title: Expression profiles at the level of miRNAs in 3D cultures.

city: Mexico City

first: Yarely M.

last: Salinas-Vera

address: Av Instituto Politécnico Nacional 2508, San Pedro Zacatenco, Gustavo A. Madero, 07360 Mexico City, CDMX

department: Biochemistry

country: Mexico

institute: Centro de Investigación y de Estudios Avanzados del IPN

summary:
Three-Dimensional Organotypic Cultures Reshape the microRNAs  Transcriptional Program in Breast Cancer Cells
Three-dimensional (3D) cell cultures have several advantages over conventional monolayer two-dimensional (2D) cultures as they can better mimic tumor biology. This study delineated the changes in microRNA (miRNA) expression patterns of breast cancer cells cultured in 3D and 2D conditions. 3D organotypic cultures showed morphological changes such as cell–cell and cell–extracellular matrix interactions associated with a loss of polarity and reorganization on bulk structures in both basal Hs578T and luminal T47D breast cancer cells. Data indicate that down-regulated miRNAs in Hs578T 3D cultures, relative to the 2D condition, contribute to a positive regulation of biological processes such as response to hypoxia and focal adhesion, whereas over-expressed miRNAs were related to negative regulation of the cell cycle. Remarkably, the repro-gramming of miRNAs’ transcriptional profiles was accompanied by changes in the expression of key miRNA/mRNA coregulation networks, such as miR-935/HIF-1A, which correlated with the expression found in clinical breast tumors and predicted poor patient outcomes. These data have implications in our understanding of cancer biology and impact the miRNA/mRNA regulatory axes of cells grown in 3D cultures. Our data represent a guide for novel miRNA candidates for functional analysis, including the response to therapy and biomarker discovery in breast cancer.

overall_design: We analyzed 3D culture samples compared to 2D cultures of the Hs578T triple-negative breast cancer cell line, using the Affymetrix GeneChip miRNA 4.0 platform. Array data were processed with the Affymetrix GeneChip command console software v4.0 computational tool. Samples were run in triplicate.

first: Y

first: J

last: Valdés

first: A

last: Hidalgo-Miranda

first: M

last: Cisneros-Villanueva

first: L

last: Marchat

first: SI

last: Nuñez-Olvera

first: R

last: Ramos-Payán

first: C

last: Pérez-Plasencia

last: Arriaga-Pizano

last: Prieto-Chávez

last: López-Camarillo


title: Analysis of the effect of TSLP stimulated CD4+T cells on epigenetic markers in PyMT primary tumors

status: Public on May 15 2022

city: Boston

first: Margherita

last: Boieri

state: MA

address: 55 Fruit Street

country: USA

institute: Masachusetts General Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: TSLP-stimulated CD4+ T cells block the promotion of breast cancer in a spontaneous PyMT mouse model. The goal of this project is to investigate what are the epigenetic changes induced by CD4+ T cells that lead to diminished proliferation of cancer cells

overall_design: K14-TSLPtg;PyMT;Rag1KO, and PyMT;Rag1KO mice were injected with wt CD4+ T cells at 4 weeks of age. Tumors were collected when they reached terminal size and tissue was processed for ChIP seq analysis.

first: Shadmehr

last: Demehri

first: Miguel

last: Rivera

first: Mary

last: Awad

first: Sowmya

last: Iyer


title: Anoctamin 1 controls bone resorption by coupling Cl- channel activation with RANKL-RANK signaling transduction

status: Public on May 17 2022

city: Beijing

first: Weijia

last: Sun

address: No. 26 Beiqing Road, Haidian District

country: China

institute: China Astronaut Research and Training Center

summary: Osteoclast over-activation leads to bone loss and chloride homeostasis is fundamental for osteoclast function. The calcium-activated chloride channel Anoctamin 1 (also known as TMEM16A) is an important chloride channel involved in many physiological processes. However, its role in osteoclasts remains unresolved. Here, we identify the existence of Anoctamin 1 in osteoclasts and show that its expression positively correlates with osteoclast activity. Osteoclast-specific Anoctamin 1 knockout mice exhibit increased bone mass and decreased bone resorption. Mechanistically, Anoctamin 1 deletion increases intracellular Cl- concentration, decreases H+ secretion and reduces bone resorption. Notably, Anoctamin 1 physically interacts with RANK and this interaction is dependent upon Anoctamin 1 channel activity, jointly promoting RANKL-induced downstream signaling pathways. Anoctamin 1 protein levels are substantially increased in osteoporosis patients and this closely correlates with osteoclast activity. Finally, Anoctamin 1 deletion significantly alleviates ovariectomy induced osteoporosis. These results collectively establish Anoctamin 1 as an essential regulator in osteoclast function and suggest a potential therapeutic target for osteoporosis.

overall_design: 6 samples, 3 in the control group, 3 in the cko group

first: Shuai

last: Guo

first: Yuheng

last: Li

first: Jianwei

first: Caizhi

last: Liu

first: Yafei

last: Chen

first: Xuzhao

last: Wang

first: Yingjun

last: Tan

first: Hua

last: Tian

first: Cheng

first: Ruikai

last: Du

first: Guohui

last: Zhong

first: Sai

last: Shi

first: Biao

last: Ma

first: Chang

last: Qu

first: Jingxuan

last: Fu

first: Xiaoyan

last: Jin

first: Dingsheng

last: Zhao

first: Yong

last: Zhan

first: Shukuan

last: Ling

first: Hailong

last: An

first: Yingxian


title: Expression data from Saccharomyces cerevisiae to evaluate the impact of  suppressors of Aβ42 cytotoxicity on recombinant protein production

status: Public on May 16 2022

city: Göteborg

first: Xin

address: Kemigården 4

department: Department of Biology and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

type: Expression profiling by high throughput sequencing

summary: High-level production of pharmaceutical proteins in industrial microorganism is often limited due to the increased cellular stress from misfolded proteins or protein aggregates. Here, we explore the feasibility of applying a yeast Alzheimer’s disease (AD) model with accumulation of amyloid-β peptides (Aβ42), which presents similar phenotypes of cellular stress. We utilize the suppressors of Aβ42 cytotoxicity as potential metabolic engineering targets to improve industrial protein production. The transcriptomics analyses provide new insights towards developing synthetic yeast cell factories for biosynthesis of valuable pharmaceutical proteins.

overall_design: The goal of the present study is to evaluate the impact of  suppressors of Aβ42 cytotoxicity on recombinant protein production in yeast. Four engineered strains (A02, A05, A08, and A16) and control strain A01 were collected from early exponential phase (OD600nm 1.0). Samples were taken from three biological replicate cultures.

first: Xiaowei

last: Li

first: Boyang

last: Ji

first: Yanyan

first: Olena

middle: P

last: Ishchuk

first: Egor

last: Vorontsov

first: Martin

middle: K

last: Engqvist

first: Verena

last: Siewers

first: Dina

last: Petranovic


title: Differential expression and functional analysis of circular RNA in Alzheimer’s disease

status: Public on May 13 2022

city: Urumqi

first: juan

last: Bu

address: 29 Tianchi Road

institute: People's Hospital of Xinjiang Uygur Autonomous Region

summary: This study investigated the pathogenesis of Alzheimer’s disease by analyzing the differential expression of circular RNAs (circRNAs), and their interactions with microRNAs (miRNAs). A circRNA microarray was used to screen expressed circRNAs in peripheral blood leukocytes from three patients with AD and four healthy control participants. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were used to annotate the functions of the circRNAs. Changes in expression of six circRNAs [0045808/0070162/0001929/0092270/0092222/0092223]) was confirmed by RT-qPCR, of which three (hsa_circ_[0045808/0070162/0092270]) were further verified by RT-qPCR using a large sample of 23 patients with AD and 25 healthy controls. A circRNA-miRNA-mRNA interaction network, constructed using TargetScan, miRanda, and Cytoscape, revealed upregulated (n=311) and downregulated (n=433) circRNAs, whereaswhile 443 circRNAs were downregulated. GO and KEGG analyses associated differentially expressed circRNAs to neurotransmitters, cell senescence, P53, mTOR, and PI3K-AKT. Microarray sample verification using RT-qPCR confirmed the microarray analysis results on changes in the six circRNAs. Contrary to the microarray analysis, large-sample verification of significantly elevated circRNA expression was partially consistent (hsa_circ_0092270), and inconsistent (hsa_circ_0045808, hsa_circ_0070162), with the microarray results. The findings highlight the significance of circRNAs in AD and that hsa_circ_0092270 represents a promising biomarker for future studies.

overall_design: The circRNA microarray was used to screen the differentially expressed circRNAs in peripheral blood leukocytes from 3 patients with AD and 4 healthy control participants

first: Juan

first: Weidong

last: Wu


title: A pilot prevention study of the effects of the anti- progestin Ulipristal Acetate (UA) on surrogate markers of breast cancer risk

city: Manchester

first: Sacha

last: Howell

address: Oglesby Cancer Research Centre

department: Faculty of Biology, Medicine and Health

country: United Kingdom

institute: The University of Manchester

summary: The Illumina Infinium Epic Human DNA methylation Beadchip was used to obtain DNA methylation profiles across more than 850,000 CpGs.

overall_design: Bisulphite converted DNA was hybridised to the Illumina Epic Human Methylation Beadchip.


title: Whole genome expression profile of human decidual PMN-MDSC and autologous neutrophils in normal pregnancy

city: Shanghai

first: Qiaohong

last: Wang

address: 160 Pujian Road

department: OB & GYN

institute: Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University

summary: It is suggested that decidual polymorphonuclear myeloid-derived suppressor cell (PMN-MDSCs) are a group of activated suppressive neutrophils. Decidual microenvironment can facilitate circulating neutrophils with phenotypes and functions of PMN-MDSCs. The mechanism of PMN-MDSCs differentiation induced by decidual microenvironment has not been fully understood. Here we performed whole genome expression profile of 3 decidual PMN-MDSCs and autologous neutrophils from normal early pregnancy. Total RNA were extracted. The arrays were scanned by the Agilent Scanner G2505C. There were differences of gene expression pattern between decidual PMN-MDSCs and autologous neutrophils in early normal pregnancy.

overall_design: Total RNA of 3 decidual PMN-MDSC and autologous neutrophils from normal early pregnancy.  were analyzed and compared in this study.

first: Aimin


title: ssDNA is an allosteric regulator of the C. crescentus SOS-independent DNA damage response transcription activator, DriD

city: Cambridge

first: Kevin

last: Gozzi

address: 31 Ames St

institute: Massachusetts Institute of Techonology

summary: DNA damage repair systems are critical for genomic integrity. However, they must be coordinated with DNA replication and cell division to ensure accurate genomic transmission. In most bacteria this coordination is mediated by the SOS response through LexA , which triggers a halt in cell division until repair is completed. Recently, an SOS-independent damage response system was revealed in Caulobacter crescentus. This pathway is controlled by the transcription activator, DriD, but how DriD senses and signals DNA damage is unknown. To address this question we performed biochemical, cellular, and structural studies. We show that DriD binds a specific promoter DNA site via its N-terminal HTH domain to activate transcription of genes including the cell division inhibitor didA. A structure of the C-terminal portion of DriD revealed a  WYL-motif domain linked to a WCX dimerization domain. Strikingly, we found that DriD binds ssDNA between the WYL and WCX domains. Comparison of apo and ssDNA-bound DriD reveals that ssDNA binding orders and orients the DriD domains, indicating a mechanism for ssDNA-mediated DNA-binding activation.  Biochemical and in vivo studies support the structural model. Our data indicate this as a conserved mechanism of signaling for WYL-containing regulators.

