

first: Carlos

last: Arevalo

first: Marc

middle: N

last: Wein


title: Early establishment of neuronal transcriptome signatures is critical for nervous system differentiation

city: Freiburg

first: Valérie

last: Hilgers

address: Stübeweg 51

institute: MPI of Immunobiology and Epigenetics

summary: Cell-type-specific gene regulatory programs are crucial for cell differentiation and function. In animal neurons, the highly conserved ELAV/Hu family of proteins promotes alternative splicing and alternative polyadenylation of mRNA precursors to create unique neuronal transcript isoforms. Here, we show in Drosophila that the ELAV-mediated establishment of neuron-specific mRNA isoforms at the onset of neuronal differentiation constitutes a developmental bottleneck. While ELAV loss during a critical developmental time window is lethal and cannot be rescued later by the activation of the ELAV-like paralogue FNE, loss of ELAV function outside of that window results in neurological defects of differing nature and degree. FNE can effectively perform all molecular functions of ELAV, and, when activated early enough, fully rescue neuronal development. Our findings demonstrate the essential role of robust ELAV activity and intact neuronal signatures in the differentiation and function of the nervous system.

overall_design: mRNA-seq in Drosophila embyros and adults in different genotypes and stages of development. Three (adults) or four (embryos) replicates containing each 12-15 individuals were sequenced.

first: Judit

last: Carrasco

first: Fernando

last: Mateos


title: Glucocorticoids Unmask Silent Non-Coding Genetic Risk Variants for Common Diseases [STARR-seq]

city: Rochester

first: Thanh Thanh

last: Nguyen

address: 200 1st St. SW

institute: Mayo Clinic

summary: 30 B-lymphoblastoid cell lines (LCLs) with genome-wide genotype data were treated with hydrocortisone (GR agonist) and CORT108297 (GR modulator), followed by RNA-seq to identify PGx-eQTLs. We then integrated GR chromatin immunoprecipitation-sequencing (ChIP-seq) to characterize the epigenetic function of PGx-eQTLs that interfere with GR response elements. We also applied a high-throughput enhancer assay (STARR-seq) using PGx-eQTL loci DNA sequences to “scan” for drug-dependent SNPs.

overall_design: STARR-seq of targeted loci before and after hydrocortisone (GR agonist) and CORT108297 (GR modulator) treatment

middle: L

first: Huanyao

first: Duan

last: Liu

first: Lingxin

last: Zhang

first: Liewei

last: Wang

first: Richard

last: Weinshilboum


title: Cell-specific Studies Through Novel Mouse Model Reveal the Transcriptomic Response of Retinal Müller Glia to Acute and Chronic Stress [Aging]

city: Oklahoma City

first: Michael

last: Stout

state: OK

address: 825 N.E. 13th Street

department: Aging and Metabolism

institute: Oklahoma Medical Research Foundation

summary: Epigenetic regulation of the genome through DNA modifications, mainly methylcytosine (mC) and hydroxymethylcytosine (hmC), alters DNA accessibility, genomic organization and gene expression and is thought to be altered during neurodegenerative diseases, such as  age-related macular degeneration (AMD). Analysis of retina epigenetic and transcriptomic signatures at the cell-type specific level is crucial to understanding the pathophysiology of retinal degeneration. We have discovered that Aldh1l1 is specifically expressed in the major macroglia of the retina, the Müller glia, and, unlike the brain, is not expressed in retinal astrocytes. This allows a novel model to study paired epigenetic and transcriptomic signatures in Müller glia using Nuclear Tagging and Translating Ribosome Affinity Purification (NuTRAP) for temporally controlled labeling and isolation of Müller glial DNA and RNA. As validated through a variety of approaches, the Aldh1l1cre/ERT2-NuTRAP model provides Müller glia specific translatome and epigenome profiles. Application of this approach to models of acute injury (optic nerve crush) and chronic stress (aging) uncovered common Müller glia-specific transcriptome changes in inflammatory pathways, as well as differential signatures for each stimulus. The expression of components of the IL1b signalling axis, complement system, and markers of gliosis was enhanced in Müller glia in response to optic nerve crush but not in response to aging. The expression of components of the purinergic receptor and focal adhesion signalling pathways changed uniquely in response to aging but not with optic nerve crush. The Aldh1l1cre/ERT2-NuTRAP model allows focusing molecular analyses to a single, minority cell type within the retina, providing more substantial effect sizes than whole tissue analyses. The NuTRAP model, nucleic acid isolation, and validation approaches presented here can be applied to any retina cell type for which a cell type-specific cre is available.

