title: NLRP3 inflammasome activation aggravates skeletal muscle atrophy in experimental model of denervation

status: Public on Dec 29 2022

city: Shanghai

first: Zongqi

last: You

address: #12, Wulumuqi M Road

institute: Huashan Hospital

summary: The innervation of skeletal myofibers exerts a crucial influence on the maintenance of muscle tone and normal operation, but little is known concerning atrophy and its underlying mechanisms in denervated muscle to date. Here, we reported that activated NOD-like receptor protein 3 (NLRP3) inflammasome with pyroptotic cell death occurred in denervated gastrocnemius in the mouse model of sciatic denervation. This damage causes interleukin 1 beta (IL-1β) release，facilitating the ubiquitin proteasome system (UPS) activation, which was responsible for muscle proteolysis. Conversely, genetic knock-out of muscular NLRP3 inhibited the pyroptosis-associated protein expression and ameliorate muscle atrophy significantly. Meanwhile, co-treatment with shRNA-NLRP3, also remarkably attenuated NLRP3 inflammasome activator (NIA)-induced C2C12 myotube pyroptosis and atrophy. Interestingly, we also observed a correlation between NLRP3 inflammasome activation and muscular apoptosis possibly via caspase 1 mediation after denervation. This work for the first time elucidates on the roles and mechanisms of NLRP3 inflammasome in skeletal muscle atrophy during denervation and suggests the potential contribution to the pathogenesis of neuromuscular diseases.

overall_design: Examination of 32 different gastrocnemius muscles post denervation

first: Xinying

last: Huang

first: Junjian

last: Jiang

first: Jianguang

last: Xu


title: Biochronicity Challenge Study Gene Expression Data

status: Public on Dec 30 2022

city: ANN ARBOR

first: ALFRED

middle: Olivier

last: HERO

state: MI

address: 1301 BEAL AVE

country: USA

institute: UNIVERSITY OF MICHIGAN

type: Expression profiling by high throughput sequencing

summary: A longitudinal human rhinovirus (HRV) challenge study with 19 volunteers was performed at University of Virginia in Sept 2015. The study collected  peripheral blood samples 3 times/day over a 8 day time period,  where an incoculation with live virus (RV39) was administered on the 4th day (Day 0). The obective was to quantify changes in gene expression induced by the viral challenge.

overall_design: RNAseq gene expression profiling in whole blood, covering both pre-inoculation (baseline) and post-inoculation time periods. 24 volunteers were recruited into the study, labeled from 01 to 24,  of which 18 sucessfully completed the study. Samples were collected from each volunteer in the morning around 8am (AM), in the afternoon around 4pm (PM1) and in the evening around 12pm (PM2).

first: Yaya

last: Zhai

first: Alfred

last: Hero

first: Thomas

last: Burke

first: Murali

last: Doraiswamy

first: Geoffrey

last: Ginsburg

first: Ricardo

last: Henao

first: Chrissy

last: Nix

first: Ronald

middle: B

last: Turner

first: Christopher

middle: W

last: Woods


title: Sperm Energy Restriction and Recovery (SER) Alters Epigenetic Marks during the First Cell Cycle of Development in Mice

status: Public on Dec 27 2022

city: Boston

first: Qiangzong

last: Yin

state: MA

address: 3 Blackfan St, CLS building 440A

department: Medicine

institute: BIDMC/Harvard Medical School

summary: The sperm energy restriction and recovery (SER) treatment developed in our laboratory was shown to improve fertilization and blastocyst development following in vitro fertilization (IVF) in mice. Here, we investigated the effects of SER on early embryogenesis. Developmental events observed during the first cell cycle indicated that progression through the pronuclear stages of SER-generated embryos is advanced in comparison with control-generated embryos. These findings prompted further analysis of potential effects of SER on pronuclear chromatin dynamics, focusing on the key H3K4me3 and H3K27ac histone modifications. Nearly all the SER-generated embryos displayed H3K4me3 in the male pronuclei at 12 hours post-insemination (HPI), while a subset of the control-generated embryos did not. Additionally, SER-generated embryos dis-played a more homogenous intensity of H3K27ac at 8 and 12 HPI compared to control embryos. These changes in histone modifications during the first cell cycle were accompanied by differences in gene expression at the two-cell stage; both of these changes in early embryos could potentially play a role in the improved developmental outcomes of these embryos later in development. Our results indicate that sperm incubation conditions have an impact on early embryo develop-ment and can be useful for the improvement of assisted reproductive technology outcomes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control and Sperm Energy Restriction and Recovery (SER) 2-Cell embryos in mice.

first: Darya

middle: A

last: Tourzani

first: Erica

last: Jackson

first: Oliver

middle: J

last: Rando

first: Pablo

middle: E

last: Visconti

first: Maria

middle: G

last: Gervasi


title: Histone methylation regulator PTIP orchestrates inflammatory responses via modulating acetylation state of cis-regulatory elements [ChIP-Seq]

city: wuhan

first: Haojian

last: Zhang

state: Hubei

address: Donghu Rd

department: Medical Research Institute

country: China

institute: Wuhan university

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Innate immune cells including myeloid cells exhibit dynamic cellular switches during inflammatory and immune responses against infection. These processes are tightly regulated at different levels including the cis-regulatory elements of immune cells. However, it remains unclear how the dynamic states of cis-regulatory elements of innate immune cells are controlled during inflammatory responses. Here we found that histone methylation regulator PTIP orchestrates inflammatory responses of macrophages through regulating acetylation state of enhancers and promoters. Rapid elevated expression of PTIP is observed in primary human and mouse macrophages upon lipopolysaccharide (LPS) stimulation. Loss of PTIP represses transcription of pro-inflammatory genes, and activates expression of anti-inflammatory genes. Mechanistically, we found that, independent of its function in histone methylation, PTIP interacts with acetyltransferase p300 and deacetylase HDACs, and serves as a beacon to recruit them to specific sites of inflammatory genes respectively. PTIP deficiency alters H3K27 acetylation state of cis-regulatory elements of inflammatory genes. Moreover, PTIP and c-JUN shape a positive and feedforward regulatory circuit. In addition, PTIP deletion sustains immunosuppressive function of tumor-associated macrophages (TAMs) and promotes tumor growth. Overall, our findings uncover a critical role of PTIP in altering the acetylation state of cis-regulatory regions and fine-tuning the inflammatory responses of innate immune cells.

overall_design: [BMDM- ChIP -seq] ChIP-seq analysis of epigenetic changes in BMDMs from PtipWT or PtipcKO mice stimulated with LPS (100 ng/ml) for 0 or 6 hours. We performed ChIP-seq for H3K4me1, H3K4me3, H3K27ac, p300 and Hdac3 in BMDMs with two biological replicates.

first: Qifan

last: Wang

first: Jin

last: Hu

first: Guoqiang

last: Han


title: Histone methylation regulator PTIP orchestrates inflammatory responses via modulating acetylation state of cis-regulatory elements

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

overall_design: Refer to individual Series


title: The Poly(C)-binding protein Pcbp2 is essential for CD4+ T cell development and proliferation.

city: Philadelphia

first: David

middle: Sheng Ming

last: Lee

state: Pennsylvania

address: 1500 Chestnut St Apt 12D

department: Genetics

institute: University of Pennsylvania

summary: Defining the molecular mechanisms that impact T cell maturation and function is important because abnormalities in these processes can lead to immunodeficient states or autoimmunity. RNA-binding proteins (RBPs) have emerged as critical factors in thymopoiesis, immune cell lineage commitment and maintenance, and as modulators of immune responses. The RBP paralogs Pcbp1 and Pcbp2 are widely expressed in the innate and adaptive immune systems and are each essential for mouse development. Pcbp1 has been shown to prevent conversion of CD4+ effector T cells into Foxp3+ regulatory T cells (Treg), with loss of Pcbp1 resulting in increased Treg differentiation. To determine whether Pcbp2 also is required for CD4+ T cell development and function, we derived mice with conditional Pcbp2 deletion in CD4+ T cells and assessed their overall phenotype and proliferative responses to activating stimuli. We found that Pcbp2 is essential for CD4+ T conventional cell (Tconv) proliferation, working through regulation of CD4 receptor co-stimulatory signaling. In addition, our data demonstrate a clear association between Pcbp2 control of Runx1 exon 6 splicing in CD4+ T cells and a specific role for Pcbp2 in the maintenance of peripheral CD4+ lymphocyte population size. Pcbp2 deficiency in the CD4+ lineage did not impact Treg abundance in vivo or function in vitro. Last, we show that Pcbp2 function is required for optimal in vivo Tconv cell activation in a T cell adoptive transfer colitis model system. These data lead us to conclude that Pcbp2 is a critical regulator of T cell signaling and function in the CD4+ lineage.

overall_design: Examination of differentially expressed genes in splenic T effector cells with or without PCBP2 CKO

first: Massimo

last: Martinelli

first: Gabrielle

last: Aguilar

middle: S

first: Andrew

last: Kromer

first: Nhu

last: Nguyen

first: Bejnamin

last: Wilkens

first: Tatiana

last: Akimova

first: Ulf

middle: H

last: Beier

first: Louis

middle: R

last: Ghanem


title: Changes in undifferentiated and differentiated human primary epithelial cells of antrum, corpus, and fundus

status: Public on Dec 28 2022

city: Berlin

first: Thomas

middle: F

last: Meyer

address: Chariteplatz 1

department: Molecular Biology

country: Germany

institute: Max Planck Institute for Infection Biology

type: Methylation profiling by genome tiling array


title: Gene expression changes in undifferentiated and differentiated human primary epithelial cells of antrum, corpus, and fundus

summary: Gene expression changes specific for healthy undifferentiated and differentiated human gastric primary epithelial cells of different regions of the stomach were here determined in order to describe the transcriptomic profile of these cells in correlation to their DNA methylation pattern. In addition, gene expression changes upon 5-aza-2'-deoxycytidine treatment of antral gastric primary cells compared to mock-treated cells were deterimend.

overall_design: Primary gastric epithelial cells were isolated from gastric sleeve resection material and cultivated as musosoids for 1-2 passages. RNA was isolated from the filter following the Trizol extraction method and gene expression was determined by Agilent 8x60k human custom single-color arrays. Three biological replicates of six different conditions (undifferentiated and differentiated antrum, corpus, and fundus samples) were analyzed as healthy gastric primary cells and two biological replicates of 5-aza-2'-deoxycytidine-treated and mock-treated undifferentiated antral  samples were analyzed.

first: Kristin

last: Fritsche

first: Hilmar

last: Berger


title: Single cell RNA-seq data for mouse fallopian tube and ovary

first: Zhe

last: Li

address: 77 Avenue Louis Pasteur, Room 466

department: Medicine, Genetics Division

institute: Brigham and Women's Hospital

summary: Epithelial ovarian cancer (EOC) is the most lethal malignancy of the female reproductive system. In order to improve EOC patient outcomes, it is crucial to have a better understanding of how EOC develops from its cellular origin. EOCs can originate from either fallopian tube epithelial (FTE) cells or ovarian surface epithelial (OSE) cells, but with different courses of development. The basis for this difference is unclear. To address this, we performed single cell RNA-sequencing of mouse cells isolated from the distal portion of fallopian tubes (i.e., oviducts) and surface layer of ovaries. Analysis of this single cell dataset revealed distinct niche organizations for murine FTE cells and OSE cells.