overall_design: Chromatin-immunoprecipitation with deep sequencing experiments (ChIP-seq) were performed on mid exponential-phase Caulobacter crescentus treated with and without DNA damage (see the Materials and Methods for the exact treatment that were applied to each strain).

first: Raul

last: Salinas

first: Viet

middle: D

last: Nguyen

first: Michael

middle: T

last: Laub

first: Maria

middle: A

last: Schumacher


title: Adipose-derived stromal/stem cells for bio-root regeneration

city: Chongqing

first: Jie

state: Chongqing

address: 426# Songshibei Road, Yubei District

department: College of Stomatology

institute: Chongqing Medical University

summary: To explore molecular mechanisms of different seed cells in bio-root regeneration, RNA sequencing (RNA-seq) was performed on adipose-derived stromal/stem cells (ASCs) and two dental derived stem cells

overall_design: Comparative gene expression profiling analysis of RNA-seq data for adipose-derived stromal/stem cells (ASCs), dental follicle cells (DFCs), and stem cells from human exfoliated deciduous teeth (SHEDs).


title: Orgo-Seq integrates single-cell and bulk transcriptomic data to identify cell type specific-driver genes associated with autism spectrum disorder

city: Worcester

first: Elaine

last: Lim

address: 366 Plantation Street, Paul J DiMare 5-1025

institute: UMass Chan Medical School

summary: To investigate the cell types and driver genes perturbed by 16p11.2 deletions using cerebral organoids

overall_design: We performed RNA sequencing on cerebral organoids differentiated from 9 donors with 16p11.2 deletions versus 12 control donors.


title: Pilot Trial of Arginine Deprivation plus Nivolumab and Ipilimumab in Patients with Metastatic Uveal Melanoma

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

summary: Metastatic uveal melanoma (UM) remains challenging to treat, with objective response rates to immune checkpoint blockade (ICB) much lower than in primary cutaneous melanoma (CM). Besides a lower mutational burden, the overall immune-excluded tumor microenvironment of UM might contribute to the poor response rate. We therefore aimed at targeting deficiency in argininosuccinate synthase 1, which is a key metabolic feature of UM. This study aimed at investigating safety and tolerability of a triple combination consisting of ipilimumab and nivolumab immunotherapy and the metabolic therapy ADI-PEG 20. 9 patients were enrolled in this pilot study. The combination therapy was safe and tolerable with absence of immune related adverse events (irAE) of special interest but with 4 of 9 patients experiencing a CTCAE grade 3 AE. No objective responses were observed. All except one patient developed anti-drug antibodies (ADA) within a month of treatment initiation and therefore did not maintain arginine depletion. Further, an IFNg-dependent inflammatory signature was observed in metastatic lesions in patients pre-treated with ICB compared with patients with no pretreatment. Multiplex immunohistochemistry demonstrated variable presence of tumor infiltrating CD8 lymphocytes and PD-L1 expression at baseline in metastases.

overall_design: Patients with metastatic uveal melanoma with various pretreatments/first line were enrolled in this pilot clinical trial. Samples were collected at baseline.

first: Alexander

middle: N

last: Shoustari

first: Taha

last: Merghoub

first: Levi

last: Mangarin

first: Lukas

last: Kraehenbuehl


title: Next Generation Sequencing of human circulating neutrophils treated with decidual  explant supernatant or not

summary: Decidual microenvironment can induce circulating neutrophils to acquire the phenotypes and functions of decidual polymorphonuclear myeloid-derived suppressor cell (PMN-MDSCs). The mechanism of PMN-MDSCs differentiation induced by decidual microenvironment has not been fully understood. Here we performed whole genome expression profile of neutrophils treated with decidual explant supernatant (DES) or not (n=3). Total RNA were extracted. Transcriptome libraries were generated with the Illumina TruseqTM RNA sample prep Kit, and sequencing was performed on the Illumina Novaseq 6000 platform. There were differences of gene expression after DES treatment.

overall_design: Retinal mRNA profiles of human circulating neutrophils treated with decidual  explant supernatant or not (n=3).

last: Zhao


title: RNA seq analysis of human monocyte subsets in healthy and dengue subjects

city: New Delhi

first: Anmol

last: Chandele

state: Delhi

address: Aruna Asaf Ali Marg

country: India

institute: International Center for Genetic Engineering and Biotechnology

summary: In this analysis, sorted classical (CM), intermediate (IM) and non-classical (NCM) monocyte subsets from children under steady state (healthy, H) and dengue febrile illness (Dengue, D) were analyzed for their transcriptional profiles using RNA seq. The monocyte subsets were sorted from peripheral blood cells after excluding CD3, CD19, CD20, CD56, CD66b and NKp30 positive cells and then gating on HLADR positive population to identify CM, IM and NCM subsets based on surface expression of CD16 and CD14. The transcriptional profile of the three monocyte subsets was separately compared in healthy children, in dengue febrile children and in dengue versus healthy states. This study highlights hierarchy of gene expression in classical, intermediate and non-classical monocytes in healthy and dengue febrile conditions.

overall_design: Expression analysis of  CD14+ CD16 low classical monocytes, CD14+ CD16+ intermediate monocytes and CD14 low CD16+ non-classical monocytes sorted from healthy and dengue subjects.

first: Murali

last: Kaja


title: Gene regulation in CXCL4 and TLR8 signaling crosstalk

first: Mahesh

last: Bachu

email: bmahesh07@gmail.com, bachum@hss.edu

state: New York

address: 535 E 70th St 6th Floor

institute: Hospital For Special Surgery

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

overall_design: Refer to individual Series


title: Developmental dynamics of the neural crest-mesenchymal axis in creating the thymic microenvironment

city: Oxford

first: Adam

last: Handel

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: The thymic stroma is composed of epithelial and non-epithelial cells that collectively provide separate microenvironment controlling the homing of blood-born precursors to the tissue, and their subsequent differentiation to functionally mature and correctly selected T cells. While thymic epithelial cells are well characterised for their role in thymopoiesis, a comparably comprehensive analysis of the non-epithelial thymic stroma is lacking. Here we explore at single cell resolution the complex composition and dynamic changes that occur over time in the non-epithelial stromal compartmenti. We detail across different developmental stages in human and mouse thymus tissues and in an experimental model of the most common form of human thymus hypoplasia the separate transcriptomes of mouse mesothelium, fibroblasts, neural crest cells, endothelial and vascular mural cells. The detected gene expression signatures identify novel stromal subtypes and relate their individual molecular profiles to separate differentiation trajectories and functions. Specifically, we demonstrate an abundance and unprecedented heterogeneity of diverse fibroblast subtypes that emerge at discrete developmental stages and vary in their expression of key regulatory signalling circuits and components of the extracellular matrix. Taken together, these findings highlight the dynamic complexity of the non-epithelial thymus stroma and link the cells’ specific gene expression profiles to separate instructive roles essential for normal thymus organogenesis and tissue maintenance. The study has been granted ethical approval and is publicly listed (IRAS ID 156910, CPMS 19587).

overall_design: Human thymic stromal cells - 10x Genomics multiomics (gene expression [GEX] and Assay for Transposase-Accessible Chromatin [ATAC]): 14 post-conceptional weeks (n=1) and 17 post-conceptional weeks (n=1)

first: Fatima

last: Dhalla

first: Stefano

last: Maio

first: Georg

last: Holländer


title: Quantitative Analysis of CXCL4 and TLR8 signaling crosstalk in human primary monocytes by RNA-Seq

summary: To gain a comprehensive understanding of gene regulation in CXCL4 and TLR8 signaling crosstalk, we treated primary human blood monocytes with CXCL4 and TLR8 ssRNA ligand ORN8L for 6 h and performed transcriptomic analysis via RNA-seq. We observed that CXCL4 interacted with TLR8 ssRNA ligand and triggered inflammatory cytokine storm including IL6, IL12p40, TNF and IFNβ, and pro-fibrotic gene expression and activated NLRP3 inflammasome leading to interleukin-1β (IL-1β) secretion and pyroptosis in human blood monocytes.

overall_design: mRNA of human primary monoyctes from 3 healthy donors after 6 h of 10 ug/ml CXCL4 and/or 20 ug/ml ORN8L stimulation were used for library preparing and RNA sequencing.

first: Giancarlo

last: Chesi

first: Chao

last: Yang


title: Distinct regulation of gene promoters and enhancers by CXCL4 and TLR8 in human CD14+ monocytes

overall_design: Examination of open chromatin regions by ATAC-seq in human CD14+ monocytes exposed for 6 h to CXCL4 ( 10 ug/ml) or ORN8L( 20 ug/ml) or both CXCL4 and ORN8L

first: Yang

last: Chao


title: RNA from RAW 264.7 cells treated with miR-loaded extracellular vesicles

city: New Orleans

first: Tina

middle: M

last: O'Grady

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

summary: RNA was harvested from RAW 264.7 cells treated with miR-loaded extracellular vesicles

overall_design: 3 replicates each of RAW 264.7 cells treated with miR-loaded extracellular vesicles

first: Makon-Sébastien

last: Njock

first: Ingrid

last: Struman

first: Franck

last: Dequiedt


title: Small RNA in endothelial cells and EVs cultured alone or with tumor cells

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA was harvested from endothelial cells cultured alone or with tumor cells and the associated endothelial extracellular vesicles.

overall_design: 3 replicates each of EVs from HUVECs cocultured with tumor cells or HUVECs cultured alone


title: Essential role of Cp190 in physical and regulatory boundary formation in Drosophila [Capture-C]

status: Public on May 12 2022

city: Lausanne

first: Maria Cristina

last: Gambetta

address: Genopode Building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

summary: While Drosophila has widespread contact domains, most domain boundaries are formed independently of CTCF by unclear mechanisms. We genetically ablate the ubiquitous boundary-associated factor Cp190 and examine impacts on genome folding and developmental gene regulation in Drosophila embryos. We find that Cp190 is widely required to form fly domain boundaries that are distal from transcribed gene promoters, while promoter proximal boundaries are unaffected by Cp190 loss.

overall_design: About 100 2-6 hour old embryos that were wildtype, Cp190[0], or SF1[KO] mutants were mechanically disrupted and fixed in biological triplicates, and Hi-C libraries were prepared using MseI and Csp6I as restriction enzymes. Multiplexed Hi-C libraries were subjected to two successive rounds of capture using 5'-biotinylated 120 nt oligos with viewpoints in HOX genes and control loci. Capture-C libraries were then sequenced 150 bp paired-end on a Novaseq 6000 instrument.