overall_design: Mouse retinal RNA from Muller glia in young (4 mo.) and old mice (24 mo.) (n = 7)

first: Ana

last: Chucair-Elliott

first: Sarah

last: Ocanas

last: Van Der Veldt

first: Kevin

last: Pham

first: Ashley

last: Cheyney

first: David

last: Stanford

first: Jami

last: Gurley

middle: H

last: Elliott

first: Willard

last: Freeman


title: Characterizing microglial gene expression in a model of chronic-relapsing EAE

city: Groningen

first: Bart

last: Eggen

state: Groningen

address: Antonius Deusinglaan 1

department: Department of Biomedical Sciences

institute: UMCG Groningen

summary: Multiple sclerosis (MS) is the most common inflammatory, demyelinating and neurodegenerative disease of the central nervous system in young adults. Chronic-relapsing experimental autoimmune encephalomyelitis (crEAE) in Biozzi ABH mice is an experimental model of MS. This crEAE model is characterized by an acute phase with severe neurological disability, followed by remission of disease, relapse of neurological disease and remission that eventually results in a chronic progressive phase that mimics the secondary progressive phase (SPEAE) of MS. In both MS and the SPEAE  the role of microglia is poorly defined. We used the crEAE model to characterize microglia in the different phases of crEAE phases using morphometric and RNA sequencing analyses. At the initial, acute inflammation phase, microglia acquired a pro-inflammatory phenotype. At remission phase, expression of standard immune activation genes was decreased while expression of genes associated with lipid metabolism and wound healing was increased. Chronic phase microglia partially regain inflammatory gene sets and increase expression of genes associated with proliferation. Together, the data presented here indicates that microglia obtain different features at different stages of crEAE and a particularly mixed phenotype in the chronic stage. Understanding the properties of microglia that are present at the chronic phase of EAE may help understand the role of microglia in progressive neurological disease to better aid the development of therapies for secondary progressive MS.

overall_design: Microglia were sorted from the spinal cord by FACS-gating CD11b-postive, CD45-intermediate, and Ly-6C-negative cell populations. RNA-sequencing was performed for microglia from 3 control mice, 3 crEAE mice in acute phase, 3 crEAE mice in remission phase and 3 crEAE mice in chronic phase.

first: Ilia

last: Vainchtein

first: Astrid

last: Alsema

first: Marissa

last: Dubbelaar

first: Corien

last: Grit

first: Jonathan

last: Vinet

last: Al-Izki

first: Giuseppe

last: Biagini

first: Nieske

last: Brouwer

first: Sandra

last: Amor

last: Baker

middle: J

first: Erik

last: Boddeke

first: Susanne

last: Kooistra


title: Effects of itaconate on gene expression in mouse CD8 T cells

city: Bad Nauheim

first: Lei

last: Gu

state: MASSACHUSETTS

address: parkstreet 1

institute: Max Planck Institute for heart and lung research

summary: The tumor microenvironment possesses multiple overlapping mechanisms that suppress anti-tumor immunity. Itaconate is a metabolite produced from the Krebs cycle intermediate cis-aconitate by the activity of immune-responsive gene 1 (IRG1). While it is known to be immune modulatory, the role of itaconate in anti-tumor immunity is unclear. Here, we demonstrate that myeloid-derived suppressor cells (MDSCs) secreted itaconate that can be taken up by CD8+ T cells and suppress their proliferation, cytokine production, and cytolytic activity. Metabolite profiling, stable-isotope tracing and metabolite supplementation studies indicated that itaconate suppressed biosynthesis of aspartate and serine/glycine in CD8+ T cells to attenuate their proliferation. Moreover, stromal deletion of IRG1 in mice bearing allografted tumors resulted in decreased tumor growth, inhibited the immune suppressive activities of MDSCs, reduced levels of itaconate in tumors, promoted anti-tumor immunity of CD8+ T cells, and enhanced the anti-tumor activity of anti-PD-1 antibody treatment. Importantly, we found a significant negative correlation between IRG1 expression and response to PD-1 immune checkpoint blockade in melanoma patients. Our findings not only reveal a previously unknown role of itaconate as an immune checkpoint metabolite secreted from MDSCs to suppress CD8+ T cells, but also establish IRG1 as a novel myeloid-selective target in immunometabolism to promote anti-tumor immunity and enhance the efficacy of immune checkpoint protein blockade.