overall_design: Fallopian tube and ovarian tissues from two wild-type adult FVB female mice were isolated. Single cells were prepared from the distal half (i.e., the portion close to ovary, thus including the fimbrial region) of fallopian tubes and from the stripped surface layer of each ovary. The resulting single cells were subjected to barcoding using the inDrop platform. The resulting expression libraries were then subjected to high throughput sequencing.

first: Eunsil

last: Park


title: Arid1b ChIP-seq

status: Public on Dec 25 2022

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

summary: Arid1b ChIP-seq

overall_design: two replicates of Arid1b ChIP-seq and one input sample in Human HEK293FRT cells.

first: Divya

last: Reddy

first: Jerry

last: Workman


title: RNAseq data of frontal cortex of Sprague Dawley rats expressing rat amylin (WT), human amylin (HIP), and rat amylin knock-out (AKO) rats

city: Lexington

first: Nirmal

last: Verma

state: Kentucky

address: 900 S Limestone

department: Pharmacology and nutritional sciences

institute: University of Kentucky

summary: To investigate the effect of pancreatic human amylin protein on the gene expression profiles of the brain

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of Sprague Dawleys rat expressing rat amylin, and Sprague Dawley rats expressing human amylin and rat amylin in pancreas

first: Florin

last: Despa


title: Gene network analysis for identification of microRNA biomarkers for asthma [Serum_miRNASeq]

status: Public on Dec 26 2022

city: Reno

first: Mariam

last: Ba

address: 1664 N. Virginia St

institute: University of Nevada, Reno

type: Non-coding RNA profiling by high throughput sequencing

summary: To analyze circulating miRNA signatures using a house dust mite model (HDM) of asthma. microRNA sequencing (miRNA-seq) was performed using serum from BALB/c mice (male and female, ages 6-8 weeks old).

overall_design: Circulating miRNA signatures from HDM-exposed mice (n=16) were compared to the miRNA profiles of  Saline-treated (controls, n=14)  mice.

last: BA

first: Cherie

last: Singer

first: Paulene

last: Cay


title: Gene network analysis for identification of microRNA biomarkers for asthma [Lung_miRNASeq]

summary: To analyze lung miRNA signatures using a house dust mite model (HDM) of asthma. microRNA sequencing (miRNA-seq) from BALB/c mice (male and female, ages 6-8 weeks old) lung tissue was performed.

overall_design: Lung miRNA profile from HDM-exposed mice (n=16) was compared to the profile of  Saline-treated (controls, n=14)  mice.


title: Single-cell transcriptomics unveils xylem cell development and evolution

city: Taipei

first: Ying-Chung Jimmy

last: Lin

address: No. 1, Sec. 4, Roosevelt Rd.

department: Department of Life Science

country: Taiwan

institute: National Taiwan University

summary: The plant xylem tissue is responsible for water transportation, mechanical support and lateral growth, and can be utilized as wood. The seed plant xylem has a radial system composed of ray parenchyma cells and an axial system of fusiform cells, including tracheids in gymnosperms and vessel elements and libriform fibers in angiosperms. Little is known about the developmental programs and evolutionary relationships of these xylem cell types. Here we show that the radial and axial systems of stem-differentiating xylem are differentially conserved across four divergent woody angiosperms. Through transcriptomic profiling of single cells and cell-type regions isolated by laser capture microdissection, we identified cell types corresponding to single-cell clusters in Populus trichocarpa. Cross-species analyses of single-cell trajectories demonstrated highly conserved development in ray lineages across angiosperms. While the core eudicots P. trichocarpa and Eucalyptus grandis share nearly identical fusiform cell lineages, the tracheids in the basal eudicot Trochodendron aralioides, an evolutionarily reversed character, exhibited an expression pattern highly similar to that of vessel elements. It suggests that water transportation, instead of mechanical support, is the dominant feature of tracheary elements. Furthermore, we found that the more basal angiosperm Liriodendron chinense has a distinct fusiform lineage. This evo-developmental framework of xylem cell lineages provides a comprehensive understanding of the formation of the most abundant tissue on Earth.

sample_organism:
Liriodendron chinense
Populus trichocarpa
Trochodendron aralioides
Eucalyptus grandis

overall_design: Single-cell RNA sequencing of stem differentiating xylem (SDX) of Populus trichocarpa, Eucalyptus grandis, Trochodendron aralioides, Liriodendron chinense. Laser capture microdissection and RNA sequencing of three xylem cell types.

first: Chia-Chun

last: Tung

first: Shang-Che

last: Kuo

first: Chia-Ling

last: Yang

first: Jhong-He

last: Yu

first: Chia-En

last: Huang

first: Pin-Chien

last: Liou

first: Ying-Hsuan

last: Sun

first: Peng

last: Shuai

first: Jung-Chen

last: Su

first: Chuan

last: Ku

first: Ying-Chung


title: Race-specific patterns of epigenetic aging and age-associated differential methylation in normal rectal biopsies: Implications for the biology of aging and its relationship to rectal cancer

status: Public on Dec 23 2022

city: Charlottesville

first: Matthew

last: Devall

state: Virginia

address: 1335 Lee Street

institute: University of Virginia

summary: Approximately 90% of colorectal cancer (CRC) develop over the age of 50, highlighting the im-portant role of aging in CRC risk. African Americans (AAs) shoulder a greater CRC burden than European Americans (EA), and are more likely to develop CRC at a younger age. The effects of aging in AA and EA normal rectal tissue have yet to be defined. Here, we performed epige-nome-wide DNA methylation analysis in the first, large-scale biracial cohort of normal rectum (n=140 samples)

overall_design: Horvath clock was used to analyze epigenetic age acceleration in human rectum. DMRcate was performed to identify differences in DNA methylation associated with aging in AA and EA rectum. Differences were related to existing rectal cancer.

first: Xiangqing

first: Stephen

last: Eaton

first: Fangcheng

last: Yuan

first: Gregory

last: Cooper

first: Joseph

last: Willis

first: Daniel

last: Weisenberger

first: Graham

last: Casey

first: Li

last: Li


title: miRBind: a Deep Learning Method for miRNA Binding Classification

status: Public on Dec 22 2022

city: Brno

first: Vaclav

last: Hejret

address: Kamenice 5

country: Czech Republic

institute: Masaryk University

summary: Here we present miR-eCLIP analysis of AGO2 in HEK293 cells to address the small RNA repertoire and uncover their physiological targets. We developed an optimized bioinformatics approach of chimeric read identification to detect chimeras of high confidence, which were useed as an biologically validated input for miRBind, a deep learning method and web-server that can be used to accurately predict the potential of miRNA:target site binding.

overall_design: miR-eCLIP analysis of AGO2 in HEK293 cells in 2 replicates with overexpressed tRNA fragment

first: Eva

last: Klimentova

first: Jan

last: Krcmar

first: Katarina

last: Gresova

first: Ilektra-Chara

last: Giassa

first: Panagiotis

last: Alexiou


title: The meningeal transciptional response to traumatic brain injury and aging [Bulk-seq]

last: Shapiro

state: VA

address: 1340 Jefferson Park Ave

department: Neuroscience

institute: University of Virginia School of Medicine

summary: Emerging evidence suggests that the meningeal compartment plays instrumental roles in various neurological disorders and can modulate neurodevelopment and behavior. While this has sparked great interest in the meninges, we still lack fundamental knowledge about meningeal biology. Here, we utilized high-throughput RNA sequencing (RNA-seq) techniques to investigate the transcriptional response of the meninges to traumatic brain injury (TBI) and aging in the sub-acute and chronic time frames. Using single-cell RNA sequencing (scRNA-seq), we first explored how mild TBI affects the cellular and transcriptional landscape in the meninges in young mice at one week post-injury. Then, using bulk RNA sequencing, we assessed the differential long-term outcomes between young and aged mice following a TBI. In our scRNA-seq studies, we found that mild head trauma leads to an activation of type I interferon (IFN) signature genes in meningeal macrophages as well as the mobilization of multiple distinct sub-populations of meningeal macrophages expressing hallmarks of either classically activated or wound healing macrophages. We also revealed that dural fibroblasts in the meningeal compartment are highly responsive to TBI, and pathway analysis identified differential expression of genes linked to various neurodegenerative diseases. For reasons that remain poorly understood, the elderly are especially vulnerable to head trauma, where even mild injuries can lead to rapid cognitive decline and devastating neuropathology. To better understand the differential outcomes between the young and the elderly following brain injury, we performed bulk RNA-seq on young and aged meninges from mice that had received a mild TBI or Sham treatment 1.5 months prior. Notably, we found that aging alone induced massive upregulation of meningeal genes involved in antibody production by B cells and type I IFN signaling. Following injury, the meningeal transcriptome had largely returned to its pre-injury signature in young mice. In stark contrast, aged TBI mice still exhibited massive upregulation of immune-related genes and markedly reduced expression of genes involved in extracellular matrix remodeling and maintenance of cellular junctions. Overall, these findings illustrate the dynamic and complex transcriptional response of the meninges to mild head trauma. Moreover, we also reveal how aging modulates the meningeal response to TBI.

overall_design: We performed bulk RNA sequencing on the meningeal tissue at 1.5 months post TBI or Sham treatment in both young (10 weeks of age) and aged (20 months of age)

first: Ashley

middle: C

last: Bolte

first: Arun

last: Dutta

first: Wei

last: Ma

first: Katherine

last: Bruch

first: Ana

last: Marco

first: John

last: Lukens


title: CD52 and OXPHOS - potential targets in ibrutinib treated mantle cell lymphoma

city: Würzburg

first: Hilka

last: Rauert-Wunderlich

address: Josef-Schneider-Str. 2 , E2

department: Institute of Pathology

institute: University of Würzburg

summary: We performed a RNA-seq analysis of an ibrutinib-sensitive mantle cell lymphoma cell line treated with ibrutinib for up to 4 d to study transcriptomic adaptations to the BTK inhibitor in surviving cells.

overall_design: Differential gene expression analysis across ibrutinib treatment in the ibrutinib-sensitive mantle cell lymphoma cell line REC-1.

first: Viktoria

last: Fuhr

first: Shanice

last: Heidenreich

first: Mugdha

last: Srivastava

first: Angela

last: Riedel

first: Johannes

last: Düll

first: Elena

last: Gerhard-Hartmann

first: Andreas

last: Rosenwald


title: The meningeal transciptional response to traumatic brain injury and aging [scRNA-seq]

first: Daniel

overall_design: We subjected mice to a mild closed-skull injury and then performed scRNAseq on whole dorsal meningeal tissue one week post injury. The meninges from 5 mice that had received TBI 1 week prior were pooled as one biological replicate. The meninges from 5 mice that had received a Sham procedure 1 week prior were pooled as one biological replicate.


title: Deep dive to the immune response against murine mesothelioma delineates a roadmap for preclinical investigations to advance anti-mesothelioma immune therapeutics

city: Paris

first: Sandrine

last: Imbeaud

address: 15 rue de l'Ecole de Médecine

department: INSERM UMRS1138-EQUIPE 28, Sorbonne Université-Inserm-Université de Paris

country: France

institute: Centre de Recherche des Cordeliers

summary: RNA sequencing data from syngeneic peritoneal tumors induced by the AB12 biphasic murine mesothelioma cell line were generated to determine molecular and immune changes during the kinetics of tumor growth.

overall_design: At least 3 tumor samples  of early-, intermediate- and advanced- phase AB12 tumors with or without anti-CTLA4 treatment  were analyzed by RNA sequencing in order to assess tumor transcriptomic changes as well as immune infiltration evolution.

