title: Exosomes released from embryonic hippocampal cells under ceramide treatment carry a specific miRNA signature for sphingolipid pathway and cell differentiation

city: Udine

first: Emiliano

last: Dalla

state: UD

address: Piazzale Kolbe 4

department: Department of Medicine

institute: Università degli Studi di Udine

summary:
Purpose: Identification of the miRNA signature carried by the exosomes released from embryonic hippocampal cells under ceramide treatment
Outcome: We investigated the role of ceramide in amplifying the differentiation signal of HN9.10 cells. Treatment of HN9.10 cells with ceramide caused the release of exosomes carrying neutral sphingomyelinase and neutral ceramidase. The analysis of exosomal miRNAs showed that 38 miRNAs were differentially expressed in a statistically significant manner, with some overexpressed miRNAs regulating genes encoding for proteins involved in biological, homeostatic, biosynthetic and small molecule metabolic processes, embryo development and cell differentiation, all phenomena that could be relevant for HN9.10 cell differentiation.

overall_design: Identification of differentially expressed miRNAs secreted in the exosomal vesicles of HN9.10 cells treated with ceramide, added to the culture medium at the 100 nmol/L concentration corresponding to the amount of ceramide present in exosomes released under vitamin D3 treatment, as previously reported (Conte et al., 2021).

first: Federico

last: Fiorani

first: Rossana

last: Domenis

first: Samuela

last: Cataldi

first: Carmela

last: Conte

first: Martina

last: Mandarano

first: Mercedes

last: Garcia-Gil

first: Adriana

last: Cifù

first: Cataldo

last: Arcuri

first: Alessandra

last: Mirarchi

first: Tommaso

last: Beccari

first: Francesco

last: Curcio

first: Elisabetta

last: Albi


title: Effect of deficiency of Elk4 on transcriptome changes in murine bone marrow derived mast cells upon FcϵRI mediated activation

status: Public on Jul 12 2023

city: Hongkong

first: Yuji

last: Huang

address: Road 86 wujin

country: China

institute: Shanghai Jiao Tong University

type: Expression profiling by high throughput sequencing

summary: The proliferative potential of mast cells after activation for 3-4h was found to be decreased, which suggests that mast cell degranulation and cell proliferation are differentially regulated. ELK4, a member of the ternary complex factor (TCF) subfamily of Ets transcription factors, is one of the downstream effectors of MAPK signaling that is critical for cell proliferation. And Elk4 has been identified to be vital for macrophage activation in response to zymosan and the transcriptional response to 12-O-tetrade canoyl phorbol-13-acetate (TPA) stimulation in fibroblast. However, the effect of ELK4 on the mast cell transcriptional response to FcϵRI and GPCR mediated activation and its potential functional significance in mast cells remain unclear. Here, We characterised the transcriptional program downstream of FcϵRI signalling using IgE-DNP/HSA stimulation by RNA-seq. The investigation of the transcriptional response was performed using murine bone marrow derived mast cells(BMMCs) from different animals: (i) wild type mice, (ii) Elk4 heterozygous mice, (iii) Elk4 knockout mice. Overall, our study identifies a new physiological role of the transcription factor ELK4 in mast cell proliferation and activation.

overall_design: To investigate the function of Elk4 on mast cell proliferation and activation, we cultured murine bone marrow derived mast cells(BMMCs) from  littermate wild type(WT), Elk4 heterozygous(HZ), Elk4 knockout(KO) mice, and observed the effects of Elk4 deficiency in WT, HZ and KO BMMCs upon IgE-DNP/HSA stimulation. We then performed gene expression profiling analysis  using data obtained from RNA-seq of 3 different cells in control and stimulated group. Comparative gene expression proliling analysis of RNA-seq data for WT, HZ and KO BMMCs with or without IgE-DNP/HSA stimulation.

first: Zhehui

last: Zhu

first: Weize

last: Li

first: Chen-Ying

last: Liu

first: Li


title: Next Generation Sequencing Facilitates Quantitative Analysis of DLBCL Cell Line SU-DHL-4 Cells with P2X7 Receptor Signaling Activation or Inhibition

city: Xi'an

first: Xiao

last: Yang

state: Shaanxi

address: 157#, Xiwu Road, Xincheng District

department: The Second Affiliated Hospital

institute: Xi'an Jiaotong University

summary: The goals of this study aim to reveal the role of P2X7 receptor signaling in DLBCL

overall_design: Compare transcriptomes of SU-DHL-4 cells treated with PBS (Control), Bz-ATP (P2X7 specific agonist) or A740003 (P2X7 specific antagonist)


title: Endothelial Map2k1 mutation affects vasculogenesis: RNA sequencing analysis in a conditional murine model

city: Boston

first: Christopher

last: Sudduth

state: MA

address: 300 Longwood Ave

country: USA

institute: Boston Children's Hospital

summary: To determine RNA expression changes caused by AVM MAP2K1 K57N mutation

overall_design: Conditional mouse model expressing MAP2K1 K57N in endothelial cells after recombination at day 1 of life produced mice with brain AVM lesions. Endothelial cells from mutant and wild type mice were compared at day 9 to determine changes in RNA expression

first: Sudduth

last: Christopher

first: Smits

last: Patrick

first: Greene

last: Arin


title: Vitamin D promotes tissue repair and host defense responses against microbial infection in airway organoids

city: Shenzhen

first: Shumin

last: Liao

address: No. 1088 Xueyuan Avenue, Nanshan District

institute: Southern University of Science and Technology

summary:
To clarify the relationship between VD deficiency and airway epithelial disorders, we investigated the effects of VD on 2.5-D airway epithelial organoids cultured at the air–liquid interface (ALI) and performed an in-silico analysis.
We performed gene expression profiling analysis using data obtained from RNA-seq of 14 mature airway organoids with 1,25(OH)2D3 treatment followed by HI1N1 infection.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mature airway organoids with 1,25(OH)2D3 treatment and H1N1 infection.

first: Liang


title: Single nuclei RNAseq of male rat area postrema and nucleus tractus solitarius after cisplatin treatment

city: Philadelphia

first: Benjamin

middle: C.

last: Reiner

state: PA

address: 125 S 31st St

institute: University of Pennsylvania

summary: We performed single-nuclei RNAseq of Sprague Dawley rat area postrema and nucleus tractus solitarius brain samples from animals treated with cisplatin to identify cellular subtype specific changes in the neural transcriptome.

overall_design: We performed the 10x Genomics 3' gene expression assay (v3.1) on nuclei isolated from frozen Sprague Dawley rat area postrema and nucleus tractus solitarius combined brain punches. At the onset of the dark cycle, rats (~400 g) were injected with cisplatin (6mg/kg, n=4) (i.p.). After six hours, rats were deeply anesthetized with a triple cocktail of ketamine, xylazine and acepromazine (180 mg/kg, 5.4 mg/kg and 1.28 mg/kg, respectively; i.p.) in the middle of the dark phase. Brains were removed and snap-frozen in dry ice-cold hexane. Three adjacent micro-punch samples (each ~1 cubic mm) containing the AP and left and right NTS were collected from coronally-prepared brains on a cryostat, pooled together, and stored at -80°C until further processing. Nuclei were isolated by differential centrifugation and microfluidically captured using the 10x Genomics Chromium controller. Sequencing libraries were constructed and sequenced on an Illumina NovaSeq 6000.

middle: C

first: Richard

last: Crist

first: Matthew

middle: R

last: Hayes

first: Bart

last: De Jonghe

first: Tito

last: Borner


title: Boldine increases functional recovery and response to physical rehabilitation in a mouse model of contusion spinal cord injury

city: New York

first: Jens

last: Hansen

state: NY

address: 1425 Madison Ave

department: Department of Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Membrane channels such as connexins (Cx), pannexins and P2X7 receptors are permeable to calcium, ATP and other small molecules. Release of ATP and glutamate through these channels is a key mechanism driving tissue response to traumas such as spinal cord injury (SCI). Boldine, an alkaloid isolated from the Chilean boldo tree, blocks both Cx hemichannels and pannexins. To test if boldine improved function after SCI, boldine or vehicle was administered to mice with a moderate severity contusion SCI. Boldine increased spared white matter and locomotor function as determined by the Basso Mouse Scale and horizontal ladder rung walk tests. Increases in locomotor function observed after treadmill walking at a slow speed were further augmented by boldine. Boldine reduced immunostaining for activated microglia (Iba1) and astrocytic (GFAP) markers while increasing that for axon growth and neuroplasticity (GAP-43). Cell culture studies demonstrated that boldine blocked hemichannels, specifically Cx26 and Cx30, on cultured astrocytes and blocked calcium entry through activated P2X7R. Studies by RT-qPCR showed that boldine reduced expression of chemokine Ccl2, cytokine IL-6 and microglial gene CD68, while increasing expression of the neurotransmission genes SNAP25 and Grin2b, as well as GAP-43. Bulk RNA sequencing revealed that boldine modulated a large number of genes involved in neurotransmission in in spinal cord tissue just below the lesion epicenter at 14 days after SCI and that numbers of genes regulated by boldine was much lower at 28 days after injury. These results indicate that boldine spares tissue and increases locomotor function through mechanisms that may include reduced expression of pro-inflammatory molecules resulting in greater remodeling of surviving circuits

overall_design: At 4 months of age, male and female animals of similar weight were randomly assigned to SCI or a sham-SCI. Each group was then randomly assigned to boldine or vehicle treated groups. For treadmill training studies, SCI animals were randomly assigned to vehicle with no treadmill, vehicle with treadmill or boldine with treadmill. The experimental design and timeline for the study procedures is shown in Figure 1 of the article

first: Carlos

middle: A

last: Toro

first: Kaitlin

last: Johnson

first: Mustafa

middle: M

last: Siddiq

first: Walter

last: Vásquez

first: Wei

last: Zhao

first: Zachary

last: Graham

first: Juan

last: Sáez

first: Ravi

last: Iyengar

middle: P

last: Cardozo


title: Beta cell dysfunction and dedifferentiation induced by Bone Morphogenetic Protein (BMP)-2 is associated with histone modifications and decreased NeuroD1 chromatin binding [NeuroD1 ChIP-seq]

city: La Jolla

last: Wortham

state: CA

address: 2880 Torrey Pines Scenic Drive, Sanford Consortium for Regenerative Medicine, Room 3102

institute: University of California, San Diego

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Insufficient insulin secretion is a hallmark of type 2 diabetes and has been attributed to beta cell identity loss characterized by decreased expression of several key beta cell genes. The pro-inflammatory factor BMP-2 is upregulated in islets of Langerhans from diabetic individuals and acts as an inhibitor of beta cell function and proliferation. Exposure to BMP-2 induces expression of Id1-4, Hes-1 and Hey-1, transcriptional regulators associated with loss of differentiation. The aim of this study was to investigate the mechanism of BMP-2 induced beta cell dysfunction and maturity. Mouse islets exposed to BMP-2 for 10 days showed impaired insulin secretion and beta cell proliferation. BMP-2-induced beta cell dysfunction was associated with decreased expression of beta cell specific identity and proliferation markers such as Ins1, Ucn3 and Ki67 but increased expression of Id1-4, Hes-1 and Hey-1. Top 30 most regulated proteins significantly correlated with corresponding mRNA expression. BMP-2 induced gene expression changes were associated with a predominant reduction in acetylation of H3K27 and a decrease in NeuroD1 chromatin binding activity. These results show that BMP-2-induced beta cell dysfunction is associated with epigenetic changes, predominantly a reduction in H3K27ac and a decrease in NeuroD1 DNA binding resulting in altered beta cell gene expression.

