title: A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2 [ATAC-seq]

overall_design: ATAC-seq of hindlimb buds from e10.5 mouse embryos.

first: M

last: Losa

first: I

last: Osterwalder

first: P

last: Zarrineh

first: J

middle: D

last: Benazet

first: B

last: Chacon

first: A

last: Girdzuisaite

last: Morabito

first: F

last: Blasi

last: Zhu

first: S

last: Mackem

first: T

last: Capellini

first: N

last: Bobola

first: D

last: Dickel

last: Zuniga

last: Visel

first: R

last: Zeller

first: L

last: Selleri


title: Glycerol metabolism supports oral commensal interactions.

status: Public on Apr 26 2023

city: Portland

first: June

last: Treerat

state: Oregon

address: 3181 SW Sam Jackson Park Rd, MRB 433

department: Restorative Dentistry

country: USA

institute: Oregon Health & Science University

type: Expression profiling by high throughput sequencing

summary:
To understand what molecular mechanisms determine the unique interspecies interactions between two predominant oral commensals Streptococcus sanguinis and Corynebacterium durum in the healthy oral cavity.
We further investigated the regulatory connection between lipid metabolism and chain elongation based on the global gene expression profiling of the dual species cultures, as well as characterized S. sanguinis glycerol kinase (glpK) as a key gene involved in the interspecies interactions.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for S.sanguinis at late log phase growth in the presence and absence of C. durum. Moreover, generation of the S. sanguinis glpK deletion mutant for phenotypic characterizations.

first: Puthayalai

first: Jens

last: Kreth


title: Identification of Distinct Impacts of CovS Inactivation on the Transcriptome of Acapsular Group A Streptococci

status: Public on Apr 25 2023

city: Houston

first: William

middle: Charles

last: Shropshire

state: TX

address: 1901 East Road

institute: The University of Texas MD Anderson Cancer Center

summary: To determine the impact of CovS inactivation in acapsular GAS (Streptococcus pyogenes) strains

overall_design: Differential gene expression analyses across multiple acapsular GAS backgrounds of WT vs CovS knockout strains

first: Sruti

last: DebRoy

middle: C

first: Luis

last: Vega

first: Chau

last: Tran

first: Nicola

last: Horstmann

first: Piyali

last: Mukherjee

first: Selvalakshmi

last: Selvaraj Anand

first: Truc

middle: T

first: Jordan

middle: A

last: Bremer

first: Marc

last: Gohel

first: Cesar

last: Arias

first: Anthony

middle: R

last: Flores

first: Samuel

last: Shelburne


title: Single cell RNA sequencing data of neuroblastoma infiltrated bone marrow

city: Salzburg

first: Wolfgang

last: Esser-Skala

address: Hellbrunner Strasse 34

country: Austria

institute: University of Salzburg

summary: We report transcriptional analyses at single cell resolution of 16 bone marrow samples with and without neuroblastoma infiltration. Our samples span across several neuroblastoma models, including MYCN amplified, ATRX mutated, and sporadic (lacking either alteration).

overall_design:
17 scRNA-seq samples on bone marrows derived from 16 patients. The sequencing dataset consists of 5 samples without bone marrow infiltration, defined as controls (C1, C2, C3, C4, and C5) and 11 neuroblastoma infiltrated bone marrow samples from patients with MYCN amplification (M1, M2, M3, M4), ATRX mutations (A1, A2), and cases lacking either alteration (S1, S2, S3, S4, S5).
*** Submitter declares:  Due to data protection regulations, raw data have been uploaded, but rather deposited in the EGA (accession EGAS00001006106).***

first: Irfete

middle: S

last: Fetahu

first: Rohit

last: Dnyansagar

last: Sindelar

first: Fikret

last: Rifatbegovic

first: Andrea

last: Bileck

first: Lukas

last: Skos

first: Eva

last: Bozsaky

first: Daria

last: Lazic

first: Lisa

last: Shaw

first: Marcus

last: Tötzl

first: Dora

last: Tarlungeanu

first: Marie

last: Bernkopf

last: Weninger

first: Eleni

middle: M

last: Tomazou

first: Christoph

last: Bock

first: Christopher

last: Gerner

first: Ruth

last: Ladenstein

first: Matthias

last: Farlik

first: Nikolaus

last: Fortelny

first: Sabine

last: Taschner-Mandl


title: FOXD1 is associated with poor outcome and maintains tumor-promoting enhancer-gene programs in basal-like breast cancer.

city: Tokyo

first: Kohei

last: Kumegawa

address: 3-8-31 Ariake, Koto-ku

country: Japan

institute: Japanese Foundation for Cancer Research

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: AZA+atRA reprogramming of head and neck squamous cell carcinoma cell line T-HEp3, and enhancer analysis by H3K27ac ChIP-seq in HNSCC T-HEP3 and D-HEp3 cell lines

status: Public on Apr 27 2023

city: Bronx

first: Julio

last: Aguirre-Ghiso

state: NY

address: 1301 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine


title: In vivo single-cell profiling of lncRNAs during Ebola virus infection.

city: Barcelona

first: luisa

last: santus

address: Plaça d'Eusebi Güell, 1-3

country: Spain

institute: Barcelona Supercomputing Center

overall_design:
Refer to individual Series

Please note that the rheMac10_EBOV_and_novel_genenames.gtf represents the merging of two subseries datasets.


title: Tumor-derived Small Extracellular Vesicles Inhibit CAR T Cells

city: PHILADELPHIA

first: Wei

last: Guo

state: PENNSYLVANIA

address: 433 S. University Avenue

institute: University of Pennsylvania

summary: To examine the effect of tumor-derived small extracellular vesicles on Meso-CAR T cells. Series of genes of CAR T cells treated with or without tumor-derived small extracellular vesicles were detected.

overall_design: Meso-CAR T cells were treated with or without tumor-derived small extracellular vesicles. Those small extracellular vesicles were purified from tumor cells with or without PD-L1 KO cells

first: Wenqu

last: Zhong


title: Plasma cell infiltrate populating the muscle tissue of patients with inclusion body myositis feature distinct BCR repertoire properties

city: New Haven

first: Steven

last: Kleinstein

state: Ct

address: 300 George St.

department: Pathology

institute: Yale University

summary: Inclusion body myositis (IBM) is an autoimmune and degenerative disorder of skeletal muscle. The B cell infiltrates in IBM muscle tissue are predominantly fully differentiated antibody-secreting plasma cells, with scarce naïve or memory B cells. The role of this infiltrate in the disease pathology is not well understood. To better define the humoral response in IBM, we used adaptive immune receptor repertoire sequencing to generate large B cell receptor (BCR) repertoire libraries from IBM muscle biopsies and compared them to those generated from dermatomyositis (DM), polymyositis (PM), and circulating CD27+ memory B cells, derived from healthy controls and antibody secreting cells (ASC) collected following vaccination. The repertoire properties of the IBM infiltrate included: expanded clones that equaled or exceeded the highly clonal vaccine-associated ASC repertoire; reduced somatic mutation selection pressure in the complementary determining regions and framework regions; and enriched usage of class switched IgG and IgA isotypes, with a minor population of IgM expressing cells. These IBM IgM-expressing population revealed unique features, including an elevated somatic mutation frequency and distinct CDR3 physicochemical properties., These findings demonstrate that the IBM muscle BCR repertoire is highly distinct from DM and PM and circulating antigen-experienced subsets, suggesting that it may form through selection by a disease-specific set of antigens.

overall_design:
Bulk BCR was performed on muscle specimens that were colected from three PM (polymyositis), three DM (dermatomyositis) and four IBM (inclusion body myositis) patients. The analysis also included bulk BCR data from peripheral blood collected from six healthy donors used in previous studies, as well as single-cell repertoires from three ASC subsets from previous studies.
This series includes re-analyzed data from:SRX8984266, SRX8984267, SRX8984268, SRX10918775, SRX1816135, SRX1816143, SRX1816152, SRX2018047, SRX2018081, SRX2018050, SRX2018060, SRX3791988, SRX3791985, SRX3791983
Re-analyzed data are included in the tar archive available at the foot of this record.

first: Ruoyi

last: Jiang

first: Roy

last: Bhaskar

first: Qian

last: Wu

first: Subhasis

last: Mohanty

first: Richard

middle: J

last: Nowak

first: Albert

last: Shaw

first: Kevin

last: O'Connor


title: FOXD1 is associated with poor outcome and maintains tumor-promoting enhancer-gene programs in basal-like breast cancer [ChIP-seq]

summary: Breast cancer biology varies markedly among patients. Basal-like breast cancer is one of the most challenging subtypes to treat because it lacks effective therapeutic targets. Despite numerous studies on potential targetable molecules in this subtype, few targets have shown promise. However, the present study revealed that FOXD1, a transcription factor that functions in both normal development and malignancy, is associated with poor prognosis in basal-like breast cancer. We analyzed publicly available RNA sequencing data and conducted FOXD1-knockdown experiments, finding that FOXD1 maintains gene expression programs that contribute to tumor progression. We first conducted survival analysis of patients grouped via a Gaussian mixture model based on gene expression in basal-like tumors, finding that FOXD1 is a prognostic factor specific to this subtype. Furthermore, our RNA sequencing and chromatin immunoprecipitation sequencing experiments on the basal-like breast cancer cell lines BT549 and Hs578T with FOXD1 knockdown revealed that FOXD1 regulates enhancer-gene programs related to tumor progression. These findings suggest that FOXD1 plays an important role in basal-like breast cancer progression and may represent a promising therapeutic target.

overall_design: Comparative peak profiling analysis of H3K27ac ChIP-seq data for BT549 and Hs578T and their KD derivatives (siFOXD1).

first: Liying

last: Yang

first: Kenichi

last: Miyata

first: Reo

last: Maruyama


title: Persistent mTORC1 activation due to loss of liver tuberous sclerosis complex 1 promotes liver injury in alcoholic hepatitis.

city: Kansas City

first: Hongmin

last: Ni

state: KS

address: 3901 Rainbow Blvd, MS-1018

institute: The University of Kansas Medical Center

summary:
The aim of the study is to investigate the role and mechanisms of tuberous sclerosis complex 1 (TSC1) and mechanistic target of rapamycin complex 1 (mTORC1) in alcohol associated liver disease
Hepatic RNA profiles of WT and hepatic TSC1 KO mice fed with alcohol or control diet using Gao binge alcohol model.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  TSC1 WT and hepatic TSC1 KO mouse livers.

first: Wen-Xing

last: Ding

first: Wanqing

last: Liu

first: Hong-Min

first: Xiaojuan

last: Chao


title: Regulatory variants of blood pressure genes (Omni-C)

first: Winona

middle: Oliveros

last: Diez

state: Barcelona

address: C. Maria Cubi 92, 2-2

institute: BSC

summary: Genome-wide association studies (GWAS) have identified blood pressure-related loci, but functional insights into causality and related molecular mechanisms lag behind. We functionally characterize 4608 genetic variants in linkage with blood pressure loci in vascular smooth muscle cells (VSMCs) and cardiomyocytes (CMs) by massively parallel reporter assays (MPRAs). Regulatory variants are in non-conserved loci, enriched in repeats, and alter trait-relevant transcription factor binding sites. Higher-order genome organization indicates that loci harboring regulatory variants converge in spatial hubs to control specific signaling pathways required for proper cardiovascular function. Modelling different variant allele frequencies by CRISPR prime editing led to expression changes of KCNK9, SFXN2, and PCGF6. We provide mechanistic insights into how regulatory variants converge their effects on blood pressure genes (i.e. ULK4, MAP4, CFDP1, PDE5A, 10q24.32), and cardiovascular pathways. Our findings support advances in molecular precision medicine to define functionally relevant variants and the genetic architecture of blood pressure genes.

