title: Transcriptome studies reveal the regulation of m6A in testis development and spermatogenesis in yak

city: Lanzhou

first: shaoke

last: guo

state: Gansu

address: West Lake Street

department: Lanzhou institute of husbandry and pharmaceutical sciences

institute: Chinese Academy of Agricultural Sciences

summary: Studying spermatogenesis is the key to understanding the development mechanism of the yak reproductive system. Although N6-methyladenosine (m6A) RNA modification has been reported to regulate spermatogenesis and reproductive function in mammals, the molecular mechanism of m6A in yak testis development and spermatogenesis remains largely unknown. Therefore, we collected testicular tissue from junile and adult yaks, and found that the m6A level significantly increased after sexual maturity in yak. In MeRIP-seq, 1,702 hypermethylated peaks and 724 hypomethylated peaks were identified. The hypermethylated differentially methylated RNAs (DMRs) (CIB2, AK1, FOXJ2, PKDREJ, SLC9A3, and TOPAZ1) mainly regulated spermatogenesis, while the hypomethylated DMRs (BCL6, USP25, CD96, EPHA2, and TAF12) mainly participated in immune response. Functional enrichment analysis showed that DMRs were significantly enriched in the adherens junction, gap junction, and Wnt, PI3K, and mTOR signaling pathways, regulating cell development, spermatogenesis, and testicular endocrine function. The functional analysis of differentially expressed genes showed that they were involved in the biological processes of mitosis, meiosis, and flagellated sperm motility during sexual maturity of yak testis. We also screened the key regulatory factors of testis development and spermatogenesis by combined analysis, which included BRCA1, CREBBP, STAT3, and SMAD4. This study has important research value and practical guiding significance for yak genetic improvement, particularly in understanding the molecular mechanism and evolutionary dynamics of the progression of testis developmental stages in yaks.

overall_design: Detection of m6A in yak testis before and after sexual maturity

first: Shaoke

last: Guo

first: Xingdong

first: Jie

last: Pei

first: Xian


title: Cell lineage specific mitochondrial resilience during mammalian organogenesis

status: Public on Apr 17 2023

city: London

first: Florian

last: Klimm

address: Exhibition Rd, South Kensington

country: United Kingdom

institute: Imperial College London

type: Expression profiling by high throughput sequencing

summary: Mitochondrial activity differs markedly between organs, but it is not known how and when this arises. Here we show that cell lineage specific expression profiles involving essential mitochondrial genes emerge at an early stage in mouse development,  including tissue-specific isoforms present before organ formation. However, the nuclear transcriptional signatures were not independent of organelle function. Genetically disrupting intra-mitochondrial protein synthesis with two different mtDNA mutations induced cell lineage specific compensatory responses, including molecular pathways not previously implicated in organellar maintenance. We saw down regulation of genes whose expression is known to exacerbate the effects of exogenous mitochondrial toxins, indicating a transcriptional adaptation to mitochondrial dysfunction during embryonic development. The compensatory pathways were both tissue and mutation specific, and under the control of specific transcription factors which promote organelle resilience. These are likely to contribute to the tissue specificity which characterizes human mitochondrial diseases, and are potential targets for organ-directed treatments.

overall_design: Single-cell RNA-sequencing from whole mice embryos

first: Stephen

middle: P

last: Burr

first: Angelos

last: Glynos

first: Malwina

last: Prater

first: Pamella

last: Sendon

first: Pavel

last: Nash

first: Marie-Lune

last: Simard

first: Nina

last: Bonekamp

first: Hector

last: Diaz

first: Maria

last: Falkenberg

first: Michal

last: Minczuk

first: Nick

middle: S

last: Jones

first: James

middle: B

last: Stewart

first: Patrick

middle: F

last: Chinnery


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [10G_190423]

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

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 (10G).

first: Hanqing

last: Liu

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

first: Julia

middle: K

last: Osteen

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Rosa

middle: G

last: Castanon

last: Nery

first: Peter

last: Berube

first: Huaming

last: Chen

first: Michael

last: Nunn

first: Jesse

last: Dixon

first: M

middle: M

last: Behrens


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [10G_190523]


title: Analyses of circRNAs and mRNAs profiling in the submandibular gland in hypertension [mRNA]

status: Public on Apr 15 2023

city: Beijing

first: Jinghua

last: Yang

address: 32 North Third Ring Road West, Haidian District, Beijing

country: China

institute: Beijing Zhiyun data technology co. LTD

summary: The aim of this study is to explore the role of circRNAs in the mechanism of submandibular gland (SMG) dysfunction in hypertension.

overall_design: Five male 14-week-old SHRs were purchased from Charles River Laboratories. Five age- and weight-matched WKY rats were used as the control group. The microarray hybridization analyses were performed to determine the circRNAs and mRNAs expression profiles in SMG and were confirmed by qRT-PCR. The bioinformatics analysis including gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway functional enrichment analysis were used to investigate the potential mechanisms. The coding-non-coding co-expression network and competing endogenous RNA  network were established.

first: Zhujun

last: Shen

first: Yechen

last: Han

first: Muwen

last: Nie

first: Hongzhi

last: Xie


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [10C_190418]

first: Joseph

last: Ecker

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 (10C).

first: Hanqing

last: Liu

last: Bartlett


title: Analyses of circRNAs and mRNAs profiling in the submandibular gland in hypertension [circRNA]


title: Genome-wide association study and transcriptome analysis discover novel genes for bacterial leaf streak resistance in rice

city: 广州

first: huabin

last: xie

state: 广东

address: 广东

institute: 没有

summary: Using 15 resistant materials and 15 susceptible materials, PBS was inoculated as the control group, and Xoc was inoculated as the experimental group. After 12 h of inoculation, RNA-Seq was performed and high-quality differential expression profiles were obtained.

overall_design: Comparative gene expression analysis of RNA-seq data for resistant accessions and susceptible accessions (XKH, XKJ, XSH, XSJ).

first: Jiafeng

last: Wang


title: Effect of depletion of ESRRB on gene expression in HeLa cells

status: Public on Apr 14 2023

city: Xi'an

first: Qinshu

last: Li

address: No.277, West Yanyan Road

institute: Xi'an Jiaotong University

summary: To investigate the role of ESRRB in cervical carcinogenesis, we established an ESRRB knockout HeLa cell line.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 different cells (3 HeLa_CRISPR_Ctrl and 3 HeLa_CRISPR_ESRRB).

first: Peng‒Sheng

last: Zheng

first: Qin‒Shu


title: Transcriptional analysis of the expression and prognostic value of lipid droplet-localized proteins in hepatocellular carcinoma

status: Public on Apr 16 2023

city: Zheng zhou

first: Yi

middle: ze

last: Zhang

state: He nan

address: The No.1, Long hu zhong huan road, Zhengzhou

institute: The First Affiliated Hospital of Zhengzhou University

summary: The accumulation of lipid droplets (LDs) in hepatocytes is the main pathogenesis in nonalcoholic fatty liver disease (NAFLD), which is also the key risk factor for the progression of hepatocellular carcinoma (HCC). LDs behaviors are demonstrated to be associated with HCC advancement, and are tightly regulated by a subset protein localized on the surface of LDs. However, the role of LDs-localized protein in HCC has been rarely investigated. This study is focused on the transcriptional dynamic and prognostic value of LDs-localized protein in HCC. Firstly, we summarized the known LDs-localized proteins, which are demonstrated by immunofluorescence according to previous studies. Next, by the use of GEPIA/UALCAN/The Human Protein Atlas databases, we screened the transcriptional change in tumor and normal liver tissues, and found that 13 LDs-localized proteins may involve in the progression of HCC. Then we verified the transcriptional changes of 13 LDs-localized proteins by the use of HCC samples. Moreover, based on the assays of fatty liver of mice and human NAFLD liver samples, we found that the hepatic steatosis mainly contributed to the transcriptional change of selected LDs-localized proteins, indicating the involvement of these LDs-localized proteins in the negative role of NAFLD in HCC progression. Finally, we focused on the role of PLIN3 in HCC, and revealed that NAFLD status significantly promoted PLIN3 transcription in HCC tissue. Functional studies revealed that PLIN3 knockdown significantly limited the migration and chemosensitivity of hepatoma cells, suggesting the positive role of PLIN3 in HCC progression. Our study not only revealed the transcriptional change and prognostic value of lipid droplet-localized proteins in HCC, but also built the correlation between HCC and hepatic steatosis.

overall_design: Total of 6 six-week old C57BL/6 mice were randomly divided into control and experimental groups (3 per group) treated with CSAA (Dyets, 518754, USA) and CDAA (Dyets, 518753, USA) feed respectively. After one week acclimatization, the experimental group was to be fed with the transitional feed for one week. During this transitional stage, the CSAA and CDSS feeds were mixed at 2:1 on the first three days, 1:1 on the fourth to fifth days, 1:2 on the sixth to seventh days, and CDAA feed was completely added after this period. At the 6th week after transitional feeding, the animals of each group were sampled. The pathological feature and steatosis of the mouse livers were confirmed by H&E staining and Oil red staining, respectively. Furthermore, mRNA expression of the selected LDs localized proteins was examined by the transcriptome.

first: Yize

first: Xue

last: Liang

first: Liwen

first: Zihui

last: Dong

first: Kunpeng


title: Single -cell type transcriptomic and imprintomic analysis in the mouse cerebral cortex

city: Taipei

first: Hsien-Sung

last: Huang

address: Rm: 1547, 15th Floor, No.1, Sec.1, Ren-ai Rd.

country: Taiwan

institute: National Taiwan University

summary: Some imprinted genes were observed in a cell-type-specific manner. However, genome-wide profiling of cell-type-specific genes has not been performed in the brain. We addressed this question and identified cell-type-specific and strain-specific monoallelically expressed genes in the mouse cerebral cortex.

overall_design: We performed RNA-Seq and followup statistical analysis on excitatory neurons, inhibitory neurons, and astrocytes of mouse cerebral cortex.


title: Transcriptome profiling of Aim29-knockout S.cerevisiae cells

city: Cambridge

first: Vladimir

last: Denic

state: MA

address: 52 Oxford St, Room 442

department: Molecular and Cellular Biology

institute: Harvard University

summary: The aim of this study was to gain insight into the transcriptome on knockout of eukaryotic gene AIM29 in S.cerevisiae.

overall_design: Comparative gene expression profiling of bulk RNA-seq data on deletion of AIM29 in a S.cerevisae strain.

