title: Analysis of the role of microbiota in macrophages using single cell RNA sequencing (scRNA-seq).

summary: Single-cell sequencing of intestinal macrophage was peformed with mice colony stimulating factor 1 receptor promoter (CSF1R) positive cells isolated from the 1/3 distal part of the small intestine of male MaFIA mice at postnatal day 17. Intestinal secretory Paneth cells become differentiated during the first two weeks after birth, which coincides with initial gut microbiota exposure. Their number is significantly reduced in cases of necrotizing enterocolitis (NEC), a deadly disease affecting premature infants. Although known to be associated with intestinal immaturity, its underlying disease mechanisms are unclear. Our analysis of mice treated with antibiotics reveals Paneth cell defects, which promote NEC pathogenesis. Our single cell and genetic analyses demonstrate that gut microbiota induces stem cell differentiation into Paneth cells by controlling the number and heterogeneity of macrophage populations that secrete Wnt ligands. Moreover, differentiated M2 macrophages are able to restore Paneth cell differentiation and rescue NEC-like pathology, while the ablation of Paneth cells is sufficient to induce it, leading to lethality. Our work reveals an unexpected requirement for Paneth cell differentiation through the regulation of gut microbiota-macrophage niches in early postnatal development.

overall_design: Examination of control group and Antibiotics treated group of the macrophage isolated from postnatal day17 mice


title: The three-dimensional genomic organization changes in terminal erythropoiesis reveal independence of chromatin condensation from nuclear condensation

status: Public on Dec 16 2022

city: Chicago

first: Peng

last: Ji

state: Illinois

address: Ward Building Room 3-230/45, 303 E Chicago Avenue

department: Pathology

country: USA

institute: Northwestern University

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Differential expression in T47-D human breast cells  after baiclalein treatment

status: Public on Dec 15 2022

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary: Investigate differences in gene expresion profiles of T47-D human breast cancer cells  when treated with baicalein.

overall_design: Gene expression profiling analysis from polyA RNA-seq of 2 replicates of T47-D cell lines treated with baicalein and controls.

first: Besa

last: Xhabija


title: Compendium of functional regulatory variants in human neuropsychiatric disease (ATAC-Seq)

city: Stanford

first: Margaret

last: Guo

state: CA

address: 269 Campus Dr. CCSR Room 2150

institute: Stanford University

summary:
Abstract: Noncoding variants of presumed regulatory function contribute to neuropsychiatric disease heritability. 4442 noncoding variants connected to risk for 10 neuropsychiatric disorders, including autism spectrum disorder, attention deficit hyperactivity disorder, bipolar disorder, borderline personality disorder, major depression, generalized anxiety disorder, panic disorder, post-traumatic stress disorder, obsessive-compulsive disorder, and schizophrenia, were studied within developing human neural cells. Integrating epigenomic and transcriptomic data with massively parallel reporter assays identified 637 disease-associated single-nucleotide variants (daSNVs) with altered transcription-regulating activity. Expression-gene mapping, network analyses, and chromatin looping identified 619 candidate disease-relevant target genes modulated by these daSNVs. Specific daSNV-associated molecular pathways mapped to prevalent mental health symptoms. These data provide a framework resource to study inherited pathogenic risk for human neuropsychiatric disorders.
Purpose: To place disease-associated single nucleotide variants (daSNVs) in genomic context within human neural cells, matched RNA-seq, chromatin accessibility profiling via ATAC-seq, and enhancer-promoter looping via H3K27ac HiChIP was performed in ES cells and at day 2 (N-D2), 10 (N-D10), and 28 (N-D28) of neuronal differentiation. Additionally, anterior (A-NPC) and posterior (P-NPC) neuronal stem cells were generated and studied. Matched sequencing was also performed on primary human astrocytes from adult brains. Processed and raw data for all cell types can be found in this repository.  All biological replicates (n=2) are merged using the ENCODE pipeline.