overall_design: Examination of  NEUROD1 binding site in primary mouse islets exposed or non-exposed to BMP2 for 10 days

first: Adriana

middle: I

last: Urizar

first: Michala

last: Prause

first: Lars

last: Ingerslev

first: Yinghui

last: Sui

first: Maike

last: Sander

first: Kristine

last: Williams

first: Roman

last: Barrès

first: Martin

last: Larsen

first: Gitte

middle: L

last: Christensen

first: Nils

last: Billestrup


title: Beta cell dysfunction and dedifferentiation induced by Bone Morphogenetic Protein (BMP)-2 is associated with histone modifications and decreased NeuroD1 chromatin binding {RNA-seq]

first: Matthew

overall_design: RNA-seq of pancreatic islets were cultured in the absence or presence of 50ng/ml BMP2


title: Role of Circulating Exosomal miRNAs in early diabetic retinopathy

city: Wuhan

first: Songtao

last: Yang

address: Jiefang Avenue 1277

department: Department of Endocrinology, Union Hospital

institute: Huazhong university of science and technology, Wuhan union hospital

type: Non-coding RNA profiling by high throughput sequencing

summary:
To investigate the possibilities of circulating exosomal miRNAs in the early screening and prevention of diabetic retinopathy(DR), and to explore how the exosomal miRNAs functioning in DR.
We then performed gene expression profiling analysis using data obtained from small RNA-seq of 3 diabetes mellitus(DM) patients and 3 DR patients.

overall_design: Comparative gene expression profiling analysis of small RNA-seq data for DM patients and DR patients.

first: Jiaoyue

last: Zhang

first: Lulu

last: Chen


title: Beta cell dysfunction and dedifferentiation induced by Bone Morphogenetic Protein (BMP)-2 is associated with histone modifications and decreased NeuroD1 chromatin binding [Histone ChIP-seq]

overall_design: Examination of 3 histone modifications (H3K27ac; H3K27me3 and H3K4me3) in primary mouse islets exposed or non-exposed to BMP2 for 10 days


title: Alalysis of gene expression sigunature in WT and Menin KO CD8 T cells.

city: Toon

first: Junpei

last: Suzuki

address: Shitukawa

department: Graduate School of Medicine

country: Japan

institute: Ehime University

summary: To elucidate the effect of menin on the differentiation of CD8 T cell, the gene expression were measured in WT and Menin KO CD8 T cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and Menin KO CD8 T cells at indicated days after TCR stimulation.


title: Transcription and DNA methylation signatures of paternal care in hippocampal dentate gyrus of prairie voles (RRBS)

city: Tallahassee

first: Nicholas

middle: James

last: Waddell

state: FL

address: 319 Stadium Dr

department: Biological Sciences

institute: Florida State University

type: Methylation profiling by high throughput sequencing

summary:
In socially monogamous prairie voles (Microtus ochrogaster), parental behaviors not only occur in mothers and fathers, but also can exist in virgin males. However,  some virgin males display aggressive behaviors towards conspecific pups. Although this behavioral dichotomy in response to pup exposure has been well documented in male virgin voles, little is known about the gene expression changes underlie the parental behavioral differences and their regulatory mechanisms. To address this, we profiled the transcriptome and DNA methylome of hippocampal dentate gyrus of four prairie vole groups, attacker virgin males, parental virgin males, fathers, and mothers.
We found a concordant pattern of gene transcription in parental virgin males and fathers, when comparing to the attacker group.  The methylome analysis also revealed pathways with genes enriched for epigenetic changes involving both receptor-mediated and secondary messenger signaling across both behavioral phenotypes and sexual experiences. Furthermore, we found correlations between gene expression changes and DNA methylation differences between attacker and parental virgin males, which suggests a canonical gene expression regulatory role of DNA methylation in paternal care. Therefore, our study presents an integrated view of transcriptome and epigenome that provides a DNA epigenetic based molecular insight of paternal behavior.

overall_design: Comparative Gene Expression and DNA Methylome profiling of Prairie Vole Dentate Gyrus cells from different groups based on behavioral response to pup-exposure

middle: J

first: Yan

last: Liu

first: Javed

last: Chitaman

first: Graham

last: Kaplan

first: Zuoxin

last: Wang

first: Jian

last: Feng


title: Transcription and DNA methylation signatures of paternal care in hippocampal dentate gyrus of prairie voles

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

overall_design: Refer to individual Series


title: Alalysis of gene expression sigunature in CD8 T cells from young and aged mice.

summary: To elucidate the effect of aging on the function of CD8 T cell, the gene expression were measured in CD8 T cells from young (6 weeks of age) and aged (around 65 weeks of age) mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for young and aged CD8 T cells at seven days after TCR stimulation.

first: Toshio

last: Kakuda


title: Beta cell dysfunction and dedifferentiation induced by Bone Morphogenetic Protein (BMP)-2 is associated with histone modifications and decreased NeuroD1 chromatin binding

last: Wortham


title: Analysis of gene expression sigunature in Utx KO CD8 T cells

summary: To elucidate the effect of Utx, histone demethylase, on CD8 Tcell diferentiation, The gene expression were measured in WT and Utx KO CD8 T cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and Utx KO CD8 T cells at five days after TCR stimulation.

first: Haruna

last: Noda


title: Defining function of wild-type and three patient specific TP53 mutations in a zebrafish model of embryonal rhabdomyosarcoma

city: San Antonio

first: Yidong

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: RNAseq analyses comparing gene expression in zebrafish embryonal rhabdomyosarcoma tumors expressing kRASG12D/tp53-/-/GFP or /kRASG12Dtp53-/- + TP53-P153△/GFP

overall_design: The RNAseq samples being submitted are of zebrafish  embryonal rhabdomyosarcoma tumors generated in th CG1 syngeneic background expressing kRASG12D/tp53-/-/GFP and /kRASG12Dtp53-/- + TP53-P153△/GFP

first: Jiangfei

first: Kunal

last: Baxi

first: Myron

middle: S

last: Ignatius

first: Zhao

last: Lai


title: Snip1  and PRC2 coordinate the intrinsic apoptosis, cell division,   and neurogenesis in the developing brain [RNA-seq]

city: Doha

first: Mohamed Nadhir

last: Djekidel

state: Doha

address: Gharafa

department: Translational Medicine Department

country: Qatar

institute: Sidra Medicine

summary: RNAseq was performed on brain cells conditionally depleted from Snip1, and the PRC2 subunit Eed.

overall_design: Snip1-tm1a (Infrafrontier/EMMA 04224) were first crossed with Actin-FLPe to generate the Snip1-flox line. To genetically label NPCs, Snip1-flox; Nestin-Cre mice were crossed with Sox2-eGFP transgenic mice. Embryos were harvested at embryonic day E13

first: Yurika

last: Matsui

first: Mohamed

middle: N

first: Katherine

last: Lindsay

first: Parimal

last: Samir

first: Nina

last: Connolly

first: Hongfeng

first: Yiping

last: Fan

first: Beisi

last: Xu

first: Jamy

last: Peng


title: USP11/LSH/CYP24A1 axis activation underlies calcium homeostasis and potentiates the resistance of colorectal cancer cells to ferroptosis

city: Beijing

first: Daoyuan

last: Huang

address: 45 Changchun Street, Xicheng District

institute: Xuanwu Hospital Capital Medical University

summary:
To explore the key downstream factors for USP11 stable LSH regulation, we performed transcriptome analysis using controls, USP11 knockdown, and LSH knockdown HCT116 cells
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HCT116 cells and its KD derivatives (shLSH, shUSP11).

first: Junyi

last: Duan


title: Snip1 and PRC2 coordinate the intrinsic apoptosis, cell division, and neurogenesis in the developing brain [CUT&RUN]

summary: Approximately 3 × 105 NPCs sorted for Sox2-eGFP were mixed with 3 × 104 Drosophila S2 cells per reaction. We performed CUT&RUN using the protocol developed by the Henikoff lab (Skene and Henikoff, 2017). In brief, Bio-Mag®Plus Concanavalin-A (Con A) coated beads (Bangs Laboratories BP531) were washed and activated with Binding buffer. Nuclei of NPCs with S2 spike-in were gently prepared (see Subcellular Protein Extraction section). Activated Con A beads and nuclei were then mixed and rotated for 5 min at room temperature. They were then blocked with Digitonin block buffer for 5 min at room temperature. 0.5-1 μg of primary antibody with 0.25 μg Spike-in antibody (Active Motif 61686) diluted in Digitonin block buffer was added to the bead-nuclei mixture and incubated for 3 hours (histone marks) or O/N (the rest) at 4 °C. Beads were washed three times with Digitonin block buffer and incubated with pA-MNase for 1 hour at 4 °C. Beads were washed three times with Wash buffer and incubated in Wash buffer for 10 min on ice. The pA-MNase was activated by incubating the beads with 2 mM CaCl2 for 25 min on ice and quenched by adding the Stop buffer. DNA was released from the beads by incubating them for 30 min at 37 °C and collected by centrifugation at 16,000 x g for 5 min at 4 °C. DNA was then isolated by using a phenol/chloroform extraction method.

last: Chen


title: YAP1 maintains active chromatin state in head and neck squamous cell carcinomas that promotes tumorigenesis through cooperation with BRD4

first: Srinivas Vinod

last: Saladi

state: Massachusetts

address: 20 Staniford St

institute: Harvard Medical School

summary: The conserved Hippo-YAP signaling pathway is involved in homeostasis and organ development through the regulation of cell growth and cell death. Its downstream effectors YAP1, WWTR1 (TAZ), and TEAD are transcriptionally active in the majority of human cancers, often as a result of copy-number variation or inactivating mutations of core components and upstream regulators. Analysis of The Cancer Genome Atlas and other published data of head and neck squamous cell carcinoma (HNSCC) reveals somatic alterations of the Hippo-YAP pathway in approximately 50% of HNSCC, making it the most altered pathway in these cancers. Unfortunately, highly specific inhibitors targeting the YAP1 transcriptional complex are not available, and better strategies to target this pathway are sought. Here, we show that FAT1 (FAT Atypical Cadherin 1), an upstream inhibitor of YAP1, is mutated either by missense or truncating mutation in 29% of HNSCC. Comprehensive proteomic and drug-screening studies across pan-cancer models confirm that FAT1-mutant HNSCC exhibit selective and higher sensitivity to BRD4 inhibition by JQ1. Epigenomic analysis reveals an active chromatin state in FAT1-mutant HNSCC cells that is driven by the YAP/TAZ transcriptional complex through recruitment of BRD4 to deposit active histone marks, thereby maintaining an oncogenic transcriptional state. This study reveals a detailed cooperative mechanism between YAP1 and BRD4 in HNSCC and suggests a specific therapeutic opportunity for the treatment of this subset of head and neck cancer patients.