overall_design: MPRA pool of 232,975 oligonucleotides, 1 sample for input library and then 5 replicates for CMs and 4 for VSMCs. The plasmid pool as DNA input and each TagSeq replicate (CMs = 5 replicates, VSMCs = 4 replicates) was sequenced on the HiSeq 2500 platform (Illumina), single end with 50 bp. Prime Editing (CRISPR/Cas9) using HEK293 with 3 replicates per allelic frequency of each SNP.

first: Philipp

middle: G

last: Maass

first: Marta

last: Melé

first: Kate

last: Delfosse

last: Oliveros

first: Daniella

middle: F

last: Lato

first: Katerina

last: Kiriakopulos

first: Milad

last: Mokhtaridoost

first: Abdelrahman

last: Said

first: Brandon

last: McMurray

first: Jared

middle: W

last: Browning

first: Kaia

last: Mattioli

first: Guoliang

last: Meng

first: James

last: Ellis

first: Seema

last: Mital


title: Regulatory variants of blood pressure genes


title: Huangqi Decoction ameliorates kidney injury in db/db mice by regulating the BMP/Smad signaling pathway

city: Shanghai

first: Aili

last: Cao

state: Shanghai

address: 600 Yishan Road

country: China

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary:
Purpose: Our study clarifies the mechanism of Huangqi decoction (HQD) against DKD in diabetic db/db mice.  Methods: Eight-week-old male diabetic db/db mice were randomly divided into four groups: Model (1% CMC), HQD-L (0.12 g/kg), HQD-M (0.36 g/kg), and HQD-H (1.08 g/kg) groups. Non-diabetic db/m mice were used as a control group. These mice received HQD treatment for 8 weeks continuously. After 8 weeks of feeding, kidneys were harvested to observe the kidney function, pathological changes, micro-assay study, and the protein expression levels.  Results: HQD treatment improved the albumin/creatine ratio (ACR) and 24 h urinary albumin, prevented the pathological phenotypes of increased glomerular volume, widened mesangial areas, the proliferation of mesangial matrix, the disappearance of foot processes, the decreased expression of nephrin and the number of podocytes. The expression profile chips were assessed to reveal the global transcriptional response and predict related functions, diseases and pathways. To verify this, we found that HQD treatment activated the protein expressions of BMP1, BMP7, BMPR2, and active-Rap1 and inhibited Smad1 and phospho-ERK. In addition, HQD could improve lipid deposition in the kidneys of db/db mice.  Conclusion: HQD prevents the progression of DKD in db/db mice by regulating the transcription of BMPs and their downstream target genes, inhibiting the phosphorylation of ERK and Smad1 by promoting the binding of Rap1 to GTP and regulating the lipid metabolism dysfunction. These provide a new idea for the treatment of DKD.
Overall, HQD had a significant protective effect against DKD. This may be related to the fact that HQD promotes the transcription of BMPs and their downstream target genes by upregulating BMPR-II and regulates the phosphorylation of ERK and Smad by promoting the binding of Rap1 to GTP. In addition, HQD also has a noticeable role in regulating lipid metabolism dysfunction in DKD, which provides a new idea for future research on HQD.

overall_design: Micro-array gene expression analysis was used to identify the DEGs in renal cortex after HQD treatment. The samples (n=3 for each group) with TNA integrity number above 7 were accepted and performed by Wanyen Biotechnologies Inc. (Shanghai).

first: Ying

last: Chen

first: Rui

last: Rong

first: Li

last: Wang

first: Hao

first: Bingbing

last: Zhu


title: GLUT3 salvage with vitamin C treatment altered gene expression landscape of OCI-AML3

city: Seoul

first: Junshik

last: Hong

state: Seoul

address: 101 Daehak-ro, Jongno-gu

department: Department of Internal Medicine

country: South Korea

institute: Seoul National University

summary: To investigate the GLUT3 salvage-induced transcriptome changes, we performed RNA-seq on the SLC2A3 overexpressed and the empty control OCI-AML3 cell lines treated with 250 µM of vitamin C.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for SLC2A3 overexpressed OCI-AML3 cell line and its empty control.

first: Jun

last: Liu


title: Hi-TrAC Detects Active Sub-TADs and Reveals Internal Organizations of Super-Enhancers

city: Bethesda

first: Yaqiang

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

institute: NHLBI

summary: Eukaryotic genome spatial folding plays a key role in genome function. Decoding the principles and dynamics of 3D genome organization depends on improving technologies to achieve higher resolution. Chromatin domains have been suggested as regulatory micro-environments, whose identification is crucial to understand the genome architecture. We report here that our recently developed method, Hi-TrAC, which specializes in detecting chromatin loops among genomic accessible regulatory regions, allows us to examine active domains with limited sequencing depths at a high resolution.  Hi-TrAC can detect active sub-TADs with a median size of 100kb, most of which harbor one or two cell specifically expressed genes and regulatory elements such as super-enhancers organized into nested interaction domains. These active sub-TADs are characterized by highly enriched signals of histone mark H3K4me1 and chromatin-binding proteins, including Cohesin complex. We show that knocking down core subunit of the Cohesin complex using shRNAs in human cells or decreasing the H3K4me1 modification by deleting the H3K4 methyltransferase Mll4 gene in mouse Th17 cells disrupted the sub-TADs structure. In summary, Hi-TrAC serves as a compatible and highly responsive approach to studying dynamic changes of active sub-TADs, allowing us more explicit insights into delicate genome structures and functions.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Hi-TrAC, ChIP-seq and RNA-seq were used to study the chromatin interaction changes  in wild type and Mll4  knockout mice Th17 cells. Hi-TrAC and RNA-seq were used to study the chromatin interaction changes in active sub-TADs boundary deletion cells and CTCF-AID cells.

first: Shuai

first: Kairong

last: Cui

first: Qingsong

last: Tang

first: Keji

last: Zhao


title: Methylation profiling in human primary leukemia samples and cell lines

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

institute: St. Jude Children's Research Hospital

type: Methylation profiling by high throughput sequencing

summary: Structural variants (SVs) involving enhancer hijacking can disrupt chromatin topologies to cause oncogene activation in cancer genomes, yet the molecular determinants for the transcriptional output of enhancer hijacking remain largely unknown. We developed a multimodal approach to integrate genome sequencing, chromosome conformation, and sequence-based deep learning for quantitative analysis of transcriptional effects and structural reorganization imposed by SVs in leukemic genomes. We identified candidate pathogenic SVs including recurrent t(5;14) translocations that cause the hijacking of BCL11B enhancers for oncogenic activation of TLX3-dependent transcriptional programs. By engineering patient-associated t(5;14) in isogenic leukemia cells, we uncovered an uncharacterized mechanism whereby DNA methylation serves as an epigenetic barrier to enhancer hijacking and loss of epigenetic barrier is a molecular determinant for the transcriptional output of pathogenic SVs. Hence, leveraging the epigenetic barriers of SV-mediated oncogenic programs may provide new opportunities to reprogram gene regulation as epigenetic therapies in human disease.

overall_design: RRBS was performed to determine methylation level at CpG islands and CpG-rich promoters in two human leukemia samples and two human leukemia cell lines

first: Giovanni

last: Botten

first: Yuannyu

last: Zhang


title: 4C-seq analysis of chromatin interactions at the TLX3 and BCL11B loci in human primary leukemia samples and cell lines

overall_design: 4C-seq was performed to determine the interactions using the TLX3 and BCL11B promoters as viewpoints in two leukemia patients and two human leukemia cell lines


title: N6-Adenosine methylation regulates the translation of insulin mRNA

city: Ann Arbor

first: Monica

last: Dus

state: MI

address: 1150 N. University Ave.

department: Department of Molecular, Cellular and Developmental Biology

institute: The University of Michigan

summary: Relatively little is known about the first step of insulin synthesis: the translation of the mRNA. Here we show that the translation of D. melanogaster insulin 2 mRNA (dilp2) is controlled by methylation of N6-adenosine (m6A) in the 3’ UTR. Mutations in the m6A writer Mettl3 and methylated residues in the dilp2 3’UTR decreased the levels of dilp2 mRNA associated with the polysomes and the total amount of dilp2 protein produced. This resulted in aberrant energy homeostasis and diabetic-like phenotypes consistent with the specific function of dilp2 in adult metabolism. Conserved m6A signatures were also identified in the 3’ UTRs of vertebrate insulin mRNAs. These data identify m6A as a key regulator of insulin protein synthesis and energy homeostasis in metazoans with important implications for diabetes and metabolic disease.

overall_design: Identification of N-6 methyladenosine in mRNAs from heads of Drosophila melanogaster by m6A-CLIP.

first: Daniel

last: Wilinski


title: ATAC-seq analysis of wild-type Jurkat, SV engineered Jurkat, DND-41 and LOUCY leukemia cell lines

overall_design: ATAC-seq was performed to determine the chromatin accessibility in human leukemia cell lines


title: Hi-C analysis of 3D chromatin structure of leukemia cells

overall_design: We performed Hi-C experiments for leukemia cells from UT424 with TLX3 translocation


title: SHP2 Blockade Sensitizes Metastatic Triple Negative Breast Cancer to PI3K Inhibition

city: Basel

first: Mohamed

last: Bentires-Alj

address: Hebelstrasse 20

department: DBM

country: Switzerland

institute: University Hospital Basel

summary: Next Generation Sequencing was applied to investigate the effects of PI3K inhibition and/or SHP2 inhibition on the mouse mammary carcinoma 4T1.

overall_design: RNA-Seq in 4 different treatment conditions to investigate PI3K/SHP2 signalling role in primary tumors.

first: Atul

last: Sethi


title: RNA-seq analysis of transcriptomic changes in human primary leukemia samples and cell lines

overall_design: RNA-seq was performed to determine the transcriptomic changes in human primary leukemia samples and cell lines


title: Effect of MYC expression on mouse PyMT tumor

status: Public on Apr 24 2023

city: New York

first: Xian

address: 417 E 68th St

institute: MSKCC

summary: S100a8-cre driven expression of Rosa26-LSL-MYC in mouse PyMT cancer cells

overall_design: Bulk tumor tissues from control-PyMT and S100a8-creRosa26-LSL-MYCPyMT (MYC-PyMT) mice were collected and homogenized in liquid nitrogen for TRIZOL RNA extraction and RNAseq

first: Ming

middle: O

last: Li


title: Gene expression profile at single nucleus level for tumor associated macrophage (TAMs) nuclei sorted from tumor of control-PyMT and S100a8-creRosa26-LSL-MYCPyMT (MYC-PyMT) mice treated with low protein diet

summary: Nuclei of TAMs were sorted for single nucleus RNA sequencing from control-PyMT and MYC-PyMT tumor treated with low protein diet, and compare their transcriptome differences.

overall_design: 7-week-old Control-PyMT and MYC-PyMT mice were lethally irradiated and reconstituted with 3 million total bone marrow cells from Fcgr1-cre-Rosa26LSL-H2B-mCherry/+ mice as described previously. Two weeks later, mice were switched to a low protein diet. 6-week post dietary switch, mice were sacrificed, and tumors were collected for immune cell isolation. TAMs were sorted based on their cell surface markers (DAPI-CD45+SiglecF-Ly6G-B220-Ly6C-F4/80+Vcam+). Nuclei were isolated with an EZ PREP kit (Sigma, Cat #NUC-101) according to the manufacturer's protocol, and intact nuclei without cell contamination were further sorted by fluorescent markers (mCherry+CD11b-SYTO9+) for downstream processes.


