title: Single-cell RNA sequencing identifies Fgf23-expressing osteocytes

city: Tokyo

first: Ayako

last: Hanai

address: 3-6-6, Asahi-machi, Machida-shi

institute: Kyowa Kirin Co., Ltd.

summary: Fibroblast growth factor 23 (FGF23), a hormone, mainly produced by osteocytes, regulates phosphate and vitamin D metabolism. By contrast, 1,25-dihydroxyvitamin D3, the active form of vitamin D, has been shown to enhance FGF23 production. While it is likely that osteocytes are heterogenous in terms of gene expression profiles, specific subpopulations of Fgf23-expressing osteocytes have not been identified. Single-cell RNA sequencing (scRNA-seq) technology can characterize the transcriptome of an individual cell. Recently, scRNA-seq has been used for bone tissue analysis. However, owing to technical difficulties associated with isolation of osteocytes, studies using scRNA-seq analysis to characterize FGF23-producing osteocytes are lacking. In this study, we characterized osteocytes secreting FGF23 from murine femurs in response to calcitriol (1,25-dihydroxyvitamin D3) using scRNA-seq. We first detected Dmp1, Mepe, and Phex expression in murine osteocytes by in situ hybridization and used these as marker genes of osteocytes. After decalcification, enzyme digestion, and removal of CD45+ cells, femoral bone cells were subjected to scRNA-seq. We identified cell clusters containing osteocytes using marker gene expression. While Fgf23 expression was observed in some osteocytes isolated from femurs of calcitriol-injected mice, no Fgf23 expression was detected in untreated mice. In addition, the expression of several genes which are known to be changed after 1,25-dihydroxyvitamin D3 treatment such as Ccnd2, Fn1, Igfbp7, Pdgfa, and Timp1 was also affected by calcitriol treatment in Fgf23-expressing osteocytes, but not in those lacking Fgf23 expression, even after calcitriol administration. Furthermore, box-and-whisker plots indicated that Fgf23 expression was observed in osteocytes with higher expression levels of the Fam20c, Dmp1, and Phex genes, whose inactivating mutations have been shown to cause FGF23-related hypophosphatemic diseases. These results indicate that osteocytes are heterogeneous with respect to their responsiveness to 1,25-dihydroxyvitamin D3, and sensitivity to 1,25-dihydroxyvitamin D3 is one of the characteristics of osteocytes with Fgf23 expression. It is likely that there is a subpopulation of osteocytes expressing several genes, including Fgf23, involved in phosphate metabolism.

overall_design: Femoral cells of untreated or calcitriol-injected C57BL/6J mice were isolated by collagenase digestion and EGTA treatment and analyzed using scRNAseq.

last: Kawabata

first: Kenta

last: Nakajima

first: Kazuhiro

last: Masuda

first: Itaru

last: Urakawa

first: Yuji

last: Yamazaki

first: Seiji

last: Fukumoto


title: ERR2 and ERR3 promote the development of gamma motor neuron functional properties required for proprioceptive movement control

status: Public on Dec 16 2022

city: Tübingen

first: Vikas

last: Bansal

state: BW

address: Otfried Müller Strasse 23

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)-Tübingen

type: Expression profiling by high throughput sequencing

summary: The transcription factors ERR2 and ERR3 promote promote the development of functional properties in gamma motor neurons necessary for executing precise movements.

overall_design: Comparative transcriptome profiling by RNA sequencing of chick motor neurons forcedly expressing eGFP, Err2 or Dlk1.

first: Mudassar

middle: N

last: Khan

first: Stefan

last: Bonn

first: Till

last: Marquardt


title: DNA-Methylation Analysis as a Tool for Thymoma Classification

city: Heidelberg

first: Daniel

last: Schrimpf

address: Im Neuenheimer Feld 224

department: Neuropathology

institute: University Hospital Heidelberg, Intitute of Pathology

summary: Thymomas are malignant thymic epithelial tumors that are difficult to diagnose due to their rarity and complex diagnostic criteria. They represent a morphologically heterogeneous class of tumors mainly defined by “organo-typical” architectural features and cellular composition. The diagnosis of thymoma is burdened with a high inter-observer variability and with the problem that some type-specific morphological alterations are rather a continuum than clear-cut. Methylation pattern-based classification may help to increase diagnostic precision, particularly in borderline cases.

overall_design: retrospective study of archival FFPE tissues

first: Andreas

last: von Deimling

first: Timo

last: Gaiser


title: RNA-seq transcriptional profiling in the Fah-/- livers after transplantation and YC treatment

status: Public on Dec 17 2022

city: Shanghai

first: Meng

middle: meng

last: Jiang

address: number 3728, Jinke Road

country: China

institute: Shanghai Institute of Materia Medica

summary: The transplanted mature hepatocytes were found to dedifferentiate into hepatic progenitor cells (HPCs), which proliferate and then convert back to mature state at the completion of liver repopulation. The combination of two small molecules Y-27632 (Y, Rock inhibitor) and CHIR99021 (C, Wnt agonist) could convert mouse primary hepatocytes into HPCs, which could be passaged for more than 30 passages in vitro. Moreover, YC could stimulate the proliferation of transplanted hepatocytes in Fah-/- liver by promoting the conversion into HPCs. Netarsudil (N) and LY2090314 (L), two clinically used drugs which target the same pathways as YC, could also promote hepatocytes proliferation in vitro and in vivo, by facilitating HPC conversion.

overall_design: To further confirm that YC stimulated growth of transplanted hepatocytes via dedifferentiation, the global gene expression profiles in the livers were compared.

first: Xin

last: Xie

first: Mengmeng

first: Ren

last: Guo


title: Chromatin complex dependencies reveal novel targeting opportunities in leukemia [40k]

city: Cambridge

first: Fadi

middle: John

last: Najm

state: Massachusetts

address: 415 Main Street 6043

department: Epigenomics

country: USA

institute: Broad Institute

summary: Combinatorial CRISPRko screening data in leukemia cell lines

overall_design: Leukemia cell lines were transduced with lentivirus to deliver sgRNA pairs for pairwise gene knockout.

first: Bradley

middle: E

last: Bernstein

first: Chadi

middle: A

last: EL Farran

middle: J


title: Chromatin complex dependencies reveal novel targeting opportunities in leukemia [RNA-seq]

summary: Knockout of NuRD complex members in THP-1, Reh, and MV4-11 leukemia cell lines.

overall_design: Leukemia cell lines were treated with Cas9 and guides targeting MTA1, MTA2, MTA1 and MTA2, CHD4, or a safe harbor genomic site.

first: Samantha

last: Bevill


title: SFRP2 Overexpression Induces an Osteoblast-Like Phenotype in Prostate Cancer Cells

city: München

first: Elif

last: Akova Ölken

state: Baveria

address: Fraunhofer Str. 20

department: Department of Orthopaedics and Trauma Surgery

institute: Ludwig-Maximilians-University

summary: Abstract: Prostate cancer bone metastasis is still one of the most fatal cancer diagnosis for men. Survival of the circulating prostate tumor cells and their adaptation strategy to survive in the bone niche is the key point to determining metastasis in early cancer stages. The promoter of SFRP2, a WNT signaling regulator, is hypermethylated in many cancer types including prostate cancer. Moreover, SFRP2 can positively modulate osteogenic differentiation in vitro and in vivo. Here, we showed SFRP2 overexpression in the prostate cancer cell line PC3 induces an epithelial mesenchymal transition (EMT), increases the attachment, and modifies the transcriptome towards an osteoblast-like phenotype (osteomimicry) in a collagen 1‑dependent manner. Our data reflects a novel molecular mechanism how metastasizing prostate cancer cells might increase their chance to survive within bone tissue.

overall_design: Nunc-PC3, Nunc PC3SFRP2, COL1-PC3 and COL1-PC3SFRP2.

first: Attila

last: Aszodi

first: Hanna

last: Taipaleenmäki

first: Hiroaki

last: Saito

first: Veronika

last: Schönitzer

first: Michael

last: Chaloupka

first: Maria

last: Apfelbeck

first: Wolfgang

last: Böcker

first: Maximilian

middle: M

last: Saller


title: Chromatin complex dependencies reveal novel targeting opportunities in leukemia [300K]

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct


title: Hyaluronan driven by epithelial aPKC deficiency remodels the microenvironment and creates a therapeutic vulnerability in mesenchymal colorectal cancer II

city: New York

first: Jorge

last: Moscat

state: NY

address: 1188 York Avenue

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICINE

summary: Mesenchymal colorectal cancer (mCRC) is microsatellite stable (MSS), highly desmoplastic, with CD8+ T cells excluded to the stromal periphery, resistant to immunotherapy, and is driven by low levels of the atypical PKCs (aPKCs). We show here that a salient feature of these tumors is the accumulation of hyaluronan (HA), which along with reduced aPKC levels, predict poor survival. HA promotes epithelial heterogeneity, and the emergence of a fetal metaplastic cell population (TFSC) endowed with invasive cancer features through a network of interactions with activated fibroblasts and components of the immune system. TFSCs are sensitive to HA deposition in vivo and organoids, and their gene expression signature has prognostic value. We demonstrate that in vivo HA degradation with a clinical dose of hyaluronidase impairs mCRC tumorigenesis and enables immune checkpoint blockade therapy by promoting the recruitment of B and CD8+ T cells, including a proportion with resident memory features.

overall_design: Prkcif/fPrkczf/f;Villin-Cre Veh- (n=3) and PEGPH20-treated (n=3) small intestine tumors were profiled

first: Anxo

last: Martinez-Ordoñez

first: Angeles

last: Duran

first: Marc

last: Ruiz-Martinez

first: Tania

last: Cid-Diaz

first: Xiao

last: Zhang

first: Qixiu

last: Han

first: Hiroto

last: Kinoshita

first: Yu

last: Muta

first: Juan

middle: F

last: Linares

last: Kasashima

first: Mohamed

last: Omar

first: Masakazu

last: Yashiro

last: Pannellini

first: Alessio

last: Pigazzi

first: Giorgio

last: Inghirami

first: Luigi

last: Marchionni

first: Darren

last: Sigal

middle: T

last: Diaz-Meco


title: Hyaluronan driven by epithelial aPKC deficiency remodels the microenvironment and creates a therapeutic vulnerability in mesenchymal colorectal cancer III

last: Moscat

overall_design: sgPrkci/Prkcz Veh- (n=3) and PEGPH20-treated (n=4) MTOs tumors  were profiled after mice xonograft injection

last: Martinez-Ordoñez

last: Duran

first: Hiroaki

first: Maria


title: c-Jun and CREB1 transcription factor binding analysis in wild type bone marrow-derived macrophages in response to type II interferon and stress

status: Public on Dec 18 2022

city: Vienna

first: Laura

last: Boccuni

address: Dr-Bohr-Gasse, 9

department: Department of Microbiology, Immunobiology and Genetics

country: Austria

institute: University of Vienna

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The innate immune system acts as the first line of defense against invasion of microbial pathogens. Here, macrophages play a substantial role in recognition, phagocytosis and killing of pathogens and the regulation of the innate immune response. Here, interferons play a crucial role in augmenting the antimicrobial functions of macrophages and their ability to produce mediators of immunoregulation. Pathogen recognition activates many different signaling pathways that interact to produce an innate response commensurate with the microbial challenge. The co-occurrence of signaling by sensors of stress and IFN receptors is a hallmark of innate responses to many viral and bacterial pathogens. Our results show c-Jun and CREB binding upon Anisomycin, a drug that induces stress-activation of MAPK pathways, IFNg stimulation and the combination of both or with p38 inhibitor PH-797804 and JNK inhibitor SP600125, Anisomycin and IFNg.