first: Anjali

last: Nelliat

first: Alexander

middle: J

last: McQuown

first: Dvir

last: Reif


title: Analyses of circRNAs and mRNAs profiling in the submandibular gland in hypertension

first: Jinghua

last: Yang

type:
Expression profiling by array
Non-coding RNA profiling by array

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

overall_design: Refer to individual Series


title: A specific protective mechanism against chloroplast photo-reactive oxygen species in phosphate-starved rice plants [ChIP-seq]

city: Yangzhou

first: Mingnan

last: Qu

state: Jiangsu

address: Pazhou Dadao Rd, 17-19

institute: Yangzhou Univerisity

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Phosphorus (Pi) starvation prevents a good match between light energy absorption and photosynthetic carbon metabolism. Photosynthetic electron-transport chain switches to use molecular oxygen as an electron carrier, generating photo-reactive oxygen species (photo-ROS) in chloroplast. In rice (Oryza sativa), DEEP GREEN PANICLE1 (DGP1) is robustly up-regulated in response to Pi-deficiency stress. DGP1 decreases the DNA-binding activities of the photosynthetic activators GLK1/2 on the genes involved in chlorophyll biosynthesis, light harvesting and electron transport. This Pi-starvation-induced mechanism dampens electron transport rates (ETRI and ETRII) and alleviates the electron-excessive stress in mesophyll cells. Meanwhile, DGP1 hijacks glycolytic enzymes GAPC1/2/3, redirecting glucose metabolism toward pentose phosphate pathway with superfluous NADPH production. Phenotypically, light irradiation induces O2– accumulation in Pi-starved WT leaves, but was observably accelerated in dgp1 mutant and impaired in GAPCsRNAi line and glk1glk2 double mutant. Interestingly, overexpression of DGP1 in rice caused hyposensitivity to the ROS-inducers (catechin and methyl viologen) and dgp1 mutant shows a similar inhibitory growth with the WT plants. We conclude that DGP1 gene serves as a specific antagonizer against Pi-starvation-induced photo-ROS, which integrates light-absorbing and anti-oxidative systems by orchestrating transcriptional and metabolic regulations, respectively.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for GLK1 and GLK2 in rice leaves under control or Pi-starved conditions (3 d after transferring to non-Pi medium).

first: Zhan

last: Xu


title: GATA2 restricts genomic actions of innate immune mediators  on fetal hematopoietic progenitor cells

city: Madison

first: Emery

middle: H

last: Bresnick

address: 1111 Highland Avenue

institute: University of Wisconsin-Madison

summary: Innate immune signaling protects against pathogens, controls hematopoietic development and functions in oncogenesis, yet the relationship between these mechanisms is incompletely defined. Downregulating the GATA2 transcription factor in fetal hematopoietic progenitor cells upregulates genes encoding innate immune regulators, increases Interferon-g (IFNg) signaling and disrupts differentiation. Here, we demonstrate that deletion of an enhancer that confers GATA2 expression in fetal progenitor cells elevated Toll-Like Receptor (TLR) TLR1/2 and TLR2/6 expression and signaling. Genetic rescue by expressing GATA2 downregulated the elevated TLR signaling. IFNg amplified TLR1/2 and TLR2/6 signaling in GATA2-deficient progenitor cells, synergistically activating cytokine/chemokine genes and elevating cytokine/chemokine production in their myeloid cell progeny. Genome-wide analysis of how IFNg and TLR signaling remodels the progenitor cell transcriptome in GATA2-deficient cells revealed exaggerated responses at innate immune genes harboring motifs for signal-dependent transcription factors. Thus, GATA2 establishes a transcriptome that constrains innate immune signaling, and insufficient GATA2 renders fetal progenitor cells hypersensitive to innate immune signaling.

overall_design: ER-HOXB8-immortalized hi-77+/+ and hi-77-/- cells were treated with vehicle, IFNg, Pam3CSK4, or both agonists for 4 h

first: Vu

middle: L

last: Tran

first: Peng

last: Liu

first: Sean

last: McIlwain


title: The Alzheimer’s disease risk factor INPP5D restricts neuroprotective microglial responses in amyloid beta-mediated pathology [snRNA-seq]

city: Charlottesville

first: Joshua

last: Samuels

state: Virginia

address: 409 Lane Road

department: Neuroscience

institute: University of Virginia

summary: INTRODUCTION: Gain-of-function mutations in INPP5D, which encodes for the SH2-domain-containing inositol phosphatase SHIP-1, have recently been linked to an increased risk of developing late-onset Alzheimer’s disease (LOAD). Yet, little is currently known in regards to how SHIP-1 affects neurobiology or neurodegenerative disease pathogenesis. METHODS: To bridge this knowledge gap, we generated 5xFAD Inpp5dfl/flCx3cr1Ert2Cre mice to investigate the function of microglial SHIP-1 signaling in response to amyloid beta (Aβ)-mediated pathology.  RESULTS: In our studies, we found that SHIP-1 deletion in microglia leads to substantially enhanced recruitment of microglia to Aβ plaques, altered microglial gene expression, and marked improvements in neuronal health. Further, SHIP-1 loss enhanced microglial plaque containment and Aβ engulfment when compared to microglia from Cre-negative 5xFAD Inpp5dfl/fl littermate controls.  DISCUSSION: These results define SHIP-1 as a pivotal regulator of microglial responses during Aβ-driven neurological disease.

overall_design: Flash-frozen corticies from 5xFAD Inpp5dfl/flCx3cr1ERT2Cre mice and 5xFAD littermate controls underwent nuclei extraction and single-nucleus RNA sequencing (snRNAseq).

middle: D

first: Katelyn

middle: A

last: Moore

first: Hannah

middle: E

last: Ennerfelt

first: Alexis

last: Johnson

first: Adeline

last: Walsh

first: Richard

last: Price

first: John

last: Lukens


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [10B_190730]

first: Joseph

last: Ecker

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 (10B).

first: Hanqing

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

first: Julia

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: Alternative 3’UTRs play a widespread role in mRNA association with the endomembrane system

city: Newark

first: Bin

last: Tian

email: btian@wistar.org, dinghaiz@gmail.com

state: NJ

address: 205 South Orange Ave., F-Bay 7

department: Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers University, New Jersey Medical School

summary: Transcripts encoding membrane and secreted proteins are known to have translation on endoplasmic reticulum (ER) through the signal recognition particle (SRP)-mediated mechanism. Translation-independent association of mRNAs with ER has also been reported, but poorly understood. Here, using 3’ end sequencing, we examine transcripts associated with polysomes on ER in mouse C2C12 cells. We identify transcript features that facilitate translation-independent ER association, including CDS size, 3’UTR size, and GC content. Interestingly, transcripts encoding nuclear proteins tend to have a higher ER association potential than other transcripts, suggesting localized translation to facilitate nuclear import. We show long 3’UTR isoforms are generally more likely to be associated with ER than short isoforms. Consistently, global shortening of 3’UTRs by knocking down CFI-25 expression leads to substantial alternation of mRNA association with ER. While ER association potentials of transcripts undifferentiated myoblasts are similar to those in differentiated myotubes, 3’UTR lengthening in differentiation leads to more transcripts associated with ER in myotubes. Moreover, translation-independent ER association correlates with low mRNA stability, which is exacerbated in cells with oxidative stress. Together, our data indicate that sequence and structure features of mRNAs facilitate ER association and translation, potentially impacting localization dynamics of protein products, and cellular stress remodels membrane-associated transcripts through mRNA stability regulation.

overall_design: Three RNAseq samples without replicate plus 37 3'READS+ samples with 1 or 2 replicates.

first: Dinghai

last: Zheng

first: Wei

last: Wang


title: TRIM28 establishes skeletal stem cell identity and safeguards skeletogenesis (scRNA-Seq)

city: Grand Rapids

first: Tao

last: Yang

state: MI

address: 333 Bostwick Ave NE

department: Department of Cell Biology

institute: Van Andel Institute

summary: The identity, renewal, and multipotency of stem cells are controlled by epigenetic mechanisms. DNA methylation and trimethylation on histone H3K9 (H3K9me3) are two epigenetic marks that coordinate gene silencing in early embryogenesis. Yet whether they also play a role in regulating somatic stem cell activities governing organogenesis, particularly in the skeletal system, is unknown. Here we show that chromatin silencing, established by TRIM28 (aka. KAP1 and TIF1β) via DNA methylation and H3K9me3 during early organogenesis is crucial for skeletal development. Loss of TRIM28 in skeletal stem cells unsilences the promoter and two previously uncharacterized enhancers of the Grem1 gene, leading to GREM1 hyperexpression, which further activates AKT/mTORC1 signaling to promote skeletal stem cell renewal while restricting osteogenesis and chondrogenesis. Notably, loss of Trim28 in the growth plate also leads to the emergence of a novel stem cell cluster with neural crest cell properties and a distinctive neurogenic tendency. These collectively result in a wide range of skeletal abnormalities. Taken together, our data suggest that TRIM28 coordinates methylation of DNA and histone H3K9 to safeguard the identity and fate determination of skeletal stem cells by epigenetically silencing the GREM1/AKT/mTORC1 signaling axis.

overall_design: Single cell RNA profiles of E17.5 WT and Trim28 KO mouse rib cartialge cells.

first: H

last: Liu

first: Y

first: S

last: Jin

first: J

last: Johnson

first: G

last: Pfeifer

first: T


title: Gene expression profiling of Cav1 knock down in murine hepatic stellate cell

city: Guangzhou

first: Yijie

last: Zhang

state: Guangdong

address: Nanfang Hospital

institute: Nanfang Hospital

summary: Activated primary murine hepatic stellate cells were transfected with siRNA targeting Caveolin-1 directly after attachment (o/n). Experiment was performed in triplicate using primary cells from 3 donor mice.

overall_design: RNA was isolated from quiescent primary hepatic stellate cells, Activated hepatic stellate cells and siRNA targeting Caveolin-1 in activated stellate cells .

first: Yan

first: Tingting

first: Yin

last: Ling

first: Jiacheng

last: Gong

first: Jun

first: Jierui

last: Li

first: Qihan

last: Xu

first: Ying

last: Meng

first: Yang

first: Xu


title: TRIM28 establishes skeletal stem cell identity and safeguards skeletogenesis (ChIP-Seq)

first: Tao

overall_design: Examination of H3K27ac in E17.5 WT and Trim28 KO mouse rib cartialge cells.

first: H


title: TRIM28 establishes skeletal stem cell identity and safeguards skeletogenesis (WGBS)

overall_design: Examination of DNA methylation in  E17.5 WT and Trim28 KO mouse rib cartialge cells.

first: Y

first: S


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [10C_190411]

first: Joseph

last: Ecker

first: Hanqing

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

first: Julia

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

first: M


title: Spatial transcriptome of muscle sample from the main electric organ of electric eel

first: Xidong

last: Mu

address: No.1 Xingyu Road

institute: Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences

summary:
To investigate the distribution and abundance of electrocytes, three 10-μm-thick sections from the main electric organ were sequenced.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 sections.

overall_design: Spatial RNA-seq for muscles cells from the main electric organ of electric eel.