first: Anjali

last: Kaushal

first: Julien

last: Dorier

first: Bihan

last: Wang

first: Pascal

last: Cousin

first: Michael

last: Taschner

first: Giriram

last: Mohana

first: Arina

last: Omer

first: Anastasiia

last: Semenova

first: Christian

last: Iseli

first: Patrice

last: Waridel

first: Manfredo

last: Quadroni

first: Nicolas

last: Guex

first: Erez

middle: L

last: Aiden

first: Maria

middle: C


title: The circadian clock in the retinal pigment epithelium controls the diurnal rhythm of phagocytic activity

city: Atlanta

first: Gianluca

last: Tosini

state: GA

address: 720 Westview Drive

institute: Morehouse School of Medicine

summary: The diurnal peak of phagocytosis by the retinal pigment epithelium (RPE) of photoreceptor outer segments is under circadian control, and it is believed that this process involves interactions from both the retina and RPE. Previous studies have demonstrated that a functional circadian clock exists within multiple retinal cell types and RPE cells. Thereby, the aim of the current study was to determine whether the circadian clock in the retina and or RPE controls the diurnal phagocytic peak of photoreceptor outer segments and whether selective disruption of the circadian clock in the RPE would affect RPE cells function and the viability during aging. To that aim, we first generated and validated an RPE tissue-specific KO of the essential clock gene, Bmal1, and then we determined the daily rhythm in phagocytic activity by the RPE in mice lacking a functional circadian clock in the retina or RPE. Then using electroretinography, spectral domain-optical coherence tomography, and optomotor response measurements of visual function we determined the effect of Bmal1 removal in young (6-month-old) and old (18-months old) mice. RPE morphology and lipofuscin accumulation was also determined in young and old mice. Our data show that the circadian clock in the RPE controls the daily diurnal phagocytic peak of POS. Surprisingly, the lack of a functional RPE circadian clock or the diurnal phagocytic peak does not result in any detectable age-related degenerative phenotype in the retina or RPE. Thus, our results demonstrate that the circadian clock in the RPE controls the daily peak in the phagocytic activity. However, the loss of the circadian clock in the RPE does not result in deterioration of photoreceptors or the RPE during aging.

overall_design: Retinal pigment epithelium samples from Bmal1-specific KO from RPE cells in mouse, three replicates from a pool of two RPE isolates for each replicate, samples collected at ZT1, ZT7, ZT13, ZT19

first: Christopher

last: DeVera

first: Jendayi

last: Dixon

first: Micah

last: Chrenek

first: Kenkichi

last: Baba

first: P

last: Iuvone


title: Dosage-sensitive miRNAs trigger modulation of gene expression during genomic imbalance in maize

city: Hangzhou

first: Xiaowen

last: Shi

state: Zhejiang

address: 866 Yuhangtang Road NongshenghuanA443

department: College of Agriculture and Biotechnology

institute: Zhejiang University

summary: Genomic imbalance caused by varying the dosage of individual chromosomes or chromosomal segments (aneuploidy) has more detrimental effects than altering the dosage of complete chromosome sets (ploidy). Previous analysis on RNA-sequencing data of varied dosage of various chromosomal regions in maize (Zea mays) revealed global modulation of gene expression both on the varied chromosome (cis) and the remainder of the genome (trans). Dysregulation of microRNA (miRNA) dosage has been reported to have profound deleterious effects in many species. miRNAs are preferentially retained as duplicates following whole-genome duplication in grass species and are postulated to be dosage-sensitive. However, little is known regarding the role of miRNAs under genomic imbalance. We examined the impact of increased and/or decreased dosage of 1 interstitial and 19 distal chromosomal regions in concert with a whole-genome ploidy series of haploid, diploid, triploid, and tetraploid via small RNA-sequencing of diploid and haploid maize mature leaf tissue to investigate the impact of aneuploidy and polyploidy on expression of miRNAs. In general, cis miRNAs in aneuploids present a predominant gene-dosage effect, whereas trans miRNAs trend toward the inverse level, although other types of responses including dosage compensation, increased effect, and decreased effect also occur. Significant correlations between expression levels of miRNAs and their targets were identified in aneuploids, indicating the regulatory role of miRNAs on gene expression triggered by genomic imbalance. The findings provide novel insights into understanding of gene balance from the aspect of the function of miRNAs.

overall_design: Small RNA sequencing was performed to the maize mature leaf tissue of a collection of 20 maize B-A translocation lines created by translocations between the normal chromosomes and the supernumerary B chromosome containing various copies of chromosomal segments covering 82.1% of the maize W22 genome, in concert with a whole-genome ploidy series of haploid, diploid, triploid and tetraploid lines.

first: James

last: Birchler

first: Hua

last: Yang


title: Simultaneous Detection of DNA Adenine and Cytosine Methylation using NT-seq

city: Houston

first: Tao

middle: P.

last: Wu

state: TX

address: One Baylor Plaza, MS BCM225

department: Molecular and Human Genetics

institute: Baylor College of Medicine

type: Methylation profiling by high throughput sequencing

sample_organism:
Helicobacter pylori
Escherichia coli
Oxytricha trifallax
mixed culture metagenome


title: Essential role of Cp190 in physical and regulatory boundary formation in Drosophila [ChIP-seq]

first: Maria Cristina

last: Gambetta

overall_design: Chromatin was prepared from 0-14 hour old embryos that were wildtype, Cp190[0], CTCF[0] or double[0] (i.e. CTCF[0] and Cp190[0]), in biological triplicates. Chromatin was also prepared from wildtype (WT), Cp190[KO] and su(Hw)[KO] mutant third instar larval central nervous systems (CNSs) in biological duplicates. ChIP-seq was performed with antibodies recognizing CTCF or Cp190. Multiplexed ChIP-seq libraries were sequenced paired-end on 2 (for embryo ChIP) or 1 (for larval CNS ChIP) lanes of a HiSeq4000 instrument.

first: Anjali

last: Kaushal

first: Julien

last: Dorier

first: Bihan

last: Wang

first: Pascal

last: Cousin

first: Michael

last: Taschner

first: Giriram

last: Mohana

first: Arina

last: Omer

first: Anastasiia


title: Polycomb-mediated genome architecture enables long-range spreading of H3K27 methylation [Cut&Tag]

city: Stanford

first: Howard

middle: Y

last: Chang

state: CA

address: CCSR 2130, 269 Campus Drive

department: Center for Personal Dynamic Regulomes

institute: Stanford University

summary: Polycomb-group proteins play critical roles in gene silencing through the deposition of histone H3 lysine 27 trimethylation (H3K27me3) and chromatin compaction. This process is essential for embryonic stem cells (ESCs) pluripotency, differentiation, and development. Polycomb repressive complex 2 (PRC2) can both read and write H3K27me3, enabling processive spread of H3K27me3 on linear genome and epigenetic memory. Long-range Polycomb-associated DNA contacts have also been described, but their regulation and role in gene silencing remains unclear. Here, we develop H3K27me3 HiChIP and apply optical reconstruction of chromatin architecture to reveal long-range Polycomb-associated DNA loops that span tens to hundreds of megabases and across multiple topological associated domains in mouse ESCs and human induced pluripotent stem cells. H3K27me3 loop anchors are enriched for Polycomb nucleation points and coincide with key developmental genes, such as Hmx1, Wnt6 and Hoxa. Genetic deletion of H3K27me3 loop anchors causes spatially proximal partner chromosomal loci to break apart, and alters H3K27me3 deposition, both locally and megabases away on the same chromosome. A selective EZH2 mutant deficient in RNA binding but intact H3K27me3 enzymatic activity leads to global alteration in H3K27me3 loops, decreased spatial proximity, and failure to spread Polycomb from PRC2 nucleation points to partner loci at developmental genes. Together, these results suggest PRC2 acts as a “genomic wormhole”, using RNA binding to enhance long range chromosome folding and H3K27me3 spreading. Developmental gene loci have novel roles in Polycomb spreading, emerging as key architectural elements of the epigenome.

overall_design: H3K27me3 Cut&Tag of CRISPR-Cas9 edited mouse embryonic stem cells (mESCs).

first: Katerina

last: Kraft

first: Kathryn

middle: E

last: Yost

first: Sedona

last: Murphy

first: Andreas

last: Magg

first: Yicheng

last: Long

first: M

middle: R

last: Corces

first: Jeffrey

last: Granja

first: Stefan

last: Mundlos

first: Thomas

last: Cech

first: Alistair

last: Boettiger


title: Simultaneous Detection of DNA Adenine and Cytosine Methylation using NT-seq [series2: 6mA DIP enrichment]

first: Tao

last: Wu

summary: DNA methylation plays important roles in foreign DNA defense, mismatch repair, and gene regulation in prokaryotic genomes. Existing methods for DNA methylation detection using next-generation sequencing (NGS) are incapable of simultaneously detecting multiple types of DNA methylation. Here, we present nitrite treatment followed by sequencing (NT-seq), a sequencing method to simultaneously detect adenine and cytosine methylation. We demonstrated that NT-seq reliably detects three types of methylation motifs in E. coli and H. pylori genomes. We further applied NT-seq to a microbial community standard for de novo methylation motif discovery. Finally, by coupling methyl DNA immunoprecipitation and NT-seq (DIP-NT-seq), we showed that 6mA could be accurately mapped at single-base resolution in the bacterial and eukaryotic genomes. NT-seq thus provides a simple and reliable solution for detecting multiple types of DNA methylations.

sample_organism:
Escherichia coli
Oxytricha trifallax

platform_organism:
Escherichia coli
Oxytricha trifallax

overall_design: NT-seq in both native and amplified DNA after 6mA DIP enrichment

first: Xuwen

last: Li


title: Simultaneous Detection of DNA Adenine and Cytosine Methylation using NT-seq [series1: no enrichment]

sample_organism:
Helicobacter pylori
Escherichia coli
mixed culture metagenome

overall_design: NT-seq in both native and amplified genomic DNA without any enrichment


title: Essential role of Cp190 in physical and regulatory boundary formation in Drosophila

first: Maria Cristina

last: Gambetta


title: RNA from 4T1 tumors in mice treated with miR-loaded EVs

first: Tina

last: O'Grady

summary: RNA was harvested from 4T1 tumors in mice treated with miR-loaded EVs

overall_design: 3 replicates each of 4T1 tumors in mice treated with miR-loaded EVs

first: Makon-Sébastien

last: Njock

first: Ingrid

last: Struman

first: Franck

last: Dequiedt


title: Pore-C: Combination of chromatin capture assay and Oxford Nanopore Technology long read sequencing.

first: Marcin

last: Imielinski

address: 413 E 69th Street

department: Pathology and Laboratory Medicine

institute: Weill Cornell Medicine

summary: Higher-order chromatin structure arises from the combinatorial physical interactions of many genomic loci. To investigate this aspect of genome architecture we developed Pore-C, which couples chromatin conformation capture with Oxford Nanopore Technologies (ONT) long reads to directly sequence multi-way chromatin contacts without amplification.

overall_design: 4 samples with several replicates to investigate 3D chromatin conformation

first: Eoghan

last: Harrington


title: RNA-SEQ OF APOCC and GOCA2 ovarian cancer cell lines

status: Public on May 11 2022

city: Doha

first: Najeeb

last: Halabi

address: Education City

country: Qatar

institute: Weill Cornell Medicine in Qatar

summary: The aim of this study was to establish baseline gene expression data for two primary ovarian cancer cell lines.