title: Effect of low protein diet on parenchymal tumor associated macrophages (TAMs) and stromal mammary tissue macrophages (MTMs) in control-PyMT and  MYC overexpressing PyMT ( S100a8-creRosa26-LSL-MYCPyMT ) tumor

summary: To study the low protein diet and cancer genetic effect on the macrophage in tumor, we treated the control-PyMT and S100a8-creRosa26-LSL-MYCPyMT (MYC-PyMT) mice reconstituted with wt bone marrow with low protein diet for 6 weeks

overall_design: Compare the gene expression between TAMs and MTMs isolated by FACS from tumor of control-PyMT and MYC-PyMT mice treated with low protein diet


title: A global survey of phytoviral RNA 3' uridylation identifies extreme variations and virus-specific patterns

city: Strasbourg

first: Dominique

last: Gagliardi

address: 12, rue du General Zimmer

department: IBMP

country: France

institute: CNRS

sample_organism:
Spinacia oleracea
Arabidopsis thaliana
Nicotiana benthamiana
Vitis vinifera
Chenopodium quinoa
Nicotiana obtusifolia

overall_design: Refer to individual Series


title: BACE1 regulates expression of Clusterin in astrocytes for enhancing clearance of β-amyloid peptides

city: Farmington

first: John

last: Zhou

state: CT

address: 263 Farmington Avenue, E4030

institute: University of Connecticut Health Center

summary: BACE1 role in reactive astrocytes are unknown. We used single cell RNA sequencing (scRNA-seq) to analyze reactive astrocytes in mice with and without germline Bace1.  We also examine reactive astrocytes in the case of adult Bace1 conditional knockout on a 5xFAD  Alzheimer's disease mouse model.

overall_design: Astrocytes of the Bace1-/-, Bace1+/+, 5xFAD; Bace1fl/fl, and 5xFAD; Bace1fl/fl; UBC-creER mice were isolated from brains by magnetically-activated cell sorting (MACS) according to the presence or absence of ACSA2+ and resulting cells were analyzed using scRNAseq.  3 samples of each Bace1-/- and Bace1+/+ were submitted, while 1 sample containing 3 pooled brains each from 5xFAD; Bace1fl/fl and 5xFAD; Bace1fl/fl; UBC-creER were analyzed.

first: Zhou

last: John


title: Lung microhemorrhage drives macrophage activation and oxidative/inflammatory damage in α-1 antitrypsin deficiency

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

summary: Background. Animal models of elastase intratracheal instillation have shown that elastase, unopposed by α-1 antitrypsin (AAT), can induce alveolar hemorrhage with ensuing macrophage inflammation and lung damage. Aim. To identify markers of alveolar hemorrhage and damage using bronchoalveolar lavage (BAL) samples and lung tissue explants from AAT deficient (AATD) subjects. Methods. BAL samples (17 patients, 15 controls) were evaluated for free heme and iron concentrations. Alveolar macrophage (AlvMac) activation patterns were assessed by RNA sequencing and validated in vitro using heme-stimulated monocyte-derived macrophages (MDM). Lung explants (7 patients, 4 controls) were evaluated for iron sequestration patterns, by Prussian blue stain and ferritin immunohistochemistry, and for ferritin iron imaging and elemental analysis by electron microscopy (EM). Tissue oxidative damage was assessed by 8-OHdG immunohistochemistry. Results. BAL showed significantly elevated free heme and iron concentrations at lobar level. BAL macrophage RNA sequencing showed innate proinflammatory activation, consistent with free heme activation. AATD tissue alveolar and interstitial macrophages showed elevated iron and ferritin accumulation in large lysosomes packed with iron oxide cores with degraded ferritin protein cages. AATD explants showed massive oxidative DNA damage in lung epithelial cells and macrophages. Conclusions. Identification of BAL and tissue markers of alveolar hemorrhage, together with the molecular and cellular evidence of macrophage innate pro-inflammatory activation and oxidative damage, consistent with free heme stimulation, provides ex vivo evidence for the pathogenetic role of elastase-induced alveolar hemorrhage AATD emphysema as shown in animal studies.

overall_design: Alveolar Macrophages were obtained by bronchoalveolar lavage from 6 patients affected by Alpha-1 Antitrypsin deficiency and 6 helthy controls. Levels of unopposed Neutrophil elastase, Alpha-1 Antitrypsin, free Heme and Iron were measure in bronchoalveolar lavage fluid. Macrophages were isolated from lavage fluid by plastic adherence, RNA was extracted and sequenced for DGE and SGEA. Alveolar macrophage-like monocyte-derive macrophages were exposed to Heme in vitro to validate the expression of of BAL alveolar macrophage innate immune response genes expression identified by DGE and GSEA in Alph-1 Antitrypsin deficiency affected subjectswere stimulat in vitro.

first: Cesare

last: Saltini

first: Naweed

last: Mohammad

first: Yan

last: Xin

first: Rodolfo

last: Alvarado

first: Andew

last: Ghio

first: Craig

last: Moneypenny

first: Dongtaqo

last: Fu

first: Tammy

last: Flagg

first: Ivan

last: Arisi

first: Kristiann

last: Fredenburg

first: Yang

first: Jorge

last: Lascano

first: Mark

middle: L

last: Brantly


title: Effect of subcutaneous tocilizumab on gene expression of neutrophils in fibromyalgia patients

city: Taichung

first: Kuo Tung

last: Tang

address: No. 1650, Sec. 4, Taiwan Blvd.

department: Division of Allergy, Immunology and Rheumatology

country: Taiwan

institute: Taichung Veterans General Hospital

summary:
Differentially expressed genes were identified in neutrophils of 5 primary FM patients, when compared with controls.
Differentially expressed genes were also identified in neutrophils of 2 primary FM patients at baseline and 12 weeks after tocilizumab treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for blood neutrophils.

first: Kuo

first: Tsai

last: Liao


title: Gene expression profiling of whole blood and peripheral neutrophils from asthma.

city: Taipei

first: Yungling

middle: Leo

last: Lee

address: Sec. 2, Academia Rd.

department: Institute of Biomedical Sciences

institute: Academia Sinica

summary: As part of the Taiwanese Consortium of Childhood Asthma Study (TCCAS), a new prospective sub-study was conducted to investigate the effectiveness of inhaled corticosteroids (ICS) treatment. Patients were categorized as either responders (R) or non-responders (NR), based on the improvement of their pulmonary function after ICS treatment. We analyzed the transcriptomes of asthma with ICS non-responsers and responders.

overall_design: Analysis of gene expression obtained from human whole blood and peripheral neutrophils comparing ICS non-responders and responders in asthma.

first: Ching-Hui

last: Tsai


title: Identification of bivalent genes in CD14+ Monocytes

city: Rouen

first: Sylvain

last: Fraineau

address: 22 Gambetta Boulevard

department: UMR Inserm U1096

institute: Université de Rouen Normandie

summary: Identification of bivalent genes, marked with both H3K4me3 and H3K27me3, in CD14+ Monocytes. Used previously published data sets for histone marks GSM1003536 and GSM1003564.

relation:
Reanalysis of: GSM1003536
Reanalysis of: GSM1003564

overall_design: We used previously published ChIP-Seq data from ENCODE in CD14+ cells for histone markd H3K4me3 (GSM1003536) and H3K27me3 (GSM1003564) from the data series GSE29611 and called peaks with MACS2 with default parameters with the exception of H3K27me3 with the additional --broad parameter. Intersecting peaks were identified with the bedtools intersect tool.  Processed data file generated for GSM1003536 and GSM1003564:  CD14+_H3K27me3_H4k4me3_Intersection.bed.gz.

first: Alphonse

last: Chu


title: Direct enzymatic sequencing of 5-methylcytosine at single-base resolution [4]

city: Philadelphia

first: Rahul

middle: M.

last: Kohli

state: Pennsylvania

address: 3610 Hamilton Walk, 502B Johnson Pavilion

department: Department of Medicine

institute: University of Pennsylvania

summary: 5-methylcytosine (5mC) is the most important DNA modification in mammalian genomes as a lineage-defining mark dynamically altered in development and disease. The ideal method for 5mC localization would be both non-destructive of DNA and direct, without requiring inference based on detection of unmodified cytosines. Here, we present Direct Methylation Sequencing (DM-Seq), a bisulfite-free method for profiling 5mC at single-base resolution, using nanogram quantities of input DNA. DM-Seq employs two key DNA modifying enzymes: a neomorphic DNA methyltransferase engineered to generate the unnatural base 5-carboxymethylcytosine, and a DNA deaminase capable of precise discrimination between cytosine modification states. Coupling these activities requires a novel adapter strategy employing 5-propynylcytosine, ultimately resulting in the accurate and direct detection of only 5mC via a C-to-T transition in sequencing. In performing comparisons to DM-Seq, we uncover a systematic bias in 5mC  detection seen with the hybrid enzymatic-chemical TAPS sequencing approach. Furthermore, by applying DM-Seq to a human glioblastoma tumor, we demonstrate that DM-Seq, unlike bisulfite-sequencing, detects 5mC at prognostically-important CpGs, without confounding by 5-hydroxymethylcytosine. DM-Seq thus leverages unnatural DNA modifications to create the first method for direct 5mC profiling entirely using enzymes rather than chemical reagents.

sample_organism:
Cloning vector pUC19
Escherichia phage T4
Escherichia phage Lambda

overall_design: DNA (no deamination), BS, DM, TAPS, or TAPS-beta sequencing experiments

first: Tong

last: Wang

first: Hao

last: Wu


title: Direct enzymatic sequencing of 5-methylcytosine at single-base resolution

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

sample_organism:
Homo sapiens
Cloning vector pUC19
Escherichia phage T4
Escherichia phage Lambda


title: Direct enzymatic sequencing of 5-methylcytosine at single-base resolution [1]


title: Direct enzymatic sequencing of 5-methylcytosine at single-base resolution [3]

platform_organism:
Cloning vector pUC19
Escherichia phage T4
Escherichia phage Lambda


title: mRNA expression data from RalGAPβ-deficient human pancreatic ductal adenocarcinoma cells (MIA PaCa-2), MIA PaCa-2 parental cells, and MIA PaCa-2 control cells

city: Tianjin

first: Mingxin

last: Cao

address: NO.22, Qixiangtai Road

institute: Tianjin medical university

summary:
Pancreatic ductal adenocarcinoma, caused by activating mutation in K-Ras, is an aggressive malignancy due to its early invasion and matastasis. Ral GTPases, negatively regulated by RalGAP, are activated downstream of Ras and play a crucial role in development and progression of pancreatic ductal adenocarcinoma. However, the underlying mechanisms remain unclear.
We used microarrays to detail the global programme of gene expression underlying the human pancreatic ductal adenocarcinoma cell line, MIA PaCa-2 with RalGAPβ deficiency or not, and identified distinct classes of Ral activation-related mRNA.

overall_design: We used two clonal RalGAPβ-deficient human pancreatic ductal adenocarcinoma cell lines of MIA PaCa-2 (KO1 and KO2) established by the CRISPR-Cas9 system, and each was compared with parental cells (WT) and control cells (Con) using microarray analysis. WT refers to parental MIA PaCa-2 cells without any treatments. Con refers to a clonal MIA PaCa-2 cell line obtained through the same RalGAPβ CRISPR-Cas9 treatment but also no indel mutation in the RalGAPβ genomic region. These cells were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Hisanori

last: Horiuchi


title: RNA-seq data of human enteroid- Giardia intestinalis infection

city: Uppsala

first: Staffan

middle: Gunnar

last: Svärd

address: Husargatan 3

department: Department of Cell and Molecular Biology

country: Sweden

institute: Uppsala University

summary:
To investigate the transcriptional responses of intestinal epithelial cells and Giardia intestinalis, assemblage A isolate WB-C6, trophozoites during infection, we infected human enteroids with preconditioned trophozoites for 1h and 3h.
Giardia intestinalis trophozoites were preconditioned before the infection with either DMEM/F-12 or DMEM/F-12 supplemented with 10% FBS to modify the trophozoites’ fitness.

sample_organism:
Homo sapiens
Giardia duodenalis assemblage A

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human enteroids and Giardia intestinalis trophozoites.