first: Esther

last: Stern

first: Clément

last: Meiller

first: Didier

last: Jean

first: Ori

last: Wald


title: The meningeal transciptional response to traumatic brain injury and aging

last: Shapiro


title: DNA methylation changes in undifferentiated and differentiated human primary epithelial cells of antrum, corpus, and fundus

first: Thomas

last: Meyer

summary: DNA methylation changes specific for healthy undifferentiated and differentiated human gastric primary epithelial cells of different regions of the stomach were here determined in order to describe the epigenetic profile of these cells in correlation to their gene expression pattern.

overall_design: Primary gastric epithelial cells were isolated from gastric sleeve resection material and cultivated as musosoids for 1-2 passages. DNA was isolated from the filter using the QIAamp DNA mini kit and DNA methylation patterns were determined using the Illumina Infinium EPIC methylation beadchip. Three biological replicates of six different conditions (undifferentiated and differentiated antrum, corpus, and fundus samples) were analyzed.

first: Kristin

last: Fritsche

first: Hilmar

last: Berger


title: Gene network analysis for identification of microRNA biomarkers for asthma [Lung_RNASeq]

first: Mariam

last: Ba

summary: To identify relevant mRNA targets of differentially dysregulated lung miRNA signatures of a house dust mite mouse (HDM) model of asthma. cDNA libraries were constructed using the same lung RNA samples as the miRNA libraries preparation.

overall_design: Lung mRNA profile from HDM-exposed mice (n=16) was compared to the profile of  Saline-treated (controls, n=14)  mice.

last: BA

first: Cherie

last: Singer

first: Paulene

last: Cay


title: Gene network analysis for identification of microRNA biomarkers for asthma

overall_design: Refer to individual Series


title: The hippocampal response to acute corticosterone elevation is altered in a mouse model for Angelman syndrome

city: Leiden

first: Eva

last: Viho

email: e.viho@lumc.nl, viho.eva@gmail.com

address: Albinusdreef 2

country: Netherlands

institute: Leiden University Medical Center

summary: Angelman Syndrome (AS) is a severe neurodevelopmental disorder, caused by the neuronal absence of the ubiquitin protein ligase E3A (UBE3A).  UBE3A promotes ubiquitin-mediated protein degradation and functions as a transcriptional coregulator of nuclear hormone receptors, including the glucocorticoid receptor (GR). Previous studies showed anxiety-like behavior and hippocampal-dependent memory disturbances in AS mouse models. Hippocampal GR is an important regulator of the stress response and memory formation, and we therefore investigated whether the absence of UBE3A in AS mice disrupted GR signaling in the hippocampus.  We first established a strong cortisol-dependent interaction between the GR ligand binding domain and a UBE3A nuclear receptor box in a high-throughput interaction screen. In vivo, we found that UBE3A-deficient AS mice displayed significantly more variation in circulating corticosterone levels throughout the day compared to wildtypes (WT), with low to undetectable levels of corticosterone at the trough of the circadian cycle. Additionally, we observed an enhanced transcriptomic response in the AS hippocampus following acute corticosterone treatment. Surprisingly, chronic corticosterone treatment showed less contrast between AS and WT mice in the hippocampus and liver transcriptomic responses.  This suggests that UBE3A limits the acute stimulation of GR signaling, likely as a member of the GR transcriptional complex. Altogether, these data indicate that AS mice are more sensitive to acute glucocorticoid exposure in the brain compared to WT mice. This suggests that stress responsiveness is altered in AS which could lead to anxiety symptoms.

overall_design:
Gene expression profiling was performed using RNA-seq in hippocampus and liver tissue of wildtype (WT) and Angelman syndrome (AS) mice after acute or continuous corticosterone exposure.
WT C57BL/6J male and female 129sv Ube3am+/p- mice (Ube3atm1Alb; MGI 2181811), were crossed to generate F1 hybrid WT and Ube3am-/p+ (AS) offspring. The Ube3atm1Alb strain resulted from the deletion of the exon 5 of Ube3a, leading to an out-of-frame mutation and loss of UBE3A protein expression in neurons. Adult 10-18-week-old male mice were used in the experiments.

first: Eva M. G.


title: Beneficial and detrimental genes in the cellular response to replication arrest

status: Public on Dec 21 2022

city: Cambridge

first: Alan

last: Grossman

address: 31 Ames St.

department: Biology

institute: MIT

summary: DNA replication is essential for all living organisms. Several events can disrupt replication, including DNA damage (e.g., pyrimidine dimers, crosslinking) and so-called “roadblocks” (e.g., DNA-binding proteins or transcription). Bacteria have several well-characterized mechanisms for repairing damaged DNA and then restoring functional replication forks. However, little is known about the repair of stalled or arrested replication forks in the absence of chemical alterations to DNA. Using a library of random transposon insertions in Bacillus subtilis, we identified 35 genes that affect the ability of cells to survive exposure to an inhibitor that arrests replication elongation, but does not cause chemical alteration of the DNA. Genes identified include those involved in iron-sulfur homeostasis, cell envelope biogenesis, and DNA repair and recombination. In B. subtilis, and many bacteria, two nucleases (AddAB and RecJ) are involved in early steps in repairing replication forks arrested by chemical damage to DNA and loss of either nuclease causes increased sensitivity to DNA damaging agents. These nucleases resect DNA ends, leading to assembly of the recombinase RecA onto the single-stranded DNA. Notably, we found that disruption of recJ increased survival of cells following replication arrest, indicating that in the absence of chemical damage to DNA, RecJ is detrimental to survival. In contrast, and as expected, disruption of addA decreased survival of cells following replication arrest, indicating that AddA promotes survival. The different phenotypes of addA and recJ mutants appeared to be due to differences in assembly of RecA onto DNA. RecJ appeared to promote too much assembly of RecA filaments. Our results indicate that in the absence of chemical damage to DNA, RecA is dispensable for cells to survive replication arrest and that the stable RecA nucleofilaments favored by the RecJ pathway may lead to cell death by preventing proper processing of the arrested replication fork.

overall_design: Identification of genes involved in survival of treatment with the DNA replication inhibitor HPUra (6-(p-hydroxyphenylazo)-uracil) using a transposon insertion library

first: Luciane

last: Schons-Fonseca

first: Milena

middle: D

last: Lazova

first: Janet

middle: L

last: Smith

first: Mary

last: Anderson


title: DC vaccines loaded with glioma killed by photodynamic therapy induce Th17 anti-tumor immunity and provide a 4-gene signature for glioma prognosis

city: Gent

first: Dmitri

last: Krysko

address: C. Heymanslaan 10, 4B3

department: Department of Human Structure and Repair

country: Belgium

institute: Ghent University

summary: Gliomas are the most frequent type of primary tumor of the central nervous system in adults with significant morbidity and mortality. Despite the development of novel, complex, multidisciplinary, and targeted therapies, glioma therapy has not progressed much over the last decades. Therefore, there is an urgent need to develop novel patient-adjusted immunotherapies that actively stimulate antitumor T cells generating long-term memory and thus resulting in significant clinical benefits. This work aimed to investigate the efficacy and molecular mechanism of dendritic cell (DC) vaccines loaded with glioma cells undergoing immunogenic cell death (ICD) induced by photosens based photodynamic therapy (PS-PDT) and to identify reliable prognostic genes’ signatures for predicting patients’ overall survival (OS). The analysis of the transcriptional program of the ICD-based DC vaccine led to the identification of robust induction of Th17 signature when used as a vaccine, these DCs demonstrate retinoic acid receptor-related orphan receptor-γt dependent efficacy in orthotopic mouse model. Moreover, by comparative analysis of transcriptome program of the ICD-based DC vaccine with transcriptome data from the TCGA-low grade glioma (LGG) dataset the four-gene signature (CFH, GALNT3, SMC4, VAV3) associated with OS of glioma patients have been identified. This model has been validated on OS of CGGA-LGG, TCGA-glioblastoma multiforme (GBM) and CGGA-GBM datasets to determine whether it has a similar prognostic value. For this the sensitivity and specificity of the prognostic model for predicting the OS were evaluated by calculating the area under curve (AUC) of the time-dependent receiver operating characteristic (ROC) curve. The values of AUC for TCGA-LGG, CGGA-LGG, TCGA-GBM and CGGA-GBM were, respectively, 0.75, 0.73, 0.9 and 0.69 for predicting 5-year survival rates. These data open attractive prospects for improving glioma therapy by employing ICD and PS-PDT-based DC vaccines to induce Th17 immunity and to use this prognostic model to predict the OS of glioma patients.

overall_design: Examination of the efficacy of DC vaccines and unraveling the immunogenic signature triggered in the DCs by dying GL261 cells treated with PS-PDT or MTX cells.

first: Maria

last: Vedunova

first: Victoria

last: Turubanova

first: Olga

last: Vershinina

last: Savyuk

first: Iuliia

last: Efimova

first: Robrecht

last: Raedt

first: Tatiana

last: Mishchenko

first: Anne

last: Vral

first: Christian

last: Vanhove

first: Daria

last: Korsakova

first: Claus

last: Bachert

first: Frauke

last: Coppieters

first: Abhishek

last: Garg

first: Patrizia

last: Agostinis

first: Mikhail

last: Ivanchenko

middle: V


title: Single cell multi-omic reference atlases of non-human primate immune tissues reveals CD102 as a biomarker for long-lived plasma cells.

city: West Point

first: Ryan

last: Staupe

state: PA

address: 770 Sumneytown Pike

institute: Merck & Co., Inc.

summary: In response to infection or immunization, antibodies are produced that provide protection against re-exposure with the same pathogen. These antibodies can persist at high titers for decades and are maintained by bone marrow-resident long-lived plasma cells (LLPC). However, the durability of antibody responses to immunization varies amongst vaccines. It is unknown what factors contribute to the differential longevity of serum antibody responses and whether heterogeneity in LLPC contributes to this phenomenon. While LLPC differentiation has been studied extensively in mice, little is known about this population in humans or non-human primates (NHP). Here, we use multi-omic single-cell profiling to identify and characterize the LLPC compartment in NHP. We identify LLPC biomarkers including the marker CD102 and show that CD102 in combination with CD31 identifies LLPC in NHP bone marrow. Additionally, we find that CD102 is expressed by LLPC in mouse and humans. These results further our understanding of the LLPC compartment in NHP, identify biomarkers of LLPC, and provide tissue-specific single cell references for future studies.

overall_design: Mononuclear cells were isolated from rhesus macaque bone marrow, lymph nodes, and peripheral blood and subjected to single-cell RNA and surface protein profiling by CITEseq. Paired biological replicates from each of the 3 tissues profiled were obtained from 5 individual rhesus macaques.

middle: P

first: Nicole

last: Sullivan

first: Kalpit

last: Vora


title: A modular CRISPR screen identifies individual and combination pathways contributing to HIV-1 latency

city: Seattle

first: Emily

last: Hsieh

state: WA

address: 1100 Fairview Ave N, Mail Stop C2-023

institute: Fred Hutchinson Cancer Center

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


summary: The goal of this CRISPR-based screen (Latency HIV-CRISPR) is to identify HIV-1 latency factors by evaluating multiple pathways simultaneously. Here are Illumina sequencing data and counts files from a Latency HIV-CRISPR screen using a custom guide RNA library targeting human epigenome genes (HuEpi). The Latency HIV-CRISPR screens described here were performed in clonal ZAP knockout J-Lat 10.6 (PMID: 12682019) or J-Lat 5A8 (PMID: 24204950) cells lines as ZAP inhibition of the HIV-CRISPR vector has been previously described (PMID: 30520725). The screens were performed in the presence or absence of AZD5582, a SMAC mimetic and latency reversal agent, in order to identify factors that are dependent and independent of this transcriptional activator.