overall_design: Methods: Bone marrow derived-macrophages (BMDM) chromatin of wild-type (WT) untreated, as well as 2h20 Anisomycin, 2h IFNg treated or pre-treated with Anisomycin (20min) and then stimulated with IFNg for for 2h or pre-treated with PH-797804 and SP600125 followed by pre-treatment with Anisomycin and stimulated with IFNg and then were generated by deep sequencing, in triplicate, using Illumina sequencing.

first: Thomas

last: Decker


title: Single-cell profiling of cell cultures during endoMT induction.

city: Ann Arbor

first: Dogukan

last: Mizrak

state: MI

address: NCRC Building 26, 263S

department: Cardiac Surgery

institute: University of Michigan

summary: Single-cell RNA sequencing (scRNAseq) data from EndoMT Day 1 dcas9-KRAB-MeCP2 (KRAB Control Day1), EndoMT Day 3 dcas9-KRAB-MeCP2 (KRAB Control Day3), and EndoMT Day 3 dcas9-KRAB-MeCP2 + rs117430032 gRNA (rs117430032i) cells.

overall_design: Using automated microwell array platforms and mRNA capture beads, we generated single-cell transcriptomic profiles of cells during endoMT induction.


title: Analysis of lung transcriptome of  Mice under normoxia or hypoxia conditions and treated with ABT-263 or its vehicle during 8 days

city: Créteil

first: Emmanuelle

last: Born

address: 8 rue du Général SARRAIL

department: Faculté de Santé

country: France

institute: IMRB, Inserm U955

summary:
To explore the role played by senescent cells in mice models of pulmonary hypertension we exposed young C57BL6/j mice to 8 days hypoxia or normoxia and treated with senolytic drug ABT-263 (50mg/kg/day) or its vehicule.
We then performed lung gene expression profiling analysis using data obtained from RNA-seq of 4 groups of mice (Normoxia+Vehicule; Normoxia+ABT-263; Hypoxia+Vehicule; Hypoxia+ABT-263)

overall_design: Comparative RNA-seq analysis has been performed on total RNA extracted from lungs of young C57BL6/j mice under hypoxia or normoxia conditions and treated with senolytic drug ABT-263 (50mg/kg/day) or its vehicule  during 8 days. Mice under Normoxia condition and treated with vehicule is defined as the control condition.

first: Larissa

last: Lipskaia

first: Elisabeth

last: Marcos

first: Jean-Michel

last: Flaman

first: David

last: Bernard

first: Serge

last: Adnot

first: Denis

last: Mestivier


title: Systematic interrogation of tumor cell resistance to chimeric antigen receptor T cell therapy in pancreatic cancer

status: Public on Dec 15 2022

city: BOSTON

first: William

middle: C

last: Hahn

address: 450 Brookline Avenue

institute: DANA-FARBER CANCER INSTITUTE

summary: TFAP4 scored strongly in our screen for MSLN CAR T cell resistance; to interogate its function, we performed RNAseq following TFAP4 knockdown and overexpression in HupT3 pancreatic cancer cells.

overall_design:
For TFAP4 knockdown experiments, we compared gene expression in control HupT3 cells (generated using two different intergenic guides ) to TFAP4 knockout HupT3 cells (generated using two different TFAP4 guides) (all samples in triplicate)
For TFAP4 overexpression experiments, we compared gene expression in HupT3 cells following overexpression of control (eGFP) or TFAP4  (all samples in triplicate)

first: Hahn

last: William

first: Hagel

last: Kimberly


title: The Impact of Pro-Inflammatory Cytokines on Alternative Splicing Patterns in Human Islets

city: Indianapolis

first: Carmella

last: Evans-Molina

state: Indiana

address: 1210 Waterway Blvd, 4108G, Indianapolis, IN

department: Pediatrics

institute: Indiana University School of Medicine and the Center for Diabetes and Metabolic Diseases

summary: Alternative splicing (AS) within the β cell has been proposed as one potential pathway that may exacerbate autoimmunity and unveil novel immunogenic epitopes in type 1 diabetes (T1D). We employed a computational strategy to prioritize pathogenic splicing events in human islets treated with IL-1β + IFN-γ as an ex vivo model of T1D and coupled this analysis with a k-mer based approach to predict RNA binding proteins involved in AS events.  In total, 969 AS events were identified in cytokine-treated islets, with the majority (44.8%) involving a skipped exon.  AS events occurred with high frequency in MHC Class II-related mRNAs, and targeted qPCR validated reduced inclusion of Exon5 in the MHC Class II gene HLA-DMB, while RNA FISH confirmed HLA-DMB splicing in pancreatic sections from human T1D donors.  Together, these data suggest that dynamic control of AS plays a role in the β cell response to inflammatory signals during T1D evolution.

overall_design: Examination of cytokines impacts on alternative splicing patterns in human islets.

first: Wenting

last: Wu


title: A stimulus-contingent positive feedback loop enables IFN-β dose-dependent activation of pro-inflammatory genes

city: Los Angeles

first: Quen

last: Cheng

address: 10833 LeConte Ave

institute: UCLA

summary: Type I interferons (IFN) induce powerful anti-viral and innate immune responses via the transcription factor, IFN-stimulated gene factor (ISGF3). However, in some pathological contexts type I IFNs are responsible for exacerbating inflammation. Here, we show that a high dose of IFN-β also activates an inflammatory gene expression program in contrast to IFN-λ3, a type III IFN, which elicits only the common anti-viral gene program. We show that the inflammatory gene program depends on a second, potentiated phase in ISGF3 activation. Iterating between mathematical modeling and experimental analysis we show that the ISGF3 activation network may engage a positive feedback loop with its subunits IRF9 and STAT2. This network motif mediates stimulus-specific ISGF3 dynamics that are dependent on ligand, dose, and duration of exposure, and when engaged activates the inflammatory gene expression program. Our results reveal a previously underappreciated dynamical control of the JAK-STAT/IRF signaling network that may produce distinct biological responses, and suggest that studies of type I IFN dysregulation, and in turn therapeutic remedies, may focus on feedback regulators within it.

overall_design: RNA-seq time course from MLE12 cells stimulated with varying doses of Type I and III interferons

first: Catera

middle: L

last: Wilder

first: Diane

last: Lefaudeux

first: Raisa

last: Mathenge

first: Kensei

last: Kishimoto

first: Alma

last: Zuniga Munoz

first: Minh

last: Nguyen

first: Aaron

middle: S

last: Meyer

first: Alexander

last: Hoffmann


title: Spatially resolved epigenomic profiling of single cells in complex tissues

city: Stanford

first: Cheen Euong

last: Ang

state: CA

address: 265 Campus Drive, G3145

institute: Stanford University

summary: The recent development of spatial omics enables single-cell profiling of the transcriptome and the 3D organization of the genome in a spatially resolved manner. A spatial epigenomics method would expand the repertoire of spatial omics tools and accelerate our understanding of the spatial regulation of cellular processes and tissue functions. Here, we developed an imaging approach for spatially resolved profiling of epigenetic modifications in single cells

overall_design: Examination of the epigenome using single cell epigenomic methods

first: Tian

last: Lu

first: Xiaowei

last: Zhuang


title: Human PSEN1 Mutant Glia Improve Spatial Learning and Memory in Aged Mice

city: Helsinki

first: Iiris

last: Hovatta

address: Haartmaninkatu 3

department: Department of Psychology and Logopedics

country: Finland

institute: University of Helsinki

summary: PSEN1 ΔE9 mutation causes a familial form of Alzheimer's disease. We have previously shown that human induced pluripotent stem cell (iPSC)-derived astrocytes carrying PSEN1 ΔE9 mutation exhibit transcriptional and functional abnormalities (Stem Cell Reports. 2017;9:1885-1897). Here we injected glial progenitors derived from 2 pairs of PSEN1 ΔE9 mutant- isogenic CTRL iPSCs intracerebroventricularly into newborn mice. At the age of 18 months, mouse hippocampi containing human cells (5 x PSEN1 ΔE9  + 6 x CTRL, all from male mice) were quickly dissected out and bulk RNA sequencing analysis was performed. Our results shed more light on the efffect of  PSEN1 ΔE9 mutation on human glia in vivo as well as on the effect of the presence of mutant human glia on the surrounding healthy mouse cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Human iPSC-derived glial progenitors were injected intracerebroventricularly into newborn immunedeficient mice and were let to proliferate and maturate in the mouse brain for 18 months. Ribo-depleted RNA was then sequenced with Illumina Next-seq 500 from mouse hippocampi containing human cells (5 x PSEN1 ΔE9  + 6 x CTRL). Sequences from human and mouse origin were analyzed separately.

first: Jari

last: Koistinaho

first: Taisia

last: Rolova


title: CDK4/6 inhibitors reverse primary resistance to anti-PD-1 therapy in LKB1-deficient lung adenocarcinoma

city: Guangzhou

first: Xue

last: Bai

address: No. 1023-1063, Shatai South Road, Baiyun District

institute: Southern Medical University

summary: LKB1 deficiency in lung adenocarcinoma (LUAD) leads to primary resistance to immune checkpoint inhibitors. However, the underlying molecular mechanism remains unclear. Here, we showed that LKB1 deficiency significantly affected the tumor immune landscape by decreasing the infiltration of most immunocyte populations and downregulating the expression of intercellular adhesion molecule-1 (ICAM1). LKB1 deficiency promoted cancer evasion due to loss of ICAM1-mediated antitumor immunity, including immune-competent cell cytotoxicity and tumor infiltration. CDK4/6 inhibitors reversed this process in a targeted manner. A tailored combination strategy using CDK4/6 inhibitors and anti-PD-1 antibodies slowed tumor growth and increased survival in syngeneic mouse models of LKB1-deficient lung adenocarcinoma. Combining a CDK4/6 inhibitor, which is clinically approved, with PD-1 blockade therapy is thus a promising option for lung adenocarcinoma patients harboring LKB1 mutations.

overall_design: RNA-sequencing of murine tumor specimens administered with different treatments: vehicle, palbociclib, anti-PD-1 antibody, or their combination. 3 replicates for each group.

first: Zeqin

last: Guo

first: Yanpei

last: Zhang

first: Lili

last: Long

first: Zhongyi

last: Dong


title: Expresssion data from primary mouse prostate tumor cells (primary prostate tumor cells; PPC, shrunken prostate tumor cells; S-PC, castration-resistant prostate tumor cells; CRPC)

city: Daegu

first: Ji-Hak

last: Jeong

address: 80 Daehakro, Bukgu

country: South Korea

institute: Kyungpook National University

summary:
To investigate the mechanisms underlying castration-resistant prostate cancer (CRPC) development, we used a prostate cancer (PCa) allograft mouse model. In this model, an androgen-dependent (AD) mouse prostate cancer cell line, Myc-CaP, was used. Myc-CaP cells can grow as primary prostate tumors (PPC) in immune competent FVB mice in an AD manner, when host mice are castrated, Myc-CaP allografts shrink (shrunken prostate tumor, S-PC), and later re-grow and become AR-positive CRPC. To compare the gene expression of different stage of PCa, primary cells from PPC, S-PC, and CRPC were isolated and purified.
We used RNA-seq to detail the global programme of gene expression underlying castration-resistant prostate cancer (CRPC) development and identified distinct classes of up-regulated or down-regulated genes during this process.

overall_design: Prostate tumors were selected at three different stages of CRPC development (PPC, S-PC, and CRPC) for RNA extraction and hybridization on Affymetrix microarrays.