first: Jana

last: Grüttner


title: Direct enzymatic sequencing of 5-methylcytosine at single-base resolution [2]


title: Cell-type specific transcriptomics of the the dlPFC in females with MDD [single-nucleus RNA-seq]

city: Montreal

first: Gustavo

last: Turecki

state: Quebec

address: 6875 Boulevard LaSalle

department: Psychiatry

country: Canada

institute: McGill University

summary: We performed high-throughput snRNA-seq using the 10X Genomics Chromium platform on archived post-mortem dorsolateral prefrontal cortex (BA9) tissue in female MDD subjects who died by suicide and in female control subjects to identify cell-type specific differentially expressed genes. We further re-processed in parallel a previously generated snRNA-seq dataset in males with or without MDD to generate comparable differential expression results and compare the cell-type specific MDD-associated differences between the sexes.

overall_design: 10X Genomics Chromium snRNA-seq was performed on nuclei extracted from BA9 of the post-mortem brain tissue of 18 control subjects and 20 MDD cases who died by suicide. All subjects were female. We performed unsupervised clustering and pseudobulk differential gene expression was performed between cases and controls for each cluster and each broad brain cell type. The library preparation was performed with the Chromium Single Cell 3’ Reagent Kits v3.1 or v2. Paired-end sequencing was performed on the Illumina NovaSeq 6000 or with BGI DNBSeq. FASTQ files were produced with Cellranger v3.1.0 mkfastq. Alignments and gene counts were generated with Cellranger v5.1.0 count. Additionally, FASTQ files previously produced from a male cohort (GSE144136) were realigned and recounted, and raw count data from both sexes, which were input into differential expression analysis, along with the cell type annotations are included in the counts matrix provided.


title: Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy

city: Brisbane

first: Katia

last: Nones

state: QLD

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer Medical Institute

summary: Oesophageal adenocarcinoma (OAC) is a poor prognosis cancer and the molecular features underpinning response to treatment remain unclear. We investigated whole genome, and where possible transcriptomic and methylation data from 115 OAC patients mostly from the DOCTOR phase II clinical trial (ANZCTR-ACTRN12609000665235). We identified genomic features associated with poorer overall survival, such as the APOBEC mutational and RS3-like rearrangement signatures. We also showed that positron emission tomography non-responders have more sub-clonal genomic copy number alterations. Transcriptomic analysis categorised patients into four immune clusters correlated with survival. The immune suppressed cluster was associated with worse survival, enriched with myeloid-derived cells, and an epithelial-mesenchymal transition signature. The immune hot cluster was associated with better survival, enriched with lymphocytes, myeloid-derived cells, and an immune signature including CCL5, CD8A, and NKG7. The immune clusters highlight patients who may respond to immunotherapy and thus may guide future clinical trials.

overall_design: This study used 34 public 450K methylation arrays (GSE72874) and 38 new EPIC arrays in this submission. Normalized data of all 72 samples provided plus raw idat for the new 38 EPIC arrays.

first: Marjan

last: Naeini

first: Felicity

last: Newell

first: Lauren

last: Aoude

first: Vanessa

last: Bonazzi

first: Kalpana

last: Patel

first: Guy

last: Lampe

first: Lambros

last: Koufariotis

last: Lakis

first: Venkateswar

last: Addala

first: Olga

last: Kondrashova

first: Rebecca

last: Johnston

first: Sowmya

last: Sharma

first: Sandra

last: Brosda

first: Oliver

last: Holmes

first: Conrad

last: Leonard

first: Scott

last: Wood

first: Qinying

last: Xu

first: Janine

last: Thomas

first: Euan

last: Walpole

first: G

last: Mai

first: Stephen

middle: P

last: Ackland

first: Jarad

last: Martin

first: Matthew

last: Burge

first: Robert

last: Finch

first: Christos

last: Karapetis

first: Jenny

last: Shannon

first: Louise

last: Nott

last: Bohmer

first: Kate

last: Wilson

first: Elizabeth

last: Barnes

first: John

last: Zalcberg

first: B

last: Smithers

last: Simes

first: Timothy

last: Price

first: Val

last: Gebski

first: David

middle: I

last: Watson

middle: V

last: Pearson

first: Andrew

last: Barbour

first: Nicola


title: Epigenome analysis of NNMT KO versus WT cells

first: Mohamed

last: Bentires-Alj

type: Methylation profiling by genome tiling array

summary: Genome wide methylation profiling of SUM159PT NNMT WT, KOs and KOd cells. The Illumina human Infinium Methylation EPIC BeadChip was used to measure global DNA methylation on CpG from 850 k probes. Samples include three experimental replicates from each cell line.

overall_design: Bisulphite-converted DNA from 9 samles were hybridized to the 850 k Human Infinium Methylation EPIC BeadChip.

first: Milica

last: Vulin


title: The gene regulatory landscape of kidney organoid differentiation revealed by single nucleus multiomic analyses

city: St. Louis

first: Yasuhiro

last: Yoshimura

state: MO

address: 660. S Euclid Ave., CB 8118

department: Medicine / Nephrology

institute: Washington University in St. Louis


title: Integration of a multi-omics stem cell differentiation dataset using a dynamical model

city: Leiden

first: Stefan

last: Semrau

address: Einsteinweg 55

department: Physics

country: Netherlands

institute: Leiden University

summary: Stem cell differentiation is a highly dynamic process involving pervasive changes in gene expression. The large majority of existing studies has characterized differentiation at the level of individual molecular profiles, such as the transcriptome or the proteome. To obtain a more comprehensive view, we measured protein, mRNA and microRNA abundance during retinoic acid-driven differentiation of mouse embryonic stem cells. We found that mRNA and protein abundance are typically only weakly correlated across time. To understand this finding, we developed a hierarchical dynamical model that allowed us to integrate all data sets. This model was able to explain mRNA-protein discordance for most genes and identified instances of potential microRNA-mediated regulation. Overexpression or depletion of microRNAs identified by the model, followed by RNA sequencing and protein quantification, were used to follow up on the predictions of the model. Overall, our study shows how multi-omics integration by a dynamical model could be used to nominate candidate regulators.

overall_design: mRNA profiles of mouse embryonic stem cells (E14) during retinoic acid mediated differentiation. Samples were collected at 0h (duplicate), 6h, 24h, 36h, 48h, 72h and 96h (duplicate). Additionally, 2 samples were collected at 96h after sorting cells into extra-embryonic endoderm-like (XEN) and ectoderm-like (ECT) fractions.

first: Patrick

last: van den Berg

first: Nikolai

last: Slavov


title: Long non-coding RNA LIPTER effect on human iPSC-CMs and mouse heart

city: Indianapolis

first: Lei

last: Yang

state: Indiana

address: 1044 W Walnut Street, R4 272

department: Department of Pediatrics

institute: Indiana University School of Medicine

overall_design: Analysis of human lncRNA LIPTER effect on human WT or LIPTER KO iPSC-CMs.  which were cultured in high glucose DMEM for 40 days. To analyse the LIPTER effect in vivo, WT and LIPTER transgenic mice were fed with high fat diet for 7 months. And then heart RNA profile were analyzed by RNA-seq. Results provide the LIPTER functiions on both human iPSC-CMs and mouse heart.

last: Han


title: RNAseq of dauer-forming C. elegans L2d in daf-2 and daf-2;daf-42

status: Public on Apr 23 2023

city: Seoul

first: Daisy

middle: Sunghee

last: Lim

address: 1 Gwanak-ro, Gwanak-gu

institute: Seoul National University

summary: Under adverse environmental conditions, nematodes arrest into dauer, an alternative developmental stage for diapause. Dauers endure unfavorable environment and interact with host animals to access favorable environments, thus playing a critical role in the survival of both free-living and parasitic nematodes. Here, we discovered that in Caenorhabditis elegans, daf-42 is essential for development into dauer stage, as the null mutant shows lethal phenotype during dauer entry. To examine the transcriptional changes accompanied by the absence of DAF-42 during dauer entry, we performed RNA-sequencing on daf-2 and daf-2; daf-42 worms at 52 hours after egg laying (HAE) and 60 HAE, the time at which 0% and about 40% of daf-2; daf-42 mutants form dead dauer at 25 degrees Celcius, respectively. daf-2 control worms develop into dauer stage after 60 HAE, and half of its population develop into dauer by 72 HAE, when raised at 25 degrees Celcius.

overall_design: daf-2(e1370) and daf-2(e1370);daf-42(ys54) C.elegans at late L2d stages, at 52 and 60 hours after eggs were laid, raised at 25°C

first: Jun

last: Kim

first: Junho

last: Lee


title: Pro-inflammatory polarization and colorectal cancer modulate alternative and intronic polyadenylation in primary human macrophages

city: Porto

first: Joana

last: Wilton

address: Rua Alfredo Allen, 208

department: IBMC

country: Portugal

summary: Macrophages are essential cells of the immune system that alter their inflammatory profile depending on their microenvironment. Alternative polyadenylation in the 3'UTR (3'UTR-APA) and intronic polyadenylation (IPA) are mechanisms that modulate gene expression, in particular in cancer and activated immune cells. Yet, how polarization and colorectal cancer (CRC) cells microenvironment affect 3'UTR-APA and IPA in primary human macrophages remains unknown. Here, primary human monocytes were isolated from healthy donors, differentiated and polarized into a pro-inflammatory state and ChrRNA-Seq and 3'RNA-Seq were performed to quantify gene expression and characterize new 3’UTR-APA and IPA mRNA isoforms. Our results show that polarization of human macrophages from naïve to a pro-inflammatory state causes a marked increase both in proximal polyA site selection in the 3'UTR and in IPA events, in genes relevant for macrophage functions. Additionally, we found a negative correlation between differential gene expression and IPA during pro-inflammatory polarization of primary human macrophages. As macrophages are abundant immune cells in the CRC microenvironment that either promote or abrogate cancer progression, we investigated how indirect exposure to CRC cells affects macrophage gene expression and 3'UTR-APA and IPA mRNA events. Co-culture with CRC cells alters the inflammatory phenotype of macrophages, increases the expression of pro-tumoral genes and induce 3’UTR-APA alterations. Notably, some of these gene expression differences were also found in tumour-associated macrophages of CRC patients, indicating that they are physiological relevant. Upon macrophage pro-inflammatory polarization SRSF12 is the pre-mRNA processing gene that is most upregulated. After SRSF12 knockdown in M1 macrophages there is a global downregulation of gene expression, in particular in genes involved in gene expression regulation and in immune responses. Our results reveal new 3’UTR-APA and IPA mRNA isoforms produced during pro-inflammatory polarization of primary human macrophages and CRC co-culture that may be used in the future as diagnostic or therapeutic tools.

overall_design: After treating primary human macrophages for 24 hours with pro-inflammatory stimuli - LPS + IFN-gamma - and 24 hours of exposure to CRC cells, we performed chromatin-bound RNA-Seq and 3'RNA-Seq. In unpolarised macrophages (M0), we performed 3'RNA-Seq

first: Michael

last: Tellier

first: Takayuki

last: Nojima

first: Isabel

last: Pereira-Castro

first: Jaime

last: Freitas

first: Angela

last: Costa

first: Shona

last: Murpy

first: Maria

last: Oliveira

first: Nicholas

last: Proudfoot

first: Alexandra

last: Moreira

first: Filipa

last: Lopes de Mendonça


title: Gene Expression by RNA-Seq of Peripheral Blood Monocyte with the EZH2 inhibitor GSK-343

first: Sylvain

last: Fraineau

summary: Epigenetic regulation of histone H3K27 methylation has recently emerged as a key step during alternative M2-like macrophage (M2) polarization, essential for cardiac repair after Myocardial Infarction (MI). We hypothesized that EZH2, responsible for H3K27 methylation, could act as an epigenetic checkpoint regulator during this process. We demonstrate for the first time inactivation of EZH2 activity, linked to ectopic cytoplasmic localization of the epigenetic enzyme, during monocyte differentiation in vitro as well as in M2 macrophages in vivo during post-MI cardiac inflammation. Moreover, we show that pharmacological EZH2 inhibition, with GSK-343, resolves H3K27 methylation at the promoter of bivalent genes, thus enhancing their expression to promote human monocyte repair functions. In line with this protective effect, GSK-343 treatment accelerated cardiac inflammatory resolution preventing infarct expansion and subsequent cardiac dysfunction after MI in vivo. In conclusion, our study reveals that epigenetic modulation of cardiac-infiltrating immune cells may hold promise to limit adverse cardiac remodeling after MI.