overall_design: Latency HIV-CRISPR is performed by generating a pool of ZAP-knockout J-Lat 10.6 and 5A8 cells that are each knocked out for human epigenome genes using the HuEpi guide RNA library. Each knockout pool is then treated with or without a low-activating dosage (10 nM) of AZD5582 for 24 hours. Each screen is performed in two biological replicates. Afterwards, for each condition, the cell pellets were harvested, genomic DNA (gDNA) was extracted, and sequencing was performed to evaluate the single guide RNA (sgRNA) representation of the library. Simultaneously, the viral supernatant was harvested, viral RNA (vRNA) was extracted, and sequencing was performed. By comparing the sgRNA representation of the viral RNA to the library representation of the genomic DNA, the sgRNAs that are enriched and depleted in the viral population are associated with potential HIV-1 latency factors. The plasmid library of the HIV-CRISPR HuEpi guide RNA library was also sequenced.

first: Michael

last: Emerman


title: A trio of bipotent precursors seeds the mesenchymal, haematopoietic, and endothelial lineages of the yolk sac

city: Melbourne

first: Samir

last: Taoudi

address: 1G Royal Parade

country: Australia

institute: The Walter and Eliza Hall Institute

summary: During embryogenesis, haematopoietic and endothelial lineages emerge closely in time and space. It is thought that the first blood and endothelium derive from a common clonal ancestor, the haemangioblast. However, investigation of candidate haemangioblasts in vitro has revealed a mesenchymal differentiation potential, a feature more compatible with an earlier mesodermal precursor. To date, no evidence for an in vivo haemangioblast has been discovered. Using single cell RNA-Sequencing and in vivo cellular barcoding, we have unraveled the ancestral relationships that give rise to the haematopoietic lineages of the yolk sac, the endothelium, and the mesenchyme. We show that the mesodermal derivatives of the yolk sac are produced by three distinct bipotential precursors: the haemangioblast, mesenchymoangioblast, and a novel cell type: the haematomesoblast. Between E6.5 and E7.5, this trio of precursors seeds haematopoietic, endothelial, and mesenchymal trajectories.

overall_design: This single cell RNAseq dataset was aimed at characterising non-blood, non endothelial components of the yolk sac. A pool of 33 C57BL/6 yolk sacs was enzymatically dissociated to generate a single cell suspension. 6 populations were sorted (primitive erythrocyte (EryP: TER119+ CD45-), haematopoietic progenitor/colony forming cell (HPC: TER119- CD41low CD45+), Megakaryocyte (Mk: TER119- CD41high CD45-), macrophage (Mac: TER119- CD41- CD45+), endothelium (Endo: TER119- CD41- CD45- PECAM+ PDGFRA-), mesenchyme (Mes: TER119- CD41- CD45- PECAM-)).  Each population was labelled with a unique MultiSeq hashtag to identify population of origin. Sorted cells were combined and loaded on the 10X Chromium.

first: Christine

last: Biben

first: Tom

last: Weber


title: Next generation sequencing identifies lncRNAs on replication forks of mouse embryonic stem cells

city: Kunming

first: Ping

last: Zheng

address: Qingsong Road 21

institute: Kunming Institute of Zoology, Chinease Academy of Sciences

summary: Purpose: The goals of this study are to identify lncRNAs on replication forks of embryonic stem cells.

overall_design: mouse embryonic stem cells or NIH3T3 cells were treated or untreated with HU, and RNAs on nascent DNA were isolated in mouse embryonic stem cells and NIH3T3 cells using iROND protocol.

first: Lin

last: Wang

first: Bo

last: Zhao

first: Weidao

last: Zhang


title: Fibroblast Growth Factor-2 bound to specific dermal fibroblasts-derived extracellular vesicles is protected from degradation: relevance to wound healing

city: Nijmegen

first: Jo Huiqing

last: Zhou

address: Geert Grooteplein 26/28

institute: Radboud University

summary: Fibroblast growth factor-2 (FGF2) has multiples roles in cutaneous wound healing but its natural low stability prevents the development of its use in therapeutic for impaired skin repair. Here we show that FGF2 binds the outer surface of dermal fibroblast (DF)-derived extracellular vesicles (EVs) and this association protects FGF2 from fast degradation. We performed RNA-seq analysis after EV treatment to examine modulated genes in DFs.

overall_design: Twenty-four hours after stimulation with CTL-EVs or FGF2-EVs, RNA was extracted, amplified and sequencedand used for RNA-seq

first: Jieqiong

last: Qu

first: Huiqing

first: Isabelle

last: Petit


title: Transcriptomic analysis of human podocytes [total RNA]

city: Bethesda

first: Teruhiko

last: Yoshida

state: Maryland

address: 10 Center Drive, 9N208

department: NIDDK - KDB

institute: National Institutes of Health

summary: We analyzed the transcriptomic profiles of human podocyte-like epithelial cells (HUPEC) obtained from urine of two subjects with APOL1 low-risk (G0/G0) genotypes and two subjects with APOL1 high-risk (G1/G2) genotypes.

overall_design: Transcriptomic profiles of differentiated and undifferentiated HUPECs using HUPECs with APOL1 low-risk and high-risk genotype.

first: Khun

last: Zaw Latt

first: Avi

middle: Z

last: Rosenberg

first: Shashi

last: Shrivastav

first: Jurgen

last: Heymann

first: Marc

middle: K

last: Halushka

first: Cheryl

last: Winkler

first: Jeffrey

last: Kopp


title: Transcriptomic analysis of human podocytes


title: The histone acetyltransferase KAT6A is recruited to unmethylated CpG islands via a DNA binding winged helix domain

status: Public on Dec 20 2022

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

institute: Philipps University of Marburg

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Effect of human beta defensin-2 (hBD-2) on T cells [human]

city: Freiburg

first: Natalie

last: Koehler

address: Breisacher Str. 115

institute: University Medical Center Freiburg

summary: In this experiment, we studied how human beta defensin-2 (hBD-2) affects kinase activity of T cells.

overall_design: Human PBMC isolated CD4/CD8 T cells were treated with hBD-2 or vehicle (PBS) control for 20 min (n=3 per group). T cells from 3 individual healthy donors

first: Tamina

last: Rueckert

first: Lukas

last: Braun


title: Comparison of high throughput RNA sequences between Babesia bigemina and Babesia bovis revealed consistent differential gene expression that is required for Babesia life cycle in the vertebrate and invertebrate hosts.

city: Pullman

first: Massaro

middle: Wilson

last: Ueti

state: Washington

address: 3003 ADBF Washington State Univ, 3003 ADBF, Grimes Way

institute: USDA ARS Animal Disease Research Unit

summary: To understand Babesia gene regulation during tick and mammalian host infection, we performed high throughput RNA-sequencing using samples collected from calves and Rhipicephalus microplus ticks infected with Babesia bigemina. We evaluated gene expression differences between B. bigemina kinetes and blood-stage parasites

overall_design: Parasite mRNA isolated from 3 biological replicates for each of bovine blood stage and tick kinete stage parasites were compared by RNAseq methodology using Illumina technology.

first: Janaina

last: Capelli-Peixoto

first: Perot

last: Saelao

first: Wendell

last: Johnson

first: Lowell

last: Kappmeyer

middle: W


title: Transcriptomic analysis of human podocytes [small RNA]

first: Teruhiko

last: Yoshida

summary: We analyzed the small RNA profiles of human podocyte-like epithelial cells (HUPEC) obtained from urine of two subjects with APOL1 low-risk (G0/G0) genotypes and two subjects with APOL1 high-risk (G1/G2) genotypes.

overall_design: Small RNA profiles of differentiated and undifferentiated HUPECs using HUPECs with APOL1 low-risk and high-risk genotype.

middle: A

first: Sanga

last: Mitra

first: Pavol

last: Genzor

first: Astrid

last: Haase

middle: B


title: The RNA-binding proteins TIA1 and TIAL1 are required for the expression of the DNA damage repair machinery during B cell lymphopoiesis.

city: Toulouse

first: Manuel

last: Diaz-Munoz

address: CHU Purpan, BP3028

institute: INSERM

summary: B-cell lymphopoiesis requires dynamic modulation of the B-cell transcriptome at the post-transcriptional level, although the implication of RNA binding proteins (RBPs) remain largely unknown. Here we show that the RBPs TIA1 and TIAL1 are essential in B cells and, if deleted, there is a developmental block at the pro-B cell stage. TIA1 and TIAL1 have redundant functions. They act together as global splicing regulators for the expression of mRNAs including those involved in DNA damage repair in pro-B cells. Mechanistically, TIA1 and TIAL1 bind to 5’splice sites for exon definition, splicing and expression of DNA damage sensors like Chek2 and Rif1. In their absence, pro-B cells show exacerbated DNA damage, altered P53 expression and increased cell death. Altogether, our study uncovers the importance of tight regulation of mRNA splicing by TIA1 and TIAL1 for the expression of integrative transcriptional programs for DNA damage sensing and repair during B-cell development.

overall_design: Pro B cells were expanded from total bone marrow of C57BL/6 mice in cell stroma-free cultures in the presence of recombinant mouse IL7.

last: Diaz-Muñoz

first: Ines

last: Osma-Garcia

first: Mailys

last: Mouysset

first: Dunja

last: Capitan-Sobrino

first: Yann

last: Aubert

first: Orlane

last: Maloudi

first: Martin

last: Turner


title: Effect of human beta defensin-2 (hBD-2) on T cells

first: Natalie

last: Koehler


title: Effect of human beta defensin-2 (hBD-2) on T cells [mouse]

overall_design: Murine splenic CD4/CD8 T cells were treated with hBD-2 or vehicle (PBS) control for 20 min (n=3 per group). T cells from 2 individual C57BL/6 mice.

first: Tamina

last: Rueckert

first: Lukas

last: Braun


title: Epigenetic and transcriptional impairments in a retina of SCA7140Q/140Q and  SCA7140Q/5Q knock-in mouse model of spinocerebellar ataxia type 7 [ChIP-seq]

city: Illkirch

first: Anna

last: Niewiadomska-Cimicka

address: 1 rue Laurent Fries

institute: IGBMC

summary: Spinocerebellar Ataxia Type 7 (SCA7) belonging to ADCAs is pathomechanistically related to a group of polyglutamine expansion disorders. SCA7 affects primarily brainstem, retina and cerebellum. The distinctive feature of SCA7 among ADCAs is a progressive visual impairment due to a cone-rod photoreceptor dystrophy. Ultrastructural analysis of SCA7 mouse models revealed that photoreceptors progressively lose their outer segments, a structure essential for phototransduction, which requires daily renewal. The lack of outer segment renewal correlates with decreased expression of photoreceptor-specific genes, suggesting that progressive breakdown of photoreceptor cell identity accounts for SCA7 retinopathy. SCA7 is due to a polyglutamine expansion in ATXN7, a component of the multiprotein SPT-ADA-GCN5 Acetyltransferase (SAGA) complex, a highly conserved coactivator of transcription. SAGA harbors two chromatin remodeling activities: acetylation and deubiquitynation of histones crucial for transcription initiation and elongation. The role of SAGA in SCA7 pathogenesis and the tissue specific genetic breakdown remains to be elucidated. We addressed this issue using our new SCA7 knock-in mouse model (SCA7140Q/140Q), which recapitulates cardinal features of SCA7. Using ChIP-seq approach, we confirmed the general decrease of H3K9ac in most gene promoters in SCA7 retina, which alone cannot explain the specific gene deregulation. Interestingly, we discovered that photoreceptor identity genes, which are strongly downregulated in SCA7, harbor an unusual broad profile of H3K9ac that encompasses the entire gene. We further show that H3K9ac broad profiles at photoreceptor gene loci coincide with the presence of a broad H3K27ac, a signature of superenhancers. Furthermore, using vicinity criteria we identified enhancer RNAs (eRNAs), annotated to the photoreceptor identity genes possessing an atypical H3K9ac/H3K27ac enhancer signature. Finally, we found a synchronized expression of eRNAs and photoreceptor identity genes during retinal development, suggesting a regulatory role of these eRNAs. The decreased eRNA levels on hypoacetylated loci in the retina correlate with the downregulation of photoreceptor identity genes in symptomatic but not in pre-symptomatic SCA7 mice.