overall_design: Mouse CD8+ T cells were treated with 5 mM itaconate or NaCl, as a control, for 48 hours.

first: Zhao

last: Hongyun

first: Gu

last: Lei

first: Zheng

last: Bin


title: MEK inhibition enhances presentation of targetable MHC-I tumor antigens in mutant melanomas

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

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

overall_design: Refer to individual Series


title: Transcriptome profiling of hESC-derived endoderm progenitors by single-cell RNA-seq

city: Copenhagen

first: Josh

last: Brickman

address: 3B Blegdamsvej

department: reNEW

country: Denmark

institute: Copenhagen University

summary: In this study, we characterised transcriptomes of hESC-derived transient anterior definitive endoderm (ADE) and expanding ventral foregut (VFG) culture by single-cell sequencing. We also examined the effect of BMP4 withdrawal and FGF2 stimulation in the VFG culture.

overall_design: This study contains 4 conditions and 8 samples of human embryonic stem cells differentiated into definitive endoderm and ventral foregut progenitors under different conditions.  The single cells were specifically sorted for CD117 and/or CXCR4 protein.

first: Yan

last: Wong

first: Martin

last: Proks

first: Michaela

last: Rothová

first: Joshua


title: Cell-specific Studies Through Novel Mouse Model Reveal the Transcriptomic Response of Retinal Müller Glia to Acute and Chronic Stress

first: Michael

last: Stout


title: Epigenetic clocks are not accelerated in COVID-19 patients

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

type: Methylation profiling by genome tiling array

summary: In this study, we used blood samples of nine patients with severe SARS-CoV-2 infection either with or without acute respiratory distress syndrome (ARDS) and analyzed them on the Illumina EPIC methylation microarray.

overall_design: Bisulfite converted DNA from whole blood of nine COVID-19 patients was analyzed with Illumina EPIC BeadChip microarrays.

first: Julia

last: Franzen

first: Selina

last: Nüchtern

first: Vithurithra

last: Tharmapalan

first: Margherita

last: Vieri

first: Miloš

last: Nikolić

first: Yang

last: Han

first: Paul

last: Balfanz

first: Nikolaus

last: Marx

last: Dreher

first: Tim

last: Brümmendorf

first: Edgar

last: Dahl

first: Fabian

last: Beier


title: Next Generation Sequencing Facilitates Quantitative Analysis of watermelon fruit Whole Genome BS-Seq

city: Beijing

first: Yi

last: Zuo

address: No. 50 Road Zhanghua

institute: Beijing Academy of Agriculture and Forestry Science

summary: Analysis of genome DNA methylation level

overall_design: WGBS-Seq profiles of six stages in watermelon fruit (97103) were generated by deep sequencing, in triplicate, using Illumina NovaSeq6000 (Citrullus lanatus).

first: Yong

last: Xu


title: Effect of Hypoxia Preconditioning on the Regenerative Capacity of Adipose Tissue-Derived Mesenchymal Stem Cells in an Experimental Model of Atherosclerotic Renal Artery Stenosis

first: Naba

last: Farooqui

state: MN

address: 200 1st St SW

summary: DNA hydroxymethylation reflects gene activation. Hypoxia preconditioning can alter stem cell functioning by affecting gene activation. We wanted to assess the gene groups which would be activated and suppresed with hypoxia preconditioning to investigate and functionally correlate whether this strategy can enhance the regenerative capacity of adipose derived mesenchymal stem cells, which is a promising upcoming therapy for tissue regeneration especially for organs with a fixed tissue reserve such as the kidneys.

overall_design: Comparison of DNA 5hmC residues in Mesenchymal Stem Cells cultured under different conditions

first: Arjunmohan

last: Mohan

first: Busra

last: Isik

middle: B

last: Goksu

first: Roman

last: Thaler

first: Xiang

middle: Y

last: Zhu

first: James

last: Krier

first: Ishran

last: Saadiq

first: Christopher

last: Ferguson

first: Kyra

last: Jordan

first: Hui

last: Tang

first: Stephen

middle: C

last: Textor

first: LaTonya

last: Hickson

first: Andre

last: van Wijnen

first: Alfonso

last: Eirin

first: Lilach

middle: O

last: Lerman

first: Sandra

last: Herrmann


first: Josh

middle: M

last: Brickman

summary: Transcriptome profiling of hESC-derived endoderm progenitors by RNA-seq. RNA-seq analysis during the stepwise progression of hESC toward the pancreatic progenitors, at five defined stages of differentiation and expansion: hESC, ADE, VFG.p3, VFG.p6. PE.