overall_design: Chromatin accessibility analysis of ATAC-seq data for CAL33 cells with or without JQ1(6 hrs and 24 hrs) treatment

first: Nana

first: Gabriel

last: Golczer

first: Brian

last: Lin

first: Adam

last: Langenbucher

first: Richard

last: Joh

first: Michael

last: Lawrence

first: Srinivas

middle: V


title: Evasion of antiviral innate immunity by SARS-CoV-2 NSP1 is exerted through H3K9 di-methylation

city: Bethesda

first: Markus

last: Hafner

state: MD

address: 50 South Drive

department: NIAMS

institute: NIH

summary: The pathogen causing the current COVID-19 pandemic, the severe acute respiratory syndrome coronavirus (SARS-CoV-2), evades the innate immune machinery through the independent action of several viral proteins, including the nonstructural protein 1 (NSP1). NSP1 has multiple functions, but the relative contribution of NSP1-mediated translational repression, ribosome-proximate degradation of host mRNA, or other molecular mechanisms to viral immune evasion remains unclear. Here we combined several genome wide approaches, including RNA-seq, ribosome footprinting, and ChIP-seq to find that NSP1 predominantly affects transcription of immune-related genes. NSP1 expression in A549 cells induced Histone 3 Lysine 9 (H3K9) methylation of antiviral gene loci, leading to specific suppression of type I and type III interferon pathways. Treatment with the G9a/GLP H3K9 methyltransferase inhibitor UNC0638 reverses this suppression of antiviral genes and blocks viral replication after SARS-CoV2 infection of A549 cells. Our results call attention to epigenetic reprogramming induced by SARS-CoV2 and highlight the importance to identify innate factors regulating histone modification of gene loci targeted by SARS-CoV-2, with possible relevance to the understanding and therapy of other immunomodulatory diseases.

overall_design: Herin several high throughput approaches including total RNA-Seq, Ribosome footprinting and ChIP-seq are combined to probe NSP1 function. Our results lead us to propose that NSP1 is a multifunctional protein that promotes innate antiviral immune evasion by inducing H3K9 dimethylation. Treatment with the specific H3K9 methyltransferases inhibitor UNC0638 attenuated suppression of antiviral genes by NSP1. In addition, UNC0638 treatment restored antiviral gene expression and blocked viral replication during SARS-CoV2 infection of human lung epithelial cells.

first: Dimitrios

middle: G

last: Anastasakis

first: Daniel

last: Benhalevy

first: Nicolas

last: Çuburu

first: Nihal

last: Altan-Bonnet


title: Obesity enhances antiviral immunity in the genital mucosa through a microbiota-mediated effect on γδ T cells

city: Daejeon

first: Heung Kyu

last: Lee

address: 291 Daehak-ro, Yuseong-gu

department: Graduate School of Medical Science and Engineering

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: Obesity is detrimental to the immune system. It impairs lymphatics, T cell development, and lymphopoiesis; induces dysfunction of antitumor immunity; and also promotes tumor progression. However, direct evidence of the impact of obesity on viral infection is lacking. We found an unexpected protective role of obesity against herpes simplex virus 2 infection of the genital mucosa in mice. Although conventional antiviral immunity was comparable between obese mice and lean mice, obesity enhanced the cytotoxic subset of γδ T cells. This effect was mediated by L-arginine produced by commensal microbiota in the genital mucosa, which induced “pseudonormoxia” of γδ T cells, resulting in increased NKG2D expression of γδ T cells through the downregulation of HIF1A by inducing NO production, thereby protecting mice from lethal genital herpes. Thus, our work illuminates one mechanism by which obesity-induced compositional changes in the vaginal microbiota can affect mucosal immune responses against viral infection.

overall_design: 5 wks-old female C57BL/6J mice were fed with SCD or 60%kcal HFD for 10 weeks. MPA was subcutaneously injected to the mice at the 9 weeks of feeding. At 10 weeks of feeding, mice were infected with 10^4 pfu of HSV-2 WT intravaginally. At 0 or 3 days post infection, vagina were harvested and single cell suspensions were isolated. 10 0 dpi mice were pulled for one sample and 5 3 dpi mice were pulled for one sample.  By FACS Aria II, 7-AAD- live cells were sorted. 10,000 cells per sample were sequenced.

first: JangHyun

last: Park

first: In

last: Kang

first: HyeonCheol

last: Kim

first: Younghoon

first: SungKi

first: JiEun

last: Oh

first: HeungKyu


title: Snip1  and PRC2 coordinate the intrinsic apoptosis, cell division,   and neurogenesis in the developing brain

first: Mohamed Nadhir

last: Djekidel


title: Construction of GBM patient-derived xenograft mouse models

city: Cincinnati

first: Frank

last: Huang

state: OHIO

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: Our adult GBM patient-derived xenograft mouse models keep the genomics characteristics of GBM patient tumors.

sample_organism:
Homo sapiens
Homo sapiens/Mus musculus xenograft

overall_design: To understand the difference between GBM patient tumor and the GBM patient-derived xenograft mouse models, we conducted bulk RNA sequencing analysis of patient-derived xenograft mice model of GBM


title: Cardiomyocyte-specific PCSK9 deficiency compromises mitochondrial bioenergetics and heart function

city: Gothenburg

first: Muhammad

last: Arif

state: Västra Götaland

address: Blå Straket 5/WLAB

department: Department of Molecular and Clinical Medicine

country: Sweden

institute: University of Gothenburg

summary:
Purpose: PCSK9, which regulates hepatic lipid homeostasis by modulating LDL levels, is expressed in small quantities in the heart, but its role is unknown. Here, we sought to determine its cardiac function and identify the mechanisms. Mice with heart-specific deletion of Pcsk9 had reduced contractile capacity, heart failure with preserved ejection fraction, and left ventricular dilatation at 28 weeks of age and died prematurely.
Results: Transcriptomic analyses revealed alterations of signaling pathways linked to cardiomyopathy and energy metabolism. Mitochondrial membrane lipid composition and cristae morphology were also altered, impairing the assembly and activity of mitochondrial respiratory complexes. Mitochondrial oxidation was reduced and compensatory glycolytic energy production was insufficient to support demand.
Conclusions: Thus, PCSK9 is a key factor in cardiac metabolic function and PCSK9 deficiency is linked to cardiomyopathy, impaired heart function, and compromised energy production.

overall_design: We performed a genome-wide transcriptomic analysis on tissue samples obtained from 10- and 28-week-old male C57B1/6N mice (hPcsk9–/– and hPcsk9+/+)

first: Marion

last: Laudette

first: Malin

last: Lindbom

first: Mathieu

last: Cinato

first: Mario

last: Ruiz

first: Stephen

last: Doran

first: Azra

last: Miljanovic

first: Mikael

last: Rutberg

first: Linda

last: Andersson

first: Martina

last: Klevstig

first: Marcus

last: Henricsson

first: Per-Olof

last: Bergh

first: Marc

last: Pilon

first: Tuulia

last: Hyötyläinen

first: Matej

last: Orešič

first: Adil

last: Mardinoglu

last: Levin

first: Jan

last: Boren


title: Sequencing of  mRNAs with N6-methyladenosine modifications in Diabetic Nephropathy (DN) with and without forced expression of FTO

city: Yiwu

first: Qiang

last: Sun

state: Zhejiang

address: No. N1, Shangcheng Avenue

institute: Zhejiang University

summary: To identify potential mRNA targets of FTO whose m6A levels are affected by FTO in Diabetic Nephropathy (DN), we conducted m6A-seq for messenger RNAs isolated from HMC cells with and without forced expression of FTO.

overall_design: HMC cell line; control vs FTO overexpression

first: Mengzhe

last: Guo

first: Qian

last: Sha

first: Xi

last: Chen


title: Oral air pollution exposure mediates diabetes by disrupting intestinal macrophage differentiation

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: We performed a single-cell transcriptome analysis of colon monocytes and macrophages in 2 control mice and 2 mice orally treated with diesel exhaust particles.

overall_design: Lamina propria cells positive for Cd11b and positive for Ly6c2 or Cd64 were sorted for each replicate mouse, and used for single cell RNA Seq (10x genomics platform)

first: Angela

last: Bosch

first: Claudia

last: Cavelti

first: Julien

last: Roux


title: Dynamics of reactive astrocytes fosters tissue regeneration after cuprizone-induced demyelination

status: Public on Jul 11 2023

city: Hannover

first: Ulrich

last: Kalinke

state: Lower Saxony

address: Feodor-Lynen-Str. 7

department: Institute for Experimental Infection Research

country: Germany

institute: Twincore, Centre for Experimental and Clinical Infection Research


title: The 31 pairs of FF and FFPE data for the development of 72GC for FFPE in 2014

city: Suita

first: Yoshiaki

last: Sota

state: Osaka

address: Yamadaoka 2-15

department: Breast and Endocrine Surgery

institute: Osaka University

summary: The study aimed to develop the 72GC (the 72-gene classifier) for recurrence-risk prediction for patients with estrogen receptor positive and node-negative breast cancer. 72-GC could differentiate the high-risk from the low-risk patients with a high statistical significance, and is considered to be applicable to formalin-fixed, paraffin embedded (FFPE) tumor tissues because the results of 72-GC on FF (fresh-frozen) tissues and FFPE tissues showed a high concordance.  J06 31 pairs of FF (fresh‑frozen) and FFPE data are included in the concordance analysis of 72GC high/low results between FF and FFPE (Table 3). A long time passed, and now it is unclear how these 31 cases were distributed among the analysis.    *Note: This old data has been updated multiple times by the other members.  Then, there are some differences from the original paper and unclear points still remain.  Therefore, do not use it for formal analysis aimed at public insurance coverage etc. This is for research purposes only. Please cite this paper when writing a new paper.   PMID: 24461457  DOI: 10.1016/j.clbc.2013.11.006

overall_design: RNA was extracted from 31 pairs of FF (fresh frozen) and FFPE (Formalin-fixed paraffin-embedded) tumor samples obtained from radical breast cancer surgery and hybridized on Affymetrix microarrays.

first: Ryo

last: Tsunashima

first: Yasuto

last: Naoi


title: Transcription and DNA methylation signatures of paternal care in hippocampal dentate gyrus of prairie voles (RNA-Seq)

first: Nicholas

last: Waddell

first: Yan

last: Liu

first: Javed

last: Chitaman

first: Graham

last: Kaplan

first: Zuoxin

last: Wang

first: Jian

last: Feng


title: Revealing and harnessing CD39 for the treatment of colorectal cancer and liver metastases by engineered T cells

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Scientific Institute


title: Laminar shear stress regulated gene expression in HUVECs II

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: To identify genes whose expression is regulated by laminar flow in HUVECs.

overall_design: HUVECs were subjected to laminar shear stress (12 dynes/cm2) or were kept under static conditions for 48 hours. Then total RNA was isolated from HUVECs and RNA-sequencing was performed.

first: Liang

last: Guozheng

first: Wang

last: Lei

first: Guenther

last: Stefan


title: CRISPR/Cas9 in vivo screens in patients’ leukemias growing in mice

city: Munich

first: Tobias

last: Herold

address: Marchioninistr. 15

department: Department of Internal Medicine III

institute: University Hospital Grosshadern, Ludwig-Maximilians-University (LMU)

summary: Functional genomic screens were mostly performed in cell lines and mouse models so far. To approximate the clinical situation, we established customized CRISPR/Cas9 screens in patient-derived xenograft (PDX) leukemia models in vivo. Ninety-two surface molecules were tested; sgRNAs against CXCR4 and ITGB1 dropped out and single knockouts validated their essential function. Our method allows determining patient-specific tumor dependencies in vivo which might facilitate personalized medicine of cancer in the future.

overall_design:
Whole-Transcriptome analysis of 36 pediatric and adult patient-derived xenograft (PDX) acute lymphoblastic leukemia (ALL) samples. Samples were taken in the majority in the relapsed/refractory setting.
*** Submitter states that German law does not allow raw data to be submitted for public access.
The raw data of this study is available, but German law restrictions apply to the availability of these data, which were used for the current study, and so are not publicly available. Data are however available from the authors upon reasonable request and with permission of the local ethics committee.