overall_design: Retinal genome-wide chromatine (ChIP-seq) and transcriptome (total RNA-seq) profiling of a knock-in mouse model of spinocerebellar ataxia type 7 (SCA7).

first: Stephanie

last: Le Gras

first: Yvon

last: Trottier


title: Epigenetic and transcriptional impairments in a retina of SCA7140Q/140Q and  SCA7140Q/5Q knock-in mouse model of spinocerebellar ataxia type 7 [RNA-seq]

summary: Spinocerebellar Ataxia Type 7 (SCA7) belonging to ADCAs is pathomechanistically related to a group of polyglutamine expansion disorders. SCA7 affects primarily brainstem, retina and cerebellum. The distinctive feature of SCA7 among ADCAs is a progressive visual impairment due to a cone-rod photoreceptor dystrophy. Ultrastructural analysis of SCA7 mouse models revealed that photoreceptors progressively lose their outer segments, a structure essential for phototransduction, which requires daily renewal. The lack of outer segment renewal correlates with decreased expression of photoreceptor-specific genes, suggesting that progressive breakdown of photoreceptor cell identity accounts for SCA7 retinopathy. SCA7 is due to a polyglutamine expansion in ATXN7, a component of the multiprotein SPT-ADA-GCN5 Acetyltransferase (SAGA) complex, a highly conserved coactivator of transcription. SAGA harbors two chromatin remodeling activities: acetylation and deubiquitynation of histones crucial for transcription initiation and elongation. The role of SAGA in SCA7 pathogenesis and the tissue specific genetic breakdown remains to be elucidated. We addressed this issue using our new SCA7 knock-in mouse model (SCA7140Q/140Q), which recapitulates cardinal features of SCA7. Using ChIP-seq approach, we confirmed the general decrease of H3K9ac in most gene promoters in SCA7 retina, which alone cannot explain the specific gene deregulation. Interestingly, we discovered that photoreceptor identity genes, which are strongly downregulated in SCA7, harbor an unusual broad profile of H3K9ac that encompasses the entire gene. We further show that H3K9ac broad profiles at photoreceptor gene loci coincide with the presence of a broad H3K27ac, a signature of superenhancers. Furthermore, using vicinity criteria we identified enhancer RNAs (eRNAs), annotated to the photoreceptor identity genes possessing an atypical H3K9ac/H3K27ac enhancer signature. Finally, we found a synchronized expression of eRNAs and photoreceptor identity genes during retinal development, suggesting a regulatory role of these eRNAs. The decreased eRNA levels on hypoacetylated loci in the retina correlate with the downregulation of photoreceptor identity genes in symptomatic but not in pre-symptomatic SCA7 mice. Our results support the view that epigenetic and enhancer alterations compromise the maintenance of neuronal identity in SCA7.

first: Celine

last: Keime


title: Culture protocol and transcriptomic analysis of murine SVZ NPCs and OPCs

status: Public on Dec 19 2022

city: Edmonton

first: Anastassia

last: Voronova

state: Alberta

address: 8-43A Medical Sciences Building

department: Medical Genetics

country: Canada

institute: University of Alberta

summary: The mammalian adult brain contains two neural stem and precursor (NPC) niches: subventricular zone [SVZ] lining the lateral ventricles and subgranular zone [SGZ] in the hippocampus. From these SVZ NPCs represent the largest NPC pool. Notably, while SGZ NPCs typically only produce neurons and astrocytes, SVZ NPCs produce neurons, astrocytes and oligodendrocytes throughout life. Of particular importance is the generation and replacement of oligodendrocytes, the only myelinating cells of the central nervous system (CNS). SVZ NPCs contribute to myelination by regenerating oligodendrocyte precursor cell (OPC) pool and by differentiating into oligodendrocytes in the developing and demyelinated brain. The neurosphere assay has been widely adopted by the scientific community to facilitate the study of NPCs in vitro. Here, we present a streamlined protocol for culturing postnatal and adult SVZ NPCs and OPCs from primary neurosphere cells. We characterize the purity and differentiation potential as well as provide RNA-sequencing profiles of postnatal SVZ NPCs, postnatal SVZ OPCs and adult SVZ NPCs. We show that primary neurospheres cells generated from postnatal and adult SVZ differentiate into neurons, astrocytes and oligodendrocytes concurrently and at comparable levels. SVZ OPCs are generated by subjecting primary neurosphere cells to OPC growth factors fibroblast growth factor (FGF) and platelet-derived growth factor-AA (PDGF-AA). We further show SVZ OPCs can differentiate into oligodendrocytes in the absence and presence of thyroid hormone T3. Transcriptomic analysis confirmed the identities of each cell population and revealed novel immune and signalling pathways expressed in an age and cell type specific manner.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for primary postnatal or adult SVZ neural stem cells (neurospheres) and postnatal oligodendrocyte precursor cells generated from neurospheres. Cultures were generated from 4 independent litters of CD1 mice to achieve n=4 biological replicates, each sequenced separately for a total of 12 individual datasets (adult neural stem cells [2 months], postnatal neural stem cells [P0-2], postnatal oligodendrocyte precursor cells [P0-2])

first: Nicole

last: Dittmann


title: The RNA-binding proteins TIA1 and TIAL1 are required for the expression of the DNA damage repair machinery during B cell lymphopoiesis

last: Diaz-Munoz

summary: B-cell lymphopoiesis requires dynamic modulation of the B-cell transcriptome at the post-transcriptional level, although the implication of RNA-binding proteins (RBPs) remain largely unknown. Here we show that the RBPs TIA1 and TIAL1 are essential in B cells and, if deleted, there is a developmental block at the pro-B cell stage. TIA1 and TIAL1 have redundant functions. They act together as global splicing regulators for the expression of mRNAs including those involved in DNA damage repair in pro-B cells. Mechanistically, TIA1 and TIAL1 bind to 5’splice sites for exon definition, splicing and expression of DNA damage sensors like Chek2 and Rif1. In their absence, pro-B cells show exacerbated DNA damage, altered P53 expression and increased cell death. Altogether, our study uncovers the importance of tight regulation of mRNA splicing by TIA1 and TIAL1 for the expression of integrative transcriptional programs for DNA damage sensing and repair during B-cell development.

overall_design: Pro B cells (CD19+ B220+ surface IgM- CD43+ CD25- CD24+ BP1-) from control and Tia1 Tial1 double conditional knock out mice were sorted by FACs for RNA extraction. 10 ng of RNA were then used to prepare RNAseq libraries using the SMART-Seq Stranded mRNA kit following the instruction of the manufacturer (TakaraBio).


title: scRNAseq of mouse corneal epithelium in homeostasis

city: Saint Louis

first: Joseph

last: Lin

address: 660 South Euclid Ave, MSC-8096-06-07

department: Ophthalmology & Visual Sciences

institute: Washington University School of Medicine

summary: We performed single cell transcriptional profiling of mouse corneal epithelium under homeostatic conditions.

overall_design: We prepared cell suspensions of corneal epithelium from healthy mice (C57BL/6J).

first: Rajendra

last: Apte


title: scRNAseq of corneal epithelium in dry eye disease

summary: We performed single cell transcriptional profiling of mouse corneal epithelium in a mouse model of dry eye disease.

overall_design: We prepared cell suspensions of corneal epithelium: one from control and one from dry eye disease (n = 7 male C57BL/6J mice, 10 weeks old). We excised the right lacrimal glands (both extra- and intra-orbital) following previously described protocols (Shinomiya et al., 2018). We sacrificed mice 9 days after lacrimal gland excision. Left control eyes were pooled (n = 7 eyes), and right dry eyes were pooled (n = 6, one was excluded due to injury during surgery).


title: In vivo clonal tracking reveals evidence of haemangioblast and haematomesoblast contribution to yolk sac haematopoiesis

first: Jarny

last: Choi

state: Victoria

address: The University of Melbourne

department: Anatomy and Neuroscience

institute: Centre for Stem Cell Systems

summary: During embryogenesis, haematopoietic and endothelial lineages emerge closely in time and space. It is thought that the first blood and endothelium derive from a common clonal ancestor, the haemangioblast. However, investigation of candidate haemangioblasts in vitro revealed the capacity for mesenchymal differentiation, a feature more compatible with an earlier mesodermal precursor. To date, no evidence for an in vivo haemangioblast has been discovered. Using single cell RNA-Sequencing and in vivo cellular barcoding, we have unraveled the ancestral relationships that give rise to the haematopoietic lineages of the yolk sac, the endothelium, and the mesenchyme. We show that the mesodermal derivatives of the yolk sac are produced by three distinct precursors with dual-lineage outcomes: the haemangioblast, the mesenchymoangioblast, and a previously undescribed cell type: the haematomesoblast. Between E5.5 and E7.5, this trio of precursors seeds haematopoietic, endothelial, and mesenchymal trajectories.

overall_design: Yolk sac lineages related to emergenece of blood and endothelial cells were collected between E7.5 and E10.5 of mouse embryonic development using Flk1-GFP mouse (Shalaby et al, DOI: 10.1016/s0092-8674(00)80283-4) and combinations of antibodies described in (Potts et al, https://doi.org/10.1182/blood-2014-02-559468).

first: Kathy

last: Potts

first: Christine

last: Biben

first: Tom

last: Weber

first: Denis

last: Miles

first: Amandine

last: Carmagnac

first: Tobias

last: Sargeant

first: Carolyn

last: de Graaf

first: Katie

last: Fennell

first: Alison

last: Farley

first: Olivia

last: Stonehouse

first: Mark

last: Dawson

first: Douglas

middle: J

last: Hilton

first: Shalin

last: Naik

first: Samir

last: Taoudi


title: scRNAseq of diabetic corneal epithelium

first: Joseph

last: Lin

summary: We performed single cell transcriptional profiling of mouse corneal epithelium in streptozotocin-induced diabetic mice.

overall_design: We prepared cell suspensions of corneal epithelium: one from control and one from diabetic C57BL/6J mice (male, 20 weeks old). Each sample is a pooled sample of 4 corneas from n = 2 mice. We induced hyperglycemia by administering a single injection of streptozotocin (STZ, 160 mg/kg bodyweight) to cause complete pancreatic β-cell necrosis and diabetes, with control mice receiving an equal volume of sodium citrate buffer (pH 4.5). We measured blood glucose weekly to certify hyperglycemia, and mice that remained hyperglycemic (blood glucose > 250 mg/dL) throughout the 12 week study were considered diabetic.


title: scRNAseq of young vs. aged corneal epithelium

summary: We performed single cell transcriptional profiling of mouse corneal epithelium in young vs. aged mice.

overall_design: We prepared cell suspensions of corneal epithelium: one from young and one from aged C57BL/6J mice (11 weeks and 18 months old, respectively). Each sample is a pooled sample of 4 corneas from n = 2 mice.

first: Rajendra

last: Apte


title: Epigenetic and transcriptional impairments in a retina of SCA7140Q/140Q and  SCA7140Q/5Q knock-in mouse model of spinocerebellar ataxia type 7

first: Anna

last: Niewiadomska-Cimicka

summary:
Background
Spinocerebellar ataxia type 7 (SCA7) is a neurodegenerative disorder that primarily affects the cerebellum and retina. SCA7 is caused by a polyglutamine expansion in the ATXN7 protein, a subunit of the transcriptional coactivator SAGA that acetylates histone H3 to deposit narrow H3K9ac mark at DNA regulatory elements of active genes. Defective histone acetylation has been presented as a possible cause for gene deregulation in SCA7 mouse models. However, the topography of acetylation defects at the whole genome level and its relationship to changes in gene expression remain to be determined.