first: Jun-Li

last: Luo


title: Combining Time-Resolved Transcriptomics and Proteomics Data for Adverse Outcome Pathway Refinement in Ecotoxicology

status: Public on Dec 21 2022

city: Amsterdam

first: Ruben

last: Bakker

state: North-Holland

address: Boelelaan 1105

department: A-Life

country: Netherlands

institute: Vrije Universiteit Amsterdam

summary: We obtained RNA-seq data from whole body springtail Folsomia candida exposed to the neonicotinoid insecticide imidacloprid or control conditions for a total of 72 hours and sampled every 12 hours .

overall_design: Imidacloprid concentration was 0.25 mg / kg dry soil equal to the EC20 (reproduction). 3 samples per condition and per time point, sampled every 12 hours for 72 hours. In total, 3 days, 6 time points, 2 conditions, 36 samples.

first: Katja

last: Hoedjes


title: Caloric restriction combined with immobilization as translational model for sarcopenia expressing key-pathways of human pathology

city: Leiden

first: Eveline

last: Gart

state: Zuid Holland

address: Sylviusweg 71

department: MHR

institute: TNO

summary: Abstract     Background: The prevalence of sarcopenia is increasing and effective interventions are required to prevent or reverse age-related muscle loss. However it is often challenging expensive and time-consuming to develop and test the effectiveness of such interventions. Furthermore translational animal models that adequately mimic underlying physiological pathways are scarce. Strong predictors for the incidence of sarcopenia include a sedentary life-style and malnutrition. Therefore our objective was to investigate the translational value of three potential mouse models for sarcopenia namely partial immobilized caloric restricted (CR) and a combination (immobilized & CR) model.    Methods: C57BL/6J mice were calorically restricted (-40%) and/or one hindleg was immobilized for two weeks to induce loss of muscle mass and function. Muscle mass function and diameter and distribution of slow (type 1) and fast ( type 2) myofibers were compared to those of young control (4 months) and old reference mice (21 months). Transcriptome analysis of quadriceps muscle was performed to identify underlying pathways and were compared with those being expressed in aged human vastus lateralis muscle-biopsies using a meta-analysis of five different human studies.    Results: Caloric restriction induced overall loss of lean body mass (-15% p<0.001) whereas immobilization decreased muscle strength (-28% p<0.001) and muscle mass of hindleg muscles specifically (on average -25% p<0.001). The proportion of slow myofibers increased with aging in mice (+5% p<0.05) and this was not recapitulated by the CR and/or immobilization models. The diameter of fast myofibers decreased with aging (-7% p<0.05) and this was mimicked by all models. Transcriptome analysis revealed that the combination of CR and immobilization recapitulated more pathways characteristic for human muscle-aging (73%) than naturally aged (21 months old) mice (45%). These pathways included critical pathways relevant for protein synthesis/ breakdown (mitochondrial) metabolism neurology and the vascular system.     Conclusions: The combination model exhibits loss of both muscle mass (due to CR) and function (due to immobilization) and has a remarkable similarity with pathways underlying human sarcopenia. Our results demonstrate that naturally aging up to 21 months in mice only partially recapitulates the human pathology with fewer overlapping pathways than the combination model. These findings underline that external factors such as sedentary behavior and malnutrition are key elements of a translational mouse model and favor the combination model as a rapid model for testing the treatments against sarcopenia.

overall_design: Five treatment groups for induction of sarcopenia (a, b, c, d, e). a) At 14 weeks, 2 weeks partial immobilized right hind leg. b) At 14 weeks, 2 weeks caloric restriction (CR). c) At 14 weeks 2 weeks combination of immobilization right leg and CR. d) 76 weeks ageing on control diet. e) 92 weeks ageing on control diet.

first: Jelle

last: de Jong

first: Martien

middle: P

last: Caspers

first: Nanda

last: Keijzer

first: Nicole

last: Worms

first: Joline

last: Attema

first: Christa

last: de Ruiter

first: Serene

last: Lek

first: Arie

middle: G

last: Nieuwenhuizen

first: Jaap

last: Keijer

first: Aswin

last: Menke

first: Robert

last: Kleemann

first: Lars

last: Verschuren

first: Anita

last: van den Hoek


title: A temporal in vivo catalog of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements

city: Beirut

first: Pierre

last: Khoueiry

address: Bliss street

department: Biochemistry and Molecular Genetics

country: Lebanon

institute: American University of Beirut

summary: Pediatric pineoblastomas (PBs) are rare and aggressive tumors of grade IV histology. Although some oncogenic drivers are characterized, including germline mutations in RB1 and DICER1, the role of epigenetic deregulation and cis-regulatory regions in PB pathogenesis and progression is largely unknown. Here, we generated genome-wide gene expression, chromatin accessibility, and H3K27ac profiles covering key time points of PB initiation and progression from pineal tissues of a mouse model of CCND1-driven PB. We identified PB-specific enhancers and super-enhancers, and found that in some cases, the accessible genome dynamics precede transcriptomic changes, a characteristic that is underexplored in tumor progression. During progression of PB, newly acquired open chromatin regions lacking H3K27ac signal become enriched for repressive state elements and harbor motifs of repressor transcription factors like HINFP, GLI2, and YY1. Copy number variant analysis identified deletion events specific to the tumorigenic stage, affecting, among others, the histone gene cluster and Gas1, the growth arrest specific gene. Gene set enrichment analysis and gene expression signatures positioned the model used here close to human PB samples, showing the potential of our findings for exploring new avenues in PB management and therapy. Overall, this study reports the first temporal and in vivo cis-regulatory, expression, and accessibility maps in PB.

overall_design: Examination of gene expression and accessible elements in 3 time-points spanning the proliferating, premalignant and tumorigenic stages.

first: P

first: R

last: Saab

first: S

last: Idriss

first: M

last: Hallal

first: A

last: El-Kurdi


title: Maternal undernutrition induces cell signalling and metabolic dysfunction in undifferentiated mouse embryonic stem cells

city: Huddersfield

first: Patrick

last: McHugh

address: Queensgate, Huddersfield

department: Pharmacy

country: United Kingdom

institute: University of Huddersfield

summary: The peri-conceptional environment can induce permanent changes in embryo phenotype which alter development and associate with later disease susceptibility. Thus, mouse maternal low protein diet (LPD) fed exclusively during preimplantation is sufficient to cause cardiovascular, metabolic and neurological dysfunction in adult offspring. Embryonic stem cell (ESC) lines were generated from LPD and control NPD C57BL/6 blastocysts and characterised by transcriptomics, metabolomics, bioinformatics and molecular/cellular studies to assess early potential mechanisms in dietary environmental programming. Previously, we showed these lines retain cellular and epigenetic characteristics of LPD and NPD embryos after several passages. Here, three main changes were identified in LPD ESC lines. First, their derivation capacity was reduced but pluripotency marker expression was similar to controls. Second, LPD lines had impaired Mitogen-activated protein kinase (MAPK) pathway with altered gene expression of several regulators (e.g., Maff, Rassf1, JunD), reduced ERK1/2 signalling capacity and poorer cell survival characteristics which may contribute to reduced derivation. Third, LPD lines had impaired glucose metabolism comprising reduced upstream enzyme expression (e.g., Gpi, Mpi) and accumulation of metabolites (e.g., glucose-6-P, fructose-6-P) above the phosphofructokinase (PFK) gateway with PFK enzyme activity reduced. ESC lines may therefore permit investigation of peri-conceptional programming mechanisms with reduced need for animal experimentation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for undifferentiated C57Bl/6 ES cells isolated from mothers on a low protein (LPD) or normal protein (NPD) diet

first: Pooja

last: Khurana

first: Andrew

last: Cox

first: Barira

last: Islam

first: Judith

last: Eckert

first: Sandrine

last: Willaime-Morawek

first: Joanna

last: Gould

first: Neil

middle: R

last: Smyth

first: Tom

last: Flemng


title: Early activated ageing-related changes in cardiac transcriptome of Tgαq*44 mice during entire HF development

city: Cracow

first: Piotr

last: Berkowicz

address: Bobrzyńskiego 14

country: Poland

institute: Jagiellonian Centre for Experimental Therapeutics

summary: To investigate ageing-related changes in cardiac transcriptome of FVB mice we performed differential gene expression profiling analysis using data obtained from RNA-seq of five life time points (4-, 8-, 10-, 12-, 14 months) by comparing older FVB mice (8-, 10-, 12-, 14 months) to young 4-month-old FVB mice (FVB vs. FVB analysis). Genes that were differentially expressed in FVB vs. FVB analysis were also annotated to the respective biological processes based on Gene Ontology database, assessed for their overrepresentation to indicate processes involved in cardic ageing process in FVB mice. To investigate heart failure-related as well as ageing-related changes in cardiac transcriptome of Tgαq*44 mice we performed differential gene expression profiling analysis using data obtained from RNA-seq of five life time points (4-, 8-, 10-, 12-, 14 months) by comparing Tgαq*44 to age-matched FVB mice (Tgαq*44 vs. FVB analysis). Genes that were differentially expressed in Tgαq*44 vs. FVB analysis were also annotated to the respective biological processes based on Gene Ontology database, assessed for their overrepresentation to indicate processes iniciated along heart failure development as well as cardiac ageing process in Tgαq*44 mice. To investigate early activated ageing-related changes in cardiac transcriptome of Tgαq*44 mice during entire heart failure development we searched for the presence of ageing-related genes (those identified in cardiac transcriptome of older FVB mice) among genes which were differentially expressed commonly at each measured time points in Tgαq*44 vs. FVB analysis. To investigate early activated aging-related biological processes in cardiac transcriptome of Tgαq*44 mice during entire heart failure development, we searched for the presence of ageing-related processes (those identified in cardiac transcriptome of older FVB mice) among processes which were overrepresented commonly at each measured time points in Tgαq*44 vs. FVB analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for older FVB mice (8-, 10-, 12-, 14 months) to young 4-month-old FVB mice as well as Tgαq*44 to age-matched FVB mice at the age of 4-, 8-, 10-, 12-, 14 months.

first: Stefan

last: Chlopicki


title: Histone variant H3.3 promotes experimental metastasis in alveolar rhabdomyosarcoma [RNA-Seq]

city: Singapore

first: Reshma

last: Taneja

address: 10 Medical Dr

country: Singapore

institute: NUS

summary: In this study, we show that histone variant H3.3 is overexpressed in ARMS patient-derived cell lines and patient tumour specimens. Functionally, knockdown of H3F3A significantly impairs the ability of ARMS cells to undertake migration and invasion and reduces Rho activation in vitro. In addition, a striking reduction in metastatic tumour burden and improved survival is apparent in vivo. Through RNA-sequencing and ChIP-sequencing analyses, we identified Melanoma Cell Adhesion Molecule (MCAM/CD146) as a direct downstream target of H3.3. Therefore, this study identifies a novel H3.3- MCAM axis involved in ARMS metastatic phenotypes, and supports the development of MCAM as a therapeutic target for this disease.

overall_design: RH41 cells were treated with control siRNA (siscr) or H3F3A-specific siRNA (siH3F3A) for 48 hours, after which total RNA was collected with TRIzol reagent. RNA was purified and quality of purified RNA was checked using Nanodrop and gel electrophoresis. Two samples of siscr and 3 samples of siH3F3A were used for sequencing analysis, done by Novogene.