first: Irmela

last: Jeremias


title: The 14 pairs of FF and FFPE data for the application of 95GC to FFPE in 2019

summary: The study aimed to apply 95GC, originally developed using fresh‑frozen (FF) tissues, to formalin‑fixed paraffin‑embedded (FFPE) tissues, because FFPE tissues are routinely prepared and are readily available. Although we previously reported the applicability of 72GC to FFPE tissues (DOI: 10.1016/j.clbc.2013.11.006), the present study aimed to improve the accuracy of 95GC for FFPE tissues using the reference robust multiarray average (refRMA) method, optimized for FFPE tissues. Therefore, a 95GC RS (Recurrence Score) was first developed and then the accuracy of the newly developed 95GC algorithm for FFPE tissues was evaluated using the 95GC RS. These 14 pairs of FF and FFPE data are included in the concordance analysis of 95GC high/low results between FF and FFPE (Figure 3B). J05 was created in a form more suited to the actual clinical setting, such as leaving the postoperative samples for 4 hours before immersing them in formalin. A long time passed, and now it is unclear how these 14 cases were distributed among the analysis.     *Note: This old data has been updated multiple times by the other members.  Then, there are some differences from the original paper and unclear points still remain.  Therefore, do not use it for formal analysis aimed at public insurance coverage etc. This is for research purposes only. Please cite this paper when writing a new paper.  PMID: 31638234  DOI: 10.3892/or.2019.7358

overall_design: RNA was extracted from 14 pairs of FF (fresh frozen) and FFPE (Formalin-fixed paraffin-embedded) tumor samples obtained from radical breast cancer surgery and hybridized on Affymetrix microarrays.


title: Dynamics of reactive astrocytes fosters tissue regeneration after cuprizone-induced demyelination [RNA-seq I]

first: Ulrich

last: Kalinke

summary: Demyelination and dysregulated myelination in the CNS are hallmarks of many neurodegenerative diseases such as multiple sclerosis (MS) and leukodystrophies. Here, we studied GFAP+ astrocytes during de- and remyelination in the cuprizone mouse by exploiting the ribosomal tagging (RiboTag) technology. Analyses were performed 5 weeks after cuprizone feeding, at the peak of demyelination in the corpus callosum, and 0.5 and 2 weeks after cuprizone withdrawal, when remyelination and tissue repair is initiated. After 5 weeks of cuprizone feeding, reactive astrocytes showed inflammatory signatures with enhanced expression of genes that modulate leukocyte migration (Tlr2, Cd86, Parp14,Cxcl10). Furthermore, demyelination-induced reactive astrocytes expressed numerous ligands including Cx3cl1, Csf1, Il34, and Gas6 that act on homeostatic as well as activated microglia and thus potentially mediate activation and recruitment of microglia as well as enhancement of their phagocytosis. During early remyelination, region-specific astrocytes displayed reduced inflammatory response signatures as indicated by shut down of CXCL10 production. During late remyelination, the signatures of GFAP+ astrocytes shifted towards resolving inflammation by active suppression of lymphocyte activation and differentiation and support of glia cell differentiation. Astrocytes showed enhanced expression of osteopontin (SPP1) as well as of factors that are relevant for tissue remodelling (Timp1), regeneration and axonal repair. In conclusion, we detected highly dynamic astroglial transcriptomic signatures in the cuprizone model, which reflects excessive communication amongst glia cells and highlights different astrocyte functions during neurodegeneration and regeneration.

overall_design: Male GFAP-Cre+/-RPL22HA/wt aged 8-9 weeks fed with 0.2% (w/w) of cuprizone blended into standard rodent chow for a total of 5 weeks to induce demyelination . Animals were fed ad libitum until defined experimental endpoints. After 5 weeks post-cuprizone feeding, mice were put on regular chow for additional 2 weeks (total 7 weeks) to examine remyelination. Natural remyelination occurs starting 0.5 weeks after Cuprizone withdrawal (total 5.5wks). For this study, brains were collected at 5, 5.5 and 7 weeks, which corresponds, to acute demyelination, earlier remyelination and late remyelination respectively. Along with this, aged-matched control mice were kept of a normal diet.At the experimental endpoint, animals were euthanized, brain harvested and corpus callosum was micro-dissected. Thereafter, corpus callosum was homogenized and lysate used to pull down HA-tagged ribosomes and to isolate RNA from the immunoprecipitate (IP) for bulk RNA-sequencing.

first: Felix

last: Mulenge

first: Lara-Jasmin

last: Schröder

first: Andreas

last: Pavlou


title: Dynamics of reactive astrocytes fosters tissue regeneration after cuprizone-induced demyelination [RNA-seq II]


title: Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale [II]

city: Seattle

first: Asia

last: Mendelevich

state: WA

address: 2211 Elliott Ave

institute: Altius

summary:
Analysis of allele-specific expression is strongly affected by the technical noise present in RNA-seq experiments. Previously, we showed that technical replicates can be used for precise estimates of this noise, and we provided a tool for correction of technical noise in allele-specific expression analysis. This approach is very accurate but costly due to the need for two or more replicates of each library. Here, we develop a spike-in approach that is highly accurate at only a small fraction of the cost.
We show that a distinct RNA added as a spike-in before library preparation reflects technical noise of the whole library and can be used in large batches of samples. We experimentally demonstrate the effectiveness of this approach using combinations of RNA from species distinguishable by alignment, namely, mouse, human, and C.elegans. Our new approach, controlFreq, enables highly accurate and computationally efficient analysis of allele-specific expression in (and between) arbitrarily large studies at an overall cost increase of ∼ 5%.

sample_organism:
Caenorhabditis elegans
Mus musculus

platform_organism:
Caenorhabditis elegans
Mus musculus

overall_design: Comparative allele-specific expression analysis of RNA-seq data with foreign RNA spike-ins (mixes of human, mouse and C.elegans).

first: Saumya

last: Gupta

first: Alexander

last: Gimelbrant


title: Characterization of MGC-803 cell line use sample HeLa and AGS

city: wuhan

first: Meimei

last: Yang

address: Bayi Road

department: China Center for Type Culture Collection

institute: Wuhan University

summary: Investigation of the mixed origins of the MGC-803 cell line reveals it is a HeLa hybrid cell line

overall_design: MGC-803 cell line


title: Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale [III]

sample_organism:
Caenorhabditis elegans
Homo sapiens
Mus musculus


title: Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale [I]

platform_organism:
Caenorhabditis elegans
Homo sapiens
Mus musculus


title: Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale

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

overall_design:
Refer to individual Series
grantee -- *Alexander Gimelbrant*
grant # -- *5 R01 CA262577-02*
grant title -- *Elucidating prostate cancer risk mechanisms through
large-scale cistrome wide association studies*
name of the funding source -- *NIH*


title: TRIM25 promotes glioblastoma cell growth and invasion via regulation of the PRMT1/c-MYC pathway by targeting the splicing factor NONO

city: Hangzhou

first: Yike

last: Chen

address: Jiefang Road 88, Hangzhou

department: Department of Neurosurgery

institute: Second Affiliated Hospital, School of Medicine, Zhejiang University

summary: Ubiquitination plays an important role in proliferating and invasive characteristic of glioblastoma (GBM), similar to many other cancers. Tripartite motif 25 (TRIM25) is a member of the TRIM family of proteins, which are involved in tumorigenesis through substrate ubiquitination. Here, we found TRIM25 is upregulated in GBM and promotes glioblastoma cell growth and invasion, both in vitro and in vivo. Subsequently, we screened a panel of proteins that interact with TRIM25; mass spectrometry and co-immunoprecipitation showed that NONO was a potential substrate of TRIM25. TRIM25 knockdown reduced the K63-linked ubiquitination of NONO, which suppressed the splicing function of NONO. The dysfunctional NONO further leads to the retention of the second intron in the pre-mRNA of PRMT1 and inhibit the activation of the PRMT1/c-MYC pathway. In summary, we demonstrated that TRIM25 promotes glioblastoma cell growth and invasion by regulating the PRMT1/c-MYC pathway through mediation of the splicing factor NONO. Efforts to target the E3 ligase activity of TRIM25 or the complex interactions between TRIM25 and NONO may be useful in the treatment of GBM.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for LN229 cells and its KD derivatives (shTRIM25).

first: Xiaohui

last: Xu

first: Jianxiong

last: Ji

first: Jianmin

last: Zhang


title: PAXIP1 and STAG2 converge to maintain 3D genome architecture and facilitate promoter/enhancer contacts to enable stress hormone-dependent transcription [ChIP-seq]

city: Amsterdam

first: Isabel

last: Mayayo-Peralta

address: Plesmanlaan 121

country: Netherlands

institute: NKI

summary: How steroid hormone receptors (SHRs) orchestrate transcriptional activity remains only partly understood. Upon activation, SHRs bind the genome and recruit their co-regulators, crucial to induce gene expression. However, it remains unknown which components of the SHR-recruited coregulator complex are essential to drive transcription following hormonal stimuli. Through a FACS-based genome-wide CRISPR screen, we comprehensively dissected the Glucocorticoid Receptor (GR) co-regulatory complex involved in gene-target regulation. We describe a novel functional cross-talk between PAXIP1 and the cohesin subunit STAG2 that is critical for regulation of gene expression by GR. Without altering the GR cistrome, PAXIP1 and STAG2 depletion alter the GR transcriptome, by impairing the recruitment of 3D-genome organization proteins to the GR complex. Importantly, we demonstrate that PAXIP1 is required for stability of cohesin on the genome, its localization to GR-occupied sites, and maintenance of enhancer-promoter interactions. Moreover, in lung cancer, where GR acts as tumor suppressor, PAXIP1/STAG2 loss enhances GR-mediated tumor suppressor activity by modifying local chromatin interactions. All together, we introduce PAXIP1 and STAG2 as novel co-regulators of GR, required to maintain 3D-genome architecture and drive the GR transcriptional programme following hormonal stimuli.

overall_design:
GR ChIPs in NT-1, PAXIP1-KO, NT-2 and STAG2-KO cells. Three biological replicates. PAXIP1, RAD21, and H3K4me1 ChIPs in NT and PAXIP1-KO cells. Two biolofical replicates. For all ChIPs, cells were treated with 100nM Dexamethasone for 2 hours.
Please note that no (narrow peak) processed data was provided for the PAXIP1* and H3K4me1* samples as enrichment of the transcription factors/histone mark on GR peaks was analyzed using BAM files.

first: Sebastian

last: Gregoricchio

first: Karianne

last: Schuurman

first: Selçuk

last: Yavuz

first: Anniek

last: Zaalberg

first: Bart

last: Geverts

first: Aleksandar

last: Kojic

first: Nina

last: Abbott

first: Suzanne

last: Beerthuijzen

first: Joseph

last: Siefert

first: Tesa

last: Severson

first: Martijn

last: van Baalen

first: Liesbeth

last: Hoekman

first: Cor

last: Lieftink

first: Maarten

last: Altelaar

first: Roderick

last: Beijersbergen

first: Adriaan

middle: B

last: Houtsmuller

first: Stefan

last: Prekovic

first: Wilbert

last: Zwart


title: PAXIP1 and STAG2 converge to maintain 3D genome architecture and facilitate promoter/enhancer contacts to enable stress hormone-dependent transcription [RNA-seq]

first: Isabel

last: Mayayo-Peralta

overall_design: RNA-seq in NT-1, PAXIP1-KO-1, PAXIP1-KO-2, and GR-KO and RNA-seq in NT-2 and STAG2-KO. A549 cells were treated with vehicle(DMSO) or 100nM Dexamethasone for 8 hours

first: Sebastian

last: Gregoricchio

first: Karianne

last: Schuurman


title: Epigenomic and Topological Mechanisms Regulate Transcriptional Programs in Hepatocellular Carcinoma Cells

city: Farmington

first: Liuyang

last: Cai

state: CONNECTICUT

address: 10 Discovery Drive

department: Ruan Lab

institute: The Jackson Laboratory for Genomic Medicine

summary: Please note: There are no data associated with this record because the submitter failed to complete the submission of the data to GEO despite numerous requests. If you are interested in accessing these data, please contact the submitter and the journal editor. Samples and data can be added to GEO records at any time.