Methods
We performed deep RNA-sequencing and chromatin immunoprecipitation coupled to high-throughput sequencing to examine the genome-wide correlation between gene deregulation and alteration of the active transcription marks, e.g. SAGA-related H3K9ac, CBP-related H3K27ac and RNA polymerase II (RNAPII), in a SCA7 mouse retinopathy model.

Results
Our analyses revealed that active transcription marks are reduced at most gene promoters in SCA7 retina, while a limited number of genes show changes in expression. We found that SCA7 retinopathy is caused by preferential downregulation of hundreds of highly expressed genes that define morphological and physiological identities of mature photoreceptors. We further uncovered that these photoreceptor genes harbor unusually broad H3K9ac profiles spanning the entire gene bodies and have a low RNAPII pausing. This broad H3K9ac signature co-occurs with other features that delineate superenhancers, including broad H3K27ac, binding sites for photoreceptor specific transcription factors and expression of enhancer-related non-coding RNAs (eRNAs). In SCA7 retina, downregulated photoreceptor genes show decreased H3K9 and H3K27 acetylation and eRNA expression as well as increased RNAPII pausing, suggesting that superenhancer-related features are altered.

Conclusions
Our study thus provides evidence that distinctive epigenetic configurations underlying high expression of cell-type specific genes are preferentially impaired in SCA7, resulting in a defect in the maintenance of identity features of mature photoreceptors. Our results also suggest that continuous SAGA-driven acetylation plays a role in preserving post-mitotic neuronal identity.

overall_design: Refer to individual Series


title: RNA-seq of SPARC-treated human corneal epithelial cells

summary: We identified that Sparc gene expression is upregulated in corneal epithelial cells in a mouse model of dry eye disease involving lacrimal gland excision. Therefore, in this experiment we assess the effect of SPARC treatment on the transcriptome of human corneal epithelial cells.

overall_design: We used a telomerase-immortalized human corneal epithelial cell line (hTCEpi) that was graciously donated by Danielle Robertson (UT Southwestern). These cells were maintained in keratinocyte growth medium 2 (PromoCell C20011) supplemented with SupplementMix, 1% penicillin/streptomycin, and 0.15 mM calcium chloride. We treated hTCEpi cells with recombinant human SPARC (PeproTech 120-36) in KGM media: 0.00, 0.05, 0.50, and 5.00 micrograms/ml for 24h. Then, we washed cells with PBS, isolated RNA, and prepared samples for RNA-sequencing using the RiboErase rRNA depletion kit.


title: Antibiotics-induced depletion of rat microbiota induces changes in the expression of host drug-processing genes and pharmacokinetic behaviors of CYPs probe drugs

status: Public on Dec 18 2022

city: Changsha

first: Qing

last: Li

state: Hunan

address: 110 Xiangya Road

department: Department of Clinical Pharmacology, Xiangya Hospital

institute: Central South University

summary: This study aimed to quantify and compare the mRNA abundance of drug-processing genes (DPGs) in liver and jejunum between wild-type rats and antibiotics-treated rats by using an unbiased quantitative RNA-Seq method. Our results show that antibiotics treatments altered the mRNA expressions of 112 DPGs in the liver and jejunum of rats. The mRNA levels of CYP2A1, CYP2C11, CYP2C13, CYP2D, CYP2E1, and CYP3A of CYP family members were significantly downregulated in antibiotics-treated rats.

overall_design: mRNA profiles of liver and jejunum of wild-type rats and antibiotics-treated rats were generated by RNA-seq, in triplicate, by Illumina NovaSeq 6000.

first: Haijun

last: Yang

first: Yanjuan

last: Zhang


title: Bacterial membrane phosphatidylglycerols activate a population of human CD1a-restricted t cells

city: New York

first: Annemieke

last: de Jong

email: ad2952@cumc.columbia.edu, mongaisha4@gmail.com, im2569@cumc.columbia.edu, gwennaelle.monnot@gmail.com

state: NY

address: 1150 st. Nicholas Avenue

department: Department of Dermatology

institute: Columbia University Irving Medical Center

summary: Expressed on epidermal Langerhans cells, CD1a presents a range of self-lipid antigens found within the skin. However, the extent to which CD1a presents microbial ligands from skin bacteria is unclear. Here, we identified CD1a-dependent T cell responses to phosphatidylglycerol (PG), a ubiquitous bacterial membrane phospholipid, as well as to lysyl phosphatidylglycerol (lysylPG), a modified PG, present in the many gram positive bacteria, and highly abundant in Staphylococcus aureus. Specifically, PG and lysylPG together constitute the vast majority of the structural membrane lipids in Staphylococcus aureus. The crystal structure of the CD1a-lysylPG complex showed that the acyl chains were buried within the A′- and F′-pockets of CD1a, while the lysine-modified phosphoglycerol headgroup protruded from the F′-portal and was available for T cell receptor contact. Using lysylPG-loaded CD1a tetramers, we identified T cells in peripheral blood and in skin that respond to this lipid in a dose dependent manner. Tetramer+ CD4+ T cell lines secreted Th2 cytokines in response to lysylPG as well as to co-cultures of CD1a+ dendritic cells and Staphylococcus aureus. The expansion of CD4+ CD1a-lysylPG tetramer+ T cells in atopic dermatitis patients, indicates a response to a lipid made by bacteria associated with atopic dermatitis, and provide a link supporting involvement of PG-based lipid-specific T cells in the pathogenesis of dermatitis.

overall_design: We identify bacterial lipids PG and lysylPG as antigens for CD1a-restricted T cells and use RNAsequencing to gain insight in the gene expression profiles and functions of CD1a-(lysyl)PG reactive T cells

first: Gwennaëlle

last: Monnot

first: Isha

last: Monga


title: Transcriptome of MRC5 fibroblasts

city: Chicago

first: Mary

last: Hummel

state: IL

address: 303 E. Chicago Ave

institute: Northwestern University

summary: Purpose: to investigate the human transcriptome in MRC5 fibroblasts

overall_design: MRC5 cells were harvested for RNAseq analyses.

first: Eleonora

last: Forte

first: Matthew

last: Schipma


title: HCMV epigenome during early lytic infection

summary: Purpose: to investigate occupancy of Pol II and H3K27Ac on the HCMV and cellular genomes at early times post-infection in a lytic model

sample_organism:
Homo sapiens
Human betaherpesvirus 5

platform_organism:
Homo sapiens
Human betaherpesvirus 5

overall_design: MRC5 cells were infected with the TB40/E wtGFP strain of HCMV. Cells were left in culture for 24 hours, and then processed for Pol 2 and H3K27Ac ChIPseq analysis.


title: HCMV transcriptome during early lytic infection

summary: Purpose: to investigate expression of HCMV and cellular RNAs at early times post-infection in a lytic model

overall_design: MRC5 cells were infected with the TB40/E wtGFP strain of HCMV.  Cells were cultured for 24 hours, and then processed for RNAseq analysis.


title: Pol II and H3K27Ac occupancy of the human genome in MRC5 cells

summary: Purpose: to investigate the epigeome of MRC5 fibroblasts

overall_design: MRC5 cells were harvested for ChIPseq analyses.


title: CBP and p300 Jointly Maintain Neural Progenitor Viability but Play Unique Roles in the Differentiation of Neural Lineages

status: Public on Dec 17 2022

city: San Juan de Alicante

first: Ángel

last: Márquez Galera

address: Av. Santiago Ramón y Cajal, s/n

country: Spain

institute: Instituto de Neurociencias

summary: The paralogous lysine acetyltransferases 3 (KAT3), CBP and P300, play critical roles during neurodevelopment, but their specific roles in neural precursors maintenance and differentiation remain obscure. In fact, it is still unclear whether these proteins are individually or jointly essential in processes such as proliferation of neural precursors, differentiation to specific neural cell types, or both. Here, we use subventricular zone-derived neurospheres as a potential ex vivo developmental model to analyze the proliferation and differentiation of neural stem cells (NSCs) lacking CBP, p300, or both proteins. The results showed that CBP and p300 are not individually essential for maintenance and proliferation of NSCs, although their combined ablation seriously compromised cell division. In turn, the absence of either of the two proteins compromised the differentiation of NSC into the neuronal and astrocytic lineages. Single-nucleus RNA sequencing analysis of neural cell cultures derived from CBP or p300 mutant neurospheres revealed divergent trajectories of neural differentiation upon CBP or p300 ablation, confirming unique functions and nonredundant roles in neural development. These findings contribute to a better understanding of the shared and individual roles of KAT3 proteins in neural differentiation and the etiology of neurodevelopmental disorders caused by their deficiency.

overall_design: snRNA-seq analysis of differentiating neurospheres lacking either CBP or p300.

first: Angel

last: Marquez-Galera

first: Rocio

last: Gonzalez-Martinez

first: Jose

last: Lopez-Atalaya

first: Eloisa

last: Herrera


title: IL-4 protects against chemically-induced retinal degeneration in AMD mouse model via Nrf2 activation

city: Guangzhou

first: xialin

last: liu

address: Jinsui Road

institute: Zhongshan Opythalmic Center, Sun yat-sen University

summary: To explore whether IL-4 could exert a novel protective role for RPE damage and attenuate the pathogenesis of dry age-related macular degeneration (AMD), we established a retinal degeneration model of dry AMD by intravenous injection of NaIO3, and explored the treatment effects of intravitreal IL-4 injection. We found exogenous IL-4 protected against retinal degeneration characterized by well-preserved structures and improved retinal function. The RNA-seq analysis revealed that IL-4 treatment suppressed the essential oxidative and pro-inflammatory pathways in the degenerative retina. IL-4 induced the expression of IL-4Rα and Nrf2 for anti-oxidative defense in vivo and in vitro. Our data provides evidences that IL-4 can be a useful neuroprotective agent against retinal degeneration due to its antioxidant and anti-inflammatory property through Nrf2 activation. The IL-4/IL-4Rα-Nrf2 axis maybe the potential targets for the development of novel therapies for dry AMD.

overall_design: Examination of bulk RNA in RPE-sclera complex derived from PBS, NaIO3 and NaIO3+IL-4 treated mice.

first: Tian

last: Zhou

first: Huiyi

last: Xu

first: Xiaojing

last: Lin

first: Hong

first: Ziqi

first: Biyan

last: Ni

first: Rong

last: Ju

first: Chunqiao

last: Liu

first: Chang

last: He

first: Xialin


title: Transcriptome profiling of wildtype C57BL/6 female mice during estrous cycle(mainly in estrus and diestrus).