first: Karthik

last: Nandini

first: Taneja

last: Reshma

first: Joshua

last: Jun


title: Spatial genomics reveals a high number and specific location of B cells in the pancreatic ductal adenocarcinoma microenvironment of long-term survivors

status: Public on Dec 14 2022

city: Rotterdam

first: Willem

last: de Koning

state: Zuid-Holland

address: Doctor Molewaterplein 40

institute: Erasmus University Medical Center

summary:
Background and aim: Only 10% of pancreatic ductal adenocarcinoma (PDAC) patients survive longer than five years. Factors underlining long-term survivorship in PDAC are not well understood. Therefore, we aimed to identify the key players in the tumor immune microenvironment (TIME) associated with long-term survivorship in PDAC patients.
Methods: The immune-related gene expression profiles of resected PDAC tumors of patients who survived and remained recurrence-free of disease for ≥36 months (long-term survivors, n=10) were compared to patients who had survived ≤6 months (short-term survivors, n=10) due to tumor recurrence. Validation was performed by the spatial protein expression profile of immune cells using the GeoMx™ Digital Spatial Profiler. An independent cohort of samples consisting of 12 long-term survivors and 10 short-term survivors, was used for additional validation. The independent validation was performed by combining qualitative immunohistochemistry and quantitative proteinexpression profiling.
Results: B cells were found to be significantly increased in the TIME of longterm survivors by gene expression profiling (p=0.018). The high tumor infiltration of B cells was confirmed by spatial protein profiling in the discovery and the validation cohorts (p=0.002 and p=0.01, respectively). The higher number of infiltrated B cells was found mainly in the stromal compartments of PDAC samples and was exclusively found within tumor cells in long-term survivors.
Conclusion: This is the first comprehensive study that connects the immune landscape of gene expression profiles and protein spatial infiltration with the survivorship of PDAC patients. We found a higher number and a specific location of B cells in TIME of long-term survivors which emphasizes the importance of B cells and B cell-based therapy for future personalized immunotherapy in PDAC patients.

first: Hosein

last: Aziz

first: Lawlaw

last: Saida

last: Stubbs

first: Yunlei

last: Li

first: Kostandinos

last: Sideras

first: Elena

last: Palacios

first: Jaime

last: Feliu

first: Marta

last: Mendiola

first: Casper

middle: H

last: van Eijck

first: Dana

last: Mustafa


title: Histone variant H3.3 promotes experimental metastasis in alveolar rhabdomyosarcoma

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

overall_design: Refer to individual Series


title: CD8+ T cells can trigger skin pathology post Zika virus infection in the absence of CD4+ T cell regulation

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

institute: Singapore Immunology Network

summary: Using a T cell deficient mouse model that retains a persistent ZIKV viral titre in the circulatory system and organs, we show that adoptive transfer of CD8+ T-cells led to a significant reduction in viral load in the blood and tissues. In addition, this animal model reveals the potential for a ZIKV induced auricular dermatitis and blepharitis, mediated by ZIKV-specific CD8+ T cells. Single cell RNA sequencing of these causative CD8+ T cells from the ears show an overactivated and elevated cytotoxic signature in mice with severe symptoms.

overall_design: Brain macrophage CD45+F4/80+CD11b+Ly6C- heterogeneity was determined by single cell RNA-Seq analysis

first: Cheryl

middle: Y

last: Lee

first: Guillaume

last: Carissimo

first: Teck-Hui

last: Teo

first: Rajarethinam

last: Ravisankar

first: Tze-Kwang

last: Chua

first: Zheyuan

last: Chen

first: Rhonda

last: Chee

first: Alicia

last: Tay

first: Shanshan

middle: W

last: Howland

first: Kok

last: Ang

first: Jinmiao

first: Laurent

last: Renia

first: Lisa

last: Ng


title: Caenorhabditis elegans RNA-seq

city: Santa Cruz

first: Joshua

last: Arribere

address: 1156 High St

department: Department of Molecular, Cell, and Developmental Biology

institute: University of California at Santa Cruz

summary: RNA-seq performed to study No-Go mRNA Decay.

overall_design: Analysis of mutant C. elegans samples expressing a No-Go mRNA Decay reporter by RNA-seq.

first: Parissa

last: Monem


title: Histone variant H3.3 promotes experimental metastasis in alveolar rhabdomyosarcoma [ChIP-Seq]

first: Reshma

last: Taneja

overall_design: Regions of H3.3 binding in RH41 cells were identified through ChIP-sequencing. H3.3 pulldown was done using ab176840. 10% of total DNA was collected prior to pulldown (as input) and used for sequencing. Two samples of input and 2 ChIP samples were used for analysis. Sequencing was done by Novogene.

first: Karthik

last: Nandini

first: Taneja

last: Reshma

last: Jun


title: The chromatin determinants and Ph1 gene effect at wheat sites with contrasting recombination frequency

city: Olomouc

first: Maciej

last: Majka

state: Please select a region, state or province.

address: Šlechtitelů 31

country: Czech Republic

institute: Institute of Experimental Botany AS CR

type: Methylation profiling by high throughput sequencing

summary: This study aims to investigate a wheat recombination hotspot (H1) in comparison with a “regular” recombination site (Rec7) on the sequence and epigenetic level in conditions with functional and non-functional Ph1 locus.

sample_organism:
Triticum aestivum
Triticum timopheevii subsp. timopheevii

overall_design: Bisulfate sequencing of the region containing two recombination sites: H1 and Rec7.

first: Eva

last: Janáková

first: Irena

last: Jakobson

first: Kadri

last: Järve

first: Petr

last: Cápal

first: Zuzana

last: Korchanová

first: Adam

last: Lampar

first: Jakub

last: Juračka

first: Miroslav

last: Valárik


title: Analysis of lung transcriptome of  Mice under normoxia or hypoxia conditions and treated with ABT-263 or its vehicle during 2 days

city: Créteil

first: Emmanuelle

last: Born

address: 8 rue du Général SARRAIL

institute: IMRB, Inserm U955

summary:
To explore the role played by senescent cells in mice models of pulmonary hypertension we exposed young C57BL6/j mice to 2 days hypoxia or normoxia and treated with senolytic drug ABT-263 (50mg/kg/day) or its vehicule.
We then performed lung gene expression profiling analysis using data obtained from RNA-seq of 4 groups of mice (Normoxia+Vehicule; Normoxia+ABT-263; Hypoxia+Vehicule; Hypoxia+ABT-263)

overall_design: Comparative RNA-seq analysis has been performed on total RNA extracted from lungs of young C57BL6/j mice under hypoxia or normoxia conditions and treated with senolytic drug ABT-263 (50mg/kg/day) or its vehicule  during 2 days. Mice under Normoxia condition and treated with vehicule is defined as the control condition.

first: Larissa

last: Lipskaia

first: Elisabeth

last: Marcos

first: Jean-Michel

last: Flaman

first: David

last: Bernard

first: Serge

last: Adnot

first: Denis

last: Mestivier


title: Control of pancreatic islet function and glucose homeostasis by a novel microexon program misregulated in type 2 diabetes

city: Barcelona

first: Manuel

last: Irimia

state: Barcelona

address: 88 Dr. Aiguader

department: MELIS

country: Spain

institute: Universitat Pompeu Fabra - Centre for Genomic Regulation

summary: Pancreatic islets control glucose homeostasis by the balanced secretion of insulin and other hormones, and its abnormal function causes diabetes or hypoglycemia. Here, we uncover a conserved program of alternative microexons included in mRNAs of islet cells, particularly in genes involved in vesicle transport and exocytosis. Islet microexons (IsletMICs) are regulated by the RNA binding protein SRRM3 and represent a subset of the larger neural program that are particularly sensitive to the levels of this protein. Both SRRM3 and IsletMICs are induced by elevated glucose levels, and depletion of SRRM3 in beta cell lines and mouse islets, or repression of particular IsletMICs using antisense oligonucleotides, leads to inappropriate insulin secretion. Consistently, SRRM3 mutant mice display defects in islet cell identity and function, leading to hyperinsulinemic hypoglycemia. Importantly, human genetic variants that influence SRRM3 expression and microexon inclusion in islets are associated with fasting glucose variation and type 2 diabetes risk.

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Srrm3 was depleted or overexpressed in different systems to investigate regulation of microexons.

first: Jonas

last: Juan-Mateu

first: Sophie

last: Bonnal

first: Simon

last: Bajew


title: Genome editing in plants using the compact editor CasΦ

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

summary: CRISPR-Cas systems have been developed as important tools for plant genome engineering. Here, we demonstrate that the hypercompact CasΦ nuclease is able to generate stably inherited gene edits in Arabidopsis, and that CasΦ guide RNAs can be expressed with either the Pol-III U6 promoter or a Pol-II promoter together with ribozyme mediated RNA processing. Using the Arabidopsis fwa epiallele we show that CasΦ displays higher editing efficiency when the target locus is not DNA methylated, suggesting that CasΦ is sensitive to chromatin environment. Importantly, two CasΦ protein variants, vCasΦ and nCasΦ, both showed much higher editing efficiency relative to the wildtype CasΦ enzyme, and yielded more offspring plants with inherited edits. Extensive genomic analysis of gene edited plants showed no off-target editing, suggesting that CasΦ is highly specific. The hypercompact size, flexible PAM and wide range of working temperatures make CasΦ an excellent addition to existing plant genome editing systems.

sample_organism:
Arabidopsis thaliana
Zea mays

platform_organism:
Arabidopsis thaliana
Zea mays

overall_design: This dataset includes amplicon sequencing data to evaluate the editing efficiencies of target loci by CasΦ, and whole genome sequencing to assess the off-target editing level by CasΦ in plants.

first: Li

last: Zheng

first: Zhong

last: Zhenhui


title: Differential gene expression in salicylic acid-deficient transgenic plants overexpressing StTGA2.1 after viral infection.

city: Ljubljana

first: Marko

last: Petek

address: Večna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

summary:
The general aim was to better understand the role of StTGA2.1 in plant immunity by transcriptional profiling of plants overexpressing the salicylic acid pathwas related TGA transcription factor StTGA2.1 after infection with potato virus Y (PVY).
Potato non-transgenic cultivar Rywal (NT), Rywal-NahG (NahG), a transgenic line unable to accumulate SA due to salicylate hydroxylase expression, and a transgenic Rywal-NahG line inducibly overexpressing StTGA2.1 (TGA2.1-NahG) using the glucocorticoid-system, in which target gene expression can be controlled by external application of dexamethasone (DEX), were used. The leaves of three plants per genotype were infected with either PVY or mock-inoculum and subsequently treated with DEX. Additionally, three TGA2.1-NahG PVY-infected or mock-inoculated plants were not treated with DEX as control. After four days, PVY infection symtoms appeared as small regions of necrotic tissue called lesions. Tissue sections, containing lesions and their immediate surrounding area, were sampled, allowing us to focus on PVY-affected cells. Total RNA was isolated, DNase treated and sent for library prep and high-throughput sequencing.

overall_design: Gene expression profiles of TGA2.1-NahG, NahG and NT plants after PVY infection.

first: Špela

last: Tomaž

first: Anna

last: Coll

first: Tjaša

last: Lukan

first: Karmen

last: Pogačar

first: Katja

last: Stare

first: Erica

last: Teixeira Prates

first: Daniel

last: Jacobson

first: Jan

last: Zrimec

first: Gregor

last: Bajc

first: Matej

last: Butala

first: Maruša

last: Pompe Novak

first: Quentin

last: Dudley

first: Nicola

last: Patron

first: Ajda

last: Taler-Verčič

first: Aleksandra

last: Usenik

first: Dušan

last: Turk

first: Salomé

last: Prat

first: Kristina

last: Gruden


title: Transcriptional changes induced by ADH5 knocking out in HeLa cells.