overall_design: Isolated peripheral blood monocytes cells (negative magnetic selection) were treated with DMSO (Vehicle Control) or 5 µM of GSK-343, an EZH2 inhibitor, and analyzed by RNA-Seq to identify differentially expressed genes.

first: Alphonse

last: Chu

first: Marjorie

last: Brand

first: Julie

last: Rondeaux


title: Bulk ATAC-seq of RPTEC with HNF1B CRISPRi

first: Yasuhiro

last: Yoshimura

summary: We performed bulk ATAC-seq of primary PRTEC after CRISPRi targeting HNF1B promoter and enhancers.

overall_design: Profiling open chromatin regions of the genome by high throughput sequencing

first: Yoshiharu

last: Muto

first: Benjamin

middle: D

last: Humphreys


title: ChIP-seq on INTS11-degron cells

city: Beijing

first: Hua

last: Wang

address: 38 Xueyuan Rd

institute: Peking University

summary: Here, we showed that acute lost H3K4me3 induces rapid reduction in global transcription with progressively increase in magnitude over the time-course cooccurrence with lost all H3K4 methylations. To further determine the effects of COMPASS subunits degradation on H3K4 methylations occupancies genome-wide, we performed time-course spike-in chromatin immunoprecipitation and sequencing (ChIP-seq, also known as ChIP-Rx) analysis in both degron systems.

overall_design: INTS11-FKBP dTAG degron tag into the 3’ end of both alleles of endogenous Ints11 locus of the E14 mESC cell line.


title: TT-seq on INTS11-degron cells

summary: Here, we use elongation velocity analysis showed that acute loss INTS11 caused a general transcriptome-wide attenuation of elongation velocity in cells.

overall_design: In order to examine and monitor the effects of INTS11 on newly synthesized RNA rates genome-wide from actively transcribing RNAPII, we performed the modified transient transcriptome sequencing (TTchem-seq) with spike-in strategy on INTS11-FKBP dTAG degron cells.


title: SLAM-seq on INTS11-degron cells

summary: Here, we showed that acute lost H3K4me3 induces rapid reduction in global transcription with progressively increase in magnitude over the time-course cooccurrence with lost all H3K4 methylations,

overall_design: To define the primary effects of rapid INTS11 removal on transcription, we measured the synthesis of newly transcribed RNAs using a Thiol(SH)-linked alkylation for the metabolic sequencing of RNA (SLAM-seq) with a time-course in the INTS11-FKBP dTAG degron cells.


title: Single-cell RNA sequencing reveals the local cell landscape in mouse epididymal initial segment during aging

city: Guangzhou

first: Yun

last: Xie

state: China

address: No. 58 Zhongshan 2nd Road, Yuexiu District, 0080, China.

institute: sun yat-sen university

summary:
Introduction: Morphological and functional alternations of the aging reproductive organs result in decreased male fertility. We previously reported that the epididymal initial segment underwent remarkable histological changes and chronic immune-activation in mouse during aging. However, the local cell landscape in the aged epididymal initial segment are poorly understood.
Objectives: We aimed to characterize the aging-associated cellular and molecular features of mouse epididymal initial segment.

overall_design: Single-cell RNA sequencing analysis was conducted on the epididymal IS of young (3-month-old) and old (21-month-old) C57BL/6 mice.

first: Jintao

last: Zhuang

first: Xiangping

last: Li

first: Jiahui

last: Yao


title: Complex regulation of Eomes levels mediated through distinct functional features of the Meteor long non-coding RNA locus (3' RNA-Seq)

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

country: Israel

institute: Weizmann Institute of Science

summary: Long non-coding RNAs (lncRNAs) are diverse transcription products emanating from thousands of loci in mammalian genomes, implicated in a wide array of cellular processes including transcriptional regulation, differentiation, cellular reprogramming, and many others. While a large majority of functional lncRNAs have been proposed to act in cis to their sites of transcription, an in-depth understanding of the functional features within such lncRNA loci, as well as their mechanisms of action, is currently lacking. Further insights are hindered by the heavy dependencies of observed phenotypes on the perturbation techniques employed. Here, we study Meteor, a lncRNA transcribed nearby the gene encoding for Eomes, a pleiotropic transcription factor with highly regulated spatiotemporal expression patterns throughout early development and in adult tissues. Using a wide array of perturbation techniques, we show that transcription elongation through the Meteor locus is required for Eomes activation in naive mouse embryonic stem cells (mESCs), with Meteor repression linked to a reduction in cells potentiated to differentiate to the mesoderm lineage. We further demonstrate that a distinct functional feature of the locus – namely, the underlying DNA element – is required for suppressing Eomes expression following neuronal differentiation of mESCs. Our results demonstrate the complex regulation that can be conferred by a single lncRNA locus, and emphasize the importance of careful selection of perturbation techniques for the study of lncRNA loci.

overall_design: 3' RNA-seq of day 4 EBs of various genotypes (WT, Meteor promoter KO, Meteor promoter inversion) or perturbations (Ctrl, Meteor CRISPR/Cas9 KD).

first: Noa

last: Gil


title: Complex regulation of Eomes levels mediated through distinct functional features of the Meteor long non-coding RNA locus (4C)

overall_design: 4C of the Meteor and Eomes loci in WT mESCs, NPCs, and neurons, as well in mESCs of various genotypes (WT, Meteor full-body KO, Rz KD, promoter KO, promoter inversion) or perturbations (Ctrl, Meteor CRISPR/Cas9 KD).


title: ChIP-seq analysis of H3K27ac, TLX3 and MYB in human primary leukemia cells and cell lines

city: Memphis

first: Jian

last: Xu

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

summary: Structural variants (SVs) involving enhancer hijacking can disrupt chromatin topologies to cause oncogene activation in cancer genomes, yet the molecular determinants for the transcriptional output of enhancer hijacking remain largely unknown. We developed a multimodal approach to integrate genome sequencing, chromosome conformation, and sequence-based deep learning for quantitative analysis of transcriptional effects and structural reorganization imposed by SVs in leukemic genomes. We identified candidate pathogenic SVs including recurrent t(5;14) translocations that cause the hijacking of BCL11B enhancers for oncogenic activation of TLX3-dependent transcriptional programs. By engineering patient-associated t(5;14) in isogenic leukemia cells, we uncovered an uncharacterized mechanism whereby DNA methylation serves as an epigenetic barrier to enhancer hijacking and loss of epigenetic barrier is a molecular determinant for the transcriptional output of pathogenic SVs. Hence, leveraging the epigenetic barriers of SV-mediated oncogenic programs may provide new opportunities to reprogram gene regulation as epigenetic therapies in human disease.

overall_design: ChIP-seq was performed to determine the chromatin occupancy of H3K27ac, TLX3 and MYB in leukemia patients and human leukemia cell lines

first: Giovanni

last: Botten

first: Yuannyu

last: Zhang


title: Complex regulation of Eomes levels mediated through distinct functional features of the Meteor long non-coding RNA locus (CUT&RUN)

overall_design: Cut&Run of H3K4me3 in WT NPCs, and of H3K27me3 in Meteor WT and promoter KO/inversion mESCs


title: Complex regulation of Eomes levels mediated through distinct functional features of the Meteor long non-coding RNA locus (ChIP-Seq)

overall_design: ChIP-seq of H3K27ac in WT NPCs, and of CTCF in Meteor WT and full-body KO and Ctrl and CRISPR/dCas9 KD mESCs


title: Global circadian transcript profile of mouse gastrocnemius muscle entrained by inverted feeding

city: Chongqing

first: Min-Dian

address: 30 Gaotanyan Main Street

department: Department of Cardiovascular Medicine

institute: Southwest Hospital, Army Medical University

summary: Circadian clocks in peripheral organs are entrained by feeding. Eating in the right time is crucial to maintain metabolic health, whereas eating in the wrong time increases the susceptibility to metabolic diseases. It is unknown how change of mealtime impacts circadian transcriptomes in peripheral organs and brain. Here, we presented global circadian transcript profile of mouse tissues (i.e. skeletal muscle) entrained by inverted feeding to compile an atlas for mechanistic insights into how feed-fast cycle regulates circadian biology.

overall_design:
RNA-seq of transcriptome in mouse gastrocnemius muscle collected from daytime-restricted feeding (DRF) or nighttime-restricted feeding (NRF, reference), totaling 56 samples

Submitter states: The raw data is deposited in CNGB (#CNP0001547, https://db.cngb.org/cnsa/project/page/sub018148/view/, release date 2023/01/12)

first: Mindian


title: RNA-seq analyses of autophagy-high and autophagy-low cells from human colon cancer organoids

city: Chuo-ku

first: Hirokazu

last: Ohata

state: Tokyo

address: Tsukiji 5-1-1

institute: National Cancer Center Research Institute

summary: We isolated the human colon cancer cells expressing high leveles and low levels of autophagic activity by introdicing an autophagic flux indicator in organoids and performed RNA-seq analyses.

overall_design: Expression profiles of autophagic activity-high and -low cells from human colon cancer organoids


title: Base-editor-mediated multiplexed inactivation of DNA methyltransferases reveals essential roles of miRNAs in mouse gastrulation

first: Jiansen

last: Lu

address: No. 5 Yiheyuan Road, Haidian District

department: Biomedical Pioneering Innovation Center (BIOPIC)

summary: Here, we first establish an easy Multi-Stop system to simultaneously inactivate genes involved in DNA methylation and demethylation in zygotes through introduction of the stop codon by hA3A-eBE-Y130F-mediated base editor (BE). While Multi-Stop-derived Dnmt-null embryos display embryonic lethal due to gastrulation failure. Moreover, mutation combinations between Tet and Dnmt families show severe embryonic lethal and Dnmt1 or Dnmt3a/3b is indispensable for mouse gastrulation. Then WGBS and RNA-seq analysis of different mutant embryos reveals genes jointly maintained by Dnmt1 and Dnmt3a/3b that are critical for gastrulation.

overall_design: We used WGBS (Whole Genome Bisulfite Sequencing) and RNA-seq to analyze the change of DNA methylation and transcription in DNMT and TET mutant embryos. WGBS data of E7.5 whole embryos from eight groups of 32 samples, including E7.5-control, E7.5-Dnmt1-KO, E7.5-Dnmt3a/3b-DKO, E7.5-Dnmt1/3a/3b-TKO, E7.5-Tet1/2/3;Dnmt1/3a/3b-6KO, E7.5-Tet1/2/3; Dnmt3a/3b-5KO, E7.5-Tet1/2/3; Dnmt1-4KO, E7.5-Tet1/2; Dnmt3a/3b-4KO. WGBS data of E6.5 and E7.5 embryo from 16 groups of 48 samples, including Ex-E6.5-control, Ex-E6.5-Dnmt1-KO, Ex-E6.5-Dnmt3a/3b-DKO, Ex-E6.5-Dnmt1/3a/3b-TKO, Em-E6.5-control, Em-E6.5-Dnmt1-KO, Em-E6.5-Dnmt3a/3b-DKO, Em-E6.5-Dnmt1/3a/3b-TKO, Ex-E7.5-control, Ex-E7.5-Dnmt1-KO, Ex-E7.5-Dnmt3a/3b-DKO, Ex-E7.5-Dnmt1/3a/3b-TKO, Em-E7.5-control, Em-E7.5-Dnmt1-KO, Em-E7.5-Dnmt3a/3b-DKO, Em-E7.5-Dnmt1/3a/3b-TKO. RNA-seq data of E6.5 and E7.5 embryo from 16 groups of 48 samples, including Ex-E6.5-control, Ex-E6.5-Dnmt1-KO, Ex-E6.5-Dnmt3a/3b-DKO, Ex-E6.5-Dnmt1/3a/3b-TKO, Em-E6.5-control, Em-E6.5-Dnmt1-KO, Em-E6.5-Dnmt3a/3b-DKO, Em-E6.5-Dnmt1/3a/3b-TKO, Ex-E7.5-control, Ex-E7.5-Dnmt1-KO, Ex-E7.5-Dnmt3a/3b-DKO, Ex-E7.5-Dnmt1/3a/3b-TKO, Em-E7.5-control, Em-E7.5-Dnmt1-KO, Em-E7.5-Dnmt3a/3b-DKO, Em-E7.5-Dnmt1/3a/3b-TKO.