overall_design: Each cell line was sequenced in two replicates under basal 2D cell culture

first: Halema

last: Al-Farsi


title: p53 regulates a miRNA-fructose transporter axis in brown adipose tissue under fasting

city: Graz

first: Ingeborg

last: Klymiuk

address: Neue Stiftingtalstrasse 6

country: Austria

institute: Medical Univ Graz

summary: Active thermogenic adipocytes voraciously consume energy substrates like fatty acids and glucose to maintain body temperature upon cold exposure. Despite strong evidence for the involvement of brown adipose tissue (BAT) in controlling systemic energy homeostasis upon nutrient excess, it is unclear how the activity of brown adipocytes is regulated in times of nutrient scarcity. Therefore, this study aimed to scrutinize factors that modulate BAT activity to balance thermogenic and energetic needs upon simultaneous fasting and cold-exposure. For an unbiased view we performed transcriptomic and miRNA sequencing analysis of BAT from acutely fasted (24 hours) mice under mild cold exposure. Combining these data with in-depth bioinformatic analyses and in vitro experiments, we defined a previously undescribed axis of p53 and miR-92a-1-5p that is highly upregulated by fasting in thermogenic adipocytes. p53, a fasting-responsive transcription factor, was previously shown to control genes involved in the thermogenic program and miR-92a-1-5p was found to negatively correlate with human BAT activity. Here, we elucidated fructose transporter Slc2a5 as one direct downstream target of this axis and show that fructose can be taken up by and metabolized in brown adipocytes. In sum, this study delineates a fasting-induced pathway involving p53 and miR-92a-1-5p impinging on Slc2a5 and suggests a contribution of fructose as an energy substrate in thermogenic adipocytes.

overall_design: 9 samples, three groups, 3 samples per group


title: Dynamic changes of nonepithelial thymic stroma during thymus organogenesis

first: Adam

last: Handel

summary: The thymic stroma provides the microenvironment for T cell lineage commitment, development, maturation, and repertoire selection. While the thymic epithelial cell (TEC) compartment is relatively well characterised, a comparably detailed analysis of the non-TEC stromal compartment including the endothelial cells and fibroblasts is currently lacking. Here, we probe the composition of thymic mesenchymal cells and their dynamic change during thymus organogenesis. Using a single cell transcriptomic approach, we identify previously unappreciated heterogeneity within the non-TEC stromal compartment and demonstrate dynamic shifts within non-TEC stromal cell populations over thymic development. We then use a compound heterozygous model (Tbx1+/-Crkl+/-) for 22q11.2DS syndrome to show that significant reductions of multiple mesenchymal subpopulations associated with functional defects and accelerated aging are associated with the thymic hypoplasia observed in this condition. Thus, we provided a comprehensive picture of non-TEC thymic stromal development and their functional defects in a disease model of thymic hypoplasia.

overall_design: Thymic stromal cells - 10X gene expression: non-TEC thymic stroma over development (n=8) and thymic stroma wild-type vs. Tbx1+/-Crkl+/- mice (n=6); RNA-seq wild-type thymic stroma mice

first: Stanley

last: Cheuk

first: Georg

last: Holländer


title: Essential role of Cp190 in physical and regulatory boundary formation in Drosophila [HiC]

overall_design: About 100 2-6 hour old embryos that were wildtype, Cp190[0], CTCF[0] or double[0] (i.e. CTCF[0] and Cp190[0]) mutants were mechanically disrupted and fixed in biological quadruplicates, and Hi-C libraries were prepared using MseI and Csp6I as restriction enzymes. Multiplexed Hi-C libraries were sequenced paired-end on HiSeq4000 instruments.

first: Anjali

last: Kaushal

first: Julien

last: Dorier

first: Bihan

last: Wang

first: Pascal

last: Cousin

first: Michael

last: Taschner

first: Giriram

last: Mohana

first: Arina

last: Omer

first: Anastasiia

last: Semenova

first: Christian

last: Iseli

first: Patrice

last: Waridel

first: Manfredo

last: Quadroni

first: Nicolas

last: Guex

first: Erez

last: Aiden

first: Maria


title: Glucocorticoid receptor-regulated enhancers play a central role in the gene regulatory networks underlying drug addiction

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

summary: Substance abuse and addiction represent a major public health problem that impacts multiple dimensions of society, including healthcare, economy, and workforce. In 2021, over 100,000 drug overdose deaths have been reported in the US with an alarming increase in fatalities related to opioids and psychostimulants. Understanding of the fundamental gene regulatory mechanisms underlying addiction and related behaviors could facilitate more effective treatments. To explore how repeated drug exposure alters gene regulatory networks in the brain, we combined capped small (cs)RNA-seq, which accurately captures nascent-like initiating transcripts from total RNA, with Hi-C and single nuclei (sn)ATAC-seq. We profiled initiating transcripts in two addiction-related brain regions, the prefrontal cortex (PFC) and the nucleus accumbens (NAc), from rats that were never exposed to drugs or were subjected to prolonged abstinence after oxycodone or cocaine intravenous self-administration (IVSA). Interrogating in total over 100,000 active transcription start regions (TSRs) revealed that most TSRs had hallmarks of bona-fide enhancers and highlighted the KLF/SP1, RFX and AP1 transcription factors families as central to establishing  brain-specific gene regulatory programs. Analysis of rats with addiction-like behaviors versus controls, identified addiction-associated repression of transcription at regulatory enhancers recognized by nuclear receptor subfamily 3 group C (NR3C) factors, which include glucocorticoid receptors. Cell-type deconvolution analysis using snATAC-seq uncovered a potential role of glial cells in driving the gene regulatory programs associated with addiction-related phenotypes. These findings highlight the power of advanced transcriptomics methods to provide insight into how addiction perturbs gene regulatory programs in the brain.

overall_design: Transcription initiation profiling (csRNA-seq), 3D genome structure (Hi-C), and single cell open chromatin profiling (snATAC-seq) all using high-throughput sequencing

first: Sascha

middle: H

last: Duttke

first: Patricia

last: Montilla-Perez

first: Max

middle: W

last: Chang

first: Hairi

last: Li

first: Hao

last: Chen

first: Lieselot

last: Carrette

first: Giordano

last: de Guglielmo

first: Olivier

last: George

first: Abraham

last: Palmer

first: Francesca

last: Telese


title: SAHA, VPA and JQ1 treatment in ISOS-1

status: Public on May 10 2022

city: Sapporo

first: Keisuke

last: Aoshima

state: Hokkaido

address: Kita 18 Nishi 9

department: Faculty of Veterinary Medicine

country: Japan

institute: Hokkaido University

summary: ISOS-1, a mouse angiosarcoma cell line, was treated with histone deacetyltransferase inhibitors (HDACI: SAHA and VPA) and a bromodomain and extraterminal domain inhibitor (BETi: JQ1).

overall_design: mRNA expression profiles of ISOS-1 cell line treated with DMAO, SAHA, VPA or JQ1.

first: Tamami

last: Suzuki


title: Perirenal Adipose Afferent Nerves Sustain Pathological High Blood Pressure

city: nanjing

first: mingyan

last: lin

address: 101Longmian Avenue, Jiangning District, Nanjing

institute: nanjing medical university

summary: Hypertension is a pathological condition of persistent high blood pressure (BP) of which the underlying mechanisms remain largely obscure. Here, we show that the afferent nerves in perirenal adipose tissue are a regulatory site in triggering and maintaining pathological high BP, without affecting physiological BP. Bilateral perirenal adipose tissue (PRAT) ablation leads to a long-term and effective reduction of BP in spontaneous hypertensive rats (SHR) and high fat and high salt diet fed rats, but has no effect on normal BP in control Wistar-Kyoto or control SD rats. Moreover, gain- and loss-of-function studies show that augmented activities of L1-L2 dorsal root ganglia (DRG) neurons are responsible for hypertension in SHR. Further, L1-L2 DRG neuron transcriptomics uncovers significant changes in neuron development, remodeling, and plasticity. Importantly, calcitonin gene-related peptide (CGRP), a systemic vasodilator, is induced after PRAT ablation. We went on to show that CGRP antagonist blocks the BP-lowering effect of PRAT ablation. CGRP is therefore a key endogenous suppressor of hypertension that is sequestered by anti-hypertensive PRAT in SHRs. Taken together, we identify PRAT afferent nerves as a pathological node of hypertension that sustains high BP via suppressing CGRP, thereby providing a therapeutic target to tackle primary hypertension.

overall_design: Examination of mRNA profiles in DRG tissues from three PRATA  spontaneously hypertensive rats and three sham-operated spontaneously hypertensive rats by Illumina RNA sequencing.

first: Peng

first: Xiaoguang

last: Wu

first: Boxun

last: Liu

first: Wei

last: Sun

first: Xiangqing

last: Kong


title: Switch tandem repeats influence the choice of the alternative end-joining pathway in class switch recombination

city: Toulouse

first: Chloé

last: Oudinet

address: 205 route de Narbonne

department: Oncology

country: France

institute: IPBS

overall_design: We performed CSR-HTGTS-Seq in mature splenic B cells with different stimulation conditions to study antibody class switching in A150 mice model

first: Frederick

last: Alt

first: Xuefei

last: Zhang


title: Gene set enrichment analysis of basal and in vitro irradiation differentiates breast cancer patients with late skin radiotherapy toxicity

city: Barcelona

first: Ester

last: Aguado-Flor

state: Barcelona

address: c/Natzaret, 115-117

country: Spain

institute: Vall Hebron Institute of Oncology (VHIO)

summary:
Radiation-induced late effects remain a common cause of morbidity amongst cancer survivors.
The purpose of this study was to investigate the molecular basis underlying the radiotherapy-induced late skin toxicity in breast cancer patients who were previously assessed for radiation-induced lymphocyte apoptosis (RILA).

overall_design: Peripheral blood mononuclear blood cells of 10 patients with severe skin late complications from radiotherapy and 10 patients without symptoms were mock-irradiated or irradiated with 8-Gy X-rays. The 48-h radiation response was analysed by gene expression profiling with Affymetrix microarrays Human Exon 1.0 ST array.Gene set enrichment analysis was performed to identify differentially expressed biological processes.

first: Sara

last: Guitérrez-Enríquez


title: RNA-sequencing of inguinal adipose tissue from wild type and adipocyte specific HIF2a knock-out mice upon thermoneutral and cold exposure

city: Seoul

first: Jae Bum

last: Kim

address: Bldg 105-Rm. 333, Seoul National University, San 56-1, Sillim Dong, Kwanak-Gu

department: Biological Sciences

country: South Korea

institute: Seoul National University

summary: Adipose tissue plays an important role in the regulation of wholebody energy homeostasis, depending on external environments. Upon cold acclimation, brown and beige adipocytes dissipate mitochondrial proton gradient generating heat via uncoupling protein 1. Due to increasing demands for oxygen during thermogenesis, adipose tissue could become hypoxic upon cold exposure. Hypoxia-inducible factors (HIFs) are one of the major transcription factors which are involved in various cellular responses under hypoxic condition. Although HIFs regulate diverse metabolic processes with selective target gene expression, their roles in thermogenic adipocytes are still elusive. In this study, we demonstrate that adipocyte HIF2a regulate thermogenic activity upon cold stimuli. To investigate molecular mechanisms of adipocyte HIF2a upon thermoneutral and cold exposure, we report the transcriptomes of inguinal adipose tissue from WT and adipocyte specific HIF2a knock-out mice.

overall_design: Examination of 12 samples derived from inguinal adipose tissue of wild type and adipocyte specific HIF2a knockout mice upon thermoneutral or cold exposure

first: Ji

middle: S

last: Han

first: Min

last: Oh

first: Yong

middle: G

last: Jeon

first: Jae

middle: B


title: Identify the role of host ATF4 on CAFs in the tumor microenvironment of large size and small size B16F10 tumors

city: Athens

first: Evdokia

last: Karagouni

state: Attica

address: 127 Vas. Sofias Avenue

department: Department of Microbiology

country: Greece

institute: Hellenic Pasteur Institute

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

overall_design: Refer to individual Series


title: RNA sequencing to profile transcriptomes in murine bone-marrow-derived macrophages upon infection with Leptospira spp.