city: Copenhagen

first: Salvatore

last: Rizza

email: salvatoreri@gmail.com, rizza@cancer.dk

address: Strandboulevarden 49

department: Redox Biology

country: Denmark

institute: Danish Cancer Institute

summary: ADH5 encodes for the protein GSNOR, an alchol dehydrogenase acting as a denitrosylase. GSNOR reduces S-nitrosoglutathione (GSNO) to an unstable intermediate, S-hydroxylaminoglutathione, which then rearranges to form glutathione sulfonamide, or in the presence of GSH, forms oxidized glutathione (GSSG) and hydroxylamine

overall_design: Four biological replicates were analyzed for each of the 2 genotypes

first: Giuseppe

last: Filomeni


title: Efficient in vivo Genome Editing Prevents Hypertrophic Cardiomyopathy in Mice [Amplified_cDNA]

status: Public on Dec 13 2022

city: Boston

last: DeLaughter

state: MA

address: 7 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: Dominant pathogenic variants encoding amino acid substitutions in cardiac myosin heavy chain cause hypertrophic cardiomyopathy (HCM), a currently incurable disorder that increases risk for stroke, heart failure, and sudden cardiac death. We assessed the efficacy of two different genetic therapies, an adenine base editor (ABE8e) and a potent Cas9 nuclease delivered by AAV9, to prevent disease in mice carrying the heterozygous HCM pathogenic variant myosin R403Q. One dose of dual AAV9 vectors, each carrying one half of RNA-guided ABE8e, corrected the pathogenic variant in ≥70% of ventricular cardiomyocytes and maintained durable, normal cardiac structure and function. An additional dose provided more global editing especially in the atria but also increased bystander editing. AAV9 delivery of RNA-guided Cas9 nuclease effectively inactivated the pathogenic allele, albeit with dose-dependent toxicities, necessitating a narrow therapeutic window to maintain health. These preclinical studies demonstrate considerable potential for single-dose genetic therapies to correct or silence pathogenic variants and prevent the development of HCM.

overall_design: Editing efficiency of the targeted MYH6 R403Q allele and insertions/deletions (indels) after a single or multiple does of AAV9 ABE8e injection was assessed by sequencing PCR amplified cDNA of Myh6 derived from RNA extracted from specific cardiac chambers.

first: Reichart

last: Daniel

first: Newby

last: Gregory A.

first: Wakimoto

last: Hiroko

first: Lun

last: Mingyue

first: Gorham

last: Joshua M.

first: Raguram

last: Aditya

first: DeLaughter

last: Daniel M.

first: Conner

last: David A.

first: Marsiglia

last: Júlia D C.

first: Kohli

last: Sajeev

first: Chmatal

last: Lukas

first: Page

last: David C.

first: Zabaleta

last: Nerea

first: Vandenberghe

last: Luk

first: Liu

last: David R.

first: Seidman

last: Jonathan G.

last: Christine


title: Transcriptome-wide analysis of pseudouridinylation in Drosophila melanogaster

city: Bloomington

first: W.

middle: Daniel

last: Tracey

address: 702 N. Walnut Grove

department: Biology

institute: Indiana University

summary: Pseudouridine (Psi) is one of the most frequent post-transcriptional modification of RNA. Enzymatic Psi modification occurs on rRNA, snRNA, snoRNA, tRNA, non-coding RNA and has recently been discovered on mRNA. Transcriptome-wide detection of Psi (Psi-seq) has yet to be performed for the widely studied model organism Drosophila melanogaster. Here, we optimized Psi-seq analysis for this species and have identified thousands of Psi modifications throughout the female fly head transcriptome. We find that Psi is widespread on both cellular and mitochondrial rRNAs. In addition, more than a thousand Psi sites were found on mRNAs. When pseudouridinylated, mRNAs frequently had many Psi sites. Many mRNA Psi sites are present in genes encoding for ribosomal proteins, and many are found in mitochondrial encoded RNAs, further implicating the importance of pseudouridinylation for ribosome and mitochondrial function. The 7SLRNA of the signal recognition particle is the non-coding RNA most enriched for Psi. The three mRNAs most enriched for Psi encode highly-expressed yolk proteins (YP1, YP2, YP3). By comparing the pseudouridine profiles in the RluA-2 mutant and the w1118 control genotype, we identified Psi sites that were missing in the mutant RNA as potential RluA-2 targets. Finally, differential gene expression analysis of the mutant transcriptome indicates a major impact of loss of RluA-2 on the ribosome and translational machinery.

overall_design: Polyadenylated RNA was enriched from total RNA using two rounds of Oligo(dT) dynabeads (Invitrogen) according to manufacturer’s protocol. To each polyA-RNA sample, spike-in RNA (~3ug) was added and then the samples were split into two equal samples for CMCT or mock treatment.

first: Wan

last: Song

first: Ram

last: Podicheti

first: Douglas

middle: B

last: Rusch

first: W

middle: D


title: Efficient in vivo genome editing prevents hypertrophic cardiomyopathy in mice

first: Daniel

last: DeLaughter


title: Multi-omics and machine learning reveal context-specific gene regulatory activities of PML-RARA in Acute Promyelocytic Leukemia

city: London

first: Cameron

last: Osborne

address: Guy's Hospital Campus

department: Medical and Molecular Genetics

institute: King's College London


title: Efficient in vivo Genome Editing Prevents Hypertrophic Cardiomyopathy in Mice [Nuc-Seq]

overall_design: Editing efficiency of the targeted MYH6 R403Q allele and insertions/deletions (indels) after a single or multiple does of AAV9 ABE8e injection was assessed by examining MYH6 reads from single nuclei RNA-sequencing  of nuclei derived from specific cardiac chambers.

first: Reichart

last: Daniel

first: Newby

last: Gregory A.

first: Wakimoto

last: Hiroko

first: Lun

last: Mingyue

first: Gorham

last: Joshua M.

first: Raguram

last: Aditya

first: DeLaughter

last: Daniel M.


title: Efficient in vivo Genome Editing Prevents Hypertrophic Cardiomyopathy in Mice [RNA-seq]

overall_design: The transcriptional responses to one and two editor doses were assessed by RNA-sequencing of LV tissues from WT, untreated, and treated R403Q 129SvEv/S4 F1 mice

first: Conner

last: David A.

first: Marsiglia

last: Júlia D C.

first: Kohli

last: Sajeev

first: Chmatal

last: Lukas

first: Page

last: David C.

first: Zabaleta

last: Nerea

first: Vandenberghe

last: Luk


title: Regulation of the alveolar regenerative niche by amphiregulin-producing Treg cells

city: New York

first: Nicholas

last: Arpaia

address: 701 W 168TH ST HHSC 910C

department: Microbiology & Immunology

institute: Columbia University Irving Medical Center


title: GPS2 sensitizes IL4 pathway via the recruitments of KDM1A

city: Nanjing

first: Zhiqiang

last: Huang

state: Jiangsu

address: Hankou 22

department: Medical School

institute: Nanjing University

summary: Here, we systemically investigated the GPS2 corepressor complex function on cyclooxygenase 1 (Ptgs1) in macrophage M2 activation. We found the inflammatory states changed the DNA topology structure along with the histone modification and the gene expression on Ptgs1 locus. GPS2 related NCOR/SMRT corepressor physically bound to Ptgs1 promoter and enhancer, and depletion of all corepressor subunits caused the basal overexpression of Ptgs1 along with the H3K27ac activation.  The corepressor subunits display a conserved function on Ptgs1 expression in M2 activation and this regulation is dependent on STAT6 but not through the direct interaction. We find the GPS2 depletion interferences the DNA accessibility on Ptgs1 locus and promotes the enhancer-promoter interaction and the transcriptional process in M2 activation. We further find the GPS2 depletion caused the recruitments of KDM1A, which specifically demethylated the H3K9me2/3 on Ptgs1 locus. In summary, these findings suggest a new paradigm of the corepressor mediated common gene repression in M2 activation and indicate the potential function of the GPS2/NCOR/SMRT function in the tissue homeostasis and wound healing during Th2-mediated immune responses.

overall_design: Use the ChIP-seq, 4C-seq, ATAC-seq, and CUT&Tag to uncover the regulation mechanism at the molecular level on IL4 target gene expression in  M2 activation and reveal a new function of GPS2 in this process.

first: Eckardt

last: Treuter

first: Rongrong

last: Fan


title: The regulons of an OmpR-like transcription factor in Pseudomonas syringae pv. Actinidiae

city: Guiyang

first: Zhibo

last: Zhao

state: China

address: The west campus of Guizhou University

institute: Guizhou University

summary: A ChIP-seq assay was performed to identify the regulons of an ompR-like transcription factor (gene name: 13375, GenBank: AYL80818.1) in Pseudomonas syringae pv. actinidiae. An 13375-overexpressing mutant G1-OE13375, which constitutively express C-terminally Myc-tagged ompR-like gene in the 13375-deletion mutant G1Δ13375, was used in this study. The bacterial cells were cultured either in nutrition-rich KB medium or hrp-derepressing medium (HDM) at 25 C for 24 hours. A PierceTM Magnetic ChIP Kit (Cat. #: 26157, Thermo Fisher Scientific) and a ChIP-grade Myc-Tag Monoclonal Antibody (Myc.A7, Cat. #: MA121316, Thermo Fisher Scientific) were used for sample pretreatment and immunoprecipitation.

overall_design: Two independent ChIP-seq assay (no replicates) for Myc-tagged OmpR-like transcription factor in bacteria cultured either in KB medium or hrp-derepressing medium.

first: Zhao

last: Zhibo

first: Zhi

last: Taihui

last: Fu


title: Multi-omics and machine learning reveal context-specific gene regulatory activities of PML-RARA in Acute Promyelocytic Leukemia [ATAC-seq]

first: Cameron

last: Osborne

summary: The PML-RARA fusion protein is the hallmark driver of Acute Promyelocytic Leukemia (APL) and disrupts retinoic acid signaling, leading to wide-scale gene expression changes and uncontrolled proliferation of myeloid precursor cells. While known to be recruited to binding sites across the genome, its impact on gene regulation and expression is under-explored. Using integrated multi-omics datasets, we characterize the influence of PML-RARA binding on gene expression and regulation in an inducible cell line model and APL patient ex vivo samples. We find that genes whose regulatory elements recruit PML-RARA are not uniformly transcriptionally repressed, as commonly suggested, but also may be upregulated or remain unchanged. We develop a novel, computational machine learning application to deconvolute the complex, local transcription factor binding site environment at PML-RARA bound positions to reveal distinct signatures that modulate how PML-RARA directs the transcriptional response.

overall_design: Application of omni ATAC-seq to the U937-PR9 cell line system, before and after PML-RARA induction. Application of omni ATAC-seq to two ex vivo APL patient samples

first: William

last: Villiers

first: Richard

last: Dillon

first: Borbala

last: Mifsud


title: SF3B1

city: Bronx

first: Teresa

last: Bowman

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

sample_organism:
Danio rerio
Homo sapiens

platform_organism:
Danio rerio
Homo sapiens

overall_design: Refer to individual Series


title: RNAseq data of T-Ctr vs T-anti-FGL2

status: Public on Dec 12 2022

first: Shan

last: Jiang

department: Taub Institute for Research on Alzheimer’s Disease and the Aging Brain

summary: To analyze wha's the function of anti-FGl2-scFv on T cells, sorted CD8+T cells transfected with empty vector or with anti-FGL2-scFv were processed RNA next generation sequencing

overall_design: T-Ctr cells were set as control, T-anti-FGl2 cells were the experimental group. N=3

first: Qingnan

first: Shulin

last: Li


title: Efficient in vivo genome editing prevents hypertrophic cardiomyopathy in mice [genomicDNA]

first: Daniel

last: DeLaughter

summary:
We assessed genome editing strategies to treat cardiomyopathy in mice including one or two doses of ABE8e, or one low, medium, or high dose of SaCas9 nuclease
We conducted RNA analysis and genomic DNA analysis at the target region and transcriptome-wide analysis to assess cellular phenotypes

overall_design: After genomic DNA extraction from mouse tissues, the a 300 bp region around the target editing site (Myh6 R403Q ) was PCR-amplified and sequenced on an Illumina MiSeq

first: Reichart

last: Daniel

first: Newby

last: Gregory A.