first: Yuanyuan

last: Wang

first: Yi

last: Liu

first: Yexin

last: Yang

first: Chao

first: Yang

last: Zhang

last: Bian


title: Increased motility and suppression of ex vivo-expanded regulatory T cells designed for adoptive transfer therapy in ulcerative colitis

city: Erlangen

first: Mark

last: Dedden

state: Bayern

address: Schwabachanlage 12

department: Department of Medicine 1

country: Germany

institute: Universitätsklinikum Erlangen

summary: We sequenced non-expanded and expanded Human regulatory T cells. Cells were expanded over the course of 21 days using our previously published GMP-compliant Treg expansion protocol.

overall_design: Differential expression analysis of non-expanded versus expanded regulatory T cells.

first: Sebastian

last: Zundler

first: Caroline

last: Voskens

first: Tanja

last: Müller


title: TRIM28 establishes skeletal stem cell identity and safeguards skeletogenesis

first: Tao


title: Gene signature profiles in whole blood cells from severe asthma patinets treated with benralizumab

city: TSUKUBA

first: Masashi

last: Matsuyama

state: IBARAKI

address: 1-1-1 AMAKUBO

department: respiratory medicine

country: Japan

institute: Tsukuba university

summary: Severe asthma is a clinically and physiologically heterogeneous disease. Benralizumab is a monoclonal antibody which binds the alpha chain of the interleukin-5 receptor and used for severe eosinophilic asthma worldwide. However, not all eosinophilic asthma patients will benefit from benralizumab due to heterogeneity of this disease. Therefore, we performed comprehensive gene expression analysis of whole blood cells that examine severe asthma disease heterogeneity in response to benralizumab.    This study is the first to perform comprehensive transcriptome analysis of whole blood cells to identify transcriptomic endotypes of severe asthma clusters that correlate with benralizumab response. The identified transcriptomic endotypes of severe asthma clusters are associated with gene signatures of eosinophils and neutrophilis.

overall_design: We prospectively studied 41 patients with severe eosinophilic asthma treated with benralizumab for 4 months. Whole blood cells for gene expression analysis were collected at baseline and 4 months after starting of benralizumab treatment, and RNA-seq was performed. Whole blood was collected with PAXgene blood RNA tubes (Qiagen). Total 82 RNA samples from whole blood cells were obtained, 41 samples at baseline and 41 samples 4 months after treatment.

first: Masayuki

last: Nakajima

first: Masafumi

last: Muratani

first: Nobuyuki

last: Hizawa


title: Identification of ADAMTS9-AS2 and MBNL1-AS1 as subtype-specific dysregulated lncRNAs in basal and luminal muscle-invasive bladder cancer via RNA sequencing

city: Nanning

first: Zhenxing

state: Guangxi

address: Zhongshan Street

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medicla University

summary:
Muscle-invasive bladder cancer (MIBC) is an aggressive disease with high morbidity and mortality that can be divided into basal and luminal subtypes based on genomic characteristics. Due to the complex heterogeneity of MIBC, specific markers are needed to distinguish MIBC subtypes to guide future clinical treatment.
In this study, we explore abnormal lncrnas that are specific to the basic and intracavitary subtypes of MIBC, which will provide potential biomarkers for precision therapy of MIBC.

overall_design: In this study, 48 MIBC tissues and 38 adjacent tissues were collected for RNA sequencing

first: Zhijian

last: Li

first: Shaomei

last: Tang

first: Xia

first: Yuqi

last: Lv

first: Liwen

last: Qin

first: Xi

last: Wng

first: Qiuyan

first: Tianyu


title: Egr2 promoter antisense RNA as coordinator of chromatin remodeling and genome reorganization in Schwann cells [Hi-C]

city: Bronx

first: Jorge

middle: Eduardo

last: Fajardo

state: NY

address: 1300 Morris Park Avenue

department: Systems and Computational Biology

institute: Albert Einstein College of Medicine

summary: The Egr2 promoter antisense RNA (Egr2-AS-RNA) recruits chromatin remodeling complexes to inhibit Egr2 transcription following peripheral nerve injury. Here we show that the Egr2-AS-RNA modulates chromatin accessibility and serves as scaffold for two distinct histone modification complexes. The Egr2-AS-RNA binds to Ezh2 and Wdr5 and enables coordinate targeting of H3K27me3 and H3K4me3 to promoters of Egr2 and c-Jun. Expression of the AS-RNA results in reorganization of the global chromatin landscape and quantitative changes in loop formation and in contact frequency at domain boundaries exhibiting enrichment for AP-1 binding events. Our results show for the first time that the Egr2 promoter AS-RNA may serve as a regulator of coordinate chromatin remodeling and genome organization to regulate transcription, with a significant role in phenotypic plasticity of SCs.

overall_design: We performed HiC on Schwann cells after ectopic expression of the Egr2-AS-RNA. We identified the static, lost and gained loops and we annotate them to their promoters.

first: Nikos

last: Tapinos

first: J

first: David

last: Karambizi

first: Jia

last: Chen

first: Hyeyeon

last: Hwang

first: Margot

last: Martinez-Moreno


title: Gene expression profile of 2-D or 3-D neural cultures derived from an H1 hESC cell line

city: Raleigh

first: Thomas

last: Rudibaugh

state: North Carolina

address: 840 Main Campus Dr, Partners II Room 3700

institute: North Carolina State University

summary: Striatal neurons and striatal DA neuron fusions make up the mesolimbic pathway and respond to substances of abuse. We use scRNAseq to define the composition of our culture conditions and study their transcriptional responses to dopamine, cocaine, and morphine.

overall_design:
We use scRNAseq to define the composition of our culture conditions and study their transcriptional responses to dopamine, cocaine, and morphine.
We then dissociated 3-D cultures using papain dissociation system and prepared libraries using Parse Biosciences protocol.

first: Ryan

last: Tam

first: Chris

last: Estridge

first: Albert

last: Keung


title: TRIM28 establishes skeletal stem cell identity and safeguards skeletogenesis (RNA-Seq)

first: Tao

last: Yang

overall_design: mRNA profiles of E17.5 WT and Trim28 KO mouse rib cartialge cells.

first: H

last: Liu

first: Y

first: S

last: Jin

last: Johnson

first: G

last: Pfeifer

first: T


title: A specific protective mechanism against chloroplast photo-reactive oxygen species in phosphate-starved rice plants

first: Mingnan

last: Qu

overall_design: Refer to individual Series


title: Bacterial TLR2/6 Ligands Block Ciliogenesis, Derepress Hedgehog Signaling, and Expand the Neocortex

status: Public on Apr 13 2023

city: Memphis

first: Jeremy

middle: Chase

last: Crawford

state: TN

address: MS 221, 262 Danny Thomas Place

department: Department of Host-Microbe Interactions

institute: St. Jude Children's Research Hospital

summary: Microbial components have a range of direct effects on the fetal brain. However, little is known about the cellular targets and molecular mechanisms that mediate these effects. Neural progenitor cells (NPCs) control the size and architecture of the brain and understanding the mechanisms regulating NPCs is crucial to understanding brain developmental disorders. We identify ventricular radial glia (vRG), the primary NPC, as the target of bacterial cell wall (BCW) generated during the antibiotic treatment of maternal pneumonia. BCW enhanced proliferative potential of vRGs by shortening the cell cycle and increasing self-renewal. Expanded vRGs propagated to increase neuronal output in all cortical layers. Remarkably, Toll-like receptor 2 (TLR2), which recognizes BCW, localized at the base of primary cilia in vRGs and the BCW-TLR2 interaction suppressed ciliogenesis leading to derepression of Hedgehog (HH) signaling and expansion of vRGs. We also show that TLR6 is an essential partner of TLR2 in this process. Surprisingly, TLR6 alone was required to set the number of cortical neurons under healthy conditions. These findings suggest that an endogenous signal from TLRs suppresses cortical expansion during normal development of the neocortex and that BCW antagonizes that signal through the TLR2/cilia/HH signaling axis changing  brain structure and function.

overall_design: Comparative spatial transcriptomics of mouse brain sections obtained at E12 after either S. pneumoniae + ampicillin challenge or after ampicillin control.

middle: C

first: Beth

last: Mann

first: Elaine

middle: I

last: Tuomanen


title: TRIM28 establishes skeletal stem cell identity and safeguards skeletogenesis (Cut&Run)

overall_design: Examination of H3K9me3 modification in E17.5 WT and Trim28 KO mouse rib cartialge cells.

first: J

middle: P


title: Egr2 promoter antisense RNA as coordinator of chromatin remodeling and genome reorganization in Schwann cells

first: Jorge

last: Fajardo


title: Proteomic discovery of chemical probes that perturb protein complexes in human cells

city: LA JOLLA

first: Hsuan-Lin

last: Her

address: 9500 Gilman Dr,

institute: UCSD

summary: Most proteins in the human proteome lack chemical probes, and several large-scale and generalizable small-molecule binding assays have been introduced to address this problem. How compounds discovered in such “binding-first” assays affect protein function, nonetheless, often remains unclear. Here, we describe a “function first” proteomic strategy that uses size exclusion chromatography (SEC) to assess the global impact of electrophilic compounds on protein complexes in human cells. Integrating the SEC data with cysteine-directed activity-based profiling identifies changes in protein-protein interactions that are caused by site-specific liganding events, including the stereoselective engagement of cysteines in PSME1 and SF3B1 that disassemble the PA28 proteasome regulatory complex and remodel the spliceosome, respectively. Our findings thus show how multidimensional proteomic analysis of focused libraries of electrophilic compounds can expedite the discovery of chemical probes with site-specific functional effects on protein complexes in human cells.   In this experiment, we probed the RNA-binding profile of DDX42 by eCLIP via an endogenously introduced HA-tag in the context of various SF3B1 ligands.

overall_design: Two independent treatments were performed for each of 4 treatment groups (3h DMSO, 5uM WX-02-23, 5uM WX-02-43, 100nM PladB). An input and an eCLIP fraction were sequenced for each individual replicate, yielding a total of 16 samples.

first: Jarrett

last: Remsberg

first: Benjamin

middle: F

last: Cravatt

first: Martin

last: Jaeger

first: Assael

last: Madrigal

first: Katherine

last: Rothamel

first: Gene

middle: W

last: Yeo


title: HNF4a regulates hepatic peroxisomal biogenesis and fatty acid elongation during the thermogenic response

first: Judith

last: Simcox

state: WI

address: 433 Babcock dr.

department: Biochemistry

institute: University of Wisconsin Madison

summary: We observed gene expression changes in livers of cold exposed mice along with changes in global genome occupancy for the transcription factor HNF4a, RNA polymerase II and the histone marker H3K27Ac, suggesting a hepatic transcriptional response to cold xposure.

overall_design: Performed RNA-seq for gene expression changes on livers of cold exposed mice during a 24 hour time course (hours 0,6,12,24). Perforemed ChIP-seq for HNF4a, Rpb1-CTD, H3K27Ac on livers from room temperture and cold exposed (6 hours) mice.

first: Gisela

last: Geoghegan


title: WDR5 is required for DUX4 expression and its pathological effects in FSHD muscular dystrophy

city: Planegg-Martinsried

first: Filippo M.