overall_design: If you are interested in accessing these data, please contact the submitter and the journal editor. The data that the submitter pledged to submit to GEO has not been uploaded.


title: PAXIP1 and STAG2 converge to maintain 3D genome architecture and facilitate promoter/enhancer contacts to enable stress hormone-dependent transcription [4C-seq]

overall_design: Cells with a non-targeting sgRNA (NT_AZ3) or with a CRISPR knock-out of PAXIP1 (IM26_PAXIP1KO1), after 3 days in hormone-deprived media conditions, were treated (Dex) or not (DMSO) with 100nM Dexamethasone for 2h. Three biological replicates have been proccessed for 3 different View-points.

first: Selçuk

last: Yavuz

first: Anniek

last: Zaalberg

first: Aleksandar

last: Kojic

first: Julien

last: Champagne

first: Remco

last: Nagel

first: Reuven

last: Agami


title: RNA sequencing in the skin of non-responders and allergic individuals exposed to p-phenylenediamine

status: Public on Jul 10 2023

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

institute: ETH ZURICH / University of Zurich

summary: p-Phenylenediamine (PPD) is a strong contact allergen used in hair dye that is known to cause allergic contact dermatitis (ACD). We investigated the effects of PPD exposure on the skin of occupationally exposed subjects with and without clinical symptoms.

overall_design: Skin biopsy specimens were collected from 4 patients with mild and 5 patients with severe PPD-related ACD and 7 hairdressers without contact dermatitis on day 4 after patch testing with 1% PPD in petrolatum or just petrolatum.

first: Sanne

last: Meisser

first: Yasutaka

last: Mitamura

first: Can

last: Altunbulakli

first: Cezmi

last: Akdis


title: Replication dynamics identifies the folding principles of the inactive X chromosome [scRepli-seq]

city: Tsu-shi

first: Rawin

last: Poonperm

state: Mie

address: 1577 Kurimamachiya

department: Graduate School of Bioresources

institute: Mie University

summary: Chromosome-wide late replication is an enigmatic hallmark of the inactive X chromosome (Xi). How it is established and what it represents remains obscure. By single-cell DNA replication sequencing, here we show that the entire Xi is reorganized to replicate rapidly and uniformly in late S-phase upon X-chromosome inactivation (XCI), reflecting its relatively uniform structure revealed by 4C-seq. Despite this uniformity, only a subset of the Xi became earlier replicating in SmcHD1-mutant cells. In the mutant, these domains protruded out of the Xi core, contacted each other, and became transcriptionally reactivated. 4C-seq suggested that they constituted the outermost layer of the Xi even before XCI and were rich in escape genes. We propose that this default positioning forms the basis for their inherent heterochromatin instability in cells lacking the Xi-binding protein SmcHD1 or exhibiting XCI escape. These observations underscore the importance of 3D genome organization on heterochromatin stability and gene regulation.

overall_design: BrdUIP Repli-seq, RNA-seq, and 4C-seq experiments were performed in wild-type and SmcHD1 mutant female JB4/EI7HZ2 mouse embryonic stem cells, day-9 differentiated cells, and neural stem cells (NSCs). Single-cell Repli-seq (scRepli-seq) was performed in wild-type and SmcHD1 mutant NSCs. We only deposited single-cell data sets which passed our filtering steps.

first: Ichiro

last: Hiratani


title: Changes in mouse epidermal DNA methylation during development of squamous cell carcinoma in response to UVR

city: Copenhagen

first: Olivia

last: Luxford Meyer

address: Frederik V's Vej 11

department: Department of Forensic Medicine

country: Denmark

institute: University of Copenhagen

type: Methylation profiling by genome tiling array

summary: Squamous cell carcinoma (SCC) is a common skin cancer, often caused by exposure to ultraviolet radiation (UVR). Recent studies have shown that changes in DNA methylation play a crucial role in the development of cancers. However, methylation patterns of SCC are not well characterised. Identifying biomarkers for the risk of developing SCC could be helpful for early detection and diagnosis, and can potentially improve treatment and prevention strategies. This study aimed to investigate methylation changes in the epidermis of mice exposed to UVR for 24 weeks. We examined the DNA methylation levels of 260,199 CpGs using the Illumina Infinium Mouse Methylation BeadChip and studied the epidermis of UVR-exposed and unexposed mice every four weeks for 24 weeks (n = 39). We identified CpGs with large differences in methylation levels (β-values) between UVR-exposed and unexposed mice. We also observed differences in the epigenetic age of these mice. We identified CpGs in Rev, Ipmk, Rad51b, Fgfr2, Fgfr3, and Ctnnb1 that may serve as potential biomarkers for SCC risk and could be helpful for the early detection and prevention of SCC. Further investigations are necessary to determine the biological functions and clinical significance of these CpGs.

overall_design: 36 mice subdivided in two groups comprising UVR-exposed (UVR group) and unexposed mice (control group). The epidermis of three mice in each group was analysed every four weeks for 24 weeks in (study) weeks 4, 8, 12, 16, 20, and 24 resulting in 36 mice. Additionally, three mice sampled in week 0 served as baseline mice resulting in a total of 39 mice.

last: Meyer

first: Jeppe

middle: D

last: Andersen

first: Claus

last: Børsting

first: Niels

last: Morling

first: Mikkel

first: Hans

last: Wulf

first: Peter

last: Philipsen

first: Catharina

last: Lerche


title: PAXIP1 and STAG2 converge to maintain 3D genome architecture and facilitate promoter/enhancer contacts to enable stress hormone-dependent transcription.

first: Isabel

last: Mayayo-Peralta

overall_design: Refer to individual Series


title: Replication dynamics identifies the folding principles of the inactive X chromosome [RNA-seq]


title: Phenylacetaldehyde inhibits development of colorectal cancer

city: shanghai

first: Kong

last: Cheng

address: 270 Dong 'an Road

institute: fudan university shanghai cancer center

summary: Phenylacetaldehyde (PAA), a product of phenylalanine metabolism, is catabolized by microbiota and has demonstrated anticancer properties in breast cancer. As intestinal homeostasis is influenced by gut microbiome, we investigated the effect of PAA on colorectal cancer (CRC). In the study, we interrogated the mechanistic pathways induced by PAA treatment using RNA sequencing.

overall_design: HCT-116 versus HCT-116 treated with PAA; RKO versus RKO treated with PAA.

first: Cheng

last: Kong


title: Single-Cell transcriptional profiling reveals immune dysregulation and abnormal immune-inflammatory communications between immune and retinal cells in uveitis

city: Jinan

first: Wei

last: Lin

state: Shandong

address: 6699 Qingdao Road, Huaiyin District, Jinan, Shandong , China

department: School of Clinical and Basic Medicine

institute: Shandong First Medical University & Shandong Academy of Medical Sciences

summary: Uveitis is an immune-inflammatory disease that can cause blindness. However, little is known about a comprehensive atlas of the ocular cellular and inflammatory components in uveitis. Here, single-cell RNA sequencing was performed to construct a transcriptomic atlas of ocular cells from experimental autoimmune uveitis (EAU) and control mice to identify disease- associated immune cell subsets and molecules. We reveal 15 cell types in eyes and found an α-Synuclein positive microglia subset and plasma cell subset with high level of cytokines. The heterogeneous plasma cells subsets communicated with DC, T cells and retinal cells via various cytokines and molecular pairing. The G protein Rab1A participated in the inflammatory response of plasma cells. Altogether, we revealed the heterogeneous inflammatory genes, EAU-specific immune cell populations, and dysregulated communications of immune and retinal cells in EAU. This result provides a systematic view of the transcriptional map of uveitis and a foundation for studying the cellular and molecular mechanisms and pathogenesis of this disease.

overall_design: Eye tissues from 15 EAU mice (after immunization for 16 days) vs  eye tissues from 15 Control mice. Eye tissues of each 15 mice were combined into one sample.

first: Meng

last: Feng

first: Songqi

last: Duan

first: Minghao

last: Li

first: Tingting

last: Liu

first: Xiaomeng

last: Yuan

first: Lijie

last: Wang

first: Xunbin

last: Wei

first: Qiang

last: Fu

first: Baofa

last: Sun


title: Replication dynamics identifies the folding principles of the inactive X chromosome [BrdU-IP Repli-seq]

first: Rawin

last: Poonperm

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

first: Ichiro

last: Hiratani


title: The compact high-fidelity EbCas12a enables all-in-one AAV delivery system

city: Wuhan

first: chen

last: peng

address: College of Life Sciences, Wuhan University

department: College of Life Sciences

summary: we characterized a novel compact Cas12a ortholog, EbCas12a, from the Erysipelotrichia bacterium with activities in mammalian cells. It is with the PAM sequence of 5’-TTTV-3’ (V=A, G, C) and the smallest size of ~3.47kb among reported Cas12a orthologs so far. Moreover, enhanced EbCas12a (enEbCas12a) was also developed to have comparable editing efficiency with higher specificity to AsCas12a and LbCas12a in mammalian cells. With the help of the compact enEbCas12a, all-in-one AAV delivery system with crRNA for Cas12a was developed for both in vitro and in vivo. Altogether, with the help of the novel smallest high fidelity enEbCas12a, this first case of the all-in-one AAV delivery for Cas12a could greatly boost future gene therapy and scientific research.

overall_design: Cells were collected after 48h post-transfection for genomic DNA extraction using FastPure Cell/Tissue DNA Isolation Mini Kit(Vazyme), Libraries were prepared according to GUIDE-seq methods. Briefly, Genomic DNA was sheared to length of about 250 bp, added Y adapter, and amplified by two rounds of nested anchored PCR. The last PCR products were GUIDE-seq libraries and sent to the company for sequencing using an Illumina sequencer

first: Lei

last: Yin


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [7C and 7D]

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. With support from NIMH and NINDS as part of the BRAIN Initiative Cell Census Network (BICCN), the Center for Epigenomics of the Mouse Brain Atlas (CEMBA) applied single nucleus methylation sequencing in 117 brain funtional regions across the whole adult male P56 C57BL/6J mouse brain. In each major brain regions, we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster. We integrate the single cell methylome with single cell gene expression and chromatin accessibility profiles from the same brain region to further identify potential enhancers and their corresponding genes for several neuronal cell types. By brain region spacial comparisons, we found spatial specificity among excitatory neuronal clusters within the same cortical layer. We identify brain-region-specific transcription factors that may regulate cortical region development of excitatory neurons. These data define the landscape of cell type and spatial heterogeneity in the mouse brain and the underlining regulatory epigenomic basis.

overall_design: Apply snmC-seq2 to 117 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (7C_191205, 7C_191212, 7D_200714, 7D_200721, 7E_201029, 7E_201105, 7F_200723).