first: Yan

last: Wong

first: Joshua


title: Next Generation Sequencing Facilitates Quantitative Analysis of watermelon fruit Transcriptomes

first: Yi

last: Zuo

summary: Analysis of gene expression level. The hypothesis tested in the present study was that 5-azacytidine affects fruit ripening.

overall_design: mRNA profiles of six stages in watermelon fruit (97103) were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500 ( Citrullus lanatus).

first: Yong

last: Xu


title: Whole blood RNA-seq of pediatric cases of natural Dengue infection

city: Chicago

last: Che

state: Illinois

address: 303 E Superior St

institute: Northwestern University

summary: The primary aim of this study was to characterize the transcriptomic changes between the acute and convalescent phase of natural Dengue infections in pediatric patients as observed in peripheral blood samples.

overall_design: 68 pediatric cases of natural Chikungunya infection were sampled for whole blood at two timepoints (1-5 and 14-30d post symptom onset). Two technical replicates were sequenced per blood sample.

first: Eun-Young

last: Kim

first: Daniela

last: Michlmayr

first: Eva

last: Harris

first: Steven

last: Wolinsky


title: MEK inhibition enhances presentation of targetable MHC-I tumor antigens in mutant melanomas [RNA-seq]

first: Charles

last: Whittaker

summary: Combining multiple therapeutic strategies in NRAS/BRAF mutant melanoma – namely MEK/BRAF kinase inhibitors, immune checkpoint inhibitors, and targeted immunotherapies – may offer an improved survival benefit by overcoming limitations associated with any individual therapy. Still, optimal combination, order, and timing of administration remains under investigation. Here, we measure how MEK inhibition alters anti-tumor immunity by utilizing quantitative immunopeptidomics to profile changes the peptide MHC (pMHC) repertoire. These data reveal a collection of tumor antigens whose presentation levels are selectively augmented following therapy, including several epitopes present at over 1000 copies-per-cell. We leveraged the tunable abundance of MEKi-modulated antigens by targeting 4 epitopes with pMHC-specific T cell engagers and antibody drug conjugates, enhancing cell killing in tumor cells following MEK inhibition. These results highlight drug treatment as a means to enhance immunotherapy efficacy by targeting specific upregulated pMHCs and provide a methodological framework for identifying, quantifying, and therapeutically targeting additional epitopes of interest.

overall_design: 3 replicates each of 100 nM binimetinib-treated and 1 uM binimetinib-treated SKMEL5 cells. DMSO control samples are available in submission GSE144373.

first: Lauren

middle: E

last: Stopfer

last: Mesfin

first: James

last: Wells

first: Forest

last: White

first: Nicholas

last: Rettko

first: Owen

last: Leddy

first: Eric

last: Brown

first: Shannon

last: Winski

first: Bryan

last: Bryson


title: Metabolic pathways that are essential for the progression of TNBC in vivo

status: Public on Nov 14 2022

city: Nanjing

first: Jie

last: Dong

address: Hankou road 22

institute: Nanjing University

summary: To identify metabolic pathways that are essential for the progression of TNBC in vivo

overall_design: 4T1 breast cancer cells were engineered to express synergistic activation mediators. Then these cells were transfected with an sgRNA library containing 69,225 sgRNAs targeting 23,439 protein-coding genes and 491 control sgRNAs.These tumor cells were transplanted into mice. The tumors on days 5 and 10 were collected for sgRNA sequencing.

first: Lingkai

last: Kong


title: A human bone marrow organoid for disease modelling and drug screening in blood cancers

city: Birmingham

first: Abdullah

middle: Obaid

last: Khan

state: West Midlands

address: MDS, Wolfson Drive

department: Institute of Cardiovascular Science

country: United Kingdom

institute: University of Birmingham

summary: Here we upload data from the 10x analysis of 2 types of human stem cell derived bone marrow organoids.

overall_design: Sequencing and analysis of 2 cytokine formulations used to generate human bone marrow organoids.