last: Cernilogar

address: Grosshaderner Strasse 9

department: Biomedical Center

institute: LMU Munich

summary: Facioscapulohumeral muscular dystrophy (FSHD) is an inherited progressive neuromuscular disorder that afflicts both children and adults regardless of gender. FSHD is caused by aberrant gain of expression of the transcription factor DUX4, which triggers a pro-apoptotic transcriptional program leading to muscle wasting. As today, no cure or therapeutic option is available to FSHD patients. Given its centrality in FSHD, blocking DUX4 expression with small molecule drugs is an attractive option. We previously showed that the long non-coding RNA DBE-T is required for aberrant DUX4 expression in FSHD. Using affinity purification followed by proteomics, we identified the chromatin remodeling protein WDR5 as a novel DBE-T interactor and a key player required for the biological activity of the lncRNA. We found that WDR5 is required for the expression of DUX4 and its targets in primary FSHD muscle cells. Moreover, targeting WDR5 rescues both cell viability and myogenic differentiation of FSHD patient cells. Notably, comparable results were obtained by pharmacological inhibition of WDR5. Importantly, WDR5 targeting was safe to healthy donor muscle cells. Our results support a pivotal role of WDR5 in the activation of DUX4 expression identifying a druggable target for an innovative therapeutic approach for FSHD.

overall_design: Comparative expression analysis of muscle cells from an healthy or FSHD donor , treated with DMSO (vehicle; 6 replicates) or OICR (active compound; 6 replicates) compounds

first: Filippo

first: Gunnar

last: Schotta

first: Emanuele

last: Mocciaro

first: Davide

last: Gabellini


title: Breast tumors interfere with endothelial TRAIL at the pre-metastatic niche to promote cancer cell seeding

city: Leuven

first: Sandrine

last: Da Cruz

state: Flemish Brabant

address: ON 5 Herestraat 49

department: KU Leuven Department of Neurosciences

country: Belgium

institute: VIB-KU Leuven Center for Brain and Disease Research

summary:
Purpose: To study the effects of endothelial cell (EC)-specific TRAIL depletion on lung endothelial cells. Here, we used RNA sequencing to explore the transcriptional changes of lung ECs upon deletion of TRAIL specifically in ECs.
RNA from 2.000.000 sorted lung ECs (viability dye- CD45- CD31+) from EC-specific TRAIL WT and KO mice (Cdh5.iCreERT2xTnfsf10Lox/Lox) were isolated and the concentration as well as purity was determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies).   Per sample, an amount of 3000ng of total RNA was used as input. Subsequently, preparation was performed with KAPA stranded mRNA seq according to the protocol and samples were pooled equimolar. Sequencing was performed as single end of 50bp on hiseq 4000 from  Illumina. 35-40 Million reads were generated per sample. Raw FASTQ reads were mapped using STAR v2.7.1a and gene reads counts were estimated by RSEM v1.2.28 using GENCODE reference annotation of the mouse genome (GRCm38), version M24 (Ensembl 99).  Gene reads counts were estimated by RSEM using GENCODE reference annotation of the mouse genome (GRCm38), version M24 (Ensembl 99). Differential expression of EC-specific TRAIL KO (EC-Tg/W) vs control (EC-W/W) was performed using the DESeq2 R package (v1.26.0). The significance was determined by padj < 0,05. The gene set enrichment analysis (GSEA) was performed using the pre-ranked gene list by log2 fold-change (EC-Tg/W vs EC-W/W control) and the MSigDB gene sets. Only gene sets containing between 5 and 500 genes were retained and the number of permutations was set at 1000.

overall_design: 5x5 design in Cdh5.iCreERT2xTnfsf10Lox/Lox mice (5 W/W and 4 Tg/W) with sorted lung ECs RNA sequencing conducted

first: Massimiliano

last: Mazzone


title: Transcriptomic analysis of Nintedanib, Alpelisib and Nintedanib;Alpelisib treated  bladder tumors

city: Madrid

first: Jaime

last: Martinez de Villarreal

state: Madrid

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

country: Spain

institute: CNIO

summary: Nintedanib is a potent anti-fibrotic angio-kinase inhibitor, which has shown clinical efficacy in combination with chemotherapy in locally advanced muscle invasive BC patients. Nintedanib inhibits Fibroblast Growth Factor receptors (FGFRs), validated targets in patients with BC harboring FGFR3/2 genetic alterations. Here, we aimed at studying its mechanisms of action to understand therapy their combination (n=4). Reads were mapped separately against the human and mouse genomes to differentiate tumor vs. stromal expression changes

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: In order to gain insight into the mechanisms underlying Nintedanib and Alpelisib synergism in vivo, we tested the effects of Nintedanib, Alpelisib (BYL719) and their combination on  Nintedanib-resistant VM-CUB-1 cells xenografts. We performed RNA sequencing of tumors treated for 7 days with either either vehicle (n=4), Nintedanib [responders (n=2) and non-responders (n=3)], Alpelisib (n=4), or their combination (n=4). Reads were mapped separately against the human and mouse genomes to differentiate tumor vs. stromal expression changes

first: Miriam

last: Marqués

first: Sonia

last: Corral

last: Martínez de Villarreal

first: Norbert

last: Schweifer

first: Roland

last: Varecka

first: Frank

last: Hilberg

first: Francisco

middle: X

last: Real


title: Egr2 promoter antisense RNA as coordinator of chromatin remodeling and genome reorganization in Schwann cells [ATAC-seq]

first: Jorge

last: Fajardo

overall_design: We performed ATAC-Seq on Schwann cells after ectopic expression of the Egr2-AS-RNA to determine changes in chromatin accessibility. Annotation of the peaks showed differential accessibility at some promoter regions, defined as the sequences from -1500 to +500 with respect to the transcription start site. TF footprinting showed an enrichment on AP-1 TF family.

first: Nikos

last: Tapinos

first: J

first: David

last: Karambizi

first: Jia

middle: S

last: Chen

first: Hyeyeon

last: Hwang

first: Margot

last: Martinez-Moreno


title: Genetic differences in conditioned medium through adding human AQP4-IgG on primary astrocytes.

status: Public on Apr 12 2023

city: Guang Zhou

first: Wei

last: Jiang

state: Guang dong

address: Tianhe street NO.600

institute: The Third Affiliated Hospital of Sun Yat-sen University

summary:
To investigate the genetic differencesin human AQP4-IgG group and control-IgG group , we established primary astrocytes line.
We then performed gene expression profiling analysis using data obtained from RNA-seq after 48h with stimulation with human AQP4-IgG and control-IgG.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  human AQP4-IgG groups and human  control-IgG groups.

first: Jiang

last: Wei

first: Tang

last: Changyong


title: Single cell RNA sequencing on rats with or without bleomycin treatemnt

city: shanghai

first: Xiucheng

last: Liu

address: zhengmin road 557

institute: Shanghai pulmonary hospital

summary: Purpose:To characterize the heterogeneity of endothelial cells in bleomycin-induced lung fibrosis in rats

overall_design: After adequate anesthesia, BLMwas administered by oral tracheal intubation via a 16-gauge catheter. One dose of BLM (5 mg/kg, the BLM-treated group) or an equal volume of saline was administered via the catheter. The rats were rotated immediately after instillation to ensure thorough drug distribution in the lungs. All rats were killed by cervical dislocation and lungs were harvested 28 days after intratracheal BLM or saline treatment. Rat lungs were harvested and 3 mm3 lung tissues were taken for digestion to generate single-cell suspensions.Beads with unique molecular identifier (UMI) and cell barcodes were loaded close to saturation, so that each cell was paired with a bead in a microwell. Whole transcriptome libraries were prepared using the BD Rhapsody system (BD Bio_x0002_sciences).

first: Hao

last: Qin


title: Egr2 promoter antisense RNA as coordinator of chromatin remodeling and genome reorganization in Schwann cells [RNA-seq]

overall_design: We performed RNA-seq on Schwann cells after ectopic expression of the Egr2-AS-RNA to determine changes in gene expression. Upregulated genes were enriched for mTOR signaling and cell cycling biological processes. Downregulated genes were enriched for Erk1/Erk2 signaling, ErbB signaling pathway, MAPK regulation and ECM organization biological processes. Additionally, upregulated genes showed enrichment for sonic hedgehog (Shh) signaling pathway.


title: RNA-seq of Notch signaling response in RTE cells

city: Toronto

first: Juan Carlos

last: Zuniga-Pflucker

state: Ontario

address: 2075 Bayview Avenue

department: Immunology

country: Canada

institute: University of Toronto

summary: We report the gene expression profile of recent thymic emigrant (RTE) that are either responsive to Notch signals, or unresponsive to Notch signals during their maturation process. Notch responsiveness is controled by the expression of RBPJ, a key mediator of the Notch signaling pathway.

overall_design: Wild type mature T cells (WT) and RTE from RBPJind mice that were Notch responsive (ON) and Notch unresponsive (OFF) during maturation stage were FACS sorted.  These cells were sent for bulk RNA sequencing.

first: Sintia

last: Teichman

first: Helen

last: Wang

first: Christina

middle: R

last: Lee

first: Mahmood

last: Mohtashami

first: Elisabeth

last: Foerster

first: Ashton

last: Trotman-Grant

first: Shawn

last: Winer

first: Hubert

last: Tsui

first: Dana

last: Philpott

first: Juan

last: Zúñiga-Pflücker


title: ATAC-seq and RNA-seq of Notch signaling response in RTE cells

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


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [10B_190725]

city: La Jolla

first: Joseph

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

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 (10B).