city: Taoyuan

first: Li-Fang

last: Chou

address: 5 Fu-Shing St., Kueishan

department: Department of Medical Research and Development

country: Taiwan

institute: Chang Gung Memorial Hospital, Linkou

summary: Leptospirosis is a re-emerging zoonosis, a globally important infectious disease, caused by an infection with the genus Leptospira. Leptospirosis is associated with acute kidney injury and progress to CKD due to sustained tubulointerstitial inflammation. Macrophages play a critical role in controlling the bacterial burden and tissue inflammation during the spirochete infections. To understand the molecular mechanisms of leptospia-induced macrophage activation and its role in the inflammatory process, we performed the transcriptome profiles of murine bone marrow-derived macrophages infected with pathogenic and non-pathogenuc Leptospira spp.at a multiplicity of infection of 100 for 2 and 24 hrs, respectively.

overall_design: Murine bone marrow-derived macrophages (BMDMs) infected with Leptospira spp. at different times after infection. The control group (n=3 per each group), non-infected BMDMs at the 2- and 24-hour time-points, respectively; the L. interrogans-infected BMDMs (n=3 per each group), BMDMs infected with pathogenic L. interrogans serovar Copenhageni Fiocruz L1-130 at the 2- and 24-hour time-points, respectively; the L. biflexa-infected BMDMs (n=3 per each group), BMDMs infected with non-pathogenic L. biflexa serovar Patoc at the 2- and 24-hour time-points, respectively.

first: Chih-Wei

last: Yang


title: miRNA pattern in hypoxic microenvironment of kidney cancer – role of PTEN

city: Warsaw

first: Klaudia

last: Brodaczewska

address: Szaserow 128

country: Poland

institute: Military Institute of Medicine

summary: MicroRNAs are post-transcriptional regulators of gene expression, disturbances of their expression are the basis of many pathological states, including cancers. The miRNA pattern in the context of tumor microenvironment, explains mechanisms related to cancer progression and pro-vides a potential target of modern therapies. Here we show how tumor hypoxia modifies the miRNA pattern in renal cancer focusing on the dysregulation PTEN being a major tumor suppressor for its regulation of others key suppressors. Methods comprised the CRSPR/Cas9 mediated PTEN knockout in Renca kidney cancer cell line and global miRNA expression analysis in both in vivo and in vitro (in normoxic and hypoxic conditions). The results were validated on human cancer models with distinct PTEN status. The increase in miR210-3p in hypoxia was universal, however, the hypoxia-induced decrease in PTEN was associated with an increase in miR-221-3p, the loss of PTEN affected differently the response to hypoxia by decreasing miR-10b-3-5p and increasing miR-206-3p. In turn, Complete loss of PTEN induces miR-155-5p, miR-100-5p. Upregulation of miR342-3p in knockout PTEN occurred in the context of whole tumor microenvironment. Thus effective identification of miRNA patterns in cancers must consider the specificity of the tumor microenvi-ronment together with the mutations of key suppressors.

overall_design: small RNA-Seq for wild type hypoxia cells (2 replicates), wild types normoxia cells (2 replicates), PTEN knock-out cells (2 replicates), control knock-out cells (2 replicates), PTEN knock-out normoxia (2 replicates) and hypoxia (2 replicates) cells

first: Aleksandra

last: Majewska

last: Filipiak-Duliban

first: Arkadiusz

last: Kajdasz

first: Claudine

last: Kieda


title: Global-run on sequencing identifies Gm11967 as an Akt-dependent long noncoding RNA involved in insulin sensitivity

city: Philadelphia

first: Paul

last: Titchenell

state: Pennsylvania

address: 3400 Civic Center Blvd.

department: Institute of Diabetes, Obesity, and Metabolism

institute: University of Pennsylvania

summary: We performed global run-on sequencing in the livers of fasted and refed mice in order to build a comprehensive map of the transcriptional changes in the liver in response to feeding. We further looked at the livers of mice lacking Akt (AktDKO) or Akt and FoxO1 (AktFoxo1TKO) to assess the role of insulin signaling in mediating this feeding response. With this method, we identified 599 feeding-regulated transcripts out of a total of 7,505. We took a particular interest in the long noncoding RNAs identified with this technique, of which there were 396, with 37 being feeding-regulated and 6 of those being dependent on Akt for their expression.

overall_design: We analyzed 2 replicates of control fasted and refed liver samples as well as 1

first: Dominic

last: Santoleri

first: Hee-Woong

last: Lim

first: Matthew

middle: J

last: Emmett

last: Gavin

first: Jaimarie

last: Sostre-Colón

first: Kahealani

last: Uehara

first: Mitchell

last: Lazar


title: Artificial neural networks enable genome-scale simulations of intracellular signaling

status: Public on May 09 2022

city: Cambridge

first: Bryan

last: Bryson

address: 77 Massachusetts Avenue

department: Department of Biological Engineering

institute: Massachusetts Institute of Technology

summary: Mammalian cells adapt their functional state in response to external signals in form of ligands that bind receptors on the cell-surface. Mechanistically, this involves signal-processing through a complex network of molecular interactions that govern transcription factor activity patterns. Computer simulations of the information flow through this network could help predict cellular responses in health and disease. Here we develop a recurrent neural network framework constrained by prior knowledge of the signaling network with ligand-concentrations as input and transcription factor -activity as output. Applied to synthetic data, it predicts unseen test-data (Pearson correlation r=0.98) and the effects of gene knockouts (r=0.8). We stimulate macrophages with 59 different ligands, with and without addition of lipopolysaccharide, and collect transcriptomics data. The framework predicts this data under cross-validation (r=0.8) and knockout simulations suggest a role for RIPK1 in modulating the lipopolysaccharide response. This work demonstrates the feasibility of genome-scale simulations of intracellular signaling.

overall_design: RNA-sequencing (Smart-seq2) was performed on primary monocyte-derived macrophages that were stimulated with ligands.

first: Avlant

last: Nilsson

first: Joshua

last: Peters

first: Nikolaos

last: Meimetis

first: Douglas

last: Lauffenburger


title: Alx function in the developing eye

status: Public on May 07 2022

city: Boston

first: Eric

last: Liao

address: CRMT, Simches Research Center, CPZN 4400, 185 Cambridge Street

institute: MGH

summary: Zebrafish with loss-of-function alx1 mutations develop with craniofacial and ocular defects of variable penetrance, likely due to compensatory upregulation in expression of a paralogous gene, alx3. We show that zebrafish alx1; alx3 mutants develop with highly penetrant cranial and ocular defects that resemble human ALX1-linked FND. alx1 and alx3 are expressed in anterior cranial neural crest (aCNC), which gives rise to the anterior neurocranium (ANC), anterior segment structures of the eye and vascular pericytes. Consistent with a functional requirement for alx genes in aCNC, alx1; alx3 mutants develop with nearly absent ANC and grossly aberrant hyaloid vasculature and ocular anterior segment, but normal retina. In vivo lineage labeling identified a requirement for alx1 and alx3 during aCNC migration, and transcriptomic analysis suggested oxidative stress response as a key target mechanism of this function. Oxidative stress is a hallmark of fetal alcohol toxicity, and we found increased penetrance of facial and ocular malformations in alx1 mutants exposed to ethanol, consistent with a protective role for alx1 against ethanol toxicity.

overall_design: Germline samples: RNAseq was performed on single zebrafish embryos  derived from an alx1;alx3/+ mutant incross.  A total of 12 samples (4 each of alx1, alx1; alx3/+ and alx1; alx3) were used  for pairwise comparisons; CRISPANTs samples: Additional samples were sequenced using 72hpf alx1; alx3 CRISPANTs (multiple alx3 guides injected into alx1 embryos). A total of 12 samples (6 from alx1; alx3 CRISPANTs and 6 WT).

first: Baul

last: Yoon

first: Pan

last: Yeung

first: Nicholas

last: Santistevan

first: Lauren

last: Bluhm

first: Kenta

last: Kawasaki

first: Janina

last: Kueper

first: Richard

last: Dubielzig

first: Jennifer

last: Vanoudenhove

first: Justin

last: Cotney

first: Yevgenya

last: Grinblat


title: Identify the role of host ATF4 on CAFs in the tumor microenvironment of small size B16F10 tumors

first: Evdokia

last: Karagouni

summary: To delineate the role of host ATF4 in the sequence of events leading to tumor growth, we performed transcriptional profiling at the single-cell level (scRNA-seq) in smaller (150 mm3) size B16F10 tumors grown in Atf4wt/wt and Atf4D/D mice. Among others, we observed striking differences in gene expression in a cluster that corresponds to CAFs. In this cluster, we identified 148 DE genes, including a significant downregulation of Col1a1 and Col1a2 in the Atf4D/D mice-grown tumors. Notably, the expression levels of aSMA and Pdgfrb were nearly absent in the tumors grown in Atf4D/D mice. Finally, after CAFs subclustering, we identified the vCAFs (vascular CAFs) that are considered essential for vascular development and angiogenesis to be significantly reduced in the Atf4D/D mice.

overall_design: Smaller size B16F10 tumors from two Atf4wt/wt and two Atf4D/D were harvested, pulled and submitted for scRNA-seq analysis.

first: Ioannis

last: Verginadis

first: Harris

last: Avgousti

first: Giorgos

last: Skoufos

first: Constantinos

last: Koumenis

first: Jonathan

last: Schug


title: Dissection of multiple sclerosis genetics identifies B and CD4+ T cells as driver cell subsets

status: Public on May 06 2022

first: Nikolaos

last: Patsopoulos

address: 60 Fenwood Road

institute: BRIGHAM AND WOMEN'S HOSPITAL

summary: We have performed ATAC-seq from FACS sorted immune cell populations from peripheral blood of human donors. All donors have a diagnosis of multiple sclerosis and some donors were treated with immunotherapy (glatiramer acetate, interferon beta, or natalizumab). We called peaks from the ATAC-seq data and tested for enrichment of open chromatin regions for each cell population in MS GWAS.

overall_design: We examined open chromatin regions in FACS-sorted immune cell populations from peripheral blood of human donors with a diagnosis of multiple sclerosis

first: Michael

last: Guo


title: Identify the role of host ATF4 on CAFs in the tumor microenvironment of large size B16F10 tumors

summary: To delineate the role of host ATF4 in the sequence of events leading to tumor growth, we performed transcriptional profiling at the single-cell level (scRNA-seq) in larger (300 mm3) size B16F10 tumors grown in Atf4wt/wt and Atf4D/D mice. We surprisingly detected impaired CAFs activation in Atf4D/D mice, based on the expression levels of Acta2 and Pdgfrb, as one of the most commonly used CAF markers. Among our key findings, we identified the vascular CAFs (vCAFs), a spatially distinct CAF subcluster featured by the highest levels of aSMA and PDGFRb, that were reduced in Atf4D/D mice.

overall_design: Large size B16F10 tumors (300 mm3) from four Atf4wt/wt and four Atf4D/D were harvested and submitted for scRNA-seq analysis.

middle: I


title: The Rho guanosine exchange factors Vav2 and Vav3 modulate epidermal stem cell function

city: Salamanca

first: L. Francisco

last: Lorenzo-Martín

state: Castilla y León

address: Campus Miguel de Unamuno

institute: University of Salamanca (USAL) – Centro de Investigación del Cáncer (CIC)

summary:
It is known that Rho GTPases control different aspects of the biology of skin stem cells (SSCs). However, little information is available on the role of its upstream regulators under normal and tumorigenic conditions in this process. To address this issue, we have used here mouse models in which the activity of guanosine nucleotide exchange factors of the Vav subfamily has been manipulated using both gain- and loss-of-function strategies.
These experiments indicate that Vav2 and Vav3 regulate the number, functional status, and responsiveness of hair follicle bulge stem cells. This is linked to gene expression programs related to the reinforcement of the SSC identity and the quiescent state. By contrast, Vav proteins promote transcriptomal programs associated with the identity and activation state of SSCs in cancer stem cells.