first: Wakimoto

last: Hiroko

first: Lun

last: Mingyue

first: Gorham

last: Joshua M.

first: Raguram

last: Aditya

first: DeLaughter

last: Daniel M.

first: Conner

last: David A.

first: Marsiglia

last: Júlia D C.

first: Kohli

last: Sajeev

first: Chmatal

last: Lukas

first: Page

last: David C.

first: Zabaleta

last: Nerea

first: Liu

last: David R.

first: Seidman

last: Jonathan G.

last: Christine


title: RNA-seq of endothelial cells  from 28 hours post fertilization sf3b1 mutant and sibling zebrafish with Stat3 overexpression

first: Teresa

last: Bowman

summary: The purpose of the experiment was to define the gene expression and splicing alterations occurring when wildtype or consitutively active Stat3 are expressed in embryonic zebrafish endothelial cells with low levels of splicing factor 3b subunit 1 (Sf3b1). Results provide insight the interplay of Sf3b1 and Stat3 in hematopoietic development.

overall_design: mRNA profiling of kdrl-positive endothelial cells isolated from 28 hours post fertilization wildtype, sf3b1 mutant and sibling zebrafish with wildtype or constitutively active Stat3 overexpression using the Novogene 6000 platform. A total of 15 samples were sequenced.

middle: V


title: RNA-seq of endothelial cells  from 28 hours post fertilization sf3b1 mutant and sibling zebrafish

summary: The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of splicing factor 3b subunit 1 (Sf3b1) are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in hematopoietic development.

overall_design: mRNA profiling of kdrl-positive endothelial cells isolated from 28 hours post fertilization sf3b1 mutant and sibling zebrafish using Illumina HiSeq4000. Four sibling control samples and Four mutant samples were sequenced.


title: An atlas of lamina-associated chromatin across thirteen human cell types reveals cell-type-specific and multiple subtypes of peripheral heterochromatin

city: Philadelphia

first: Rajan

last: Jain

state: PA

address: 09-102 Smilow TRC 3400 Civic Center Blvd

department: Departments of Medicine and Cell and Developmental Biology, Penn CVI

institute: Perelman School of Medicine, University of Pennsylvania

summary: Three-dimensional genome organization, specifically organization of chromatin at the nuclear periphery, coordinates cell type-specific gene regulation and is critical for maintenance of cell type identity. While various histone modifications and chromatin-associated proteins have provided important insights into genome organization, nuclear peripheral chromatin maps have only been generated in a few cell types. In this study, we define nuclear peripheral chromatin organization signatures based on association with LAMIN-B1 and/or the histone modification H3K9me2 across thirteen human cell types encompassing undifferentiated stem cells and intermediate and terminally differentiated cells from all three germ layers. Genomic analyses across these thirteen human cell types reveal sub-compartmentalization of peripheral heterochromatin, specifically two subtypes of LAMIN B1-associated chromatin, which appear to be physically and functionally distinct. By integrating peripheral chromatin maps with transcriptional data, we find evidence of cooperative shifts between chromatin structure and gene expression associated with each cell type. Across multiple, distinct cell cell types, this work revealed that lamina-associated chromatin is organized into at least two fundamentally different compartments, with diverse genome coverage, characteristics and gene complements, underscoring the complexity of peripheral chromatin organization. Moreover, these maps encompass an atlas of peripheral chromatin and associated features in multiple human cell types from all three germ layers, providing the largest resource to date for peripheral chromatin organization and a greater appreciation for how this organization may impact the establishment and maintenance of cellular identity.

overall_design:
LB1 and H3K9me2 ChIP-seq and RNAseq for multiple ES-derived cell types.
TPM Data from Day 3 early somite and paraxial mesoderm cells were downloaded from GSM2257301 (reanalyzed raw data from SRP073808). Data from mid-hindgut were downloaded from GSM1273677 (reanalyzed raw data from SRP033267). Data from neural ectoderm were downloaded from GSM2711696, GSM2711697, and GSM2711698 (reanalyzed raw data from SRP113027).

first: Kathleen

last: Keough

first: Parisha

last: Shah

first: Nadeera

last: Wickramasinghe

first: Carolyn

middle: E

last: Dundes

first: Angela

last: Chen

first: Rachel

last: Salomon

first: Sean

last: Whalen

first: Kyle

last: Loh

first: Nicole

last: Dubois

first: Katherine

last: Pollard


title: Coopting T cell proximal signaling molecules enables Boolean logic-gated CAR T cell control

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

summary: While CAR T cells have altered the treatment landscape for B cell malignancies, the risk of on-target, off-tumor toxicity has hampered their development for solid tumors because most target antigens are shared with normal cells. Researchers have attempted to apply Boolean logic gating to CAR T cells to prevent on-target, off-tumor toxicity; however, a truly safe and effective logic-gated CAR has remained elusive. Here, we describe a novel approach to CAR engineering in which we replace traditional ITAM-containing CD3ζ domains with intracellular proximal T cell signaling molecules. We demonstrate that certain proximal signaling CARs, such as a ZAP-70 CAR, can activate T cells and eradicate tumors in vivo while bypassing upstream signaling proteins such as CD3ζ. The primary role of ZAP-70 is to phosphorylate LAT and SLP-76, which form a scaffold for the propagation of T cell signaling. We leveraged the cooperative role of LAT and SLP-76 to engineer Logic-gated Intracellular NetworK (LINK) CAR, a rapid and reversible Boolean-logic AND-gated CAR T cell platform that outperforms other systems in both efficacy and the prevention of on-target, off-tumor toxicity. LINK CAR will dramatically expand the number and types of molecules that can be targeted with CAR T cells, enabling the deployment of these powerful therapeutics for solid tumors and diverse diseases such as autoimmunity9 and fibrosis10. In addition, this work demonstrates that the internal signaling machinery of cells can be repurposed into surface receptors, a finding that could have broad implications for new avenues of cellular engineering.

overall_design: CAR T cells were engineeried with two different signaling domains (ZAP70 and BBZ) then either rested or stimulated in the presence of CD19+ cells.

first: Aidan

last: Tousley

first: Robbie

last: Majzner


title: TCRa/b RNA seq data of CD8+TRM in brain and CD8+memory T cells in dLNs

first: Shan

last: Jiang

summary: To analyze the TCR clonal repertoire, sorted CD44+CD8+T cells from brain and draining lyph nodes of T-aFGL2 treated tumor free mice were processed TCRa or TCRb RNA sequencing

overall_design: After confirming that T-aFGL2 treatment induced long term suvival of GBM tumor bearing mice, and the formation of CD8+TRM in brain, the CD44+CD8+T cells from brain and dLNs were sorted and underwent TCR deep sequencing to analyze the TCR clone characteristics.

first: Qingnan

last: Zhao

first: Shulin

last: Li


title: Genome-wide maps of YTHDC1 upon Heat-shock (HS) or in untreated conditions (UT) in HeLa cells

city: Montpellier

first: Rosemary

last: Kiernan

address: 141 rue de la cardonille

institute: UMR9002 CNRS-UM

summary: we used the technnology of ChIP-sequencing to specifically analyze the recruitment of YTHDC1 onto active genes during heat shock

overall_design: HeLa cells unstressed or  stressed 60 minutes at 43°C were used for chromatin immunoprecipitation using YTHDC1  antibodies

first: Kalina

last: Timcheva

first: Solenne

last: Dufour

first: Callum

last: Burnard

first: Leila

last: Touat-Todeschini

first: Aude

last: Grézi

first: Yohann

last: Couté

first: Marion

last: Helsmoortel

first: Claire

last: Vourc'h

first: Daphné

last: Seigneurin-Berny

first: André

last: Verdel


title: Transcriptome profiling of cytosol, endoplasmic reticulum (ER), and pellet fraction from the Xenopus laevis oocyte and mature egg

city: Urbana

first: Jing

last: Yang

state: Illinois

address: 2001 South Lincoln Avenue

department: Comparative Biosciences

institute: University of Illinois Urbana Champaign

summary: This genome-wide transcriptome analysis was aimed to reveal dynamic regulation of mRNA-ER association during Xenopus oocyte maturation. We extracted RNAs from the cytosolic, ER, and the pellet fraction of oocytes and eggs, respectively, and performed RNA-sequencing. These results showed that mRNA-ER association is down-regulated during oocyte maturation.

overall_design: Three biological replicates were assigned for each group. Before RNA extraction, a mixture of spike-in RNAs (egfp, mCherry, mRuby2, firefly, renilla) was added to each fraction. Total RNA was extracted from the cytosol, ER, and pellet fraction in the four oocytes or four mature eggs using TRIzol reagent. Ribosomal RNA was removed with the Ribozero HMR kit (Illumina), and the RNA libraries were prepared using the TruSeq Stranded mRNAseq Sample Prep kit (Illumina). The libraries were quantitated by qPCR and sequenced on one lane for 101 cycles from each end of the fragments on a NovaSeq 6000 using a NovaSeq S1reagent kit. Fastq files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina). Transcript abundance (TPM) was quantified by Kallisto, and the TPM of each RNA-seq data was converted to absolute attomolar concentration (aM) through the regression estimation with five spike-in RNAs.

first: Taejoon

last: Kwon

first: Hyojeong

last: Hwang

first: Seungmin

last: Yun


title: Controlling human organoid symmetry breaking reveals signaling gradients drive segmentation clock waves

city: Cambridge

first: Sharad

last: Ramanathan

address: 52 Oxford St.

institute: Harvard University

summary: Axial development of mammals is a dynamic process involving several coordinated morphogenetic events, including axial elongation, somitogenesis, and neural tube formation. To gain insight into the signals control the dynamics of human axial morphogenesis, we generated hundreds of axially elongating organoids by inducing anteroposterior symmetry breaking of spatially coupled epithelial cysts derived from human pluripotent stem cells. Each organoid was composed of a neural tube flanked by presomitic mesoderm sequentially segmented into somites. Periodic activation of the somite differentiation gene MESP2 coincided in space and time with anteriorly traveling segmentation clock waves in the presomitic mesoderm of the organoids, recapitulating critical aspects of somitogenesis. Through timed perturbations of organoids, we demonstrated that FGF and WNT signaling play distinct roles in axial elongation and somitogenesis and that FGF signaling gradients drive the segmentation clock waves. By generating and perturbing organoids that robustly recapitulate the architecture and dynamics of multiple axial tissues in human embryos, this work offers a means to dissect complex mechanisms underlying human embryogenesis.

overall_design: Organoids were dissociated into a single-cell suspension using the Worthington Papain Dissociation System kit (Worthington Biochemical).

first: Yaman

last: Yusuf Ilker

first: Ramanathan

last: Sharad


title: RNA-seq of human K562 leukemia cells with or without a mutation in SF3B1 (splicing factor 3b, subunit 1) that were treated with DMSO or the STAT3 inhibitor STATTIC

first: Teresa

last: Bowman

summary: The purpose of the experiment was to define the gene expression and splicing alterations occurring when human wildtype or splicing factor 3b subunit 1 (SF3B1) mutant K562 cells had STAT3 inhibited with the small molecule STATTIC. Results provide insight the interplay of SF3B1 and STAT3 in human hematopoietic cells.

overall_design: mRNA profiling of human K562 cells with or without a mutation in SF3B1 (K666N) treated with DMSO or the STAT3 inhibitor STATTIC using a NovaSeq6000. A total of 18 samples were sequenced.