first: Hanqing

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

first: Julia

middle: K

last: Osteen

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Rosa

last: Castanon

last: Nery

first: Peter

last: Berube

first: Huaming

last: Chen

first: Michael

last: Nunn

first: Jesse

last: Dixon

first: M

last: Behrens


title: Replication dynamics identifies the folding principles of the inactive X chromosome [4C]

first: Rawin

last: Poonperm


title: Role of RelB in Suppressing NF-κB Pro-Inflammatory Gene Expression [RNA-seq]

city: Los Angeles

first: Hector

last: Navarro

state: California

address: 570 Boyer Hall

department: MIMG

institute: UCLA

summary: To investigate the gene regulatory mechanisms of RelB DNA binding function and identify regulatory mechanisms for NF-κB pro-inflammatory gene expression.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for bone marrow derived dendritic cells from WT, RelBko, RelB-DB/DB, IFNARko,  IFNARko;RelBko, and IFNARko;RelB-DB/DB Mice
Please note that the GSE224515/PRJNA931364 samples (GSM7025414-GSM7025429) have been re-analyzed in the current study:
GSM7025414, WT_Control_1hr, SAMN33059462, SRX19279645
GSM7025415, RelBko_Control_1hr, SAMN33059461, SRX19279646
GSM7025416, IFNAR_Control_1hr, SAMN33059460, SRX19279647
GSM7025417, IFNAR;RelBko_Control_1hr, SAMN33059459, SRX19279648
GSM7025418, WT_CPG_1hr, SAMN33059458, SRX19279649
GSM7025419, WT_CPG_3hr, SAMN33059457, SRX19279650
GSM7025420, RelBko_CPG_1hr, SAMN33059456, SRX19279651
GSM7025421, WT_CPG_8hr, SAMN33059455, SRX19279652
GSM7025422, RelBko_CPG_3hr, SAMN33059454, SRX19279653
GSM7025423, IFNAR_CPG_3hr, SAMN33059453, SRX19279654
GSM7025424, IFNAR_CPG_1hr, SAMN33059452, SRX19279655
GSM7025425, IFNAR;RelBko_CPG_1hr, SAMN33059451, SRX19279656
GSM7025426, IFNAR;RelBko_CPG_8hr, SAMN33059450, SRX19279657
GSM7025427, IFNAR;RelBko_CPG_3hr, SAMN33059449, SRX19279658
GSM7025428, RelBko_CPG_8hr, SAMN33059448, SRX19279659
GSM7025429, IFNAR_CPG_8hr, SAMN33059447, SRX19279660

first: Navarro

last: Hector

first: Alexander

last: Hoffmann


title: Cell cycle-linked vacuolar pH dynamics regulate amino acid homeostasis and cell growth

city: South San Francisco

first: Voytek

last: Okreglak

state: CA

address: 1170 Veterans Blvd

institute: Calico Life Sciences

summary: Amino acid homeostasis is critical for many cellular processes. It is well established that amino acids are compartmentalized using pH gradients generated between organelles and the cytoplasm; however, the dynamics of this partitioning has not been explored. We have developed a highly sensitive pH reporter, and we find that the major amino acid storage compartment in Saccharomyces cerevisiae, the lysosome-like vacuole, alkalinizes prior to cell division and re-acidifies as cells divide. The vacuolar pH dynamics require the uptake of extracellular amino acids and activity of TORC1, the v-ATPase and the cycling of the vacuolar specific lipid, PI3,5P2 which is regulated by the cyclin-dependent kinase, CDK5/Pho85. Vacuolar pH regulation enables amino acid sequestration and mobilization from the organelle, which is important for mitochondrial function, ribosome homeostasis and cell size control. Collectively, our data provide a new paradigm for the use of dynamic pH-dependent amino acid compartmentalization during cell growth/division.

overall_design: duplicate cultures wild-type, atg18∆, fab1∆ and vph1∆ S. cerevisiae cells were grown in synthetic defined media containing dextrose, yeast nitrogen base and amino acids (SDC) to early log-phase. Experiment was repeated on two different days to give 4 samples per cell line.

first: Daniel

last: Gottschling


title: Role of RelB in Suppressing NF-κB Pro-Inflammatory Gene Expression


title: Super-enhancer switching in early mammalian development involves eRNA mediated SWI/SNF recruitment [RIP-seq]

city: Houston

first: Junwoo

last: Lee

address: 2120 El Paseo Street, Apt.603

department: Epigenetics and Molecular Carcinogenesis

institute: MD Anderson Cancer Center

summary: The RNA transcribed from enhancer regions, referred to as eRNA, has been suggested to directly activate transcription by helping to recruit transcription factors and co-activators.   Although there have been specific examples of eRNA functioning in this way, it is not clear how general this may be. We find the AT-hook of SWI/SNF alone binds preferentially RNA and as part of the esBAF complexes likely associates with eRNA that are transcribed from intronic and intergenic regions.  SWI/SNF is globally recruited in cis by eRNA to cell-type specific enhancers at two distinct stages in early mammalian development and not at promoters or enhancers that are shared between the two stages. SWI/SNF recruited by eRNA facilitates recruitment and/or activation of MLL3/4, p300/CBP and Mediator co-activators to stage-specific super-enhancers that in the primed embryonic stage activate cell lineage priming related genes.  We find a strong connection between ATP-dependent chromatin remodeling and eRNA in cell identity and super-enhancer activation.

overall_design: To investigate the RNA binding affinity of Brg1 and its AT hook domain and the characteristics of Brg1 bound RNAs, we first created Brg1 HA tagged and AT hook domain knock-out E14 cell lines. After then, we identified AT hook domain dependently Brg1 binding RNAs using RIP-seq data.

first: Dhurjhoti

last: Saha

first: McKenzie

last: Murvin

first: Mauro

last: Calabrese

first: Yue

last: Lu


title: Super-enhancer switching in early mammalian development involves eRNA mediated SWI/SNF recruitment [RNAPII_inhibitor CUT&RUN]

overall_design: To understand the importance of RNA polymerase II trasnscripts in AT hook dependent Brg1 localization, we created Brg1 AT hook domain knock-out E14 cell lines. After then,  10µM Triptolide were treated for 2hr and 3µg/mL Actinomycin D was treated for 4hr to inhibit transcription initiation and elongation separately. DMSO was treated as a control. And then, we classified Brg1 peaks via transcription and/or AT hook dependency using Cleavage under targets and release using nuclease (CUT&RUN) sequencing for Brg1/SMARCA4 in mouse embryonic stem cells (E14). RNA polymerase II CUT&RUN samples were used to show the transcriptional defects in inhibitors.

first: Srinivas

last: Animireddy

first: Anna

last: Thommen


title: CITE-seq of Ewing sarcoma lines

city: Boston

first: April

last: Apfelbaum

state: MA

address: 450 Brookline Ave

department: Pediatric Oncology

institute: Dana-farber Cancer Institute

summary: CD73 marks cells with increased mesenchymal morphologies and phenotypes. To understand the transcriptional differences in CD73+ and - cells and to understand the heterogeneity, we performed CITE-seq to measure single-cell RNA expression and cell surface CD73 protein expression on 9 different EwS cell lines

overall_design: CITE-seq for CD73 protein and  total mRNA  on 9 different Ewing sarcoma cell lines.

first: Emma

last: Wrenn

first: Beth

last: Lawlor

first: Olivia

last: Waltner

first: Scott

last: Furlan


title: Gene expression profile at single cell level of cells in distal pulmonary arteries from healthy and hypoxia-induced pulmonary hypertensive calves

city: Aurora

first: Sushil

last: Kumar

institute: University of Colorado Anschutz medical campus

summary: Distal pulmonary arteries contain multipe cell types and each cell type contains multiple functional state. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of cell types in control animals and the changes of cell types and gene expression between cells from healthy and PH vessels.

overall_design: Distal pulmonary arteries (DPAs) (less than 2mm in diameter) were dissected from the lungs of control and pulmonary hypertensive calves. Single cells were generated from DPAs, in which around 10,000 DPA cells from each animal were sequenced by sc-RNA-seq at depth of 100,000 reads/per cell.

first: Kurt

last: Stenmark

first: Cheng-Jun

last: Hu

first: Hui

last: Zhang

first: Li

last: Min

first: Suzette

last: Riddle

first: B

last: McKeon


title: Resveratrol prevents corneal allograft rejection in the rat cornea

city: Guangzhou

first: Chenjia

last: Xu

address: Zhongshan Ophthalmic Center

institute: Zhongshan Ophthalmic Center

summary: Rat corneal allograft rejection models were established to investigate the effects and mechanisms of resveratrol on corneal allograft rejection after corneal transplantation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the rat corneas of the control group and the resveratrol group after corneal transplantation,including a total of 6 samples, each with 3 duplicate samples.

first: Ting

last: Huang


title: MAdCAM-1 targeting strategy can prevent colitic cancer carcinogenesis and progression via suppression of immune cell infiltration and inflammatory signals

city: Maebashi

first: Naoya

last: Ozawa

state: None Selected

address: showamachi

institute: Gunma University, Graduate School of Medicine

summary: Chronic inflammation caused by infiltrating immune cells can promote colitis-associated dysplasia/colitic cancer in ulcerative colitis (UC) by activating inflammatory cytokine signaling through the IL-6/p-STAT3 and TNFα/NF-κB pathways. Mucosal addressin cell adhesion molecule-1 (MAdCAM-1) expressed on high endothelial venules promotes the migration of immune cells from the bloodstream to the gut via interaction with α4β7 integrin expressed on the immune cells. MAdCAM-1, has therefore drawn interest as a novel therapeutic target for treating active UC. However, the role of MAdCAM-1-positive endothelial cells in immune cell infiltration in dysplasia/colitic cancers remains unclear. We evaluated the expression of MAdCAM-1, CD31, and immune cell markers (CD8, CD68, CD163, and FOXP3) in samples surgically resected from 11 UC patients with dysplasia/colitic cancer and 17 patients with sporadic colorectal cancer (SCRC), using immunohistochemical staining. We used an azoxymethane/dextran sodium sulfate mouse model (AOM/DSS mouse) to evaluate whether dysplasia/colitic cancer could be suppressed with an anti-MAdCAM-1 blocking antibody by preventing immune cell infiltration. The number of MAdCAM-1-positive vessels and infiltrating CD8+, CD68+, and CD163+ immune cells was significantly higher in dysplasia/colitic cancer than in normal, SCRC, and UC mucosa. In AOM/DSS mice, the anti-MAdCAM-1 antibody reduced the number, mean diameter, depth of tumors, Ki67 positivity, number of CD8+, CD68+, and CD163+ immune cells, and the IL-6/p-STAT3 and TNF-α/NF-κB signaling. Our results indicate that targeting MAdCAM-1 is a promising strategy for controlling not only UC severity, but also carcinogenesis and tumor progression by regulating inflammation/immune cell infiltration in patients with UC.

overall_design:
Examination of 3 different method in  2 mouse

RNA extracted from tumors arising in a mouse model of inflammatory colorectal cancer (AOM/DSS mice) treated with an anti-inflammatory MAdCAM-1 antibody and a control group treated with an IgG antibody.
two mice from each group were selected.

first: Takehiko

last: Yokobori

first: Katsya

last: Osone

first: Hiroshi

last: Saeki


title: Investigating how the loss of RelB affects RelA DNA binding [ChIP-seq]

first: Hector

last: Navarro

overall_design: ChIP-seq Sample of RelB-ChIP and RelA-ChIP in WT and RelBko BMDCs Stimulated with LPS

first: Navarro

last: Hector

first: Allison

last: Daly

first: Alexander

last: Hoffmann


title: CD73 sorted cell RNA-sequencing and GeoMX sequencing

first: April

last: Apfelbaum

summary:
CD73 marks cells with increased mesenchymal morphologies and phenotypes. To understand the transcriptional differences in CD73+ and - cells, we performed bulk RNA-seq on the CD73 sorted cells.