first: Michela

last: Colombo

first: Guanlin

last: Wang

first: Bethan

last: Psaila


title: single cell RNA sequencing of intra- and extra- articular ligaments in mice

city: Suita

first: Takashi

last: Shimbo

state: Osaka

address: 2-2 Yamadaoka

institute: Osaka university

summary: Knee ligaments, the anterior cruciate ligament (ACL) and medial collateral ligament (MCL),  have unique functions but distinct regeneration capacities. However, the landscape of cellular heterogeneity in ligaments remains unclear. Here we profile the transcriptional signatures of ACL and MCL cells using single-cell RNA-sequencing. These ligaments consist of three fibroblast types that express Col22a1, Col12a1, or Col14a1 but have distinct localizations in the tissue. In addition, we find substantial heterogeneity in Col12a1 and Col14a1 positive cell clusters when comparing the ACL and MCL. Furthermore, we identified aging related changes in both cell composition and gene expression in ligaments.

overall_design: mRNA profiles of knee joint ligaments from 10 and 100 week-old mice

last: shimbo


title: Immune cell profiling of preeclamptic pregnant and postpartum women by single-cell RNA sequencing

first: Juntao

last: Liu

address: No. 1, Shuaifu Garden, Dongcheng District

institute: Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences

summary: Preeclampsia (PE) is characterized by sustained hypertension and proteinuria at a gestational age of 20 weeks or more. Immune system alterations are associated with the origin and the pathophysiology of preeclampsia, however, little is known about the landscape and heterogeneity of maternal immune system at the single-cell level. In this study, we performed single-cell RNA sequencing of 80,429 cells in PE patients and health controls, including T cells, B cells, natural killer (NK) cells, myeloid cells in peripheral blood mononuclear cells to characterize the immune cell subgroups at the pregnant and postpartum stages of PE. Our work showed that there was excessive activation of B cells, monocytes and NK cells in PE patients at the pregnant stage. Additionally, lower immune response activation was noticed in CD4+ and CD8+ T cells in PEs, especially the low-activation of memory T cells at the pregnant and postpartum stages. Moreover, there was a higher activation of B cells in pregnancy persisted postpartum in PEs, together with lower activation of memory T cells. These indicated their persistent effects on PE and its recurrence risks.

overall_design: Single-cell RNA sequencing of 80,429 cells in PE patients and health controls, including T cells, B cells, natural killer (NK) cells, myeloid cells in peripheral blood mononuclear cells to characterize the immune cell subgroups at the pregnant and postpartum stages of PE.

first: Jing

last: Hu

first: Qi

last: Guo

first: Congcong

first: Qian

last: Yu

first: Yuan

last: Ren

first: Yueni

last: Wu

first: Yuezhen

last: Li


title: Genome-wide analysis of gene expression in brain of Neil3-deficient Alzheimer's disease mouse model

city: Trondheim

first: Katja

last: Scheffler

address: Edvard Griegs Gate 8

department: Department of Neuromedicine and Movement Sciences

country: Norway

institute: Norwegian University of Science and Technology

summary: Oxidative stress generating DNA damage has been shown to be a key characteristic in Alzheimer’s disease (AD). However, how it affects the pathogenesis of AD is not yet fully understood. NEIL3 is a DNA glycosylase initiating oxidative DNA repair and with a distinct expression pattern in proliferating cells. In brain, its function has been linked to hippocampal-dependent memory and to induction of neurogenesis after stroke and in prion disease. Here, we generated a novel AD mouse model deficient for Neil3 to study the impact of impaired oxidative base lesion repair on the pathogenesis of AD. Our results demonstrate an age-dependent decrease in amyloid-β (Aβ) plaque deposition in female NEIL3-deficient AD mice. Moreover, male NEIL3-deficient AD mice show reduced neural stem cell proliferation in the adult hippocampus and impaired working memory. These effects seem to be independent of DNA repair as both sexes show increased level of oxidative base lesions in the hippocampus upon loss of NEIL3.  Thus, our findings suggest a sex-dependent role of NEIL3 in the progression of AD by altering cerebral Aβ accumulation and promoting adult hippocampal neurogenesis to maintain cognitive function.