overall_design: Healthy skin stem cells (SSCs) (CD34+;Itga6+) from dorsal skin of 2.5-month-old WT, Vav2Onc and Vav2–/–;Vav3–/– (DKO) mice (n = 3 per genotype). Tumor stem cells (TSCs) (CD34+;Itga6+) from skin tumors obtained from 6-month-old WT and Vav2Onc mice after DMBA treatment (n = 4 per genotype)

first: L

middle: F

first: Mauricio

last: Menacho-Márquez

first: Sonia

last: Rodríguez-Fdez

first: Gloria

last: Pascual

first: Antonio

last: Abad

first: Piero

last: Crespo

first: Mercedes

last: Dosil

first: Salvador

last: Benitah

first: Xosé

last: Bustelo


title: Sequencing results of FTO overexpressing in papillary thyroid cells [meRIP-seq]

city: zhengzhou

first: xinguang

last: qiu

address: Erqi District, Zhengzhou City, Henan Province

institute: First Affiliated Hospital of Zhengzhou University

summary: We tried to analyze the effect of FTO on papillary thyroid carcinoma. We constructed a FTO overexpression stable cell line of papillary thyroid carcinoma cells. We performed meRIP-seq sequencing analysis of the FTO overexpression stable transfer cell line to try to assess which genes were changed at the m6A level in papillary thyroid cancer cells by overexpressing FTO.

overall_design: Comparative sequencing analysis of FTO overexpression stabilized cell lines of papillary thyroid carcinoma examined against normal papillary thyroid carcinoma cell lines.

first: Feihong

last: Ji

first: Xinguang

last: Qiu


title: RNA-seq and ATAC-seq of tumor resistance to immune cell attack

city: REGENSBURG

first: Claudia

last: GEBHARD

address: FRANZ-JOSEF-STRAUSS ALLEE 11

country: Germany

institute: UNIVERSITY HOSPITAL REGENSBURG


title: Trans-Seq for mammalian retinotectal circuit mapping

city: San Francisco

first: Xin

last: Duan

department: Ophthalmology

institute: UCSF

summary: The mouse visual system serves as an accessible model to understand mammalian circuit wiring. Despite rich knowledge in retinal circuits, the long-range connectivity map from distinct retinal ganglion cell (RGC) types to diverse brain neuron types remains unknown. Here we developed an integrated approach, named Trans-Seq, to map RGC to superior collicular (SC) circuits. Trans-Seq combines a fluorescent anterograde transsynaptic tracer, consisting of codon-optimized wheat germ agglutinin fused to mCherry, with single-cell RNA Sequencing. We used Trans-Seq to classify SC neuron types innervated by genetically-defined RGC types and predicted a neuronal pair from αRGCs to Nephronectin-positive wide-field neurons (NPWFs). We validated this connection using genetic labeling, electrophysiology, and retrograde tracing. We then utilized transcriptomic data from Trans-Seq to identify Nephronectin as a determinant for selective synaptic choice from αRGC to NPWFs via binding to Integrin-α8β1. The Trans-Seq approach can be broadly applied for postsynaptic circuit discovery from genetically-defined presynaptic neurons.

overall_design: Anterograde tracing with WGA-mCherry was combined with single-cell RNA sequencing to produce bioinformatic circuit maps from retinal ganglion cell subtypes into the superior colliculus. Intraocular injections of WGA-mCherry tracer were performed to transsynaptically label postsynaptic retinorecipient neurons in the superior colliculus. The superior colliculus was processed to obtain single-cell suspensions and mCherry+ connected cells were recovered by FACS. mWmC-positive SC neurons connected to all RGCs, alpha-RGCs (labelled through the reporter Kcng4-Cre), and ooDSGCs (labelled through Cart-Cre) were isolated and profiled in this study.

first: Nicole

last: Tsai


title: Sequencing results of FTO overexpressing in papillary thyroid cells


title: Interaction between stromal cells and GCB-DLBCL cells promotes the tumor cell survival through CD40-KDM6B-NF-B axis

city: Guangzhou

first: Dandan

last: Liu

state: Guangdong province

address: Xinzao, Panyu District,

department: Guangdong Provincial Key Laboratory of Protein Modification and Degradation

institute: Guangzhou Medical University

summary: Germinal center B-cell-like diffuse large B-cell lymphoma (GCB-DLBCL) is one of the most common subtypes of B-cell non-Hodgkin lymphoma. The tumor microenvironment (TME) is responsible for therapy resistance and relapse in GCB-DLBCL, while most studies have focused on targeting tumor cells instead of the TME. Stromal cells are the main component of the TME in GCB-DLBCL. How stromal cells interact with GCB-DLBCL tumor cells and protect GCB-DLBCL from cell death remain elusive. Here we reported that a CD40/RANK pathway-mediated positive feedback loop mediated the interaction of stromal cells and GCB-DLBCL to enhance the survival of GCB-DLBCL tumor cells. The viability of primary GCB-DLBCL patient-derived xenograft tumor cells was increased when they were cocultured with different tissue-derived stromal cells. We demonstrated that stromal cells promoted tumor cell survival not only through excreted cytokines but also depending more on direct contact. Furthermore, CD40 ligand (CD40L) expressed on stromal cells activated CD40 signaling in tumor cells, protecting tumor cells from apoptosis and upregulating RANK ligand (RANKL). RANK activation by RANKL in tumor cells enhanced the expression of CD40L and BAFF in stromal cells, both of which in turn promoted tumor cell survival through activating canonical and noncanonical NF-B signaling. In addition, CD40 activation upregulated the expression of KDM6B, and KDM6B further mediated the activation of canonical and noncanonical NF-B signaling, the downstream signaling pathways of the CD40 activation, all leading to tumor cell survival. These results further suggest that CD40-KDM6B-NF-B axis serve as a potential target for GCB-DLBCL therapy.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for sorted mono-cultured GCB-DLBCL PDX tumor cells and co-cultured GCB-DLBCL PDX tumor cells.

first: Haohao

last: Zhang

first: Liping

last: Xiao

first: Yiming

last: Hu


title: H3K9 methylation drives resistance to androgen receptor–antagonist therapy in prostate cancer

status: Public on May 05 2022

city: Cleveland

first: Vladimir

last: Makarov

state: OH

address: 9500 Euclid Ave

institute: CLEVELAND CLINIC LERNER COM-CWRU

summary: The study was performed to identify the role of H3K9 methylation in prostate cancer. This experiment was conducted to determine the genomic localization of H3K9me2 and H3K9me3 in naïve, short-term antiandrogen treated and antiandrogen resistant prostate cancer cells.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications H3K9me2 and H3K9me3 in naïve LNCaP, short-term antiandrogen treated LNCaP and LNCaP EnzR cells.

first: Mehdi

last: Baratchian

first: Ritika

last: Tiwari

first: Nima

last: Sharifi


title: Sequencing results of FTO overexpressing in papillary thyroid cells [RNA-seq]

overall_design: Comparative sequencing analysis of FTO overexpression stabilized cell lines of papillary thyroid carcinoma examined against normal papillary thyroid carcinoma cells


title: BCG therapy downregulates HLA-I on malignant cells to subvert antitumor immune responses in bladder cancer [RNA-seq]

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

summary: Patients with high-risk non-muscle-invasive bladder carcinoma (NMIBC) frequently relapse after standard BCG immunotherapy and have a dismal outcome after progression to muscle-invasive bladder carcinoma (MIBC). Although BCG induces potent inflammatory responses upon intravesical instillations, the mechanisms of tumor resistance to such immunotherapy remain elusive. We performed a longitudinal immune profiling of a cohort of MIBC pre- and post BCG therapy with gene and protein expression analysis to establish correlations with 5 year clinical follow up. Here, we demonstrate two distinct patterns of BCG-induced immunosubversion, which include acquired immune resistance and tumor-cell intrinsic resistance. Firstly, intracellular BCG infection of a subset of urothelial carcinoma cells downregulated HLA-I expression and induced epithelial to mesenchymal transition (EMT) characteristics. BCG treated tumors exhibiting such HLA class I loss displayed an immune desert tumor microenvironment dominated by myeloid immunosuppressive cells. Such patients presented with early cancer relapses and a bad outcome. Conversely, BCG-treated tumors which did not lose HLA class I antigens at relapse displayed an immune escape mechanism dominated by a Th1 pattern with high expression of inhibitory checkpoints and exhaustion markers. Such patients had a favorable outcome upon second surgery. We surmise that HLA class I expression does not result from immunoediting but rather from an EMT process associated to myeloid immunosuppression that predicts dismal prognosis.

overall_design: RNA-seq profile of non-muscle-invasive bladder carcinoma.

first: Mathieu

last: Rouanne

first: Julien

last: Adam

first: Camelia

last: Radulescu

first: Tuan

middle: Z

first: Aurélien

last: Marabelle


title: Gene expression of murine 3 major salivary gland organoids

first: Jae-Yol

last: Lim

address: 50-1, Yonsei-ro, Seodaemun-gu

department: Department of Otorhinolaryngology

institute: Yonsei University College of Medicine

summary: Salivary glands that produce and secret saliva, which is essential for lubrication, digestion, immunity, and oral homeostasis, consist of diverse cells. The long-term maintenance of diverse salivary gland cells in organoids remains problematic. Here, we established long-term murine salivary gland organoids from 3 major salivary glands, including parotid gland (PG), submandibular gland (SMG), and sublingual gland (SLG). Murine salivary gland organoids expressed gland-specific genes and proteins of acinar, myoepithelial, and duct cells. Organoids were maintained in growth media (named GEM) and further underwent differentiation in differentiation media (named DAM). Our study will provide an experimental platform for the exploration of mechanisms involvled in tissue regeneration, development, or several salivary gland diseases.

overall_design: Two biological replicates were analyzed for each of 7 conditions (3 gland tissues, 3 gland organoids cultured in DAM, and SMG organoids cultured in GEM)

first: Donghyun

last: Kim

first: Yeo-Jun

last: Yoon


title: DNA Methylation-Based Prediction of Post-Operative Atrial Fibrillation II

city: Los Angeles

first: Matthew

middle: A

last: Fischer

address: 650 Charles Young Dr

department: Anesthesiology and Perioperative Medicine

country: USA

institute: University of California, Los Angeles

summary: Background: Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia and post-operative atrial fibrillation (POAF) is a major healthcare burden, contributing to an increased risk of stroke, kidney failure, heart attack and death. Genetic studies have identified associations with AF, but no molecular diagnostic exists to predict POAF based on pre-operative measurements. Such a tool would be of great value for perioperative planning to improve patient care and reduce healthcare costs. In this pilot study of epigenetic precision medicine in the perioperative period, we carried out bisulfite sequencing to measure DNA methylation status in blood collected from patients prior to cardiac surgery to identify biosignatures of POAF. Methods: We enrolled 221 patients undergoing cardiac surgery in this prospective observational study. DNA methylation measurements were obtained from blood samples drawn from awake patients prior to surgery. After controlling for clinical and methylation covariates, we analyzed DNA methylation loci in the discovery cohort of 110 patients for association with POAF. We also constructed predictive models for POAF using clinical and DNA methylation data. We subsequently performed targeted analyses of a separate cohort of 101 cardiac surgical patients to measure the methylation status solely of significant methylation loci in the discovery cohort. Results: A total of 47 patients in the discovery cohort (42.7%) and 43 patients in the validation cohort (42.6%) developed POAF. We identified 12 CpGs that were statistically significant in the discovery cohort after correcting for multiple hypothesis testing. Of these sites, 6 were amenable to targeted bisulfite sequencing and chr16:24640902 was statistically significant in the validation cohort. In addition, the methylation POAF prediction model had an AUC of 0.79 in the validation cohort. Conclusions: We have identified DNA methylation biomarkers that can predict future occurrence of POAF associated with cardiac surgery. This research demonstrates the use of precision medicine to develop models combining epigenomic and clinical data to predict disease.