city: Beijing

first: Yiran

address: 38 Xueyuan Rd

institute: Peking University

summary:
Background:The morphology of vaginal secretions during estrus and diestrus is characteristic and easy to distinguish. There are also significant differences in hormone levels between the two periods in physiological condition. However, the gene changes during estrus cycle especially the two periods are still unclear. Therefore, this study plans to find out the pathway changes related to the estrus cycle of female mice, the expression of various proteins, predict the genes sensitive to hormone changes in vivo through gene analysis of 15 tissues in the two periods and construct of differential gene expression library.
Methods:The wildtype healthy female mice in estrus were compared with those in diestrus. The transcriptome changes between the two periods were probed by using high-throughput RNA-seq techniques.
Results:A comprehensive mouse transcriptome map in estrus or diestrus across fifteen tissues including aorta, vein, brown adipose tissue, white adipose tissue, heart, kidney, liver, skeletal muscle, stomach, duodenum, cerebrum, hypothalamus, ovary, womb and spleen were provided.
Conclusions:This dataset could serve as a baseline resource for investigating the potential gene changes sensitive to the estrus cycle across different tissues and provide the information for screening the key functional genes or molecular markers of estrus cycle.

overall_design: Wildtype healthy C57BL/6 female mice in estrus or diestrus (Detection of aginal secretion smear). The mRNA profiles across 15 tissues (including aorta, vein, brown adipose tissue, white adipose tissue, heart, kidney, liver, skeletal muscle, stomach, duodenum, cerebrum, hypothalamus, ovary, womb and spleen) were generated through RNA-seq technique, in triplicate for each group, using BGISEQ-500.

first: Jichun

last: Yang

first: Qinghua

last: Cui


title: HCMV epigenome and transcriptome during early lytic infection

first: Mary

last: Hummel

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


title: The histone demethylase KDM5C represses trophoblast proliferation and invasion in woman with recurrent miscarriage [CUT & Tag]

status: Public on Dec 16 2022

city: Shanghai

first: Shanhe

last: Yu

address: 197# Rui Jin Road II

institute: Shanghai Institute of Hematology，Rui Jin Hospital

summary: To characterize genome-wide  KDM5C traget genes in HTR-8/SVneo cells transduced with KDM5C-expression vector by CUT&Tag.

overall_design: Examination of KDM5C traget genes in HTR-8/SVneo cells transduced with KDM5C-expression vector cells

first: Min

last: Xiao


title: Chromatin complex dependencies reveal targeting opportunities in leukemia

city: Cambridge

first: Fadi

middle: John

last: Najm

state: Massachusetts

address: 415 Main Street 6043

department: Epigenomics

institute: Broad Institute

summary: Chromatin regulators are frequently mutated in human cancer and are attractive drug targets. They include diverse proteins that share functional domains and assemble into related multi-subunit complexes. To investigate functional relationships among these regulators, here we apply combinatorial CRISPR knockouts (KOs) to test over 35,000 gene-gene pairings in leukemia cells, using a library of over 300,000 constructs. Top pairs that demonstrate either compensatory non-lethal interactions or synergistic lethality enrich for paralogs and targets that occupy the same protein complex. The screen highlights protein complex dependencies not apparent in single KO screens, for example MCM histone exchange, the nucleosome remodeling and deacetylase (NuRD) complex, and HBO1 (KAT7) complex. We explore two approaches to NuRD complex inactivation. Paralog and non-paralog combinations of the KAT7 complex emerge as synergistic lethal and specifically nominate the ING5 PHD domain as a potential therapeutic target when paired with other KAT7 complex member losses. These findings highlight the power of combinatorial screening to provide mechanistic insight and identify therapeutic targets within redundant networks.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct


title: single-nucleus ATAC-seq in PBMCs with COVID-19

status: Public on Dec 15 2022

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: KAIST

summary: PBMCs were extracted from 8 donors (an influenza, 2 mild and 2 severe COVID-19 patients, 3 healthy donors). Datasets generated by single-cell ATAC sequencing platform from 10X genomics. The library was generated by single-cell ATAC kit v1.1 following manufacturer's instructions.

overall_design:
Single-cell ATAC sequencing performed with PBMC of 8 donors.
PBMCs were isolated from peripheral venous blood via standard Ficoll-Paque (GE Healthcare, Uppsala, Sweden) density gradient centrifugation, frozen in freezing media, and stored in liquid nitrogen until use. All samples showed a high viability of about 90% on average after thawing.

first: S

last: Park

first: I

first: E

last: Shin


title: The histone demethylase KDM5C represses trophoblast proliferation and invasion in woman with recurrent miscarriage  [RNA-seq]

summary:
KDM5C is a H3K4- specific demethylase, which has multiple biological roles in development and disease. However, the role of KDM5C in trophoblasts at the maternal-fetal interface remains unknown. Here, we showed that KDM5C was upregulated in placental trophoblasts from patient with recurrent miscarriage (RM). Trophoblasts proliferation and invasion was inhibited by KDM5C overexpression and was enhanced by KDM5C knockdown. Interestingly, KDM5C knockdown promoted trophoblast invasion in villous explant culture system. RNA-seq and ChIP-seq analyses revealed that KDM5C exerts anti-proliferation and anti-invasion effect by directly modulating H3K4 methylation level to repress the expression of a number of key regulatory genes. We show that two of these genes, TGFβ2, RAGE, are essential for the proliferation and invasion of trophoblasts. Taken together, our results show that the KDM5C is regulator of trophoblast function during early pregnancy and indicated that KDM5C may be involved in the pathogenesis of RM.
Next Generation Sequencing Facilitates Quantitative Analysis of HTR-8/SVneo cells transduced with control or KDM5C-expression vector, and HTR-8/SVneo cells transduced with NC or KDM5C shRNA-expression vector,

overall_design: mRNA profiles of HTR-8/SVneo cells were generated by deep sequencing, in triplicate, using  Illumina HiSeq 2500. Raw sequence reads were initially processed using FastQC (Babraham Institute, Cambridge, UK) for quality control, and then adapter sequences and poor quality reads were removed using Cutadapt. Quality-filtered reads were then mapped to human genome (hg19) using STAR, and only the uniquely mapped reads were kept. Read counts were calculated using HTSeq-count. Differentially expressed genes were identified using R package DESeq2.


title: The histone demethylase KDM5C represses trophoblast proliferation and invasion in woman with recurrent miscarriage [ChIP-seq]

summary:
KDM5C is a H3K4- specific demethylase, which has multiple biological roles in development and disease. However, the role of KDM5C in trophoblasts at the maternal-fetal interface remains unknown. Here, we showed that KDM5C was upregulated in placental trophoblasts from patient with recurrent miscarriage (RM). Trophoblasts proliferation and invasion was inhibited by KDM5C overexpression and was enhanced by KDM5C knockdown. Interestingly, KDM5C knockdown promoted trophoblast invasion in villous explant culture system. RNA-seq and ChIP-seq analyses revealed that KDM5C exerts anti-proliferation and anti-invasion effect by directly modulating H3K4 methylation level to repress the expression of a number of key regulatory genes. We show that two of these genes, TGFβ2, RAGE, are essential for the proliferation and invasion of trophoblasts. Taken together, our results show that the KDM5C is regulator of trophoblast function during early pregnancy and indicated that KDM5C may be involved in the pathogenesis of RM.
To characterize genome-wide H3K4me3 chromatin-state of HTR-8/SVneo cells.

overall_design: Examination of H3K4me3 in HTR-8/SVneo cells transduced with control or KDM5C-expression vector


title: Progressive development of melanoma-induced cachexia differentially impacts organ systems in mice. [Lisinopril]

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

summary: Cachexia is a systemic wasting syndrome that develops in many cancers and increases mortality. Despite its importance, it is largely unknown how cachexia progressively and differentially induces tissue wasting. Although cachexia occurs also in pediatric patients, little is known on the underlying mechanisms. Here, we have used pediatric melanoma xenografts to determine the progression and tissue-specific impact of juvenile cachexia on skeletal muscles, heart, white and brown adipose, liver, and brain. We find that the heart and muscles undergo wasting at early stages and are the tissues most strongly impacted transcriptionally. Beyond wasting, we identify general and organ-specific transcriptional changes that likely indicate derangement of organ/tissue function by cachexia.  Moreover, also the transcriptome of tissues that do not undergo wasting, such as the brain, is profoundly remodeled by cachexia. Altogether, this study provides insight into the progression of melanoma-induced pediatric cachexia and its differential impact on distinct organ systems.

overall_design: RNA-sequencing data from tibialis anterior skeletal muscles sourced from mice after 49 days from implantation of a cachexia-inducing melanoma xenograft or mock-injected (control), and either treated with the ACE inhibitor Lisinopril or mock.

first: Flavia

last: Graca

first: Anna

last: Stephan

first: Abbas

last: Shirinifard

first: Jianqin

last: Jiao

first: Peter

last: Vogel

first: Myriam

last: Labelle

first: Fabio

last: Demontis


title: Transcriptomic profiling of murine adipose endothelial cells from high-fat diet fed mice

city: Stockholm

first: Eric

last: Rullman

address: C1:82 Karolinska University Hospital, Huddinge

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

summary: Female mice display greater adipose angiogenesis and maintain healthier adipose tissue than do males upon sustained high-fat diet feeding. We utilized transcriptome analysis of endothelial cells (EC) from the white adipose tissue of male and female mice that were fed a high-fat for 7 weeks. We found that adipose EC exhibited pronouncedly sex-distinct transcriptomes. Genes upregulated in female adipose EC were associated with proliferation, oxidative phosphorylation, and chromatin remodeling contrasting the dominant enrichment for genes related to inflammation and a senescence-associated secretory of male EC. Our study provides novel insights into molecular programs that distinguish male and female EC responses to pathophysiological conditions.

overall_design: Male and female mice were fed a high fat diet for 7 weeks, starting at 7 weeks of age. Endothelial cells were purified from the white adipose tissues of these mice and RNA was extracted and analyzed by RNA-sequencing.

first: Tara

last: Haas


title: THOC5 complexes with DDX5, DDX17 and CDK12 to regulate R loop structures and transcription elongation rate

city: Hanover

first: Mareike

last: Polenkowski

address: Carl-Neuberg-Straße 1

department: Cell Biochemistry

institute: Medical School Hannover

summary: THOC5, a member of the THO complex, is essential for the 3´processing of some inducible genes, the export of a subset of genes and stem cell self-renewal. Utilising nanopore mRNA-sequencing we show that when THOC5 is depleted 50-60% of mRNAs undergo altered 3´end cleavage. Further, THOC5 depletion leads to increased RNA Polymerase II (Pol II) presence at the start site, on the gene body and close to the 3’end. Moreover, THOC5 is recruited close to high density Pol II sites suggesting that THOC5 is involved in transcriptional elongation. Indeed, DRB/TTchem-seq that measures elongation rates in vivo revealed an accumulation of released Pol II near to TSS and a decrease of elongation rates in THOC5 depleted cells. Furthermore, THOC5 is more recruited to its target genes in cells expressing slow Pol II than those expressing fast Pol II. In cells expressing slow Pol II chromatin associated THOC5 interacts with CDK12 (a protein that modulates mRNA elongation rates), RNA helicases DDX5, DDX17, and THOC6. Importantly these interactions were not observed in cells expressing fast Pol II. 3’ cleavage of 50% of THOC5 target genes is also regulated by CDK12 and THOC6. The CDK12/THOC5 interaction promotes CDK12 recruitment to R-loops in a THOC6-dependent manner. These data demonstrate that THOC5/THOC6 play a part in transcription elongation. Given the role of THOC5 in primitive cell survival its phosphorylation by agonists, oxidative stress and oncogenes the pathway we identified has relevance in the physiology and pathology of stem cells.