In this study, we investigated if and how transcriptional heterogeneity of EwS cells contributes to heterogeneity of tumor phenotypes in vivo. Digital spatial profiling and human whole transcriptome analysis interrogated transcriptomic heterogeneity in EwS CHLA10 cell line xenografts.

overall_design:
Bulk RNA-sequencing for CD73 + and - cells in A673 and CHLA10 Ewing sarcoma cell lines

GeoMx Digital Spatial Profiling (NanoString) was carried out according to manufacturer instructions. Tumor specimens were generated as follows: subcutaneous injection of 4x10^5 CHLA10 cells in 50% Matrigel, primary tumors collected 54 days post-injection; tail vein injection of 7x10^5 CHLA10 cells injected in PBS, tumors collected 28 days post-injection (NSG immunocompromised mice). Tumors were fixed for 24 hours in 10% non-buffered formalin before paraffin embedding. 3 sections of FFPE tumor tissues (1 from subcutaneous tumor, 2 from 2 different tail vein-injected mice) were sectioned and adhered to a single slide. Whole Human Transcriptome Atlas Digital Spatial Profiling was performed (GeoMx) by Nanostring according to manufacturer protocols for 12 regions of interest (4 per tumor) with NGS readout.

first: Emma

last: Wrenn

first: Lindsay

last: Clark

first: Sean

last: Taylor

first: Beth

last: Lawlor


title: BL-HiC analysis of water avoidance stressed BALB/c mice colon epithelial cells

first: Gen

last: Zheng

state: Wuhan

address: Zhongshan road

institute: Wuhan Union Hospital

summary: We profiled emotional stress caused chromatin structure changes in colon epithelial cells from BALB/c mice.

overall_design: BL-Hi-C was performed with colon epihthelial cells isolated from two control (CT) & two water avoidance stressed (WAS) BALB/c mice; data from each group were combined for visualization with hic files.


title: Tumor-infiltrating gamma delta T-cells reveal exhausted subsets with remarkable heterogeneity in colorectal cancer

first: Linyan

last: Yu

address: 44 Wenhua West Road

institute: Shandong University

summary: Here, we sought to investigate the expression pattern of inhibitory receptors and functional state of TI-γδ T-cells, and reveal the features of exhausted TI γδ T-cells in the TME of CRC. In this study, the γδ T-cell subpopulations and gene expression profiles of TI-γδ T-cells and colonic intraepithelial lymphocytes (IELs) were analyzed by single-cell RNA sequencing (scRNA-seq).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for IEL-γδT cells and TIL-γδT cells.

first: Cai

last: Zhang

last: Lu


title: Cancer-associated fibroblast-like tumor cells remodel the Ewing sarcoma tumor microenvironment

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

overall_design: Refer to individual Series


title: An EZH2-NF-kB Regulatory Axis Drives Expression of Pro-Oncogenic Genetic Signatures in TNBC

first: Jeremy

last: Simon

department: Department of Data Science

institute: Dana-Farber Cancer Institute

summary: EZH2 has been studied most extensively in the context of PRC2-dependent gene repression. Paradoxically, accumulating evidence indicates non-canonical functions for EZH2 in cancer contexts including promoting gene expression in triple negative breast cancer (TNBC) cells through interactions with the transcription factor NF-kB.  We define a genomic profile of EZH2 and NF-kB factor RelA, RelB, and NFKB2/p52 co-localization and positive regulation of a subset of NF-kB targets and genes associated with oncogenic functions in TNBC, which is enriched in patient datasets.  We demonstrate interaction between EZH2 and RelA requiring the recently identified EZH2 transactivation domain (TAD), which mediates EZH2 recruitment to and activation of certain NF-kB-dependent genes, and supports downstream stemness phenotypes in TNBC cells. Interestingly, EZH2-NF-kB positive regulation of genes and stemness does not require PRC2. This study provides new insight into pro-oncogenic regulatory functions for EZH2 in breast cancer through PRC2-independent, and NF-kB-dependent regulatory mechanisms.

overall_design: We performed ChIP-seq for EZH2, RelA, RelB, and NFKB2 alongside input control in MDA-MB-231 and SUM149 breast cancer cells in biological triplicate. We also performed RNA-seq in MDA-MB-231 breast cancer cells following control, EZH2, RelA, or RelB knockdown via siRNA in biological duplicate, and RNA-seq in SUM149 cells following control or EZH2 knockdown via siRNA in biological duplicate

first: Gabrielle

last: Dardis

first: Albert

last: Baldwin


title: Role of steroidogenic factor 1 in the regulation of the ovarian reserve

city: University Park

first: Camilla

middle: H. K.

last: Hughes

state: PA

address: 439 Shortlidge Rd

department: Animal Science

institute: Penn State University

summary: The ovarian reserve of follicles comprises all oocytes for lifetime fertility and once formed, it is non renewing. The orphan nuclear receptor steroidogenic factor 1 (SF-1; Nr5a1) is essential for steroidogenesis, but its role in the earliest stages of follicular development is not known. We therefore developed a model of conditional depletion of SF-1 from prenatal ovaries and performed RNAsequencing to identify SF-1 regulated genes.

overall_design: Mice with ovarian knockout of steroidogenic factor 1 (SF-1) were generated using Amhr2-cre (SF-1 cKO; Nr5a1 f/f, Amhr2-cre Tg/+) and compared to littermate controls with intact SF-1 expression(Con; Nr5a1 f/f, Amhr2-cre +/+). Ovaries were collected from mice on embryonic day (ED) 17.5, Postnatal day (PND) 1, and PND4.

first: Olivia

middle: E

last: Smith

first: Marie-Charlotte

last: Meinsohn

first: Mylene

last: Brunelle

first: Nicolas

last: Gévry

first: Bruce

last: Murphy


title: Blood platelet RNA profiles do not enable for nivolumab response prediction at baseline in patients with non-small-cell lung cancer

city: Amsterdam

first: Myron

last: Best

address: De Boelelaan 1117

department: Neurosurgery

institute: VU University Medical Center

summary: We report RNA-sequencing data of 286 platelet RNA samples isolated from non-small cell lung cancer patients (NSCLC) that were at baseline for nivolumab immunotherapy. This dataset was employed to test the hypothesis that platelet RNA at baseline of nivolumab treatment predicts immune responses.

overall_design: Blood platelets were isolated from whole blood in purple-cap BD Vacutainers containing EDTA anti-coagulant by standard centrifugation. Total RNA was extracted from the platelet pellet, subjected to cDNA synthesis and SMARTer amplification, fragmented by Covaris shearing, and prepared for sequencing using the Truseq Nano DNA Sample Preparation Kit. Subsequently, pooled sample libraries were sequenced on the Illumina Hiseq 2500 or 4000 platform. All steps were quality-controlled using Bioanalyzer 2100 with RNA 6000 Picochip, DNA 7500 and DNA High Sensitivity chips measurements. For further downstream analyses, reads were quality-controlled using Trimmomatic, mapped to the humane reference genome using STAR, and intron-spanning reads were summarized using HTseq.

first: Thomas

last: Wurdinger


title: CRISPR and siRNA manipulation of SOX17 in human pulmonary artery endothelial cells HPAEC

city: London

first: Christopher

last: Rhodes

state: Hammersmith and Fulham

address: Hammersmith Campus, Du Cane Rd

country: United Kingdom

institute: Imperial College London

summary: HPAEC were treated with either siRNA to SOX17 or CRISPR activating or inhibiting the promoter or an enhancer region associated with pulmonary hypertension and sequenced.

first: Rachel

last: Walters

first: Jurjan

last: Aman


title: HydRA: Deep-learning models for predicting RNA-binding capacity from protein interaction association context and protein sequence

first: Gene

middle: W

last: Yeo

address: 9500 Gilman Dr

department: Cellular and Molecular Medicine

institute: University of California, San Diego

summary: RNA-binding proteins (RBPs) control RNA metabolism to orchestrate gene expression, and dysfunctional RBPs underlie many human diseases. Proteome-wide discovery efforts predict thousands of novel RBPs, many of which lack canonical RNA-binding domains. Here, we present a hybrid ensemble RBP classifier (HydRA) that leverages information from both intermolecular protein interactions and internal protein sequence patterns to predict RNA-binding capacity with unparalleled specificity and sensitivity using support vector machine, convolutional neural networks and transformer-based protein language models. HydRA enables Occlusion Mapping to robustly detect known RNA-binding domains and to predict hundreds of uncharacterized RNA-binding domains. Enhanced CLIP validation for a diverse collection of RBP candidates reveals genome-wide targets and confirms RNA-binding activity for HydRA-predicted domains. The HydRA computational framework accelerates construction of a comprehensive RBP catalogue and expands the set of known RNA-binding protein domains.

overall_design: To characterize and validate the uncharacterized known RBPs (HSP90A, YWHAG, YWHAH, YWHAE, and YWHAZ) and candidate RBPs (INO80B, PIAS4, NR5A1, ACTN3, and MCCC1) predicted by HydRA, we V5-tagged and overexpressed them in HEK293 cell lines and implement eCLIP experiments. The same procedure was also applied on truncated proteins of INO80B, PIAS4, NR5A1, ACTN3, and MCCC1 where the HydRA predicted RNA-binding domains are deleted to validate the functions of these predicted RNA-binding domains.

first: Samuel

last: Park

first: Hui

middle: Q

last: Tan

first: Wenhao

last: Jin

first: Katannya

last: Kapeli

first: Kristopher

last: Brannan


title: Transcriptional changes and microRNA expression profiles during NeuroD1-mediated astrocyte-to-neuron conversion

city: Detroit

first: Yang

last: Shi

state: MI

address: 4100 John R St MM03BI

department: Karmanos Cancer Institute

institute: Wayne State University Schhol of Medicine

summary: To reveal the molecular mechanisms underlying astrocyte-to-neuron reprogramming, we performed RNA-seq analysis on human astrocyte cultures (HA1800) during NeuroD1(ND1)-mediated neuronal reprogramming.

overall_design: Transcriptomic and microRNA (miRNA) expression profiles of control (GFP) and ND1-transduced astrocytes at 2 and 6 days post infection were compared by RNA-seq.

first: Xuanyu

last: Chen

first: Hedong

last: Li


title: Gene expression of senescent and non-senescent AL1 cells

city: Dresden

first: Maximina

last: Yun

state: Saxony

address: Fetscherstrasse 105

department: CRTD

institute: TUD

summary: Axolotl limb regeneration proceeds through the formation of a blastema, a mound of progenitor cells that accumulate at the end of the amputated stump. These progenitor cells expand and later undergo patterning to regenerate the missing limb, restoring both form and function. A subset of cells within the blastema become senescent, a state of permanent growth arrest. Here, we address the functional relevance of cellular senescence to axolotl limb regeneration, through a combination of gain- and loss-of-function assays. Using transcriptomic analyses on in vitro and in vivo senescent cells, we gain insights into the basis of the senescent phenotype, cell-cycle arrest, and molecular mediators involved in axolotl regeneration at the molecular level.

overall_design: AL1 cells were treated with either etoposide and nutlin-3a to trigger senescence induction, or DMSO to generate proliferating controls. Their transcriptomes were analyzed through RNA-seq to obtain insights into the molecular basis of senescence induction in axolotl AL1 cells, as well as to uncover common features between in vitro and in vivo senescennce in the axolotl.