first: Li

last: Jinsong

last: Qing

last: Gao


title: SnRNA-seq of pancreas revealed the dysfunction of endocrine and exocrine cells in transgenic pig with prediabetes

status: Public on Apr 22 2023

first: Huanqi

last: Peng

address: No. 2 Yuanmingyuan West Road

institute: Chinese Academy of Agricultural Sciences

summary: Diabetes poses a tremendous threat to human health. Exocrine pancreatic dysfunction is related to diabetes, but the exact mechanism is not fully understood. In this study, the high-fat and high-sucrose dietary interventions were performed on diabetes susceptible transgenic pigs (PIGinH11) and wild pigs. And the molecular mechanism of pancreatic endocrine and exocrine damage was analyzed by histopathology and single nucleus RNA sequencing.

overall_design: single-nucleus RNA sequencing  of pancreatic cells from one wild-type pig and transgenic pig.

first: Kaiyi

first: Jiakun

last: Miao

first: Yu

last: Yang

first: Shuang

first: Tianwen

last: Wu

first: Cong

last: Tao

first: Yanfang

first: Shulin


title: RNA-seq analyses of doxycycline-induced PROX1-exprressing cells in human colon cancer spheroids

summary: We performed RNA-seq analyses of the human cancer spheroids expressing PROX1 induced by doxycycline treatment.

overall_design: Expression profiles of doxycycline-induced PROX1-expressing cells in human colon cancer spheroids


title: Autophagy restricts senescence and enables microglia to engage amyloid plagues in neuroprotection

city: New York

first: Insup

last: Choi

state: NY

address: 1 Gustave L. Levy Pl

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

summary: Microglia are essential to maintain brain homeostasis, but when dysregulated, exert pathogenic functions in Alzheimer’s disease (AD). Recent evidence has implicated senescent/dystrophic microglia in the pathological process of AD. Whether microglial senescence is a cause or consequence of AD pathogenesis however is unclear. Here we report that autophagy, a lysosomal degradation pathway, restricts cellular senescence of microglia and confer neuroprotection in AD mouse model. Autophagy-deficient microglia show hallmarks of cellular senescence evidenced by reduced proliferation, increased Cdkn1a/p21Cip, dystrophy, and typical secretory phenotype. While disease-associated microglia (DAM) surrounding amyloid plaques exhibit heightened autophagy, autophagy deficient, senescent microglia (SAM) disengage from and thus fail to limit the diffusive amyloid plaques, causing enhanced tau phosphorylation and neurotoxicity in AD model. Treatment of senolytic drugs removes senescent microglia and alleviates neuropathology. Our study demonstrates a causal role of autophagy impairment in microglial senescence and neurotoxicity and suggests therapeutic potential of senolytic treatment for AD.

overall_design:
FACS-sorted microglia from 8-month-old mice (ATG7FF and ATG7FF;Cx3cr1CreER, at 6-months post tamoxifen injection) were subject to single-cell RNA sequencing. Microglia were pooled from 3 forebrains of ATG7FF or 4 forebrains of ATG7FF;Cx3cr1CreER.
Forebrains from 8-months-old mice (ATG7FF;5xFAD, and ATG7FF;Cx3cr1CreER;5xFAD, at 6-months post tamoxifen injection) were subject to a bulk RNA RNA sequencing.

first: Zhenyu

last: Yue


title: Hepatic ChREBP activation limits NAFLD development in a mouse model for Glycogen Storage Disease type Ia/ Normalization of ChREBP activity in hepatic GSD Ia accelerates liver disease progression and sensitizes towards hepatocellular tumour formation.

city: Groningen

first: vincent

last: bloks

department: Pediatrics

institute: UMCG

summary:
abstract1: Glycogen storage disease type Ia (GSD Ia) is an inborn error of metabolism caused by defective glucose-6-phosphatase (G6PC) activity. GSD Ia patients exhibit severe hepatomegaly due to glycogen and triglyceride (TG) accumulation in the liver. We have previously shown that the activity of Carbohydrate Response Element Binding Protein (ChREBP), a key regulator of glycolysis and de novo lipogenesis, is increased in GSD Ia. In the current study we assessed the contribution of ChREBP to non-alcoholic fatty liver disease (NAFLD) development in a mouse model for hepatic GSD Ia. PMID : 32083759

Abstract2:Glycogen storage disease type 1a (GSD Ia) is an inborn error of metabolism caused by a defect in glucose-6-phosphatase (G6PC) activity, which induces severe hepatomegaly and increases the risk for liver cancer in patients. Hepatic GSD Ia is characterized by constitutive activation of Carbohydrate Response Element Binding Protein (ChREBP), a glucose-sensitive transcription factor that has been proposed as a pro-oncogenic molecular switch that supports tumour progression. Here we studied the contribution of ChREBP signalling on liver disease progression and tumour susceptibility in a mouse model for GSD Ia. Hepatocyte-specific G6pc knockout (L-G6pc-/-) mice were treated with AAV-shChREBP to normalize hepatic ChREBP activity. Hepatic ChREBP normalization induced dysplastic liver growth, massively increased hepatocyte size and sensitized to hepatic inflammation and liver fibrosis in GSD Ia mice. Furthermore, the nuclear levels of the oncoprotein YAP were increased and its transcriptional targets were induced in ChREBP normalized GSD Ia mice. Hepatic ChREBP normalization furthermore induced DNA damage and mitotic activity in GSD Ia mice, while chromosomal instability, cGAS-STING pathway, senescence, and hepatocyte dedifferentiation gene signatures emerged. Upon ChREBP silencing in immortalized human hepatocytes, on the other hand, the induction of YAP target gene expression was paralleled by cell cycle arrest, cell death, and reduced proliferation. In conclusion, our findings indicate that ChREBP activity limits hepatomegaly while protecting against liver disease progression and hepatocellular tumour induction in GSD Ia. These results underline the importance to establish the context-specific roles of ChREBP to define its therapeutic potential. PMID:37085901

overall_design: Liver-specific G6pc knockout (L-G6pc-/-) mice were treated with AAV2/8-shChREBP to normalize hepatic ChREBP activity to levels observed in wildtype (L-G6pc+/+) mice receiving AAV8-shScramble.

last: Lei

first: Joanne

middle: A

last: Hoogerland

first: Vincent

last: Bloks

first: Trijnie

last: Bos

first: Aycha

last: Bleeker

first: Henk

last: Wolters

first: Justina

middle: C

first: Brenda

middle: S

last: Hijmans

first: Theo

middle: H

last: van Dijk

first: Rachel

last: Thomas

first: Michel

last: van Weeghel

first: Gilles

last: Mithieux

first: Riekelt

last: Houtkooper

first: Alain

last: de Bruin

first: Fabienne

last: Rajas

first: Folkert

last: Kuipers

first: Maaike

last: Oosterveer


title: Long Non-coding RNA NR2F1-AS1 Induces Breast Cancer Dormancy in Lungs by Regulating NR2F1 and ΔNp63

city: Shanghai

first: Guohong

last: Hu

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health

summary: We show that the epithelial-like and mesenchymal-like subpopulations of breast cancer stem-like cells (BCSCs) demonstrate different levels dormancy and tumorigenicity in lungs. The long non-coding RNA (lncRNA) molecule NR2F1-AS1 (NAS1) is up-regulated in the dormant BCSC subpopulation, and functionally promotes tumor dissemination but reduces proliferation in lungs. Mechanically, NAS1 promotes internal ribosome entry site (IRES)-mediated NR2F1 translation, leading to inhibition of ΔNp63 transcription by NR2F1. Further, ΔNp63 downregulation results in epithelial-mesenchymal transition, reduced tumorigenicity and enhanced dormancy of cancer cells in lungs.

overall_design: Transcriptomic sequencing was firstly performed in MCF10 breast cancer cell line series that include MCF10AT, MCF10CA1h, MCF10CA1a, CA1h-P1 (CD24-CD44med subpopulation of MCF10CA1h) and CA1h-P2 (CD24-CD44high subpopulation of MCF10CA1h), while MCF10CA1h and CA1h-P2 were identified with dormant characteristics. We found that the long non-coding RNA (lncRNA) molecule NR2F1-AS1 (NAS1) is up-regulated in the dormant cells. Then the transcriptomes of CA1h-P2 with NAS1 knockdown, MCF10CA1h and MCF7 with NR2F1 overexpression, and their respective controls were sequenced to find the molecules affected by both NAS1 and NR2F1.

first: Yingjie

last: Liu

first: Peiyuan

last: Zhang


title: XRN2 Suppresses Aberrant Entry of tRNA Trailers into Argonaute in Humans and Arabidopsis

city: South Birmingham

first: Anindya

last: Dutta

state: AL

address: 720 20th Street South, Kaul 230

department: Genetics

institute: University of Alabama at Birmingham

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) are a well-characterized class of small RNAs (sRNAs) that regulate gene expression post-transcriptionally. miRNAs function within a complex milieu of other sRNAs of similar size and abundance, with the best characterized being tRNA fragments or tRFs. The mechanism by which the RNA-induced silencing complex (RISC) selects for specific sRNAs over others is not entirely understood in human cells. Several highly expressed tRNA trailers (tRF-1s) are strikingly similar to microRNAs in length but are generally excluded from the microRNA effector pathway. This exclusion provides a paradigm for identifying mechanisms of RISC selectivity. Here, we show that 5' to 3' exoribonuclease XRN2 contributes to human RISC selectivity. Although highly abundant, tRF-1s are highly unstable and degraded by XRN2 which blocks tRF-1 accumulation in RISC. We also find that XRN mediated degradation of tRF-1s and subsequent exclusion from RISC is conserved in plants. Our findings reveal a conserved mechanism that prevents aberrant entry of a class of highly produced sRNAs into Ago2.

overall_design:
Small RNA sequencing data: examination of small RNA expression following siXRN1&2.
Flag-HA-Ago2 (FH-Ago2) RNA immunoprecipitation followed by small RNA sequencing: examination of small RNAs that interact with FH-Ago2 following siXRN2.