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

middle: G

last: Castanon

last: Nery

first: Peter

last: Berube

first: Huaming

last: Chen

first: Michael

last: Nunn

first: Jesse

last: Dixon

first: M

middle: M

last: Behrens


title: Anaplastic Transformation Model in Thyroid Cancer Revealed by Single Cell Lineage and Fate Analysis

city: Chicago

first: Ruli

last: Gao

state: Illinois

address: 303 East Superior

department: Department of Biochemistry and molecular genetics

institute: Northwestern University

summary: The deadliest anaplastic thyroid cancer (ATC) often transforms from indolent differentiated thyroid cancer (DTC), however the complex intra-tumor transformation process is poorly understood.  We investigated an anaplastic transformation model by dissecting both cell lineage and cell fate transitions using single cell transcriptomes and genetic alterations data of patients with different subtypes of thyroid cancer. The resulting model started from stress-responsive DTC cells to inflammatory ATC cells, to mitotic defective ATC cells and extended all the way to mesenchymal ATC cells.  In parallel with tumor cell evolution, macrophages shifted from anti-tumor to tumor-promoting states and T cells reprogrammed from cytotoxic to exhausted states.  Further, our analysis identified two important milestones: 1) diploid stage, where ATC cells were commonly diploids with non-RAS mutations and inflammatory phenotypes.  2) aneuploid stage, where ATC cells gained aneuploidy with frequent RAS mutations and mesenchymal phenotypes leading to the extreme lethal stage of ATC progression.

overall_design: scRNA-seq of 10 ATC tumors,7 PTC tumors and 6 adjacent normal thyroid tissues, bulk RNA-seq of 9 ATC cell lines that had been passed as xenografts in mice

first: Lina

last: Lu

first: Jennifer

last: Wang

first: Ying

last: Henderson

first: Shanshan

last: Bai

first: Jie

last: Yang

first: Min

last: Hu

first: Yuanqing

last: Yan

first: Tuan

last: Tran

first: Jianzhuo

last: Li

first: Cheng-Kai

last: Shiau

first: Rachel

last: Kieser

first: Xiao

last: Zhao

first: Jiping

first: Roza

last: Nurieva

first: Michelle

last: Williams

first: Maria

last: Cabanillas

first: Ramona

last: Dadu

first: Naifa

middle: L

last: Busaidy

first: Mark

last: Zafereo

first: Nicholas

last: Navin

first: Stephen

middle: Y

last: Lai


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [10A_190525]

first: Joseph

last: Ecker

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 (10A).

first: Hanqing

last: Liu

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

first: Julia

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: Single cell sequencing of mouse vein grafts

city: Hangzhou

first: Lingxia

last: Lyu

address: No.79 Qingchun Road

institute: Zhejiang university

summary: Smooth muscle cells play a critical role in multiple cardiovascular diseases. Sca1+ cells are believed to be smooth muscle progenitors. However, the exact identity and the role of Sca1+ cells in vascular regeneration remains unclear.Here we performed single cell RNA sequencing to identify the mechanism underlying Sca1+ cells differentiate into smooth muscle cells.

overall_design: This entry contains 10x Single-cell RNA-seq data of  all cells and FACS sorted Sca1+CD45- cells from veingrafts as well as whole cells of  veingrafts from mice received adeno-associated virus to knockdown Malat1.

first: Zhoubin

last: Li

first: Ting

first: Xiaogang

last: Guo


title: Transcriptomic changes of optic nerves under crush during hibernation stage

city: Guangzhou

first: Yizhao

last: Luan

address: Xianlie South Rd. 54, Yuexiu Dist

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen university

summary: we compared the gene expression changes of crushed optic nerves from hibernating and awake squirrels.

overall_design: Optic nerves from hibernating and awake 13-lined squirrels were crushed, and total RNAs were extracted and sequenced 3 days after treated. Three replicates were included for hibernation group and awake group. Paired-end library following Illumina TruSeq stranded protocol was constructed, and subjected to RNA-Seq.

first: Wei

first: Zhi

last: Xie

first: Jingxing

last: Ou


title: RNF20 is required for male fertility through H2B ubiquitination in Sertoli cells

city: Wuhan

first: Lai

last: fengling

address: Wuhan University, Wuchang District, Hubei Province

institute: Wuhan university

summary: Spermatogenesis is an essential process to generate male gametes in vertebrates, and it has become an important social health problem caused by spermatogenesis disorder. However, the molecular mechanism underlying spermatogenesis, particularly epigenetic modification in Sertoli cells of testis, remain elusive. In this study we generated Rnf20 conditional knockout mice by recombinant mothed, and only to find that Rnf20 knockout in Sertoli cells led to male infertility.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Sertoli cells and testis tissue in WT and Rnf20 conditional knockout mice

first: Fengling

last: Lai

first: Haoyu

last: wang


title: Immune profiling of experimental murine mastitis

city: Rehovot

first: Nahum

middle: Yehuda

last: Shpigel

state: Please Select…

address: POB 12

department: Veterinary

country: Israel

institute: Hebrew University

summary: Mastitis is one of the most prevalent and economically important diseases of dairy animals. The disease is caused by ascending bacterial infection through the teat canal. Among the most common mastitis-causing bacteria are gram-negative coliforms, gram-positive streptococci and staphylococci, and mycoplasma. The most prominent cellular hallmark of acute mammary infection is a massive recruitment of blood neutrophils into the tubular and alveolar milk spaces. The complex biological processes of leukocyte recruitment, activation, adhesion, and migration in the mammary gland remain largely elusive to date. While field research of mastitis in dairy animals contributed a lot to the development of mitigation, control, and even eradication programs, little progress was made toward understanding the molecular mechanisms underlying the pathogenesis of the disease. We report here experimental mastitis model systems in lactating mice challenged with field strains of common udder pathogens in dairy cows. We used these model systems to apply recently developed multiplex gene expression technology (Nanostring nCounter), which enabled us to study the expression of over 700 immune genes. Our analysis revealed a core of 100 genes that are similarly regulated and functionally or physically interacting in E. coli, M. bovis and Strep uberis murine mastitis. Common significantly enriched gene sets include TNFɑ signaling via NFkB, Interferon gamma and alpha response, and IL6-JAK-STAT3 signaling. In addition, we show a significantly enriched expression of genes associated with neutrophil extracellular traps (NET) in glands challenged by the three pathogens. Ligand-receptor analysis revealed interactions shared by the three pathogens, including the interaction of the cytokines IL1β, IL1ɑ, and TNFɑ with their receptors, and proteins involved in immune cell recruitment such as complement C3 and ICAM1 (with CD11b), chemokines CCL3 and CCL4 (with CCR1), and CSF3 (with CSF3R). Taken together, our results show that mammary infection with E. coli, M. bovis and Strep uberis culminated in the activation of a conserved core of immune genes and pathways including NET formation.

overall_design: Lactating mice challenged by intramammary infusion of E. coli, Mycoplama bovis and Streptococcus uberis bacteria and compared to control non-challenged mice. 3 replicates per condition.

first: Inna

last: Lysnyansky


title: Transcriptional effect of EGR3 overexpression in the cell line SEM

city: Frankfurt am Main

first: Marius

last: Külp

address: Theodor-Stern-Kai 7

department: Department of Medicine II, Hematology/Oncology

institute: Goethe University Hospital Frankfurt

summary: FLAG-tagged EGR3 was overexpressed in the cell line SEM to study transcriptional consequences in the t(4;11) cellular context.

overall_design: Massive analysis of cDNA ends-sequencing (MACE-seq) of an EGR3-overexpressing SEM cell line (SEM::EGR3) in comparison to an empty vector control SEM cell line (SEM::mock). MACE-seq was performed from biological triplicates of SEM::mock and SEM::EGR3.

first: Patrizia

last: Larghero

first: Claus

last: Meyer


title: Microvascular and Macrovascuar Complications of Type 2 Diabetes Mellitus: Exome Wide Association Analyses

city: Abu Dhabi

first: Habiba

last: Al Safar

state: Abu Dhabi

address: Shakhbout Bin Sultan St

department: Biomedical Engineering

country: United Arab Emirates

institute: Khalifa University

summary: With an escalating global burden, T2DM is associated to long-term complications that have contributed to the burden of morbidity and mortality worldwide. The objective of this manuscript is to conduct an Exome-Wide Association Study (EWAS) on T2DM Emirati individuals to improve our understanding on diabetes-related complications for a more enhanced disease management and improve therapeutic targets.

overall_design: To investigate the genetic loci associated with each diabetes-related complication category ( retinopathy, neuropathy, nephropathy, and heart disease) in the Emirati population. We genotyped 384 type 2 daiabtes patients, which was conducted on the Infinium Exome BeadChip (Illumina).

first: Afnan

last: Mansour

first: Mira

last: Mousa

first: Hema

last: Vurivi

first: Dima

last: Abdelmannan

first: Guan

last: Tay

first: Ahmed

last: Hassoun

last: Alsafar


title: Transcriptomic analysis to uncover the mechanism of radiosensitization of AR-positive triple negative breast cancers with AR inhibition

city: Birmingham

first: Corey

last: Speers

state: AL

address: 1700 6th Ave S

department: Radiation Oncology

institute: University of Alabama Birmingham

summary: We used charcoal-stripped serum on AR+ breast cancer cell lines to study the gene expression changes in the presence of androgens and/or radiation treatment in breast cancer.

overall_design: Comparative gene expression analysis of charcoal-stripped AR-positive breast cancer cell lines ACC-422 and MDA-MB-453 in the presence of androgens and/or radiation treatment.

first: Anna

last: Michmerhuizen

first: Breanna

last: McBean


title: Neoadjuvant use of oncolytic herpes virus G47Δ prevents local recurrence after insufficient resection in tongue cancer models

city: Yakushiji

first: Kosuke

last: Inoue

state: Tochigi

department: Oral and maxillofacial surgery

institute: Jichi university

summary: Mice with orthotopic tongue cancer received neoadjuvant G47Δ therapy. Neoadjuvant G47Δ and resection led to 10/10 survival even with insufficient resection margins.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for murine tongue tumors after intratumoral inoculation of G47Δ.

first: Hirotaka

last: Ito

first: Miwako

last: Iwai

first: Minoru

last: Tanaka

first: Yoshiyuki

last: Mori

first: Tomoki

last: Todo


title: Transcriptomic analysis of Nintedanib, Alpelisib and Nintedanib;Alpelisib treated bladder tumors

first: Jaime

last: Martinez de Villarreal

overall_design: In order to gain insight into the mechanisms underlying Nintedanib and Alpelisib synergism in vivo, we tested the effects of Nintedanib, Alpelisib (BYL719) and their combination on  ScaBER cells xenografts. We performed RNA sequencing of tumors treated for 14 days with either either vehicle (n=4), Nintedanib  (n=4), Alpelisib (n=4), or their combination (n=4). Reads were mapped separately against the human and mouse genomes to differentiate tumor vs. stromal expression changes

first: Miriam

last: Marqués

first: Sonia

last: Corral

last: Martínez de Villarreal

first: Norbert

last: Schweifer

first: Donat

last: Alpar

first: Roland

last: Varecka

first: Frank

last: Hilberg

first: Francisco

last: Real


title: Early detection of extranodal marginal zone lymphoma in Sjögren's syndrome patients through immunogenetics

city: Rotterdam

first: Pieter Martijn

last: Kolijn

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus MC

summary: Activated B cells play a key role in the pathogenesis of Sjögren’s syndrome (SjS) through the production of autoantibodies and the development of ectopic germinal centers in the salivary glands and other affected sites. Around 5-10% of SjS patients develop B-cell lymphoma, usually extranodal marginal zone lymphomas (eMZL) of the mucosa-associated lymphoid tissue (MALT). The aim of the current study is to screen for the eMZL clonotype in prediagnostic blood and tissue biopsies of SjS patients. We studied prediagnostic tissue biopsies of 3 SjS patients diagnosed with eMZL through immunoglobulin (IG) gene repertoire sequencing. In all 3 cases, we observed the eMZL clonotype in prediagnostic tissue biopsies. To evaluate if skewing in the IGH repertoire may also be detected in the peripheral blood, we sequenced a peripheral blood mononuclear cell (PBMC) sample drawn at eMZL diagnosis and 2 years prior to eMZL relapse in two SjS patients. The eMZL clonotype was detected in the peripheral blood prior to diagnosis for both cases. Next, we selected 3 SjS patients who developed eMZL lymphoma and 3 additional SjS patients who remained cancer-free. We sequenced the IG heavy chain (IGH) gene repertoire in PBMC samples taken a median of 3 years before eMZL diagnosis. In 2 out of 3 eMZL patients, the dominant clonotype in the prediagnostic PBMC samples matched the eMZL clonotype in the diagnostic biopsy. The eMZL clonotypes observed utilized stereotypic IGHV gene combinations (IGHV1-69/IGHJ4 and IGHV4-59/IGHJ5) associated with rheumatoid factor activity, a previously reported feature of eMZL in SjS. Notably, no significant abnormalities were observed in the IGH gene repertoire of the controls. In conclusion, our results indicate that immunogenetic sequencing of the IGH gene repertoire may be an effective method of early detection of eMZL in SjS patients.