first: Qinghao

last: Yu

first: Andreas

last: Petzold


title: Differential requirements for the BAF and ncBAF subfamilies of the mammalian SWI/SNF chromatin remodeling enzymes during skeletal muscle differentiation.

city: Worcester

first: Tapan

last: Sharma

address: 368 Plantation Street

department: Gene Therapy Centre

institute: University of Massachusetts Medical School

summary: Subunit proteins BAF250a and Brd9 are specific to mammalian SWI/SNF subfamilies BAF and ncBAF respectively. We have performed RNA-seq analysis for C2C12 myoblasts stably knocked down for each subunits using specific shRNA constructs. C2C12 cells stably transfected with non-targeting scrambled shRNA construct were used as controls.

overall_design: RNA-seq data was generated from differentiated C2C12 cells. Samples from stably transfected cells were harvested at 48h post induction of differentiation (DM 48h). RNA from biological duplicates (for each treatment and timepoint) was extracted. Library preparation, sequencing and downstream analysis was performed by BGI Americas.

first: Monserrat

last: Olea-FLores

first: Sabriya

last: Syed

first: Teresita

last: Padilla-Benavides

first: Anthony

last: Imbalzano


title: AXL+SIGLEC6+ dendritic cells in cerebrospinal fluid and brain tissues of patients with autoimmune inflammatory demyelinating disease of CNS

city: Daejeon

first: Jong-Eun

address: 291, Daehak-ro, Yuseong-gu

institute: Korea Advanced Institute of Science and Technology

summary: Inflammatory demyelinating disease of the CNS (IDD) is a heterogeneous group of autoimmune diseases, and multiple sclerosis is the most common type. Dendritic cells (DCs), major antigen-presenting cells, have been proposed to play a central role in the pathogenesis of IDD. The AXL+SIGLEC6+ DC (ASDC) has been only recently identified in humans and has a high capability of T cell activation. Nevertheless, its contribution to CNS autoimmunity remains still obscure. Here, we aimed to identify the ASDC in diverse sample types from IDD patients and experimental autoimmune encephalomyelitis (EAE). A detailed analysis of DC subpopulations using single-cell transcriptomics for the paired cerebrospinal fluid (CSF) and blood samples of IDD patients (total n = 9) revealed that three subtypes of DCs (ASDCs, ACY3+ DCs, and LAMP3+ DCs) were overrepresented in CSF compared with their paired blood. Among these DCs, ASDCs were also more abundant in CSF of IDD patients than in controls, manifesting poly-adhesional and stimulatory characteristics. In the brain biopsied tissues of IDD patients, obtained at the acute attack of disease, ASDC were also frequently found in close contact with T cells. Lastly, the frequency of ASDC was found to be temporally more abundant in acute attack of disease both in CSF samples of IDD patients and in tissues of EAE, an animal model for CNS autoimmunity. Our analysis suggests that the ASDC might be involved in the pathogenesis of CNS autoimmunity.

overall_design: We have generated a single-cell transcriptome dataset for paired cerebrospinal fluid and PBMC samples from 9 Inflammatory demyelinating disease patients and 2 healthy controls without inflammatory disease of the central nervous system.

first: Sung-Min

last: Kim

first: Seok-Jin

last: Choi

first: Moonhang


title: Mitophagy promotes resistance to BH3 mimetics in acute myeloid leukemia

city: new york

first: Xufeng

state: NY

address: 550 First Avenue, Smilow 1307

institute: NYU Langone Medical Center

summary: BH3 mimetics are used as an efficient strategy to promote mitochondrial-dependent cell death in blood malignancies, including acute myeloid leukemia (AML). Venetoclax, a potent BCL2 antagonist, is used clinically in combination with hypomethylating agents for the treatment of AML, while various compounds targeting MCL1 are in clinical trials. Yet, drug resistance eventually ensues, highlighting the urgency to understand the underlying mechanisms. Our genome-wide CRISPR/Cas9 screens revealed that loss of mitophagy regulators sensitizes AML to BH3 mimetics. One such regulator is Mitofusin-2 (MFN2), a GTPase that controls mitochondrial dynamics and the degradation of damaged mitochondria through mitophagy. Resistance to BH3 mimetics is accompanied by alterations in mitochondrial morphology, enhanced mitochondria-endoplasmic reticulum interactions, and augmented mitophagy flux. MFN2 inactivation, using a novel small molecule inhibitor, and pharmacologic inhibition of mitophagy synergizes with BH3 mimetics. Overall, targeting of mitophagy along with BCL2-family members is a promising strategy to overcome drug resistance in AML.

overall_design: RNA-sequencing (RNA-Seq) was performed to explore the molecular mechanisms underpinning the MCL1 inhibitor (AMG-176) resistance

first: Christina

last: Glytsou

first: Iannis

last: Aifantis


title: Senescent cells promote progenitor cell expansion during axolotl limb regeneration


title: Gene expression profile of senescent and non-senescent cells from regenerating blastemas

overall_design: To understand what distinguishes blastemal senescent cells from their non-senescent counterparts, senescent and non-senescent cells were isolated from early, mid, late and palette stage blastemas by Fluorescence-activated Cell Sorting and analyzed using RNA-seq.


title: Gene expression profiling of adult Drosophila melanogaster prickle-prickle mutant brains

city: Iowa City

first: Krishna Madhav

last: Nukala

state: Iowa

address: 129 E Jefferson

department: Department of Biology

institute: University of Iowa

summary: Study of genome-wide differential gene expression of adult Drosophila melanogaster prickle-prickle mutant brains compared to control animals.

overall_design: Brains were dissected from prickle-prickle mutant and control adults. Total RNA was isolated and converted to cDNA for array hybridization. Each genotype was represented with two biological replicates, each with four technical replicates.

first: Krishna

middle: M

first: John

middle: R

last: Manak


title: Single-cell RNA profiling of blastemal senescent cells

first: Maximina

overall_design: Here, we performed gene expression profiling for endogenous blastemal senescent (Rho+) cells at the single-cell level. Senescent cells were isolated on the basis of GalNP-rho labelling from blastemas derived at different stages of regeneration (mid, late, and palette), and analyzed through single-cell RNA-seq.

first: Qinghao


title: Microglial gene signature reveals loss of homeostatic microglia associated with neurodegeneration of Alzheimer's disease

status: Public on Jul 09 2023

city: Nagoya

first: Akira

last: Sobue

address: Furo-cho Chikusa-ku

institute: Nagoya university

summary: Microglia-mediated neuroinflammation has been implicated in the pathogenesis of Alzheimer's disease (AD). Although microglia in aging and neurodegenerative disease model mice show a loss of homeostatic phenotype and activation of disease-associated microglia (DAM), a correlation between those phenotypes and the degree of neuronal cell loss has not been clarified. In this study, we performed RNA sequencing of microglia isolated from three representative neurodegenerative mouse models, AppNL-G-F/NL-G-F with amyloid pathology, rTg4510 with tauopathy, and SOD1G93A with motor neuron disease by magnetic activated cell sorting. In parallel, gene expression patterns of the human precuneus with early Alzheimer's change (n=11) and control brain (n=14) were also analyzed by RNA sequencing. We found that a substantial reduction of homeostatic microglial genes in rTg4510 and SOD1G93A microglia, whereas DAM genes were uniformly upregulated in all mouse models. The reduction of homeostatic microglial genes was correlated with the degree of neuronal cell loss. In human precuneus with early AD pathology, reduced expression of genes related to microglia- and oligodendrocyte-specific markers was observed, although the expression of DAM genes was not upregulated. Our results implicate a loss of homeostatic microglial function in the progression of AD and other neurodegenerative diseases. Moreover, analyses of human precuneus also suggest loss of microglia and oligodendrocyte functions induced by early amyloid pathology in human.

overall_design: We analyzed gene expression in microglia isolated by magnetic-activated cell sorting (MACS) from cerebral cortex of AppNL-G-F/NL-G-F and rTg4510 mice or lumbar spinal cord of SOD1G93A mice.

first: Okiru

last: Komine

first: Yuuichiro

last: Hara

first: Tomoo

last: Ogi

first: Koji

last: Yamanaka


title: Transcriptional network governing extraembryonic endoderm cell fate choice

city: Irvine

first: Paula Duyen

last: Pham

address: 4410 Natural Sciences

institute: UC Irvine

summary: The mechanism by which transcription factor (TF) network instructs cell-type-specific transcriptional programs to drive primitive endoderm (PrE) progenitors to commit to parietal endoderm (PE) versus visceral endoderm (VE) cell fates remains poorly understood. To address the question, we analyzed the single-cell transcriptional signatures defining PrE, PE, and VE cell states during the onset of the PE-VE lineage bifurcation. By coupling with the epigenomic comparison of active enhancers unique to PE and VE cells, we identified GATA6, SOX17, and FOXA2 as central regulators for the lineage divergence. Transcriptomic analysis of cXEN cells, an in vitro model for PE cells, after the acute depletion of GATA6 or SOX17 demonstrated that these factors induce Mycn, imparting the self-renewal properties of PE cells. Concurrently, they suppress the VE gene program, including key genes like Hnf4a and Ttr, among others. We proceeded with RNA-seq analysis on cXEN cells with FOXA2 knockout, in conjunction with GATA6 or SOX17 depletion. We found FOXA2 acts as a potent suppressor of Mycn while simultaneously activating the VE gene program. The antagonistic gene regulatory activities of GATA6/SOX17 and FOXA2 in promoting alternative cell fates, and their physical co-bindings at the enhancers provide molecular insights to the plasticity of the PrE lineage. Finally, we show that the external cue, BMP signaling, promotes the VE cell fate by activation of VE TFs and repression of PE TFs including GATA6 and SOX17. These data reveal a putative core gene regulatory module that underpins PE and VE cell fate choice.

overall_design: Gene expression profiling for Gata6, Sox17, and/or FoxA2 loss-of-function  and BMP4 stimulation time course studies in cXEN cells. Epigenetic profiling of transcription factor binding or histone marking in cXEN cells using CUT&RUN or ATAC.

first: Ken

last: Cho

first: Paula


title: Cpxm2 as a novel candidate for cardiac hypertrophy and failure in hypertension [Illumina]

city: Muenster

first: Anika

last: Witten

address: Domagkstr. 3

department: Institute of Human Genetics, Department Genetic Epidemiology

institute: University of Muenster

summary: To identify novel targets in left ventricular (LV) hypertrophy (LVH) we initiated comparative transcriptome analysis between genetic models derived from stroke-prone spontaneously hypertensive rats (SHRSP) and Fischer (F344). Previous genetic studies in the SHRSP/F344 model confirmed the presence of a major quantitative trait locus (QTL) for LV mass on rat chromosome (RNO) 1. We assigned carboxypeptidase X 2 (Cpxm2) to a genetic locus for LV mass identified in SHRSP. We assigned carboxypeptidase X 2 (Cpxm2) to a genetic locus for left ventricular mass.

overall_design: Male SHRSP and F344 rats were obtained. To develop the consomic strain SHRSP-1F344, we crossed the SHRSP strain with the F344 strain in accordance with our linkage results and introgressed the whole rat chromosome (RNO)1 from F344 into the SHRSP background as previously described. In that model, we performed whole transcriptome analysis on LV tissue of 14 weeks old male F344, SHRSP-1F344 and SHRSP (n = 8, respectively) using Illumina RatRef-12 Expression BeadChips.

first: Katja

last: Grabowski

first: Reinhold

last: Kreutz

first: Monika

last: Stoll