first: Briana

last: Wilson

first: Zhangli

last: Su


title: Effect of Zika virus (ZIKV) sfRNA on host gene expression in human brain organoids

status: Public on Apr 21 2023

city: St Lucia

first: Andrii

last: Slonchak

address: MBS Bldg 76, Cooper Rd

department: School Of Chemistry And Molecular Biosciences

institute: The University of Queensland

summary:
We employed 3D brain organoids generated from induced human pluripotent stem cells (ihPSC) as ex vivo model of viral infection in the developing brain and utilized wild type (WT) ZIKV producing sfRNA and mutant ZIKV deficient in production of sfRNA.
Global transcriptome profiling by RNA-Seq revealed that production of sfRNA affects expression of >1000 genes. We uncovered that in addition to activation of pro-apoptotic pathways, organoids infected with sfRNA-producing WT, but not sfRNA-deficient mutant ZIKV, exhibited strong down-regulation of genes involved in signaling pathways that control neuron differentiation and brain develop-ment, which indicates the requirement of sfRNA for suppression of neurodevelopment associated with ZIKV infection. Using gene set enrichment analysis and gene network reconstruction, we demonstrated that the effect of sfRNA on pathways that control brain development occurs via crosstalk between Wnt-signaling and proapoptotic pathways.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human brain organoids infected with WT and sfRNA-deficient ZIKV


title: Anti-cancer activity of verteporfin in cholangiocarcinoma

city: Bethesda

first: Margaret

last: Cam

state: MD

address: 9000 Rockville Pike

institute: NCI

summary: We investigated the antitumoral effect of verteporfin in YAP/AKT hydrodynamic tail vein injected murine models and we analyzed the correlative change of immune cell profile and stemness with the treatment of verteporfin by using flow cytometry and single-cell RNA sequencing

overall_design: Mouse liver/tumor samples were prepared with three replicate per sample. Vehicle treated sample was used as a control

first: Jihye

last: Golino

first: Xin

last: Wang

first: Jing

last: Bian

first: Benjamin

last: Ruf

first: Michael

last: Kelly

first: Baktiar

last: Karim

first: Maggie

first: Changqing

last: Xie


title: Mapping Visual Functions onto Molecular Cell Types in the Mouse Superior Colliculus

city: Charlottesville

first: Yuanming

state: Virginia

address: Gilmer Hall

department: Biology Department

institute: University of Virginia

summary: To facilitate investigation of function, connectivity, and development of superficial superior colliculus (sSC), we identified 28 neuron subtypes and subtype-enriched marker genes from tens of thousands of adult mouse sSC neurons

overall_design: The sSC was micro-dissected approximately by knife cuts, processed into a single-nuclei suspension and prepared for sequencing with 10X Chromium Next GEM 3’ reagent kit v3.1 according to the manufacturer’s protocol

first: Elise

last: Savier

first: Victor

middle: J

last: DePiero

first: Chen

last: Chen

first: Dana

last: Schwalbe

first: Ruei-Jen

last: Fan

first: Hui

first: John

middle: N

last: Campbell

first: Jianhua

last: Cang


title: CTCF facilitates subset-specific chromatin interactions to limit the formation of memory CD8+ T cells [HiC]

city: La Jolla

first: Ananda

last: Goldrath

state: CA

address: 9500 Gilman Drive

institute: UCSD

summary: CD8+ T cells provide protection from infection and tumor growth, and many current immunotherapies target molecules that enhance CD8+ T cell function and differentiation. The transcriptional programs orchestrating CD8+ T cell differentiation in response to infection has been described, but the changes in spatial chromatin organization accompanying effector and memory CD8+ T cell differentiation is unknown, despite research showing the importance of long-range chromatin interactions for transcriptional regulation in various cell types. Here, we studied how genome organization is integrated with CD8+ T cell differentiation and investigated the role of CTCF, a key factor that regulates genome organization through blocking or facilitating chromatin interactions, in regulating CD8+ T cell fates. We observed T cell subset-specific changes in chromatin organization and CTCF binding, and revealed weak-affinity CTCF binding is needed to promote terminal differentiation of CD8+ T cells by coordinating chromatin interactions that regulate transcriptional programs driving CD8+ T cell differentiation.

overall_design: Sorted OT-I cells day 0 or 7 days post infection with Lm-OVA

first: Sara

last: Quon

first: Bingfei

last: Yu

middle: W


title: CTCF facilitates subset-specific chromatin interactions to limit the formation of memory CD8+ T cells [RNA-Seq]

overall_design: Sorted OT-I cells day 0 or 8 days post infection with Lm-OVA


title: MLX siRNA knockdown in primary human hepatocytes

city: Oxford

first: Thomas

last: Monfeuga

address: Innovation Building, Old Road Campus, Roosevelt Drive

country: United Kingdom

institute: Novo Nordisk Research Centre Oxford

summary: 3' mRNA-sequencing of primary human hepatocytes treated with either non-targeting (siNT) or targeted siRNA against MLX (siMLX) (3 independent replicates with different PHH donors, n=5 prepared per donor and treatment; one siMLX sample was excluded from analysis due to low quality)

overall_design: 3' mRNA-sequencing; siCtrl n=15; siMLX n=14

first: Shilpa

middle: R

last: Nagarajan

first: Eilidh

last: Livingstone

first: Lara

last: Lewis

first: Shahul

last: Liyakath Ali

first: Anandhakumar

last: Chandran

first: David

last: Dearlove

first: Matt

last: Neville

first: Lingyan

first: Cyrielle

last: Maroteau

first: Maxwell

last: Ruby

first: Leanne

last: Hodson


title: CTCF facilitates subset-specific chromatin interactions to limit the formation of memory CD8+ T cells [ChIP-Seq]


title: Systematic elucidation of genetic mechanisms underlying cholesterol uptake

city: Boston

first: Richard

last: Sherwood

state: MA

address: 77 Avenue Louis Pasteur

institute: Brigham & Women's Hospital

overall_design: SER = cultured in serum containing media, SS = cultured overnight in optiMEM, no serum

first: Marisa

last: Hamilton


title: Towards a mechanistic understanding of response to SBRT by patients with borderline resectable pancreatic cancer

status: Public on Apr 20 2023

city: Aurora

first: Sana

last: Karam

state: CO

address: 1665 Aurora Ct.

department: Radiation Oncology

institute: CU Denver Anschutz

summary: Five year survival rates for pancreatic cancer remain low, around 11%. We assessed differential gene expression between SBRT responders and non-responders as well as expression pre and post SBRT. Samples were obtained from the University of Colorado  biorepository. All patients had borderline resectable pancreatic cancer, treated with neoadjuvant chemotherapy followed by restaging, and treatment with 30–33.6 Gy SBRT to pancreatic tumors, followed by pancreaticoduodenectomy and adjuvant chemotherapy. We observed increases in PDL1, PD1, CD25, and a decrease in CD122  expression following RT. Furthermore, we found that responders to SBRT exhibit decrased CD25 expression with increased CD122 and CD132 expression compared to non-responders. Using GSEA of responders vs. non-responders, we found responders to SBRT exhibit enrichment of inflammatory response, IFN signaling, and IL2/STAT5 signaling.

overall_design: Tumor tissue collected from patients at the time of initial biopsy (fine needle aspirate) and at time of surgery (post SBRT) were used for RNAs sequencing.

first: Maureen

last: Hoen


title: GDF15 and energy expenditure

city: Hamilton

first: Dongdong

last: Wang

state: Ontario

address: 1200 Main Street West

institute: McMaster University

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

overall_design: Refer to individual Series


title: scRNAseq characterization of synovial stromal cells in mouse STIA

city: Birmingham

first: Adam

last: Croft

state: Please Select

address: Birmingham

institute: University of Birmingham

summary:
Objective: Upregulation of glycolysis and glutaminolysis in the rheumatoid arthritis fibroblast-like synoviocytes (RAFLS) has already been established by existing literature . Henceforth, this study was undertaken to determine if dual inhibition of these processes by novel phytobiologic c28MS have the potential of promising  synergistic therapy for rheumatoid arthritis by targeting the underlying metabolic reprogramming as existing treatment strategies for RA do not target dual inhibition.
Methods: Gene associations with HK2 and GLS expression were identified by examining murine and human available scRNA-seq. The metabolic profile of FLS cells was determined by 1H magnetic resonance spectroscopy under conditions of glycolytic and glutaminolysis inhibition and HK2 and GLS1 expression was evaluated by western blot. FLS functional analysis was conducted under similar inhibitory conditions. ELISA was employed for the quantification of pivotal markers namely IL6, CCL2 and MMP3. For arthritis experiments, mice were injected with K/BxN sera on Day 0 and treated for 10 days.
Results: scRNAseq data identified... Metabolomic and functional analysis revealed that c28MS had the potential of checking the aggressive behavior of RAFLS by targeting upregulated glycolysis and glutaminolysis thereby inhibiting them. Target expression remained unaffected by the action of the dual inhibitor suggesting only potential blockage. Furthermore, the compound was able to inhibit inflammatory arthritis by decreasing the clinical score and paw inflammation in the K/BxN model.
Conclusion: Our findings imply that dual inhibition of glycolysis and glutaminolysis could be an effective strategy in the treatment of RA with chances of greater remission. It also suggests that targeting more than one pathway in the metabolome can be a novel treatment approach in non-cancer scenarios.

overall_design: STIA was induced by intravenous injection of 100 μl arthritogenic serum from KRN mice (K/BxN). Cells were extracted at various timepoints (rest d0, peak d7-9, resolving d15, resolved d22) followed by CD45neg purification of stromal cells and 3' mRNA scRNAseq (10x Genomics)

first: Chris

last: Mahony


title: Cyclic GMP–AMP Synthase (cGAS) Deletion Reduces Severity in Bilateral Nephrectomy Mice through Changes in Neutrophil Extracellular Traps and Mitochondrial Respiration

city: Worcester

first: Patipark

last: Kueanjinda

address: 368 Plantation St

institute: University of Massachusetts Medical School

summary: Uremia-induced systemic inflammation is partly caused by the dissemination of microbial molecules such as lipopolysaccharide and bacterial double-stranded DNA from leaked gut damaged by immune cells in response to the microbial molecules. Cyclic GMP–AMP synthase (cGAS) can recognize fragmented DNA and induce cGAMP synthesis for the activation of the stimulator of interferon genes (STING) pathway. To study the effect of cGAS in uremia-induced systemic inflammation, we performed bilateral nephrectomy (BNx) in wild-type and cGAS knock-out mice and found that the gut leakage and blood uremia from both groups were similar. However, serum cytokines (TNF-α and IL-6) and neutrophil extracellular traps (NETs) decreased significantly in cGAS-/- neutrophils after stimulation with LPS or bacterial cell-free DNA. Transcriptomic analysis of LPS-stimulated cGAS-/- neutrophils also confirmed the down-regulation of neutrophil effector functions. The extracellular flux analysis showed that cGAS-/- neutrophils exhibited a higher respiratory rate than wild-type neutrophils despite having similar mitochondrial abundance and function. Our results suggest that cGAS may control effector functions and the mitochondrial respiration of neutrophils in response to LPS or bacterial DNA.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for neutrophils from cGAS KO in C57b/L6 backgroud mice after treatment with or without LPS for 2 hours. RNA-seq was performed using Illumina NextSeq 500 sequencer.

first: Nattavong

last: Suksawad

first: Kanyarat

last: Udompornpitak

first: Natchapon

last: Thawinpipat

first: Pichaya

last: Korwattanamongkol

first: Peerapat

last: Visitchanakun

first: Pornpimol

last: Phuengmaung

first: Wilasinee

last: Saisorn

first: Asada

last: Leelahavanichkul


title: Circulating microRNA Biomarker for Detecting Breast Cancer in High-Risk Benign Breast Tumors

city: Honolulu

first: Mayumi

last: Jijiwa

state: HI

address: 651 Ilalo St, BSB222

department: Quantitative Health Sciences

institute: University of Hawaii

summary:
We sought to identify circulating microRNAs (miRNAs) from blood plasma that could be used as biomarkers to detect breast cancer existing in high-risk benign breast tumors.
Plasma samples were collected from patients with early-stage breast cancer (CA), high- (HB), moderate- (MB), and no-risk (Be) benign tumors.
The miRNAs we have identified have the potential to develop into a crucial blood-based screening tool to help monitor the development of breast cancer in benign breast tumors.

overall_design: small RNA-seq was performed on plasma RNA obtained from patients with early-stage breast cancer or high-, moderate-, and no-risk benign breast tumors.

first: Vedbar

last: Khadka

first: Masaki

last: Nasu

first: Youping

last: Deng


title: Conserved multitissue transcriptomic adaptations to exercise training in humans and mice

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

summary: Physical activity is associated with beneficial adaptations in human and rodent metabolism. We studied over 50 complex traits before and after exercise intervention in middle-aged men and a panel of 100 diverse strains of female mice. Candidate gene analyses in three brain regions, muscle, liver, heart, and adipose tissue of mice revealed genetic drivers of clinically relevant traits including volitional exercise volume, muscle metabolism, adiposity, and hepatic lipids. Although ~33% of genes differentially expressed in skeletal muscle following the exercise intervention were similar in mice and men independent of BMI, responsiveness of adipose tissue to exercise-stimulated weight loss appears impacted by species and underlying genotype. We leveraged genetic diversity to generate prediction models of metabolic trait responsiveness to volitional activity offering a framework for advancing personalized exercise prescription. Finally, we make the human and mouse data publicly available via user-friendly web-based application to enhance data mining and hypothesis development.