overall_design: Examination of transcriptome profiles of brain from APP/PS1 and APP/PS1 Neil3-/- C57BL/6 mice at 1 month and 6 months by RNA sequencing using Illumina Hiseq 4000

first: Milena

last: Egiazarian

first: Silje

last: Stømstad

first: Teri

last: Sakshaug

first: Ana

last: Nescolarde

first: Nicole

last: Bethge

first: Magnar

last: Bjørås


title: Gene expression profiles of primary myocardial cells treated with LPS and transfected siMETTL3 in rats

city: Shanghai

first: Cheng wu

last: Gong

address: No. 639, Shanghai Manufacturing Bureau Road

department: Department of Thoracic Surgery

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

summary: Methyltransferase-like 3 (METTL3) is the m6A methyltransferase which binds to METTL14 and wilms tumour 1-associated protein (WTAP) to form a complex catalyzing the m6A modification, the most abundant epitranscriptomic modification in eukaryotic mRNAs. And it has been demonstrated that m6A methylation mediated by METTL3 to be essential for inflammatory responses. To identify the messenger RNA (mRNA) profile in the primary myocardial cells that were treated with lipopolysaccharide (LPS) and/or small interference siMETTL3, six groups of primary myocardial cells were used for analysis.

overall_design: All primary myocardial cells were derived from the same initial isolate (pooled from multiple rats). Primary cardiomyocytes were treated with small interference siMETTL3 or siNC for 24 h and then treated with LPS for 6 h.Three replicates of each condition were used for RNA extraction, RNAseq library preparation, and paired-end Illumina sequencing.

first: Chengwu

first: Jichun


title: Next Generation Sequencing Facilitates Quantitative Analysis of watermelon fruit small RNA expression

first: Yi

last: Zuo

type: Non-coding RNA profiling by high throughput sequencing

summary: Analysis of small RNA expression level.

overall_design: Small RNA profiles of six stages in watermelon fruit (97103) were generated by deep sequencing, in triplicate, using Illumina  ( Citrullus lanatus).

first: Yong

last: Xu


title: T cells and monocyte-derived myeloid cells mediate immunotherapy-related hepatitis in a mouse model

city: San Diego

first: Richard

last: Virgen-Slane

state: CA

address: 0777 Science Center Drive, CB4-2131, Pfizer La Jolla

department: Global Computational Safety Science, DSRD

institute: Pfizer

summary: Immune checkpoint inhibitors (ICIs) are associated with immune-related adverse events (irAEs) which are more severe when ICIs are used in combination. A mouse model was developed to elucidate the molecular mechanisms of immune-related hepatitis, one of the common irAEs associated with ICIs. Molecular profiling by single cell RNA sequencing was performed on Pdcd1-/- mice treated with anti-CTLA4 and/or the IDO1 inhibitor epacadostat or a 4-1BB agonistic antibody. ICI combination-induced hepatitis and 4-1BB agonist-mediated hepatitis share similar features yet maintain distinct immune signatures. Both were characterized by an expansion of activated T cells. Single-cell transcriptomics revealed that the hepatitis induced by combination ICIs is associated with a robust immune activation signature in all subtypes of T cells and T helper 1 skewing. Expression profiling revealed a central role for IFNγ and liver monocyte-derived macrophages in promoting a pro-inflammatory T-cell response to ICI combination and 4-1BB agonism.

overall_design: Anti-CTLA4 antibody or isotype control was administered weekly to Pdcd1-/- mice. The IDO1 inhibitor, epacadostat, or vehicle control was administered by oral gavage twice daily. Anti-(4-1BB) agonistic antibody was administered intraperitoneally to mice twice weekly. Liver CD45+ cells were enriched with the Miltenyi liver dissociation kit and cells were analyzed on the 10X genomics platform.

first: Heather

last: Llewellyn

first: Changhua

last: Ji


title: Single cell atlas of epithelial and stromal cell heterogeneity by lobe and strain in the mouse prostate

first: Mindy

middle: Kim

last: Graham

state: IL

address: 303 E. Superior Street Chicago

department: Urology

institute: Northwestern University Feinberg School of Medicine

summary: Evaluating the complex interplay of cell types in the tissue microenvironment is critical to understanding the origin and progression of diseases in the prostate and potential opportunities for intervention. Mouse models are an essential tool to investigate the molecular and cell-type-specific contributions of prostate disease at an organismal level. While there are well-documented differences in the extent, timing, and nature of disease development in various genetically engineered and exposure-based mouse models in different mouse strains and prostate lobes within each mouse strain, the underlying molecular phenotypic differences in cell types across mouse strains and prostate lobes are incompletely understood.

overall_design: In this study, we used single-cell RNA-sequencing (scRNA-seq) methods to assess the single-cell transcriptomes of 6-month-old mouse prostates from two commonly used mouse strains, FVB/NJ (N = 2) and C57BL/6J (N = 3). For each mouse, the lobes of the prostate were dissected (anterior, dorsal, lateral, and ventral), and individual scRNA-seq libraries were generated.