title: Single-cell transcriptional profiles of BM, PB and lung neutrophils from naïve (C57BL/6J), AT3, and AT3-gcsf tumor-bearing mice

city: Bar Harbor

first: Guangwen

last: Ren

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary: To determine the effect of tumor-bearing vs. host neutrophilic inflammation on reinforcement of lung neutrophil-specific immunosuppressive function, we performed single-cell RNA sequencing (scRNA-seq) on BM, PB and lung neutrophils isolated from naïve (C57BL/6J), AT3, and AT3-gcsf tumor-bearing mice.

overall_design: BM, PB and lung neutrophils from naïve (C57BL/6J), AT3, and AT3-gcsf tumor-bearing mice were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.

first: Zheng

last: Gong

first: Qing

last: Li

first: Jiayuan

last: Shi


title: Single-cell transcriptional profiles of different tissue-derived myeloid cells from naïve and MDA-MB-231 tumor-bearing humanized mice

summary: To better understand how lung neutrophils transcriptionally differ from other tissue neutrophils, we performed single-cell RNA sequencing (scRNA-seq) on different tissue-derived myeloid cells isolated from naïve and MDA-MB-231 tumor-bearing humanized mice.

overall_design: Different tissue-derived myeloid cells from naïve and MDA-MB-231 tumor-bearing humanized mice were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.


title: Single-cell transcriptional profiles of BM, PB and lung neutrophils from naïve (BALBc/J) and 4T1 tumor-bearing mice

summary: To better understand how lung neutrophils transcriptionally differ from other tissue neutrophils, we performed single-cell RNA sequencing (scRNA-seq) on BM, PB and lung neutrophils isolated from naïve (BALBc/J) and 4T1 tumor-bearing mice.

overall_design: BM, PB and lung neutrophils from naïve (BALBc/J) and 4T1 tumor-bearing mice were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.


title: Preclinical Species Gene Expression Database: Development and Meta-Analysis

city: North Chicago

first: Terry

last: Van Vleet

state: IL

address: 1 N Waukegan Rd

institute: AbbVie

summary: RNA-sequencing data across a large number of tissues in mouse, rat, dog, and monkey to evaluate baseline expression levels and establish a preclinical gene expression body atlas

sample_organism:
Macaca fascicularis
Canis lupus familiaris
Mus musculus
Rattus norvegicus

overall_design: Comparative gene expression profiling analysis of RNA-seq data for tissues across preclinical species

first: Andy

last: Vo

first: Caitlin

last: Krause


title: Engineered cell entry links receptor biology with single-cell genomics

city: Stanford

first: Howard

last: Chang

state: California

address: 269 Campus Drive, CCSR 2130

department: Center for Personal Dynamic Regulomes

institute: Stanford University

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


title: Coupled induction of prophage and virulence factors during tick transmission of the Lyme disease spirochete

city: Hamilton

first: Patricia

last: Rosa

state: MT

address: 903 S 4th St

department: Laboratory of Bacteriology

institute: Rocky Mountain Labs, NIAID, NIH

summary: Lyme disease spirochetes must induce RpoS-dependent genes during tick feeding to prepare for host infection. Previous work in our lab identified bbd18 as a negative regulator of RpoS, but inactivation of bbd18 in wild-type spirochetes was never achieved. In the current study we generated an inducible bbd18 gene at the endogenous plasmid locus and demonstrated the essential nature of BBD18 for viability of wild-type spirochetes in vitro and at a unique point in vivo. Transcriptomic analyses demonstrated global induction of RpoS and RpoS-dependent genes following BBD18 depletion, culminating in spirochete lysis. Plasmid prophage genes were also induced and phage particles were detected in lysed culture supernatants, suggesting that RpoS regulates phage lysis-lysogeny decisions. The absolute requirement for BBD18 persisted following displacement of the entire set of cp32 plasmid prophages but could be circumvented by deletion of rpoS. This is the first report of a mechanistic  link between endogenous transducing prophages and the RpoS-dependent adaptive response of the Lyme disease spirochete.

overall_design: Determine differential expression in inducible bbd18 and rpoS deletion strains of Borrelia burgdorferi

first: Jenny

last: Wachter

first: Patti


title: Engineered cell entry links receptor biology with single-cell genomics [scRNA-Seq]

summary: Cells communicate with each other via receptor-ligand interactions. Here we describe lentiviral-mediated cell e¬ntry by engineered receptor-ligand interaction (ENTER) to display ligand proteins, deliver payloads, and record receptor specificity. We optimize ENTER to decode interactions between T cell receptor (TCR)-MHC peptides, antibody-antigen, and other receptor-ligand pairs. A viral presentation strategy allows ENTER to capture interactions between B cell receptor and any antigen. We engineer ENTER to deliver genetic payloads to antigen-specific T or B cells to selectively modulate cellular behavior in mixed populations. Single-cell readout of ENTER by RNA-sequencing (ENTER-seq) enables multiplexed enumeration of antigen specificities, TCR clonality, cell-type and states of individual T cells. ENTER-seq of CMV-seropositive patient blood samples reveals the viral epitopes that drive effector memory T cell differentiation and inter- vs intra-clonal phenotypic diversity targeting the same epitope. ENTER technology enables systematic discovery of receptor specificity, linkage to cell fates, and antigen-specific cargo delivery.

overall_design: Primary T cells isolated directly from patient blood samples or peptide stimulated donor PBMC were stained with a mixture of pMHC displayed ENTER viruses and oligo-barcoded antibodies. GFP+ or GFP- CD8 T cells were sorted and subjected to multiplexed single cell RNA-seq, CITE-seq, TCR-seq, and pMHC antigen profiling on the droplet based 10X Genomics platform

first: Bingfei

last: Yu

first: Quanming

first: Julia

middle: A

last: Belk

first: Kathryn

last: Yost

first: Kevin

last: Parker

first: Rui

first: Betty

last: Liu

first: Huang

last: Huang

first: Daniel

last: Lingwood

first: William

middle: J

last: Greenleaf

first: Mark

middle: M

last: Davis

first: Ansuman

last: Satpathy


title: β-catenin activity induces an RNA biosynthesis program promoting therapy resistance in T Acute Lymphoblastic Leukemia

city: Barcelona

first: Anna

last: Bigas

address: Dr. Aiguader 88

department: Cancer Research

institute: Institut Hospital del Mar d'Investigacions Mèdiques

summary:
Understanding the molecular mechanisms that contribute to the appearance of chemotherapy resistant cell populations is necessary to improve cancer treatment. We have now investigated the role of β-catenin/CTNNB1 in the evolution of T-Acute Lymphoblastic Leukemia (T-ALL) patients and its involvement in therapy resistance. We have identified a specific gene signature that is directly regulated by β-catenin, TCF/LEF factors and ZBTB33/Kaiso in T-ALL cell lines, which is highly and significantly represented in 5 out of 6 refractory patients from a cohort of 40 children with T-ALL. By subsequent refinement of this gene signature, we found that a subset of β-catenin target genes involved with RNA-processing function are sufficient to segregate T-ALL refractory patients in three independent cohorts. We demonstrate the implication of β-catenin in RNA and protein synthesis in T-ALL and provide in vitro and in vivo experimental evidence that β-catenin is crucial for the cellular response to chemotherapy, mainly in the cellular recovery phase after treatment.
We propose that combination treatments involving chemotherapy plus β-catenin inhibitors will enhance chemotherapy response and prevent disease relapse in T-ALL patients.

overall_design:
ChIPseq experiments: For b-catenin: RPMI8402 cell line: n=5 for R&D antibody in basal conditions, n =2 for R&D antibody upon LiCl treatment, n=2 for SC antibody in basal conditions, n=2 for SC antibody upon LiCl treatment. For Jurkat cell line: n=3 for R&D antibody in basal conditions in the Jurkat cell line.
For TCF1,LEF1,Kaiso: precipitating TCF1 (n=3), LEF1 (n=3) and Kaiso (n=3) in RPMI8402
For RNA-seq experiments in RPMI8402:RNAseq analysis of sh-β-catenin vs sh-control (n=3 for each condition).
For H3Ac in RPMI in basal conditions (n=2) and LiCl treated (n=2)


title: Engineered cell entry links receptor biology with single-cell genomics [bulk RNA-Seq]

first: Howard

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CMV-TCR Jurkat T cells incubated with pp65 pMHC tetramer or pp65 pMHC displayed ENTER virus-like particles.

last: Shi

last: Li

middle: T


title: Transmembrane TNF-TNFR2 axis promotes generation of human T cell precursors.

city: Ghent

first: Tom

last: Taghon

address: Corneel Heymanslaan 10

country: Belgium

institute: Ghent University

summary: The goal of this study is to dissect the impact of soluble (sTNF) and transmembrane (tmTNF) forms of tumour necrosis factor on the differentiation of human hematopoietic stem and progenitor cells (HSPCs) into T cell precursors. To achieve this, we utilized scRNA-sequencing technologies to compare the transcriptome profiles of HSPCs that had been differentiated in the artificial thymic organoid (ATO) system in the absence (control) or presence of TNF signal (soluble or transmembrane).

overall_design: CD3-CD14-CD19-CD56-CD34+ umbilical cord blood HSPCs from 4 donors were pooled and induced to undergo T cell development using the ATO system. In the absence of TNF signal (control), ATOs were supplemented with interleukin-7 and FMS-like tyrosine kinase 3 ligand. For sTNF-activated ATOs, organoids were supplemented additionally with 0.25 ng/mL of sTNF. For tmTNF-activated ATOs, 1 % of the stromal cells that were used to assemble organoids were engineered to express tmTNF. At day 10 post culture, CD45+ differentiating HSPCs were sorted from all three conditions and analysed using scRNA-seq.

first: KaiLing

last: Liang

last: Putteman

first: Lena

last: Boehme

first: Filip

last: Van Nieuwerburgh


title: Tumor cell-intrinsic BTLA receptor inhibits the proliferation of tumor cells via ERK1/2

first: Shan

last: Gao

address: No. 2 Sipailou, Xuanwu District

institute: Southeast University

summary: B and T lymphocyte attenuator (BTLA) is an immune checkpoint molecule that mediates the escape of tumor cells from immunosurveillance. Consequently, BTLA and its ligand-herpesvirus entry mediator （HVEM） are potentially immunotherapeutic targets. However, the potential effects of BTLA on tumor cells remain incompletely unknown. Here, we show that BTLA is expressed across a broad range of tumor cells. The depletion of BTLA or HVEM promotes cell proliferation and colony formation，which is reversed by re-overexpression of BTLA in BTLA knockout (KO) cells. On the contrary, overexpression of BTLA or HVEM inhibits tumor cell proliferation and colony formation. Furthermore, the proliferation of subpopulation with high BTLA is also significantly slower than that of the low BTLA subpopulation. Mechanistically, the coordination of BTLA and HVEM inhibits its major downstream ERK1/2 signaling pathway, thus preventing tumor cell growth. This study demonstrates that tumor cell-intrinsic BTLA/HVEM is a potential tumor suppressor and likely to have potential antagonist for immunotherapy, thus representing a potential biomarker for the optimal cancer immunotherapeutic treatment.

overall_design: RNA-sequence of BTLA KD with control cells and the sorting subpopulations of high BTLA expression and low BTLA expression were performed and analysed by Berry Genomics (Beijing, China).

first: Tianyou

last: Cheng

first: Yajuan

first: Hong

last: Yan

first: Yibo

last: Xi

first: Liqiang

last: Duan

first: Yang

last: Wang

first: Tiantian

last: Zhang

first: Yinmin

last: Gu

first: Xiaodong

first: Changxin

last: Wu


title: iCLIP of endogenous PURA in neuronal precursor cells

city: Würzburg

first: Kathi

last: Zarnack

address: Biocenter, Am Hubland

department: Theodor Boveri Institute

country: Germany

institute: University Würzburg

summary: The protein PURA binds to DNA and RNA and has been suggested to be implicated in different cellular functions. Here, we show that PURA predominantly resides in the cytoplasm, where it binds to a large set of transcripts.