overall_design: B-cell receptor immunoglobulin heavy chain gene repertoire sequencing of pre-diagnostic and diagnostic samples of SjS patients developing eMZL and matched controls.

first: A

last: Langerak

first: P


title: Transcriptomes of 4T1-HA tumors treated with anti-PD-1 and IL-12 micelle

city: Osaka

first: Koji

last: Nagaoka

address: 377-2 Ohno-Higashi, Osaka-Sayama

department: Department of Immunology

institute: Kindai University Faculty of Medicine

summary: IL-12 has been considered to be an ideal cytokine for cancer immunotherapy as it can activate both immune and adaptive immune systems. However, in clinical trials, severe side effects were observed in patients with IL-12 systemic administrations. In this study, we generated pH-sensitive polymeric micelle encapsulating IL-12 and compared anti-tumor activities of free IL-12, IL-12 micelle and combination of anti-PD-1 and IL-12 micelle.

overall_design: Mice were inoculated with 4T1-HA cells on day 0. Free IL-12 or IL-12 micelle were injected on days 7 and 9. Anti-PD-1 was injected on days 8 and 10. The tumors were harvested on day 17 and subjected to RNA sequencing.

first: Pengwen

last: Chen

first: Kazuhiro

last: Kakimi

first: Horacio

last: Cabral


title: Identification and characterization of extrachromosomal circular DNA in patients with high myopia and cataract

city: Tianjin

first: Jing

last: Sun

state: Tianjin

address: No. 251, Fukang Road, Nankai District, Tianjin, China

institute: Tianjin medical university eye hospital

summary: To explore the presence of extrachromosomal circular DNA (eccDNA) in the anterior capsule of the lens in the eyes of patients with cataract and with high myopia. Circle-Seq was performed to identify differences in the eccDNA and gene expression between the anterior capsule of the lens of patients with simple nuclear cataract (C, n = 6) and patients with nuclear cataract along with high myopia (HM, n = 6). The expression of eccDNA was confirmed using routine quantitative polymerase chain reaction. The eccDNA ranked in C and HM ranged in length from 0.017 kb – 9.9 Mb with two distinctive peaks detected at 0.2 kb and 0.5 kb, while eccDNA that were differentially expressed (up- and down-regulated) ranged in size from 0.05 kb – 57.8 kb with two distinctive peaks observed at 0.1 kb and 0.5 kb. Only 2.5 % of the eccDNA in C and 2 % in HM were > 25 kb in size. The gene-rich chromosomes contributed to more number of eccDNA/Mb, while several well-known high myopia candidate genes, including catenin delta 2 (CTNND2), ubiquitin-like with PHD and ring finger domains 1 binding protein 1 like (UHRF1BP1L) , exhibited significantly increased levels of eccDNA in the anterior capsule of the lens in patients with high myopia. This study highlighted the topologic analysis of the anterior capsule of eyes with high myopia, which is an emerging direction for research and clinical applications. These findings suggested that eccDNA was commonly detected in eyes with high myopia and cataracts, and the candidate genes for high myopia identified in previous studies were also observed in the eccDNA.

overall_design: Circle-Seq was performed to identify differences in the eccDNA and gene expression between the anterior capsule of the lens of patients with simple nuclear cataract (C, n = 3) and patients with nuclear cataract along with high myopia (HM, n = 3). The expression of eccDNA was confirmed using routine quantitative polymerase chain reaction.

first: Ruihua

last: Wei

first: Kai

last: Wen

first: Lujie

last: Zhang

first: Yang

last: Cai

first: He

last: Teng

first: Yi

last: Yue

first: Yaoling

last: Li


title: CMTR1 promotes colorectal cancer cell growth and immune evasion by transcriptionally regulating STAT3

city: Xiamen

first: you

middle: a

last: bin

state: Fujian

address: 55 Zhenhai Road, Siming District, Xiamen

institute: the First Affiliated Hospital of Xiamen University

summary: CMTR1, also called IFN-stimulated gene 95 kDa protein (ISG95), is elevated by viral infection in a variety of cells. However, the function of CMTR1 in colorectal cancer (CRC), especially its role in tumorigenesis and immune regulation, remains unclear. Here, we first identified CMTR1 as a novel oncogene in colorectal cancer. Based on The Cancer Genome Atlas (TCGA) database exploration and human tissue microarray (TMA) analysis, we found that CMTR1 expression was markedly higher in colorectal cancer tissues compared to that in adjacent normal tissues. High CMTR1 was correlated with poor prognosis of colorectal cancer patients. Knockdown (KD) of CMTR1 significantly suppressed cell proliferation and tumorigenicity both in vitro and in vivo, whereas overexpression of CMTR1 exhibited the opposite effects. KEGG analysis revealed that the JAK/STAT signaling pathway was differentially enriched in colorectal cancer cells with CMTR1 KD. Mechanistically, repression of CMTR1 influenced RNAPII recruitment to the TSS and repression of STAT3 expression and activation. Furthermore, PD1 blockade immunotherapy was prominently enhanced with CMTR1 KD by increased infiltration of CD8+ T cells into tumor microenvironment. Overall, it appears that CMTR1 plays a key role in regulating tumor cell proliferation and antitumor immunity.

overall_design: RNA-seq performed in this study was designed to understand the molecular mechanisms underlying CMTR1 in gene transcription regulation.

first: A-bin

last: You

last: Ding

first: Feng

last: Ye


title: Selective translational control of cellular and viral mRNAs by RPS3 mRNA binding

first: Tal

last: Havkin-Solomon

address: 234 Herzl

department: Biomolecular Sciences

institute: Weizmann Institute of Science

summary: RPS3, a universal core component of the 40S ribosomal subunit, interacts with mRNA at the entry channel. Whether RPS3 mRNA-binding contributes to specific mRNA translation and ribosome specialization in mammalian cells is unknown. Here we mutated RPS3 mRNA-contacting residues R116, R146 and K148 and report their impact on cellular and viral translation. R116D weakened cap-proximal initiation and promoted leaky scanning, while R146D had the opposite effect. Additionally, R146D and K148D displayed contrasting effects on start-codon fidelity. Translatome analysis uncovered common differentially translated genes of which the downregulated set bears long 5’UTR and weak AUG context, suggesting a stabilizing role during scanning and AUG selection. We identified an RPS3-dependent regulatory sequence (RPS3RS) in the sub-genomic 5’UTR of SARS-CoV-2 consisting of a CUG initiation codon and a downstream element that is also the viral transcription regulatory sequence (TRS). Furthermore, RPS3 mRNA-binding residues were essential for SARS-CoV-2 NSP1-mediated inhibition of host translation and for its ribosomal binding. Intriguingly, NSP1-induced mRNA degradation was also reduced in R116D cells, indicating that mRNA decay occurs in the ribosome context. Thus, RPS3 mRNA-binding residues have multiple translation regulatory functions and are exploited by SARS-CoV-2 in various ways to influence host and viral mRNA translation and stability.

overall_design: We used CRISPR-Cas9 mediated mutagenesis in mammalian cells and modified endogenous RPS3 R116, R146 and K148 amino acid residues to aspartic acids. For global translation analysis, the collected samples were merged to create the High translated fractions (3+ ribosomes). Equivalent RNA concentrations of Input and High translated ribosome were taken for the library preparation for MARS-Seq.

first: Elad

last: Itzhaki

first: Nir

last: Joffe

first: Nina

last: Reuven

first: Yosef

last: Shaul

first: Rivka

last: Dikstein


title: Characterization of immature ovarian teratomas through single-cell transcriptome

city: Chengdu

first: Heng

last: Xu

state: Sichuan

address: 17#, section 3, South Renmin Road

institute: Sichuan University

summary: Immature ovarian teratomas are malignant germ cell tumor composed of complicated cell types and are characterized by pathological features of immature neuroectodermal tubules/rosettes. To reveal the heterogeneity, evolution trajectory and cell communications among tumor microenvironment, we performed single-cell RNA sequencing (scRNA-seq) on three patient-derived immature ovarian teratomas (PDT) samples, and conducted systematically comparison with stem cell lines derived immature teratomas (CDT). A total of qualified 22,153 cells were obtained and divided into 28 clusters, which can match to the scRNA-seq annotation of CDT as well as human fetal Cell Atlas, but with higher heterogeneity and more prolific cell-cell crosstalk. Radial glia cells (tagged by SOX2) and immature neuron (tagged by DCX) exhibited mutually exclusive expression, and differentiated along distinct evolutionary trajectory from cycling neural progenitors. Proportions of these neuroectodermal cell subtypes may play important roles in PDT through contributing to the internal heterogeneity of PDTs. Moreover, the immune cells in PDTs were infiltrated rather than teratoma-derived, with more abundant macrophage in immature neuron than those in radial glia cells, and the infiltrated macrophage subtypes (i.e., M1 and M2) were significantly correlated to clinical grade. Overall, suppressed evolution process and transcriptome regulation in neuroectodermal cells, reduced cell-cell crosstalk, higher M1/M2 proportion ratio, and enhanced T cell effects in tumor microenvironment are enriched in patients with favorable prognosis. In conclusion, we provided the comprehensive profile of PDT at single cell level and highlighted the potential usage of CDTs as a model for research on PDT.

overall_design:
scRNAseq data of three patient-derived immature ovarian teratomas (PDT) grade 3 samples
-------------------------------------
Authors state "it is prohibited to upload raw human data to foreign databases by Chinese laws".