overall_design: Identification of DNA methylation biomarkers in pre-operative whole blood samples that predict post-operative atrial fibrillation after cardiac surgery

first: Douglas

last: Chapski

first: Thomas

last: Vondriska


title: BCG therapy downregulates HLA-I on malignant cells to subvert antitumor immune responses in bladder cancer

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

overall_design: Refer to individual Series


title: A single-cell transcriptomic atlas characterizes the silk-producing organ in the silkworm

city: Chongqing

first: Hanfu

last: Xu

address: 2 Tiansheng Road, Beibei District

country: China

institute: State Key Laboratory of Silkworm Genome Biology Southwest University

summary: The silk gland (SG) of the domesticated silkworm Bombyx mori, an economically important insect that has been used for silk production for over 5000 years, is a remarkable organ that produces vast amounts of silk with exceptional properties . Little is known about which SG cells execute silk protein synthesis and its precise spatiotemporal control. Here, we used single-cell RNA-seq to build a comprehensive cell atlas of the B. mori SG, consisting of 14,972 high-quality cells representing 10 distinct cell types, in three early developmental stages. We annotated all 10 cell types and determined their distributions in each region of the SG, decoded their developmental trajectory and gene-switch  status, and discovered marker genes involved in the regulation of SG development and silk protein synthesis. Our study reveals the high heterogeneity of B. mori SG cells and their gene expression dynamics for the first time, affording a deeper understanding of silk-producing organs at the single-cell level .

overall_design: SG cells collected from B. mori at three developmental stages (8 days post-egg laying, E8D; 1L1D; and first larval molting, 1LM), using single-cell RNAseq


title: Identification of (E)-β-farnesene impair the development and survival of Chilo suppressalis larval by disrupting insect hormone balance

status: Public on May 04 2022

city: nanjing

first: yang

last: niuzi

state: jiangsu

department: College of  Plant Protection

institute: jaas

summary: In this study, an artificial feeding study containing (E)-β-farnesene (0.8g/kg) with C. suppressalis larvae was conducted to investigate its physical performance, and results revealed that the average 2nd instar duration in C. suppressalis significantly increased from 4.78 days to 6.31 days after Eβf treatment (P<0.001), and in 3rd instar C. larvae also significantly increased from 5.70 days to 8.00 days (P<0.001). There were no significant differences in 4th and 5th C. suppressalis larval between Eβf treatment and control(P>0.05). The mortality rates of 2nd C. suppressalis larvae were increased by 21.00-fold, compared with control(P<0.001), 3rd C. suppressalis larval increased by 6.39-fold(P<0.001). Comparative transcriptome analysis also showed that multiple DEGs involved in insect hormone biosynthesis pathway, the results of hormone assay in 3rd instar larvae showed the balance between juvenile hormones and ecdysteroids was disrupted. Eβf treatment increased juvenile hormones titers, but not the ecdysteroids. The results of qPCR were consistent with RNA-seq. Taken together, Eβf impairs the development and survival of C. suppressalis larvae by disrupting insect hormone balance. Moreover, the altered pathways were associated with carbohydrates, xenobiotics and cofactors and vitamins in C. suppressalis larvae. Altogether, our findings identify Eβf impair the development and survival of C. suppressalis larvae. Additionally, our data also revealed a potential mechanism that Eβf impaired the development and survival of C. suppressalis larval by disrupting insect hormone balance. These findings may contribute to the integrated control of C. suppressalis.

overall_design: Examination of 2 different transcriptome in Chilo suppressalis.

first: Lei

last: Yang

first: Yang

last: Sun

first: Jichao

last: Fang


title: Global identification of RNA-binding proteins and RNA-binding domains in methicillin-resistant Staphylococcus aureus

city: Edinburgh

first: Sander

last: Granneman

address: Mayfield Road, Kings Buildings, Waddington building, room 3.06

department: Centre for Synthetic and Systems Biology

institute: University of Edinburgh

summary: Using improved and robust biochemical methods, we present the first global analysis of RNA-binding proteins (RBPs) and RNA-binding domains (RBDs) in clinically relevant and multi-drug resistant Gram-positive bacteria. To validate our results in silico, we developed novel bioinformatics tools that compare RBDome data with ligand-binding site predictions generated by five different algorithms on a large number of S. aureus crystal structures. This revealed that the putative RBDs are highly enriched for predicted RNA-binding sites and basic and aliphatic amino acids, demonstrating the robustness of our approach. Surprisingly, we found that HTH-type DNA-binding and NAD and P-loop type Rossmann-fold proteins may also play a prominent role in post-transcriptional regulation in Gram-positive bacteria and we identified a common mode of RNA recognition for these domains. Subsequent in vivo validation studies showed that the HTH-type transcription factor CcpA, a master regulator of carbon metabolism in Gram-positive bacteria, is also a global post-transcriptional regulator and binds its RNA substrates at very specific distances from transcription terminators. Our novel experimental and computations tools are widely applicable, and our work provides an extremely valuable resource for groups studying post-transcriptional regulation and RNA-binding proteins in bacteria.

overall_design: Three biological replicates with three experimental replicates each were used to generate the RNA-seq Data. RNA seq Data experiments were performed with the parental USA300 LAC strain, the ccpA gene null mutant and the ccpA deletion mutant complemented with CcpA expressed from the pCN33 plasmid. S. aureus strains were grown in TSB medium until the post-exponential phase. 10 mL of cells at an OD600 of ~3.0 were harvested by rapid centrifugation and flash-frozen. Total RNA was then extracted through acid guanidinium thiocyanate-phenol-chloroform extraction protocol.

first: Pedro

last: Rei

first: Liangcui

last: Chu


title: Dynamic mRNA Degradome Analyses Indicate a Role of Histone H3K4 Trimethylation in Association with Meiosis-coupled mRNA Decay in Oocyte Aging

city: Hangzhou

first: Yunwen

last: Wu

address: Yu Hang Tang Road

department: Life Sciences Institute

institute: Zhejiang University

summary: A decrease in oocyte developmental potential is a major obstacle for successful pregnancy in women of advanced age. However, the age-related epigenetic modifications associated with dynamic transcriptome changes, particularly meiotic maturation-coupled mRNA clearance, have not been adequately characterized in human oocytes. This study demonstrate a decreased storage of transcripts encoding key factors regulating the maternal mRNA degradome in fully grown oocytes of women of advanced age. A similar defect in meiotic maturation-triggered mRNA clearance was also detected in aged mouse oocytes. Mechanistically, the epigenetic and cytoplasmic aspects of oocyte maturation are synchronized in both the normal development and aging processes. The level of histone H3K4 trimethylation (H3K4me3) was high in fully grown mouse and human oocytes derived from young females but decreased during aging due to the decreased expression of epigenetic factors responsible for H3K4me3 accumulation. Oocyte-specific knockout of the gene encoding CxxC-finger protein 1 (CXXC1), a DNA-binding subunit of SETD1 methyltransferase, caused ooplasm changes associated with accelerated aging and impaired maternal mRNA translation and degradation. These results suggest that a network of CXXC1-maintained H3K4me3, in association with mRNA decay competence, sets a timer for oocyte deterioration and plays a role in oocyte aging in both mouse and human oocytes.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: A total of 44 samples were analyzed, including 24 human oocyte samples and 20 mouse oocyte samples. The human part included 8 individual biological cases, which were GV and MII stage oocytes from four differsnt age groups. Each case has 3 replicates. The mouse part included 7 individual biological cases, including GV and MII stage oocyte from young WT mouse (4 weeks),  GV and MII (with PB or without PB) stage oocyte from old WT mouse (14 months) and GV and MII stage oocyte from Cxxc1 conditional knock-out mouse.  Each case has 3 replicates, except that MII stage oocyte without PB from old WT mouse has only two replicates.

first: Qian-Qian

last: Sha

first: Heng-yu

last: Fan

first: Yun-Wen

first: Sen

last: Li

first: Wei

last: Zheng

first: Chu-Yan

first: Lu

last: Chen

first: Yong

last: Zhou

first: Zuo-Qi

last: Deng

first: Ge

last: Lin


title: DNA G-quadruplex structure participates in regulation of lipid metabolism through Acyl-CoA binding protein

first: Lijun

last: Xiang

state: Guangdong

address: No.55, West of Zhongshan Avenue

department: Guangzhou Key Laboratory of Insect Development Regulation and Application Research

institute: South China Normal University

summary: G-quadruplex structure (G4) is a type of DNA secondary structure that widely exists in the genomes of many organisms. G4s are believed to participate in multiple biological processes. Acyl- CoA binding protein (ACBP), a ubiquitously expressed and highly conserved protein in eukaryotic cells, plays important roles in lipid metabolism by transporting and protecting acyl-CoA esters. Here, we report the functional identification of a G4 in the promoter of the ACBP gene in silkworm and human cancer cells. We found that G4 exists as a conserved element in the promoters of ACBP genes in invertebrates and vertebrates. The BmACBP G4 bound with G4-binding protein LARK regulated BmACBP transcription, which was blocked by the G4 stabilizer pyridostatin (PDS) and G4 antisense oligonucleotides. PDS treatment with 5 th instar silkworm larvae decreased the BmACBP expression and triacylglycerides (TAG) level, resulting in reductions in fat body mass, body size and weight and growth and metamorphic rates. PDS treatment and knocking out of the HsACBP G4 in human hepatic adenocarcinoma HepG2 cells inhibited the expression of HsACBP and decreased the TAG level and cell proliferation. Altogether, our findings suggest that G4 of the ACBP genes is involved in regulation of lipid metabolism processes in invertebrates and vertebrates.

overall_design: Examination of G4 structures using BG4 antibody using HepG2 cells


title: MicroRNA-486 is an epigenetic modulator of Duchenne muscular dystrophy pathologies [eCLIP-seq]

city: Birmingham

first: Matthew

last: Alexander

state: AL

address: 1900 University Blvd. THT 929 Box# 96

department: Pediatrics

institute: University of Alabama at Birmingham

summary: Duchenne muscular dystrophy (DMD) is an X-linked progressive muscle disorder resulting in muscle weakness and cardiomyopathy. MicroRNAs have shown to play a significant role in muscle development, metabolism, and disease pathologies. We demonstrated that miR-486 expression is reduced in DMD muscles and its expression levels correlate with dystrophic disease severity. miR-486 knockout mice developed disrupted myofiber architecture, decreased myofiber size, decreased locomotor activity, increased fibrosis, and metabolic defects that were exacerbated on the dystrophic mdx5cv background. We integrated RNA-sequencing and chimeric eCLIP-sequencing data to identify direct in vivo targets of miR-486 and associated dysregulated gene signatures in skeletal muscle. Together, our studies identify miR-486 as a driver of muscle remodeling in DMD, a useful biomarker for dystrophic disease progression, and highlight chimeric eCLIP-sequencing as a useful tool to identify direct in vivo microRNA target transcripts.