overall_design: Transcriptome profiling of HEK293 cells characterized by Nanopore direct RNA-Seq. Recruitment profile of RNA PolII and THOC5 were examined by ChIP-Seq.

first: Aldrige

last: Allister

first: Sebastian

last: Burbano De Lara

first: Andrew

last: Pierce

first: Bethany

last: Geary

first: Omar

last: El Bounkari

first: Lutz

last: Wiehlmann

first: Andrea

last: Hoffmann

first: Anthony

last: Whetton

first: Teruko

last: Tamura

first: Doan

last: Tran


title: Single Cell RNA Sequencing of the Adult Drosophila Eye Reveals Distinct Clusters and Novel Marker Genes for All Major Cell Types

city: Houston

first: Kelvin

last: Yeung

state: TX

address: One Baylor Plaza, Room S242

department: Pathology

institute: Baylor College of Medicine

summary: Although the adult Drosophila eye is an important model system for phototransduction and human disease research, high quality single cell resolution transcriptome data is lacking for this tissue. To address this, we performed single cell RNA-sequencing on wild-type Canton-S adult eyes from 1 day old male and female, 3-day and 7-day old male flies.  These data sets will serve as an valuable resource for future research using the adult eye.

overall_design: Adult eyes of Canton-S flies were dissected and dissociated into single cell solution with collagenase. Single cells were analyzed with 10x Chromium based scRNA-seq

first: Komal

last: Kumar Bollepogu Raja

first: Rui

last: Chen

first: Graeme

last: Mardon


title: Progressive development of melanoma-induced cachexia differentially impacts organ systems in mice [Tumor]

first: Yong-Dong

last: Wang

overall_design: RNA-sequencing data from human melanoma cells and associated mouse stroma at different time points of cachexia progression. Female 2-month-old NCI Ath/nude mice were injected with cachectic melanoma cells (CAC), non-cachectic melanoma cells (NCAC), or mock injected (Con). The time points analyzed are 2, 4, 6, and 8 weeks (wk) post cancer cell injection.

first: Flavia

last: Graca

first: Anna

last: Stephan

first: Abbas

last: Shirinifard

first: Jianqin

last: Jiao

first: Peter

last: Vogel

first: Myriam

last: Labelle

first: Fabio

last: Demontis


title: Progressive development of melanoma-induced cachexia differentially impacts organ systems in mice [SOL]

overall_design: RNA-sequencing data from soleus skeletal muscle at different time points of cachexia progression. Female 2-month-old NCI Ath/nude mice were injected with cachectic melanoma cells (CAC), non-cachectic melanoma cells (NCAC), or mock injected (Con). The time points analyzed are 2, 4, 6, and 8 weeks (wk) post cancer cell injection.


title: Progressive development of melanoma-induced cachexia differentially impacts organ systems in mice [NEO]

overall_design: RNA-sequencing data from neocortex at different time points of cachexia progression. Female 2-month-old NCI Ath/nude mice were injected with cachectic melanoma cells (CAC), non-cachectic melanoma cells (NCAC), or mock injected (Con). The time points analyzed are 2, 4, 6, and 8 weeks (wk) post cancer cell injection.


title: Progressive development of melanoma-induced cachexia differentially impacts organ systems in mice [HIP]

overall_design: RNA-sequencing data from hippocampus at different time points of cachexia progression. Female 2-month-old NCI Ath/nude mice were injected with cachectic melanoma cells (CAC), non-cachectic melanoma cells (NCAC), or mock injected (Con). The time points analyzed are 2, 4, 6, and 8 weeks (wk) post cancer cell injection.


title: Progressive development of melanoma-induced cachexia differentially impacts organ systems in mice [CER RNA-seq]

overall_design: RNA-sequencing data from cerebellum at different time points of cachexia progression. Female 2-month-old NCI Ath/nude mice were injected with cachectic melanoma cells (CAC), non-cachectic melanoma cells (NCAC), or mock injected (Con). The time points analyzed are 2, 4, 6, and 8 weeks (wk) post cancer cell injection.


title: Progressive development of melanoma-induced cachexia differentially impacts organ systems in mice [GAS RNA-seq]

overall_design: RNA-sequencing data from gastrocnemius skeletal muscle at different time points of cachexia progression. Female 2-month-old NCI Ath/nude mice were injected with cachectic melanoma cells (CAC), non-cachectic melanoma cells (NCAC), or mock injected (Con). The time points analyzed are 2, 4, 6, and 8 weeks (wk) post cancer cell injection.


title: Progressive development of melanoma-induced cachexia differentially impacts organ systems in mice [Liver RNA-seq]

overall_design: RNA-sequencing data from liver at different time points of cachexia progression. Female 2-month-old NCI Ath/nude mice were injected with cachectic melanoma cells (CAC), non-cachectic melanoma cells (NCAC), or mock injected (Con). The time points analyzed are 2, 4, 6, and 8 weeks (wk) post cancer cell injection.


title: Progressive development of melanoma-induced cachexia differentially impacts organ systems in mice [TA]

overall_design: RNA-sequencing data from tibialis anterior skeletal muscle at different time points of cachexia progression. Female 2-month-old NCI Ath/nude mice were injected with cachectic melanoma cells (CAC), non-cachectic melanoma cells (NCAC), or mock injected (Con). The time points analyzed are 2, 4, 6, and 8 weeks (wk) post cancer cell injection.


title: The histone demethylase KDM5C represses trophoblast proliferation and invasion in woman with recurrent miscarriage

first: Shanhe

last: Yu

summary:
KDM5C is a histone H3K4-specific demethylase, which has been shown to play a key role in biological disease and development. However, the role of KDM5C in trophoblasts at early pregnancy is currently unknown. Here, we showed that KDM5C was upregulated in placental trophoblasts from recurrent miscarriage (RM) patients compared with healthy controls (HCs). Trophoblast proliferation and invasion was inhibited by KDM5C overexpression and was promoted by KDM5C knockdown. Transcriptome sequencing revealed that elevated KDM5C exerted anti-proliferation and anti-invasion effects by repressing the expression of essential regulatory genes. The combination analysis of RNA-seq, ChIP-seq and CUT&Tag assay showed that KDM5C overexpression leads to the reduction of H3K4me3 on the promoters and the corresponding downregulation of expression of several regulatory genes in trophoblasts. Among these genes, TGFβ2 and RAGE are essential for the proliferation and invasion of trophoblasts. Importantly, overexpression of KDM5C by a systemically delivered KDM5C adenovirus vector (Ad-KDM5C) promoted embryo resorption rate in mouse. Our results support that KDM5C is an important regulator of the trophoblast function during early pregnancy, and suggesting that KDM5C activity could be responsible for epigenetic alterations seen RM disease.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Progressive development of melanoma-induced cachexia differentially impacts organ systems in mice [heart RNA-seq]

overall_design: RNA-sequencing data from heart at different time points of cachexia progression. Female 2-month-old NCI Ath/nude mice were injected with cachectic melanoma cells (CAC), non-cachectic melanoma cells (NCAC), or mock injected (Con). The time points analyzed are 2, 4, 6, and 8 weeks (wk) post cancer cell injection.


title: Progressive development of melanoma-induced cachexia differentially impacts organ systems in mice [WAT]

overall_design: RNA-sequencing data from white adipose tissue at different time points of cachexia progression. Female 2-month-old NCI Ath/nude mice were injected with cachectic melanoma cells (CAC), non-cachectic melanoma cells (NCAC), or mock injected (Con). The time points analyzed are 2, 4, 6, and 8 weeks (wk) post cancer cell injection.


title: Progressive development of melanoma-induced cachexia differentially impacts organ systems in mice [BAT RNA-seq]

overall_design: RNA-sequencing data from brown adipose tissue at different time points of cachexia progression. Female 2-month-old NCI Ath/nude mice were injected with cachectic melanoma cells (CAC), non-cachectic melanoma cells (NCAC), or mock injected (Con). The time points analyzed are 2, 4, 6, and 8 weeks (wk) post cancer cell injection.


title: Single cell RNA sequencing reveals the suppressive effect of PPP1R15A inhibitor Sephin1 in antitumor immunity

status: Public on Dec 14 2022

first: Rongjing

state: Select One...

address: 320 Yueyang Road, Shanghai, China

institute: Shanghai Institute of Nutrition and Health, CAS

summary: Sephin1 is the selective inhibitor of Protein Phosphatase 1 Regulatory Subunit 15A (PPP1R15A), which is an important factor in the integrated stress response (ISR) of mammalian cells. Sephin1 can promote ISR by inhibiting the dephosphorylation of eIF2α, and preventing neurodegenerative disease occurrence in mice. However, we found that Sephin1 plays a protumorigenic role in mouse tumor models by suppressing the antitumor immune activities, which was highly relevant to the function of PPP1R15A. To fully understand the mechanism of Sephin1 to the antitumor immunity, we designed this experiment to explore the function of PPP1R15A and Sephin1 in the single-cell expression level. To understand effect of injection of Sephin1 to the immune cells in blood and tumor microenvironment in mice, we injected Sephin1 to mice intraperitoneally, and then subcutaneously inoculated with B16F1 cells. Blood before/after the tumor development and tumor tissues were collected and immune cells were isolated for single-cell sequencing and bioinformatics analysis afterwards. We found that in C57BL/6 mice, Sephin1 treatment could lead to higher levels of ISR activity and lower levels of antitumor immune activities. Specifically, Sephin1 treatment caused reductions in several tumor-killing immune cell populations, including CD8+ T cells, NK cells and NKT cells. The expression levels of cytotoxicity-related genes in lymphocytes were altered upon Sephin1 treatment. Additionally, TCR repertoire analysis demonstrated that the clonal expansion of tumor-specific T cells was inhibited by Sephin1, resulting in a compromised antitumor immune response. A special TCR+ macrophage subtype was identified to be significantly depleted upon Sephin1 treatment, implying that this type of macrophage plays a key antitumor role in the tumor microenvironment. The effects of Sephin1 were also verified in in vitro experiments and studies of other tumor cell lines. Taken together, these data suggest that inhibiting PPP1R15A promotes tumorigenesis by inducing adverse immune suppression. PPP1R15A has the potential to be an effective target for tumor therapy. Besides, a macrophage subtype, the TCR+ macrophages, played an important role in the anti-tumor immunity and can also be significantly inhibited by Sephin1.

overall_design: The cell suspension samples we obtained with this procedure were used for single-cell library construction. We performed single-cell immune profiling following the standard procedure from 10X Genomics. The library construction kit we used included the Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v1.1 (16 rxns, PN-1000165), Chromium Single Cell 5’ Library Construction Kit (16 rxns, PN-1000020), Chromium Single Cell V(D)J Enrichment Kit (Mouse T cell, 96 rxns, PN-1000071), Chromium Next GEM Chip G Single Cell Kit (48 rxns, PN-1000120) and Single Index Kit T Set A (96 rxns, PN-1000213). After single-cell library construction, all samples were sequenced on an Illumina NovaSeq PE150 platform.