first: Minyuan

last: Cao

first: Yun

last: Deng

first: Yiqi

first: Jing

last: Wu

first: Chongyi

last: Yang

first: Zijun

last: Wang

first: Qianqian

last: Hou

first: Huancheng

last: Fu

first: Zhixiang

last: Ren

first: Xuyang

last: Xia

first: Yue

first: Wei

first: Xin

last: Liao

last: Shu


title: Comparison of the dietary omega-3 fatty acids impact on murine psoriasis-like skin inflammation and associated lipid dysfunction

city: Bethesda

first: Alexander

middle: V

last: Sorokin

state: MD

address: 10 Center Drive, Bldg 10, Magnuson CC, Room 5D-03

institute: NIH, NHLBI

summary: Persistent skin inflammation and impaired resolution are the main contributors to psoriasis and associated cardiometabolic complications. Omega-3 fatty acids (FA), eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), are known to exert beneficial effects on inflammatory response and lipid function. However, a specific role in psoriasis disease and accompanied pathological mechanisms are still a matter of debate. Here, we aimed to perform a direct comparison between EPA and DHA diet treatment for 12 weeks of psoriasis-like skin inflammation in the K14-Rac1V12 mouse model. By utilizing sensitive high throughput techniques, we targeted EPA- and DHA-derived specialized pro-resolving mediators (SPMs) and identified tightly connected signaling pathways by RNA sequencing. Treatment with experimental diets significantly decreased circulating pro-inflammatory cytokines and plasma lipids, altered psoriasis macrophages phenotype and affected genes of atherosclerosis related pathways. The superficial role of these changes was related to DHA treatment and included skin abundance in resolvin D5, protectin X and maresin 2. EPA treated mice expressed less pronounced effects but resulted in decreasing skin accumulation of prostaglandin E2 and thromboxane B2. These results indicate that altering psoriasis with the omega-3 FA might have clinical significance and DHA treatment should be considered over EPA in this specific population.

overall_design: Comparison of 3 experimental diets treatment in K14-Rac1 psoriasis mouse model

first: Panagiotis

last: Papavasileiou


title: Traumatic Brain Injury Stimulates Sympathetic Tone-mediated Bone Marrow Myelopoiesis to Favor Fracture Healing

first: Liu

last: Weijian

address: Jiefang Avenue

institute: Union hospital

summary: Traumatic brain injury (TBI) accelerates fracture healing, but the underlying mechanism remains largely unknown. Accumulating evidence indicates that the central nervous system plays a pivotal role in regulating immune system and skeleton, however, the impact of TBI on hematopoiesis commitment was overlooked. Here, we found that the dramatically elevated sympathetic tone accompanied with TBI-accelerated fracture healing; chemical sympathectomy blocks TBI-induced fracture healing. Importantly, the adrenergic hypersensitivity swiftly skews bone marrow hematopoietic lineage cells toward anti-inflammation myeloid cells within 14 days, which favor fracture healing. Knockout of β3- or β2-adrenergic receptors (ARs) eliminate TBI mediated anti-inflammation macrophage expansion and TBI-accelerated fracture healing. Moreover, β3- and β2-ARs agonists synergistically promote M2 macrophages infiltration in callus and accelerate bone healing process. Our results suggest that TBI shapes the anti-inflammation environment during early stage of fracture healing, implicating the sympathetic nerve system as a potential target that can be exploited to treat fracture.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of the bone marrow cells from wild type mice, Adrb2 knockout mice, and Adrb3 knockout mice after TBI and fracture.

first: Chen

last: wei

first: Xie

last: mao

last: chao


title: Proteomic discovery of chemical probes that perturb protein complexes in human cells II

city: LA JOLLA

first: Hsuan-Lin

last: Her

address: 9500 Gilman Dr,

institute: UCSD

summary: Most proteins in the human proteome lack chemical probes, and several large-scale and generalizable small-molecule binding assays have been introduced to address this problem. How compounds discovered in such “binding-first” assays affect protein function, nonetheless, often remains unclear. Here, we describe a “function first” proteomic strategy that uses size exclusion chromatography (SEC) to assess the global impact of electrophilic compounds on protein complexes in human cells. Integrating the SEC data with cysteine-directed activity-based profiling identifies changes in protein-protein interactions that are caused by site-specific liganding events, including the stereoselective engagement of cysteines in PSME1 and SF3B1 that disassemble the PA28 proteasome regulatory complex and remodel the spliceosome, respectively. Our findings thus show how multidimensional proteomic analysis of focused libraries of electrophilic compounds can expedite the discovery of chemical probes with site-specific functional effects on protein complexes in human cells.   In this experiment, we probed the RNA-binding profile of DDX42 by eCLIP via an endogenously introduced HA-tag in the context of various SF3B1 ligands.

overall_design: Three independent treatments were performed for each of 2x4 treatment groups (pre-treatment for 1h with 500nM dTAGv-1 or DMSO; followed by 8h of DMSO, 5uM WX-02-23, 5uM WX-02-43 or 10nM Pladienolide B), yielding a total of 24 samples.

first: Jarrett

last: Remsberg

first: Benjamin

last: Cravatt

first: Martin G

last: Jaeger

first: Assael

last: Madrigal

first: Katherine

last: Rothamel

first: Gene

last: Yeo


title: Chromatin context-dependent regulation and modulation of prime editing [sci-RNA-seq3]

city: Seattle

first: Xiaoyi

last: Li

state: WA

address: 3720 15th Ave NE

department: Department of Genome Sciences

institute: University of Washington

summary: Prime editing is a powerful means of introducing precise changes to specific locations in mammalian genomes. However, the widely varying efficiency of prime editing across target sites of interest has limited its adoption in the context of both basic research and clinical settings. Here, we set out to exhaustively characterize the impact of the cis-chromatin environment on prime editing efficiency. Utilizing a newly developed and highly sensitive method for mapping the genomic locations of a randomly integrated “sensor”, we identify specific epigenetic features that strongly correlate with the highly variable efficiency of prime editing across different genomic locations. Next, to assess the interaction of trans-acting factors with the cis-chromatin environment, we develop and apply a pooled genetic screening approach with which the impact of knocking down various DNA repair factors on prime editing efficiency can be stratified by cis-chromatin context. Finally, we demonstrate that we can dramatically modulate the efficiency of prime editing through epigenome editing, i.e. enhancing (or restricting) local chromatin accessibility in order to increase (or decrease) the efficiency of prime editing at a target site. Looking forward, we envision that the insights and tools described here will broaden the range of both basic research and therapeutic contexts in which prime editing is useful.

overall_design: A pooled DNA damage response (DDR) gene-focused shRNA screen in single cells was carried out to analyze the interaction between the cis-chromatin and trans-acting regulatory factors of prime editing. Briefly, K562 PE2-Puro cells with multiple randomly integrated synHEK3 reporters were transduced with a lentiviral shRNA library (driven by a tetracycline-controlled promoter) containing 304 hairpins targeting 76 DDR-related genes. We treated the cells with Doxycycline for 2 days to fully induce knockdown effects. We then transfected pegRNAs introducing random 6-bp insertions to the synHEK3 reporters. After 3-4 days, cells were profiled using a modified version of sci-RNA-seq3 (Martin et al., 2022). In particular, a T7 in situ transcription step was used to drive expression of the synHEK3 reporter in fixed, permeabilized nuclei, such that the cellular transcriptome, the perturbation molecules (shRNAs), and prime editing outcomes recorded in synHEK3 reporters can be co-profiled. The nuclei underwent three levels of split-pool barcoding and three types of libraries were generated: the sci-RNA-seq3 transcriptome library, the synHEK3 capture library, and the shRNA capture library.

last: Chen

first: Beth

last: Martin

first: Diego

last: Calderon

first: Choli

last: Lee

first: Junhong

last: Choi

first: Florence

last: Chardon

first: Troy

last: McDiarmid

first: Haedong

last: Kim

first: Jean-Benoît

last: Lalanne

first: Jenny

last: Nathans

first: Jay

last: Shendure


title: High-resolution Nanopore methylome-maps reveal random hyper-methylation at CpG-poor regions as driver of  chemoresistance in leukemias.

city: Firenze

first: Gianluca

last: Mattei

state: FI

address: Via di S. Marta, 3

country: Italy

institute: Università degli Studi di Firenze

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

overall_design: Refer to individual Series


title: LaeA regulates mycelium growth by mediating H3K9 methylation in Myceliophthora thermophila [RNA-seq]

first: Jingen

address: Xiqi Dao 32, Tianjin Airport Economic Area

institute: Tianjin institute of industrial biotechnology,Chinses Academy of Sciences

summary: The low efficiency of fungal growth and substrate utilization is a barrier to high yield and productivity of target products during fungal fermentation. However, elaborated and intricate regulatory mechanisms of fungal growth remains inconclusive. In this study, we found deletion of putative methyltransferase LaeA enhanced sugar consumption and fungal growth rate of M. thermophila. The exploration of the mechanism of LaeA regulation revealed that transcription factor (Cre-1, Grf-1, Grf-2 and Grf-3) acted as negative repressor of intracellular metabolism, of which expression was indirectly regulated by LaeA. Moreover, higher gluconeogenesis activity is crucial for elevated fugal growth rate and PCK might be the core notes of metabolism network relative to fungal vegetative growth. Further in vivo global histone methylation assay and in vitro biochemical analysis declared LaeA was a methyltransferase with histone H3 lysine 9 (H3K9) as the substrate and regulated growth properties by directly modulating H3K9 methylation levels. ChIP-seq analysis displayed significantly reduced H3K9me3 in region of pck locus in strain ΔlaeA, implying methylation modification of pck might be the way of LaeA regulating growth phenotypes. Additionally, whole-genome bisulfite sequencing (WGBS) analysis demonstrated methylation of cytosines (5mC) in genomic DNA was carried out and correlated to the methylation of H3K9 modified by LaeA. Taken together, our research declared LaeA possessed methyltransferase activity, targeting H3K9 and participated in regulation of fugal properties, including on sugar consumption, mycelium growth, cellulase production, secondary metabolism, and oxidative stress tolerance, providing new insights into the epigenetics of filamentous fungi.

sample_organism: Thermothelomyces thermophilus ATCC 42464

overall_design: mRNA profiles of Myceliophthora thermophila cells exposed to glucose and Avicel.


title: Transcriptomic profiling of the yeast Komagataella phaffii in response to environmental alkalinization

city: CERDANYOLA DEL VALLES

first: JOAQUIN

last: ARINO

state: Barcelona

address: ED. IBB

department: Biochemistry & Mol. Biol.

institute: UNIVERSITAT AUTONOMA BARCELONA

summary: Adaptation to alkalinization of the medium in fungi involves an extensive remodeling of gene expression. Komagataella phaffii is an ascomycetous yeast that has become an organism widely used for heterologous protein expression. We explore here the transcriptional impact of moderate alkalinization in this yeast. In spite of a minor effect on growth, shifting the cultures from pH 5.5 to 8.0 or 8.2 provokes significant changes in the mRNA levels of over 700 genes. Functional categories such as arginine and methionine biosynthesis, non-reductive iron uptake and phosphate metabolism are enriched in induced genes, whereas many genes encoding iron-sulfur proteins or members of the respirasome were repressed.  We also show that alkalinization is accompanied by oxidative stress and we propose this circumstance as a common trigger of a subset of the observed changes. PHO89, encoding a Na+/Pi cotransporter, appears among the most potently induced genes by high pH. We demonstrate that this response is mainly based on two calcineurin-dependent response elements located in its promoter, thus indicating that alkalinization triggers a calcium-mediated signal in K. phaffii. Further characterization of alkaline pH responsive promoters may lead to developing novel pH-controlled systems for heterologous protein expression in this fungus.