overall_design: Expression profiling by RNA-Seq for five tissues (gonadal white adipose, heart, liver, quadriceps, brown adipose) in 50 inbred mouse strains under sedentary and exercised conditions

first: Andrea

last: Hevener

first: Tim

middle: M

last: Moore

first: Aldons

last: Lusis


title: CTCF facilitates subset-specific chromatin interactions to limit the formation of memory CD8+ T cells [ATAC-Seq]

first: Ananda

last: Goldrath

first: Sara

last: Quon

first: Bingfei

last: Yu


title: RNA binding protein PRRC2B mediates translation of specific proteins and regulates cell cycle progression

city: Rochester

first: feng

last: jiang

state: New York

address: 601 Elmwood Ave box CVRI

department: Biochemistry and Biophysics

institute: University of Rochester


title: RNA binding protein PRRC2B mediates translation of specific proteins and regulates cell cycle progression [Polysome-seq]

summary: Accumulating evidence suggests that posttranscriptional regulation of gene expression, including regulation of RNA splicing, transport, modification, translation, and degradation, primarily relies on RNA binding proteins (RBPs). However, the functions of many RBPs remain understudied. Here, we characterized the function of a novel RBP, Proline-Rich Coiled-coil 2B (PRRC2B). Through photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) and deep sequencing, we identified transcriptome-wide CU- or GA-rich PRRC2B binding sites around the translation initiation codon on a specific cohort of mRNAs in HEK293T cells. These PRRC2B target mRNAs, including oncogenes and cell cycle regulators such as CCND2 (cyclin D2), exhibited decreased translation upon PRRC2B knockdown as revealed by sequencing polysome-associated RNA, resulting in decreased G1/S phase transition and cell proliferation. Antisense oligonucleotides (ASOs) blocking PRRC2B-CCND2 mRNA interaction decreased CCND2 translation, thus inhibited G1/S transition and cell proliferation. Mechanistically, PRRC2B interactome capture analysis revealed RNA-independent interactions with eukaryotic initiation factors eIF4G2, eIF3, and FXR1. The interaction with eIF4G2 is essential for PRRC2B function since unlike wildtype PRRC2B, eIF4G2-interacting defective mutants failed to rescue the translation deficiency caused by PRRC2B knockdown. Taken together, our findings reveal that PRRC2B, by interacting with eIF4G2, is essential for efficient translation of specific proteins required for cell cycle progression and cell proliferation.

overall_design: We performed polysome-seq on HEK293T cells and its derivatives (shPRRC2B). Total RNA and polysome-associated RNA extracted from HEK293T cells and its knockdown derivatives (shPRRC2B) were subjected to RNA-seq. Biological triplicates were performed. Samples were subjected to DNA removal by DNase I and polyA enrichment before library construction by NGS Library Prep following the manufacturer's protocols. Paired-end sequencing was conducted at Novogene using NovaSeq6000 S4 with a depth of 20M reads/sample.

first: Feng

last: Jiang

first: Omar

last: Hedaya

first: EngSoon

last: Khor

first: Jiangbin

last: Wu

first: Matthew

last: Auguste


title: RNA binding protein PRRC2B mediates translation of specific proteins and regulates cell cycle progression [PAR_Clip-seq]

overall_design: We performed PAR-CLIP-seq on HEK293T cells overexpressing Flag-tagged full-length and truncated PRRC2B. PRRC2B-bound RNAs were digested by RNase T1 to 19 - 35 nt long and extracted from immunoprecipitated PRRC2B-RNA complexes. Biological replicates were performed. The samples were subjected to libraries construction using the NEBNext® Small RNA Library Prep Set following the manufacturer’s instructions. Sequencing was performed on Illumina HiSeq2500 sequencer with 75 bp single-end sequencing in the Genomic Research Center from University of Rochester Medical Center.


title: CUT&Tag result of ACTL6A, BRG1 and NRF2 related site in SNU638 gastric cancer cell line

city: Guangzhou

first: Ziqing

last: Yang

address: 26th Yuancun Erheng Road, Tianhe District

department: Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor Disease

institute: Sun Yat-sen University

summary: ACTL6A has been identified as a transcriptional regulator and driving pathways that are of specific benefit to the malignant elements within the tumor. Here, we aimed to find genes that are regulated by ACTL6A by CUT&Tag. BRG1 is the catalytic subunit of the SWI/SNF chromatin-remodeling complex. Nuclear factor (erythroid-derived 2)-like 2 (NFE2L2, NRF2) is a transcription factor that governs the antioxidant pathway. IgG was used as a control.

overall_design: CUT&Tag assay was performed in SNU638 cells, using anti-ACTL6A, anti-BRG1 and anti-NRF2 antibody or IgG.

first: Lekun

last: Fang


title: Base-editor-mediated multiplexed inactivation of DNA methyltransferases reveals essential roles of miRNAs in mouse gastrulation

first: Qing

last: Li

department: institute of biochemistry and cell biology

institute: Chinese Academy of Science

summary: Here, we establish a system to simultaneously inactivate Dnmts in one step through screening for base editors that can efficiently introduce a stop codon endogenously. Dnmt-null embryos display primitive streak elongation failure at E7.5. Interestingly, although DNA methylation is absent, gastrulation-related pathways are down-regulated in Dnmt-null embryos. Moreover, DNMT1 or DNMT3A/3B are indispensable for gastrulation and their functions are independent of TET proteins. Hypermethylation can be sustained by either DNMT1 or DNMT3A/3B at some promoters, which are mainly related to miRNAs. Strikingly, majority of hypermethylated promoter-related miRNAs are overexpressed and located at the Dlk1-Dio3 imprinted region. The predicted targets of these miRNAs tend to be down-regulated and enriched in the gastrulation-related pathways in Dnmt-null embryos. Finally, introduction of a single mutant allele of six miRNAs partially restores primitive streak elongation in Dnmt-null embryos.

overall_design: To analyze the influence of DNA methylation on miRNAs expression, we used CAS-seq to analyze different Dnmt mutant embryos, including Control, Dnmt1-KO, Dnmt3a/3b-DKO, and Dnmt1/3a/3b-TKO Exe and Epi of E6.5 and E7.5. To analyze the influence of IG-DMR methylation on Dlk1-Dio3 miRNAs expression, we used CAS-seq to analyze WT- and- DKO AG-haESCs, and WT-and DKO semi-cloned embryos at E6.5. Besides, we also analyzed DKO- and Mir-6KO semi-cloned embryos at E7.5 to describe the miRNAs expression in these samples.

first: Jinsong

first: Yunjian

last: Chang


title: Transcriptome-wide identification of the influenza A virus endoribonuclease PA-X cut sites by 5' RACE-Seq

city: Madison

first: Marta

middle: Maria

last: Gaglia

state: WI

address: 1525 Linden Dr

institute: University of Wisconsin Madison

summary: Influenza A virus induces host shutoff mainly through its endoribonuclease PA-X. Like many host shutoff nucleases, PA-X activity affects different host RNAs to varying degrees. To understand how PA-X discriminates between different mRNAs, we took a high-throughput approach to directly identify PA-X cut sites transcriptome-wide and examine PA-X cleavage characteristics. To do this, we compared RNA fragments from mock infected cells to cells infected with the wild-type (WT) A/PuertoRico/8/1934 H1N1 (PR8) influenza virus strain, or the same strain engineered to lack PA-X, referred to as PR8-PA(∆X).

overall_design: Xrn1 knock-out human lung carcinoma epithelial A549 cells were used to limit degradation of the fragments created by PA-X and identify the specific location of the initial cut (Liu and Moss, 2016). These cells were infected in triplicate with wild-type (WT) A/PuertoRico/8/1934 H1N1 (PR8) influenza virus strain, or the same strain engineered to lack PA-X referred to as PR8-PA(∆X), or mock infected. Taking advantage of the fact that RNAs cleaved by PA-X have a free 5’ phosphate, we ligated an RNA adapter at the 5’ end of every cut RNAs, then added a 3’ adapter during reverse transcription, and finally added Illumina sequencing adapters on each end through a few rounds of PCR and performed RNAseq to sequence RNA fragments.

first: Lea

last: Gaucherand

first: Amrita

last: Iyer

first: Isabel

last: Gilabert

first: Chris

last: Rycroft


title: Generation of transcriptional regulatory network of Lgr5+ small and large intestinal stem cells from mouse [ATAC-seq]

city: Seoul

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

institute: Ewha Womans University

summary: The goal of this study is to survey transcriptional machinery in intestinal stem cells from small and large intestine of mice. We established intestinal stem cell specific gene-regulatroy network to understand regional identity.

overall_design: Small intestine (2-3cm from pylorous and 2-3cm from cecum) and large intestine (cecum to rectum) of mice aged 6-12 weeks were extracted, and opened horizontally and washed with cold PBS buffer. Small intestinal stem cell (Lgr5-EGFP+/CD24-) and large intestinal stem cell (Lgr5-EGFP+) were obtained from enriched intestinal crypts by FACS analysis. Sorted cells were directly applied with TRIzol™ Reagent (invitrogen 15596026) or ATAC lysis buffer.

first: Hyo-Min

last: Kim

first: Byunghee

last: Kang


title: Generation of transcriptional regulatory network of Lgr5+ small and large intestinal stem cells from mouse [RNA-seq]


title: Generation of transcriptional regulatory network of Lgr5+ small and large intestinal stem cells from mouse


title: Mechanism-based identification of plasma metabolites associated with liver toxicity

city: Frederick

first: Venkat

last: Pannala

state: Maryland

address: 2405 Whittier Dr, #200

department: DoD BHSAI

institute: Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc.


title: Crnic Institute Human Trisome Project - Trisomy 21 Model Atlas: PolyA RNA-seq from C57BL/6 and Dp16 adult mouse heart tissue ± JAK1/2 inhibition with baricitinib

status: Public on Apr 19 2023

last: Galbraith

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

summary: Analysis of steady-state mRNA levels in adult mouse heart tissue at 7-11 weeks  from wild-type C57BL/6 and Dp16 mice ± treatment with the JAK1/2 inhibitor baricitinib. This dataset is part of the Human Trisome Project - Trisomy 21 Model Atlas run by the Linda Crnic Institute for Down Syndrome at the University of Colorado Anschutz Medical Campus. http://www.trisome.org/

overall_design: Comparison of wild-type+vehicle (n=2), wild-type+baricitinib (n=2), Dp16+vehicle (n=4), Dp16+baricitinib (n=4).

first: Kelly

last: Sullivan

first: Joaquin

last: Espinosa


title: In vivo transciptomic responses to acetaminophen exposure from liver and kidneys of Sprague Dawley rats

summary: In this study we tested the ability to identify early perturbations in the organ (liver and kidney) metabolism due to acetaminopen exposure at two early time points (5 and 10 h) using RNA-sequencing.

overall_design: We treated Sprague Dawley rats with a single dose of acetaminophen (2 g/kg) with corresponding controls given 6 ml/kg of 50% polyethylene glycol as vehicle (n =8 each for control and treatment). Liver and kidney samples for RNA-sequencing were collected 5 and 10 h post acetaminophen/vehicle treatment. Total 32 rats were used with 8 replicates for each condition and time point.

first: Shanea

last: Estes

first: Martha

last: Wall

first: Irina

last: Trenary

first: Tracy

last: OˈBrien

first: Richard

last: Printz

first: Jaques

last: Reifman

first: Tatsuya

last: Oyama

first: Masakazu

last: Shiota

first: Jamey

last: Young

first: Anders

last: Wallqvist