overall_design: We performed PURA iCLIP with a PURA specific Antibody in neuronal precursor cells in four biological replicates.

last: Molitor

first: Melina

last: Klostermann

first: Anke

last: Busch

first: Ejona

last: Rusha

first: Anna

last: Pertek

first: Julian

last: König

first: Dierk

last: Niessing


title: RNAseq of PURA knockdown in HeLa cells

summary: Here, we show that PURA predominantly resides in the cytoplasm, where it binds to a large set of transcripts. Many of these transcripts change abundance in response to PURA depletion, in parts reflected in altered protein expression levels. A closer inspection of the regulated proteins indicates a role of PURA in immune responses, mitochondrial function, autophagy and processing (P)-body activity.

overall_design: Poly A+ RNAseq of HeLa cells with 4 PURA siRNA knockdown and 4 control samples.

first: Lena


title: Genomic DNA copy number alterations of mouse B-cell lymphomas induced by ionizing radiation

city: Chiba

first: Kazuhiro

last: DAINO

address: 4-9-1 Anagawa, Inage-ku

country: Japan

institute: National Institutes for Quantum and Radiological Science and Technology

summary: To investigate DNA copy number changes in mouse B-cell lymphoma induced by ionizing radiation.

overall_design: DNA copy number changes in radiation-induced mouse B-cell lymphomas were analyzed using array-CGH microarray.

first: Hirotaka

last: Tachibana

last: Daino

first: Yi

last: Shang

first: Shizuko

last: Kakinuma


title: iCLIP of FLAG-PURA overexpression with anti-PURA12D11 antibody in HeLa cells

overall_design: We performed PURA iCLIP with a PURA specific Antibody in HeLa cells with a stable FLAG-PURA overexpression in four biological replicates.


title: Depletion of the RNA-binding protein PURA triggers changes in posttranscriptional gene regulation.

overall_design: Refer to individual Series


title: iCLIP of endogenous PURA in HeLa cells

overall_design: We performed PURA iCLIP with a PURA specific Antibody in HeLa cells in four biological replicates.


title: Direct In Vivo Cardiac Reprogramming as a Novel Therapeutic Strategy for Chronic Myocardial Infarction [Array]

city: Shinjuku

first: Taketaro

last: Sadahiro

state: Tokyo

address: 35 Shinanomachi

institute: Keio University School of Medicine

summary: Heart failure (HF) is a leading cause of morbidity and mortality. As adult cardiomyocytes (CMs) have little regenerative capacity, after myocardial infarction (MI), resident cardiac fibroblasts (CFs) synthesize extracellular matrix to form scar tissues, resulting in myocardial remodeling and HF. Thus, both cardiac regeneration and fibrosis are therapeutic targets for chronic MI. We previously reported that fibroblasts were directly reprogrammed into induced CMs (iCMs) by overexpression of cardiogenic transcription factors in vitro and in vivo in acute MI. Here we show that in vivo cardiac reprogramming generated iCMs from resident CFs, improved cardiac function, and reversed fibrosis in chronic MI using a novel transgenic mouse system. Transcriptome analysis revealed that in vivo cardiac reprogramming altered the interstitial cell landscape, suppressed signs of fibrosis and inflammation, and activated the angiogenic program. Thus, in vivo cardiac reprogramming may be a promising approach for chronic HF.

overall_design: Hearts were harvested 3 months after MI from two groups (Ctrl-MI and TTg-MI) for microarray analyses (n = 2 independent biological replicates)(Clariom S Array, Mouse, Affymetrix).

first: Hidenori

last: Tani

first: Masaki

last: Ieda


title: Therapeutic Effect of Histone Acetyltransferase Inhibitors on Galactose-Induced Cataract in Rats

status: Public on Dec 11 2022

city: Fukui

first: Masaya

last: Nagaya

address: 3-9-1 Bunkyo

institute: University of Fukui

summary:
We investigated the therapeutic effects of histone acetyltransferase (HAT) inhibitors on cataracts using an ex vivo model of galactose-induced cataracts in the rat lens.Among the tested HAT inhibitors, TH1834 was the only inhibitor that could completely reverse white opacities once formed in the lens. Combination treatment with C646/CPTH2 and CBP30/CPTH2 also had therapeutic effects.
To identify the genes regulated by HAT inhibitors, we conducted microarray analysis of treated and untreated cataract samples.

overall_design: Genes that increased in galactose-treated lenses and reverted with HAT inhibitors were extracted.

first: Risa

last: Yamaoka

first: Fumito

last: Kanada

first: Tamotsu

last: Sawa

first: Yoshihiro

last: Takamura

first: Masaru

last: Inatani

last: Oki


title: SREBP modulates the NADP+/NADPH cycle to control night sleep in Drosophila

city: Lausanne

first: Tilmann

last: Achsel

state: VD

address: Rue Bugnon 9

department: Dept. Fundamental Neurosciences

country: Switzerland

institute: University of Lausanne

summary: We investigated sleep deficits in Cyfip mutant Drosophila flies, a model for intellectual disabilities/neurodevelopmental disorders. RNA-seq was performed on heads at the circadian time point ZT16, i.e., during the night when wild-type flies are asleep.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Cyfip mutant versus control heads.

first: Vittoria

last: Mariano

first: Alexandros

last: Kanellopoulos

first: Claudia

last: Bagni


title: Direct In Vivo Cardiac Reprogramming as a Novel Therapeutic Strategy for Chronic Myocardial Infarction [scRNA-Seq]

summary: Heart failure (HF) is a leading cause of morbidity and mortality. As adult cardiomyocytes (CMs) have little regenerative capacity, after myocardial infarction (MI), resident cardiac fibroblasts (CFs) synthesize extracellular matrix to form scar tissues, resulting in myocardial remodeling and HF. Thus, both cardiac regeneration and fibrosis are therapeutic targets for chronic MI. We previously reported that fibroblasts were directly reprogrammed into induced CMs (iCMs) by overexpression of cardiogenic transcription factors in vitro and in vivo in acute MI. Here we show that in vivo cardiac reprogramming generated iCMs from resident CFs, improved cardiac function, and reversed fibrosis in chronic MI using a novel transgenic mouse system. Single-cell transcriptome analysis revealed that cardiac reprogramming shifted matrix-producing CFs, matrifibrocytes, to a quiescent state and changed the interstitial cell landscape, suppressing fibrotic and inflammatory signatures and activating angiogenic program. Thus, in vivo cardiac reprogramming may be a promising approach for chronic HF.

overall_design: Hearts were harvested 3 months after MI from three groups (Sham, Ctrl-MI, and TTg-MI) for scRNA-Seq.


title: Direct In Vivo Cardiac Reprogramming as a Novel Therapeutic Strategy for Chronic Myocardial Infarction


title: iCLIP of FLAG-PURA overexpression with anti-FLAG antibody in HeLa cells

first: Kathi

last: Zarnack

overall_design: We performed PURA iCLIP with a PURA specific Antibody in HeLa cells with a stable FLAG-PURA overexpression in two biological replicates.

first: Lena

last: Molitor

first: Melina

last: Klostermann

first: Anke

last: Busch

first: Julian

last: König

first: Dierk

last: Niessing


title: Transmembrane TNF-TNFR2 axis promotes generation of human T cell precursors

first: Tom

last: Taghon

state: East Flanders

department: Diagnostic Sciences (GE32)

summary: The goal of this study is to understand how low level of IRF8 expression promotes the differentiation of human hematopoietic stem and progenitor cells (HSPCs) into T cell precursors. To achieve this, we utilized a construct that encodes IRF8-ERT2 fusion protein where IRF8 activity is tamoxifen-dependent. We extracted genomic DNA from HSPCs that had been co-cultured with OP9-DLL4 stromal cells and tagmented by Tn5 transposase for ATAC-sequencing. This allowed us to determine the impact of low level of IRF8 activity on the chromatin accessibility landscape of differentiating HSPCs. Our analysis found significant opening of chromatin region at the TNF core promoter in the presence of low  level of IRF8 activity.

overall_design: HSPCs from 3 donors were transduced with empty vector control or IRF8-ERT2. In each condition, transduced HSPCs were sorted after 4 days of co-culture to obtain two subsets (CD45+GFP+CD7+ cells and CD45+GFP+CD34+CD7- cells) for ATAC-seq.

first: KaiLing

last: Liang

first: Juliette

last: Roels

first: Filip

last: VanNieuwerburgh


summary: The goal of this study is to understand how low level of IRF8 expression promotes the differentiation of human hematopoietic stem and progenitor cells (HSPCs) into T cell precursors. To achieve this, we utilized a construct that encodes IRF8-ERT2 fusion protein where IRF8 activity is tamoxifen-dependent. We extracted total RNA from transduced HSPCs that had been co-cultured with OP9-DLL4 stromal cells and treated with or without 4-hydroxytamoxifen (4-OHT) for sequencing. This allowed us to determine the impact of low level of IRF8 activity on the transcriptome profile of differentiating HSPCs. Our analysis found significant increase of TNF expression in the presence of low  level of IRF8 activity.

overall_design: HSPCs from 3 donors were transduced with empty vector control or IRF8-ERT2. No treatment was  performend on the control cells whereas IRF8-ERT2-transduced cells were treated with 4-hydroxytamoxifen (4-OHT) or compound solvent. For all conditions, transduced HSPCs were sorted at day 4 post co-culture to obtain CD45+GFP+CD7+ cells for RNA extraction and sequencing.

first: Laurentijn

last: Tilleman


title: TIGIT inhibition and lenalidomide synergistically promote anti-myeloma immune responses after stem cell transplantation in mice

status: Public on Dec 10 2022

city: Seattle

first: Scott

middle: N

last: Furlan

address: 1100 Fairview Ave N

country: USA

institute: CRD

summary: TIGIT inhibition and lenalidomide promote synergistic myeloma immunity by expanding non-exhausted memory CD8 T cells

overall_design: 4 samples

first: Simone

last: Minnie

first: Geoffrey

last: Hill


title: Single cell RNA-seq of fresh human cord blood mononuclear cells (CBMNCs) and umbilical vein endothelial cells (HUVECs)

city: Indianapolis

first: Jered

last: Myslinski

state: IN

address: 950 W Walnut Street

department: Nephrology and Hypertension

institute: Indiana University School of Medicine

summary: To investigate the rare circulating endothelial colony-forming cells and compare their characteristics with umblical vein endothelial cells, single-cell RNAseq was performed (10X Genomics).

overall_design: Freshly isolated and MACS sorted CBMNCs and HUVECs from a same individual human subject were applied to construct libraries.

first: Banno

last: Kimihiko

first: Myslinski

last: Jered Joseph

first: Hato

last: Takashi


title: Next Generation Sequencing Facilitates Quantitative Analysis of wild type H2AZ and H2AZ_4KR and Ino80K929R Transcriptomes

city: wuhan

first: Yu

last: Qi

state: Hubei

address: xujiapeng

department: College of life sciences

country: China

institute: Hubei university

summary: Cells need to coordinate gene expression with their metabolic states to maintain cell homeostasis and growth. However, how cells transduce nutrient availability to appropriate gene expression response via histone modifications remains poorly understood.

overall_design: Total RNA was isolated from exponential growing yeast cells by standard phenol-chloroform extraction procedures and the quality of RNA was examined using Agilent Bioanalyzer according to the manufacturer’s instructions. Library construction, sequencing and bioinformatics analysis were performed. Differential expression levels of aligned sequences were calculated using significant thresholds set at fold change over 1.5 and adjusted P-value < 0.05

first: Li

last: Xin