overall_design: comparison of mRNA levels by RNA-Seq between Komagataella phaffii yeast cells grown at pH 5.5 (referene) and 8.0 (grown on glycerol or glucose) or 8.2 (grown on glycerol). Replicates are included.

first: Joaquin

last: Arino

first: Marcel

last: Albacar

first: Antonio

last: Casamayor


title: LaeA regulates mycelium growth by mediating H3K9 methylation in Myceliophthora thermophila

last: Li

platform_organism: Thermothelomyces thermophilus ATCC 42464


title: m6A methyltransferase METTL3 programs CD4+ T cell activation and regulatory T cell differentiation in SLE

city: Changsha

first: Shuang

last: Lu

state: Hunan

address: No.139 Renmin Middle Road

institute: The 2nd Xiangya Hospital

summary: To investigate the function of METTL3 in the regulation of Treg cell differentiation, we treated inducd Tregs with STM2457 in which the catalytic activity of METTL3 has been phrmacologically inhibited. We then performed gene expression profiling analysis using data obtained from RNA-seq of 8 different cells at one time point.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for induced Treg cells and its METTL3-inhibitory derivatives.

first: Huan

last: Zhu

first: Xingyu

last: Wei


title: Mitochondrial b-oxidation of adipose-derived fatty acids by osteoblast fuels parathyroid hormone-induced bone formation

city: CHARLOTTESVILLE

first: Charles

last: Farber

state: VA

address: P.O. Box 800793, School of Medicine

institute: University of Virginia

summary: The energetic costs of bone formation require osteoblasts to coordinate their activities with tissues, like adipose, that can supply fuel molecules. In the case of intermittent parathyroid hormone treatment (PTH), a strategy used to reduce fracture risk, bone formation is proceeded by a change in lipid homeostasis. To investigate the requirement for fatty acid oxidation by osteoblasts during PTH-induced bone formation, we subjected mice with osteoblast-specific deficiency of mitochondrial long-chain b-oxidation as well as mice with adipocyte-specific deficiency for the PTH receptor or adipose triglyceride lipase to an anabolic treatment regime. PTH increased b-oxidation by osteoblasts and the release of fatty acids from adipocytes, while the genetic mouse models were resistant to the hormone’s anabolic effect. Collectively, these data suggest that PTH’s anabolic actions requires coordinated signaling in bone as well as in adipose, wherein a lipolytic response liberates fatty acids that are oxidized by osteoblasts to fuel bone formation

overall_design: RNAseq was performed on primary calvarial osteoblast cultures differentiated for 7 days and treated with PTH or Vehicle for 24 hours.

first: Nathalie

last: Alekos

first: Ryan

last: Riddle


title: Dietary induced epigenetic reprogram in mouse intestinal enterocytes

city: BRONX

first: Leonard

last: Augenlicht

state: New York

address: 1300 Morris Park Avenue

department: Cell Biology

institute: ALBERT EINSTEIN COLLEGE OF MEDICINE

summary: Bl6 mice were fed with New Western diet 1 (NWD1) or Americal Instititue of Nutrition 76A (AIN76A or AIN) diet from weaning for 3 months. Single intestinal epithelial cells were FACS isolated by the Epcam+, CD45- , and subject to scACTAseq assay.

overall_design: Examine roles of dedifferentiation of Bmi1 cell in regeneration of intestinal stem cells and its impact on mucosal homeostasis under normal physiogical condition (fed with various diets).

first: Wenge

first: Xusheng

last: Zhang

first: Michele

last: Houstopn


title: Transcriptome profiling of cardiomyocytes treated with antioxidants

city: Orlando

first: manish

middle: Kumar

last: Gupta

state: Florida

address: 6900 Lake Nona Blvd

department: Burnett School of Biomedical Sciences

institute: University of Central Florida

summary: Despite clinical advancement, ischemia-induced myocardial diseases remain an underlying cause of death among individuals throughout the world. Interestingly, we found that the administration of antioxidants can protect cardiomyocytes during ischemia. However, the mechanism involved in inducing the cytoprotective effect under ischemic conditions is not fully elucidated. In this study, we carried out RNA-sequencing data analysis of rat ventricular cardiomyocytes under normoxic, ischemic, and ischemia with eugenol.  The RNA sequencing data ascertained that the ischemic condition differentially regulated 7,694 genes in the NRVCs compared to the normoxic condition (padj<0.05). Out of 7,694 genes, 3,774 genes were up-regulated, and 3,920 genes were down-regulated. Also, the administration of eugenol in the presence of ischemic condition up-regulated 159 genes and down-regulated 111 genes. Functional enrichment analysis of differentially regulated genes was carried out using clusterProfiler R and ingenuity pathway analysis. In this study, we found that both the up-regulated and down-regulated genes regulated the post-translational modification of histone proteins during ischemia. Also, the up-regulated genes controlled cell death and survival, protein synthesis and transport etc. The down-regulated genes controlled cellular growth and development, cell signaling, cellular assembly and organization, cellular movement, cellular respiration, and cell death and survival. It was found that eugenol administration under ischemic conditions up-regulated intracellular transduction signaling and down-regulated negative regulation of the metabolic process, negative regulation of nucleic acid templated transcription, and negative regulation of the biosynthetic process. All in all, the administration of antioxidants improves cell survival via down-regulating negative regulation of biosynthetic processes.

overall_design: Evaluation of differentially expressed genes in cardiomyocytes treated with eugenol

first: Manish

first: Puneet

last: Randhawa


title: Discovery of cellular and genetic signatures of immune tolerance in kidney transplant recipients through single cell RNA sequencing analysis

city: seoul

first: Hyunjoo

last: Bae

address: 222, Banpo-daero, Seocho-gu

department: Biomedical Science, Laboratory Medicine

country: South Korea

institute: The Catholic University of Korea, College of Medicine, Seoul St. Mary’s hospital

summary: The objective of this study was to uncover distinct cellular and genetic signatures of transplant operational tolerance (TOT) in kidney transplant recipients (KTRs) through single cell RNA sequencing (scRNA-seq) using peripheral blood mononuclear cells (PBMCs). PBMCs were isolated from 12 KTRs, including those with TOT (TOT, n = 4), stable allograft function on maintenance immunosuppression (STA, n = 4) and biopsy-proven allograft rejection (BPAR, n = 4). ScRNA-seq of PBMCs was analyzed using 20 cell surface marker antibody sequencing to annotate clusters and 399 immune response panel to identify gene expression. Differences in cellular distribution and gene expression were compared among the three groups. Heatmap hierarchical clustering showed that overall cellular distribution pattern was distinct in TOT in comparison with those in the other two groups, with the proportion of B cells being higher in TOT, attributed to immature B cell fraction (TOT vs. STA vs. BPAR: 4.61% vs. 1.27% vs. 2.53%, p = 0.011). Transcript analysis of B cells revealed that genes involved in allo-immune pathway were downregulated in TOT. In T cell subset analysis, the proportion of regulatory T cells (Tregs) was increased. In transcript analysis, genes associated with inflammation were decreased, while expression levels of CCR6 in Tregs were increased in TOT. Proportions of NKT and NK cells were increased in TOT than in the other two groups. This study showed that TOT has distinct cellular and genetic signatures such as increases of immature B cells and Tregs and high expression levels of CCR6 in Tregs.

overall_design: ScRNA-seq of PBMCs from 12 KTRs, including those with TOT (TOT, n = 4), stable allograft function on maintenance immunosuppression (STA, n = 4) and biopsy-proven allograft rejection (BPAR, n = 4).

first: Hanbi

last: Lee

first: Eun

middle: J

last: Ko

first: Chan-Duck

last: Kim

first: Sang-Ho

first: Chul

last: Yang

first: Eun-Jee

last: Oh

first: Byung

middle: H

last: Chung


title: small-RNA sequencing after forced abstinence from heroin self-administration in male rats

city: Philadelphia

first: Stephanie

last: Daws

state: PA

address: 3500 N Broad St

institute: Temple University

type: Non-coding RNA profiling by high throughput sequencing

summary: We report the miRNAs differentially expressed in the orbitofrontal cortex of adult male rats that self-administered heroin after 21 days of forced abstinence.

overall_design: miRNA profiles in orbitofrontal cortex of heroin exposed animals versus naïve animals.

last: Sillivan


title: High-resolution Nanopore methylome-maps reveal random hyper-methylation at CpG-poor regions as driver of  chemoresistance in leukemias.[RNA-Seq]

first: Gianluca

last: Mattei

summary: Aberrant DNA-methylation at CpG dinucleotides is a hallmark of cancer and is associated with the  emergence of resistance to anti-cancer treatment, though molecular mechanisms and biological signifi- cance remain elusive. Genome-scale methylation maps by currently used methods are based on chemical  modification of DNA and are best suited for analyses of methylation at CpG-rich regions (CpG islands).  We report the first high-coverage whole-genome map in cancer using the long-read nanopore technol- ogy, which allows simultaneous DNA-sequence and -methylation analyses on native DNA. We analyzed  clonal epigenomic/genomic evolution in Acute Myeloid Leukemias (AMLs) at diagnosis and relapse, af- ter chemotherapy. Long-read sequencing coupled to a novel computational method allowed definition  of differential methylation at unprecedented resolution (> 99% CpGs), extending analyses of CpG is- lands to sparse CpGs, which represent half of all differentially-methylated regions. We showed that the

overall_design: relapse methylome is characterized by hypermethylation at both CpG islands and sparse CpGs. Hyper- methylated genes, however, only accounted for < 5% of all differentially-expressed genes (DEGs) in the  relapsed AMLs and were not enriched for chemoresistance genes. A few under-expressed transcription- factors (1 to 6 in the different AMLs) hyper-methylated at sparse CpGs support ∼ 40% DEGs and are  highly-enriched in chemoresistance genes. Hypermethylated regions at sparse CpGs were poorly con- served in the relapsed AMLs, under-represented at their genomic positions and showed high methylation- entropy, as compared to CpG islands. Relapsed AMLs carried a few patient-specific structural-variants  and DNA-mutations, apparently not involved in drug-resistance. Thus, drug-resistance in AMLs is due to the selection of random epigenetic alterations at sparse CpGs of a few transcription factors, which then induce reprogramming of the relapsing phenotype, independently of clonal genomic-evolution.

first: Alberto

last: Magi

first: Alessandra

last: Mingrino

first: Chiara

last: Caprioli

last: Ronchini

first: GianMaria

last: Frig`e

first: Roberto

last: Semeraro

first: Davide

last: Bolognini

first: Alessandro

last: Rambaldi

first: Anna

last: Candoni

first: Emanuela

last: Colombo

first: Luca

last: Mazzarella

first: Pier

last: Pelicci