overall_design: Whole TA muscles were isolated from male 6-month-old wild type and miR-486 KO mice (n = 3 total samples per genotype; performed in duplicate) and snap frozen in liquid nitrogen. The samples were processed for chimeric eCLIP-sequencing by Eclipse Bioinnovations Inc. (San Diego, CA). Approximately 80 mg of mouse muscles were homogenized by cryogenic pulverization. Samples were then were UV (254 nm) cross-linked twice at 400 mJ/cm2 using Stratalinker 2400 (Stratagene; San Diego, CA), on a bed of ice. Following cross-linking, the samples were sonicated (QSonica Q800R2; QSonica LLC, Newtown, CT) to shear the genomic DNA into smaller fragments. Ago2 immunoprecipitation using an Ago2 antibody (EclipseBioinnovations Inc.) was pre-coupled to anti-mouse Dynabeads (M-280 Sheep Anti-Mouse IgG Dynabeads, ThermoFisher Scientific 11201D), added to the homogenized lysate, and incubated overnight at 40C with gentile rocking. After immunoprecipitation, 2% of the sample was taken as the paired input sample. For chimeric eCLIP experiments, a standardized eCLIP protocol2 was modified to enable chimeric ligation of the miRNA and mRNA (Van Nostrand, E & Yeo, G, personal communication). miRNA-specific chimeric-eCLIP was performed by amplifying cDNA using a mouse miR-486a primer and a sequencing adapter-specific primer, following amplification with indexed primers.  Chimeric eCLIP-sequencing Library Preparation:  Whole TA muscles were isolated from male 6-month-old wild type and miR-486 KO mice (n = 5 total samples per genotype; performed in duplicate) and snap frozen in liquid nitrogen. The samples were processed for chimeric eCLIP-sequencing by Eclipse Bioinnovations Inc. (San Diego, CA). Approximately 80 mg of mouse muscles were homogenized by cryogenic pulverization. Samples were then UV (254 nm) cross-linked twice at 400 mJ/cm2 using Stratalinker 2400 (Stratagene; San Diego, CA), on a bed of ice. Following cross-linking, the samples were sonicated (QSonica Q800R2; QSonica LLC, Newtown, CT) to shear the genomic DNA into smaller fragments. Ago2 immunoprecipitation using an Ago2 antibody (EclipseBioinnovations Inc.) was pre-coupled to anti-mouse Dynabeads (M-280 Sheep Anti-Mouse IgG Dynabeads, ThermoFisher Scientific 11201D), added to the homogenized lysate, and incubated overnight at 40C with gentile rocking. After immunoprecipitation, 2% of the sample was taken as the paired input sample. For chimeric eCLIP experiments, a standardized eCLIP protocol was modified to enable chimeric ligation of the miRNA and mRNA (Van Nostrand, E & Yeo, G, personal communication). miRNA-specific chimeric-eCLIP was performed by amplifying cDNA using a mouse miR-486a primer and a sequencing adapter-specific primer, following amplification with indexed primers.

first: Hightower

last: Rylie

first: Alexander

last: Matthew


title: RNA-seq reveals differential expression of potential miR-486 target transcripts

summary: Identifying microRNA target transcripts is critical in understanding their role in modulation of disease pathology through cellular processes. Here, we used isolated 6 month mouse tibialis anterior (TA) muscle tissue for RNA extraction and sequencing in order to identify mRNA transcripts overexpressed in miR-486 knockout mice compared to wildtype.

overall_design: Tibialis anterior muscle transcriptomic profiles of 6 month male miR-486 knockout (KO) and wildtype (WT) mice were generated in triplicate.

first: Rylie

middle: M

last: Hightower


title: Gene expression analysis of differentiating skeletal muscle myoblast cell line overexpressing MyoD

status: Public on May 03 2022

city: Cincinnati

first: Jeffery

middle: D

last: Molkentin

state: Ohio

address: 240 Albert Sabin Way MLC 7020

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

summary:
We tested the hypothesis that ectopic expression of the MyoD-dependent gene program in differentiating myoblasts and myotubes compromises the integrity of the plasma membrane/sarcolemma by using a doxycycline-inducible system to overexpress MyoD in C2C12 myoblasts during differentiation. The overarching goals of this analysis pipeline were to (a) determine changes in transcriptional profiles upon sustained overexpression of MyoD during and upon differentiation; and, (b) utilize these profiles to identify potential drivers of sarcolemmal fragility that exacerbate myofiber damage and loss in dystrophic muscle.
We used microarrays to generate information about transcriptional profiles in differentiating myoblasts and myotubes overexpressing the myogenic transcription factor myoblast determination protein 1 (MyoD1).

overall_design: Low passage naïve or Lentiviral-transduced C2C12 cells were subjected to differentiation in 2% horse-serum containing media upon doxycycline (dox)-induced overexpression of MyoD. Total RNA was isolated from cells on third day of differentiation and subjected to gene array analysis

first: Justin

last: Boyer

first: Vikram

last: Prasad


title: Adjacent PTEN retained and lost sections from the same human melanoma

city: Houston

first: Lawrence

middle: N

last: Kwong

address: 1901 East Rd

institute: UT MD Anderson Cancer Center

summary: We use RNAseq to analyze the transcriptomes of adjacent tissue sections from the same melenoma, one in which PTEN protein expression is retained and one in which it is lost. This direct, intratumoral comparison provides a syngeneic background on which to assess tumor-intrinsic and -extrinsic effects of PTEN loss including cancer cell proliferation and immune cell infiltration.

overall_design: Examination of 2 adjacent tumor sections that differ in PTEN protein status

first: Michael

last: Davies


title: Activation of NOTCH and BMP signaling pathways during acute hypoxic stress in cardiac mesenchymal cells

status: Public on May 02 2022

city: Saint Petersburg

first: Pavel

last: Docshin

state: Saint Petersburg

address: 2 Akkuratova st.

department: Institute of Molecular Biology and Genetics

country: Russia

institute: Almazov National Medical Research Centre

summary:
To analyze early transcriptional events in cardiac tissue after  infarction and evaluate the genetic expression profile of post-infarction mesenchymal cells of the heart, we induced myocardial infarction in rats by ligation of the left coronary artery. 24 hours after surgery, the affected area was harvested for RNA isolation and cell culture.
We then performed a gene expression profile analysis using data obtained from RNA sequencing of 3 different postinfarction tissues and cells. Healthy tissues and cells of the left ventricle of the heart of sham-operated rats were used as controls.

overall_design: Comparative analysis of gene expression profiles of RNA sequencing data for postinfarction tissues and cardiac mesenchymal cells.

first: Andrey

last: Karpov

first: Malik

last: Mametov

first: Dmitry

last: Ivkin

first: Anna

last: Kostareva

last: Malashicheva


title: Global mapping of RNA-binding domains in multi-drug resistant Staphylococcus aureus

first: Sander

last: Granneman

country: United Kingdom

sample_organism: Staphylococcus aureus subsp. aureus USA300

overall_design: Two biological replicates of CRAC experiments with three experimental replicates each. CRAC experiments were performed with the parental USA300 strain and the strain expressing CcpA-HTF (HIS6-TEV-3xFLAG)

first: Pedro

last: Rei

first: Liangcui

last: Chu


title: RNase III CLASH in MRSA uncovers sRNA regulatory networks coupling metabolism to toxin expression

summary: Methicillin-resistant Staphylococcus aureus (MRSA) is a bacterial pathogen responsible for high levels of human morbidity and mortality. MRSA co-ordinates expression of an array of bacterial factors involved in antimicrobial resistance, nutrient acquisition and immune evasion in the host. Post-transcriptional regulation by small RNAs (sRNAs) has emerged as an important mechanism for the control of MRSA virulence. However, the function of the majority of sRNAs during infection is unknown. To address this gap in understanding, we performed UV cross-linking, ligation and sequencing of hybrids (CLASH) in MRSA to unravel sRNA-RNA interactions under conditions that mimic the host environment. Using double stranded ribonuclease III (RNase III) as a bait we not only uncovered known interactions but also hundreds of novel sRNA-RNA pairs. Strikingly, our results suggest that the production of small membrane-permeabilizing toxins is under extensive sRNA-mediated regulation and that their expression is intimately connected to metabolism. Importantly, we discovered that two sRNAs, RNAIII and RsaE, control the expression of at least four cytolytic toxins that are important for MRSA virulence. Taken together, we present a comprehensive analysis of sRNA-target interactions in S. aureus and provide detail on how these contribute to the control of virulence in response to changes in metabolism.

overall_design: CLASH was performed on RNase III in S. aureus USA300 and S. aureus JKD6009 backgrounds. As a control, CLASH was performed on the untagged parental strains. S. aureus was grown in rich medium, TSB, until the post-exponential phase and was then shifted to either RPMI medium (to mimic the human bloodstream) or LPM medium at either pH 5 or pH 7 (to mimic the intracellular host environment). S. aureus was incubated in these medium for 15 minutes and then harvested and used as inputs for CLASH. Additionally, RNA sequencing was performed on USA300 after the shifts to RPMI and LPM to understand transcriptome-level changes. For RNA sequencing, samples were taken after 5, 10, 15 and 30 minutes of exposure to the media.

first: Stuart

last: McKellar

first: Ivayla

last: Ivanova


title: RNA-sequencing analysis of pro-inflammatory cytokine stimulation of HMC3 microglia and HOG oligodendroglioma cell lines

city: Nijmegen

first: Kim

middle: de

last: Kleijn

address: Geert Grooteplein Zuid 26-28

country: Netherlands

institute: Radboud University

summary: Here we have stimulated human fetal microglia HMC3 cells and human oligodendroglioma HOG cells with LPS for 24 hours and subsequently with a combination of TNFα and IL-1β for 24 hours , and analyzed their transcriptome-wide response to compare the responsivity of the two cell lines to the pro-inflammatory stimuli.

overall_design: We analyzed the pooled RNA of three wells (technical triplicates) of unstimulated HMC3 cells and pooled RNA of three wells (technical triplicates) of HMC3 cells stimulated with 100 ng/ml LPS for 24 hours and subsequently with 5 ng/ml TNFα and IL-1β for 24 hours. We also analyzed the pooled RNA of three wells (technical triplicates) of unstimulated HOG cells and pooled RNA of three wells (technical triplicates) of HOG cells stimulated with 100 ng/ml LPS for 24 hours and subsequently with 5 ng/ml TNFα and IL-1β for 24 hours.

last: De Kleijn

first: Gerard

last: Martens

first: Kirsten

last: Straasheijm

first: Wieteke

last: Zuure


title: RNA-sequence analysis of CD3+ T cells purified from spleens in C57BL/6 recipient mice.

city: Wuhan

first: Le

last: Sheng

state: Hubei

address: JieFang Road 1277

department: Department of Cardiovascular Surgery

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: To investigate the dynamic expression of mRNAs in the regulation of  acute cardiac   allograft rejection, we isolated CD3+ T cells purified from spleens in C57BL/6 recipient mice.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of CD3+ T cells purified from spleens in C57BL/6 recipient mice.

first: Xiangchao

last: Ding

first: Jiahong

last: Xia

first: Sheng

last: Le