middle: K

first: Roshan

last: Chikarmane

first: Rulin

last: Wang

first: Srinivasan

last: Yegnasubramanian


title: Analysis of gene expression in EIF3F knockdown 22Rv1 prostate cancer cells

first: junhong

last: li

state: Shanghai

address: 801 Heqing Road, Minhang District

institute: Shanghai Fifth People's Hospital , Fudan University

summary: Total RNA was obtained from 22Rv1 cells with or without EIF3F interference to perform a High-throughput sequencing

overall_design: The prostate cancer cell line 22Rv1 expressing shRNA targeting EIF3F or a vector control. The gene transcript expression profiles were generated by deep sequencing.

first: Junhong

last: Li

first: Guowei

last: Shi


title: Sirtuin 3 is a common target of non-steroidal anti-inflammatory drugs to induce gastric cancer cell death and gastric mucosal injury.

city: Kolkata

first: Uday

last: Bandyopadhyay

state: WB

address: EN 80, Salt Lake, College More, EN Block, Sector V, Kolkata,

department: Division of Molecular Medicine

country: India

institute: Bose Institute

summary: Nonsteroidal anti-inflammatory drugs (NSAIDs), the quintessential medicines to treat pain and inflammatory conditions, induce cell death in human cancer cells, as repurposed anticancer agents, and in normal gastric mucosa, as a major side effect. The subcellular target/s of NSAIDs that leads to the cell death remained elusive so far. Here, by venturing transcriptomics followed by functional validation, we, for the first time, identified mitochondrial deacetylase Sirtuin 3 (Sirt3) as a non-canonical target of NSAIDs whose depletion induced the hyperacetylation of mitochondrial proteome, OGG1 depletion, mtDNA damage, electron transport chain defect associated mitochondrial dysfunction and finally cell death. Silencing of Sirt3 in AGS cells (a human gastric adenocarcinoma cell line) significantly aggravated NSAID-induced cytopathology. Whereas, honokiol mediated induction of Sirt3 corrected the NSAID-induced transcriptome alteration and gastropathy in rodent model. Together, the results identify Sirt3 as a common target used by NSAIDs to induce gastric carcinoma cell death and gastric mucosal injury.

overall_design: Gastric mucosal injury was developed by oral administration of typical NSAIDs including indomethacin (48 mg/kg), ibuprofen (400 mg/kg), diclofenac (75 mg/kg), aspirin (400 mg/kg) as required. Gastric injury was allowed to develop and after 4 hrs, the rats were subjected to terminal euthanasia followed by sacrifice and collection of mucosal tissue samples for transcriptome analysis and subsequent experiments. For HKL induced protection, rats were pre-treated with HKL (40 mg/kg), intraperitoneally, followed by oral administration of indomethacin after 30 minutes.


title: Identification of ethanolamine as a biomarker and therapeutic potential for diabetic retinopathy in glucose well-controlled diabetic patients

status: Public on Nov 13 2022

city: shanghai

first: Guangyi

last: Hu

state: China

address: Wujin Road 85

institute: Shanghaijaiotong University

summary:
Diabetic retinopathy (DR) is the leading cause of blindness in the working-age population, and there are no diagnostic biomarkers and intervention methods for DR developed from glucose well-controlled diabetic patients (GW-DR) to date. Here, we established a prospective cohort of 2126 diabetic Chinese adults (DM) including1134 subjects without ocular diseases at baseline. After 2-year follow-up, 42 participants (21 new-onset GW-DR and 21 matched control) with HbA1c persistently less than 7% were enrolled to profile the serum metabolic features of GW-DR through targeted metabolomics. Among different levels of metabolites, the lower level of ethanolamine with an AUC of 0.954 was significantly associated with early-stage GW-DR risk compared to HbA1c with a 0.506 AUC. Moreover, ethanolamine attenuated diabetic retinal inflammation in STZ-induced diabetic rats with inactivating microglia and DAG-PKC pathway remodeling. In conclusion, ethanolamine, as a potential metabolic biomarker for early diagnosis of GW-DR, may provide a biomarker-based treatment for DR prevention.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at two time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BV2 cells stimulated by hypoxia with or without 100μM ethanolamine and control

first: Kangjia

last: Lv


title: Effect of knockdown of Snai1 on gene expression of EndoFP during in a mouse model of pressure overload.