overall_design: ES-derived neuronal and primary astrocyte ATAC profiles in vitro


title: Enhancers display sequence flexibility constrained by transcription factor motif syntax [Drosophila motif pasting STARR-seq]

city: Wien

first: Bernardo

middle: P

last: de Almeida

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

summary: The information about when and where each gene is to be expressed is mainly encoded in the DNA sequence of enhancers, sequence elements that comprise binding sites (motifs) for different transcription factors (TFs). Most of the research on enhancer sequences has been focused on TF motif presence, while the enhancer syntax, i.e. the flexibility of important motif positions and how the sequence context modulates the activity of TF motifs, remain poorly understood. Here, we explore the rules of enhancer syntax by a two-pronged approach in Drosophila melanogaster S2 cells: we (1) replace important motifs by an exhaustive set of all possible 65,536 eight-nucleotide-long random sequences and (2) paste eight important TF motif types into 763 motif positions within 496 enhancers. These complementary strategies reveal that enhancers display constrained sequence flexibility and the context-specific modulation of motif function. Important motifs can be functionally replaced by hundreds of sequences constituting several distinct motif types, but only a fraction of all possible sequences and motif types restore enhancer activity. Moreover, TF motifs contribute with different intrinsic strengths that are strongly modulated by the enhancer sequence context (the flanking sequence, presence and diversity of other motif types, and distance between motifs), such that not all motif types can work in all positions. Constrained sequence flexibility and the context-specific modulation of motif function are also hallmarks of human enhancers and TF motifs, as we demonstrate experimentally. Overall, these two general principles of enhancer sequences are important to understand and predict enhancer function during development, evolution and in disease.

overall_design: UMI-STARR-seq was performed in S2 cells using an oligo library containing sequences for the wildtype enhancers and enhancers with mutant variants or motifs pasted at the selected positions. All experiments were performed in 3 biological replicates.

first: Franziska

last: Reiter

first: Alexander

last: Stark


title: Enhancers display sequence flexibility constrained by transcription factor motif syntax [Drosophila random variant STARR-seq]

overall_design: UMI-STARR-seq was performed in S2 cells using a enhancer libraries where we replace important motifs by an exhaustive set of all possible 65,536 eight-nucleotide-long random sequences. All experiments were performed in 2 biological replicates.


title: Analysis of plasma circRNA expression profiles in rats with myocardial ischemia-reperfusion injury

city: Jiamusi

first: Zhang

last: Meng

address: No.348 Dexiang Street, Xiangyang District, Jiamusi

country: China

institute: First Hospital of Jiamusi University

summary:
CircRNAs have complex biological functions and are involved in the development of several cardiovascular diseases. The relationship between circRNAs and myocardial ischaemia-reperfusion injury (MIRI) is not yet clear.
The aim of this study was to investigate the expression of circRNAs in rat plasma, to examine the differential expression profile of circRNAs in the plasma of MIRI rats, and to explore whether these circRNAs are potentially significant and have potential as novel markers for the diagnosis of MIRI and as therapeutic targets.

overall_design: Six adult male SD rats were randomly divided into MIRI and sham-operated groups to establish a rat MIRI model. rat plasma was taken, circRNAs were screened by high-throughput sequencing using circRNA microarrays, and circRNA differential expression was further verified using quantitative real-time polymerase chain reaction. The differentially expressed circRNAs were subjected to gene ontology analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis, and the biological functions of differentially expressed circRNAs were inferred, among others.

first: Meng

last: Zhang

first: Shan

last: Gao


title: A Potent and Selective Small-Molecule STAT5 PROTAC Degrader Capable of Achieving Tumor Regression In Vivo

first: Shaomeng

last: Wang

state: Michigan

address: 1600 Huron Parkway, Building 520 Rm 352

summary: We have developed AK2292 as a first, potent and selective small-molecule degrader of both STAT5A and STAT5B isoforms. To investigate the effect of STAT5A/STAT5B depletion on the transcriptome, we treated KU812 and NCO2 cells with AK2292 at 1 μM for 8 h and performed RNA-seq analysis. As a control, we treated KU812 and NCO2 cells with AK2292Me at 5 μM for 24 h for RNA-seq analysis. RNA-seq analysis revealed that AK2292 downregulates the transcriptome associated with STAT5A and STAT5B.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for KU812 and NCO2 cells treated with AK2292 and AK2292Me

first: Longchuan

last: Bai

first: Jelena

last: Tosovic

first: Hui

last: Jiang


title: Compendium of functional regulatory variants in human neuropsychiatric disease


title: Transcriptome-wide dynamics of m6A mRNA methylation during porcine spermatogenesis

city: Yangling

first: Xiaoxu

last: Chen

address: Litai street

institute: Northwest A&F University

type: Methylation profiling by high throughput sequencing

summary: Purpose: To understand the transcriptome-wide distribution of m6A and their roles in porcine spermatogenesis.