city: Guangzhou

first: Lu

last: Lu

address: No.12,Airport Road,Baiyun District

institute: Guangzhou University of Chinese Medicine

summary:
To investigate Snai1 in the regulation of EndoFP, we established injection of AAV containing the Snai1_KD plasmid in the mice.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 different sample 2 weeks after TAC.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Con ,TAC and its KD derivatives (shSnai1).

first: Yue


title: Transcriptomic profiling of macrophage induced breast cancer cells

city: Changsha

first: Mei

last: Yang

address: 139 Middle Renmin Road

institute: The Second Xiangya Hospital, Central South University

summary: To infestigate the effect of macrophage on breast cancer cells, we treated breast cancer cells with medium from either monocyte derived macrophages or breast cancer cell medium treated monocyte derived macrophages

overall_design:
MCF7 cells grown in dishes with medium from human monocyte derived macrophages(MDMs) or breast cancer cell MDA-MB-231medium treated monocyte derived macrophages (TAMs)

Funding Information:
Hunan Provincial Natural Science Foundation of China [Grant Number 2021JJ30971]

National Natural Science Foundation of China [Grant Number 81602445]

first: Meijun

last: Long


title: Laminin111-based defined culture promoting self-renewing human pluripotent stem cells exhibiting properties of early post-implantation epiblast cells [LN_hPSC_SC]

city: Jerusalem

first: Michal

last: Gropp

address: Hadassah Ein-Kerem

country: Israel

institute: Hadassah Medical Center

summary: In our study we sought to develop cultures highly enriched for self-renewing human pluripotent stem cells (hPSCs) with an early post-implantation phenotype, capturing the formative pluripotency phase in vitro. Our results demonstrate that hPSCs cultured on LN111 in defined conditions (LN-hPSCs) generate cultures highly enriched for genetically stable, self-renewing hPSCs exhibiting properties similar to the early-post implantation epiblast, including competence to give rise to the germ cell lineage. To analyze the global transcriptome of LN-hPSCs in comparison with conventional/primed and naive hPSCs, we performed RNA-seq of the three  hPSC lines cultured under LN, primed, and naïve conditions.

overall_design: Comparative gene expression profiling analysis of Single-cell RNA-seq (sc-RNA-seq) data for hPSC line HES-2 (ES02) (Reubinoff et al., 2000), cultured under LN and conventional/primed conditions.

first: Benjamin

last: Reubinoff


title: Tissue adaptation and clonal segregation of human memory T cells in barrier sites

city: New York

first: Peter

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

summary: T lymphocytes migrate to barrier sites after exposure to pathogen-derived antigens to provide localized immune defense and long-term surveillance. However, unique tissue adaptations of barrier T cells and the extent to which they participate in clonal networks remains unclear. In this study, we utilized our organ donor tissue resource to examine T cells in barrier sites (skin, lung, jejunum), their associated lymph nodes, other lymphoid tissues (spleen and bone marrow), and circulation. By integrating multiple single-cell protein and transcript profiling technologies, we demonstrate that human barrier sites contain site-adapted memory T cell populations, including tissue-resident memory T cells (TRM) that exhibit both shared barrier TRM signatures and tissue-specific residency profiles. Additionally, incorporating T cell receptor and RNA-sequencing analysis, we show that lung T cell clones form global networks with clones in lymphoid sites and circulation, and comprise widely disseminated clones of TEM/TEMRA subset that display distinct effector phenotypes; while T cells in skin and jejunum are predominantly TRM and participate primarily in localized clonal networks with tissue-associated lymph nodes but are largely compartmentalized.

overall_design: joint single-cell RNA/T cell receptor sequencing

first: Maya

last: Poon

first: Daniel

last: Caron

first: Zicheng

first: Yufeng

last: Shen

first: Donna

last: Farber


title: (2R,6R)-Hydroxynorketamine restores postsynaptic localization of AMPAR in the prelimbic cortex to provide sustained pain relief

city: 沙田

first: JIN

last: TINGTING

state: 沙田區

address: Prince of wales hospital

country: Hong Kong

institute: Chinese University of Hongkong

summary: To explore the molecular mechanism of R-HNK in the treatment of neuropathic pain

overall_design: Mice were divided into three groups and treated accordingly (n = 3 mice/group), namely Sham/Saline (Sham), SNI/Saline (SNI), and SNI/R-HNK (R-HNK). On the 14th day after surgery, PrL tissues were collected and perform RNA-seq

first: Xiaodong

last: LIU

first: Tingting

last: JIN