overall_design: We firstly isolated porcine spermatogonia, pachytene spermatocytes and round spermatids to analyze the transcriptome-wide distribution of m6A. Incorporation with RNA expression pattern, we systematically analyzed m6A roles in regulation of porcine spermatogenesis. Analysis revealed that m6A distributed throughout the transcripts and peaks at 3’UTR near the stop codon and located preferentially on the motif GGACU. In addition, gene expression was positively regulated by the m6A modification. Those genes regulated by m6A modification mainly participated in metabolic process in spermatogonia, cell cycle process in pachytene spermatocytes and developmental process in round spermatids.  We further demonstrated that m6A mediated SETDB1 and cell cycle associated gene expression in spermatogonia.

first: Wenxian

last: Zeng


title: Enhancers display sequence flexibility constrained by transcription factor motif syntax

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens


title: Enhancers display sequence flexibility constrained by transcription factor motif syntax [Human motif pasting STARR-seq]

overall_design: Human UMI-STARR-seq was performed in HCT-116 cells using an oligo library containing sequences for the wildtype enhancers and enhancers with mutant variants or motifs pasted at the selected positions. All experiments were performed in 3 biological replicates.


title: Transcriptome analysis of Acartia tonsa embryogenesis and its quiescent stage

city: Roskilde

first: Miguel

last: Cifuentes Acebal

state: Sjaelland

address: Universitetsvej 1

department: Department of Science and Environment

country: Denmark

institute: Roskilde university

summary: Copepods from the species Acartia tonsa, like other 41 members of Calanoida order, have the unique ability to induce quiescence in different stages during their lifetime if adverse environmental conditions occur. Here I assembled a de novo transcriptome for subitaneous and quiescent embryonic development to reconstruct the molecular processes occurring in the embryogenesis. This dataset provides a better understanding of A. tonsa embryonic development and the molecular mechanisms underlying quiescence.

overall_design: Differential expression analysis for RNA-seq data from an assemblage of eggs of Acartia tonsa. With six timepoints (3, 7, 14, 24 and 42 hours subitaneous development and 26 hours  quiescent development) and 3-5 technical replicates per timepoint

first: Tue

middle: S

last: JØrgensen

first: Benni

middle: W

last: Hansen

first: Louise

middle: T

last: Daalgard


title: Tbx5-dependent transcripts of the embryonic left ventricle

city: Cincinnati

first: Jeffrey

middle: D

last: Steimle

email: jeffrey.steimle@cchmc.org, jeffrey.steimle@bcm.edu, jsteimle@uchicago.edu, jsteimle@alumni.nd.edu

state: OH

address: 240 Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Medical Hospital Center

summary: Tbx5 is expressed in the left ventricle of the developing mammalian heart. In order to test the transcriptional requirement of Tbx5 in the fetal left ventricle and bypass its early requirement in early cardiac formation, we used a combination of the ROSA26creERT2, a ubiquitously transcribed tamoxifen-dependent cre recombinase, and the Tbx5 floxed allele to remove both copies of Tbx5 at E11.5 followed by microdissection at E12.5. In addition to several well-known targets of Tbx5, we identified a novel signature of disrupted PDGF signaling.

overall_design: The cardiac left ventricle was microdissected from 2 mutant Gt(ROSA)26Sortm1(cre/ERT2)Tyj;Tbx5flox/flox and 5 control Gt(ROSA)26Sortm1(cre/ERT2)Tyj;Tbx5+/+ mouse embryos at embryonic day 12.5 (E12.5) following maternal intraperitoneal injection of tamoxifen at E11.5. RNA was extracted, oligo-dT selected, 50bp single-ended sequenced on the HiSeq2500 (Invitrogen) to a depth of approximately 26 million reads.

first: Ivan

last: Moskowitz


title: SNP genotyping array of human naive pluripotent stem cells

city: San Francisco

first: Akira

last: Kunitomi

address: 1650 Owens Street

institute: The J. David Gladstone Institutes

summary: We introduce a method for generating transgene-free and high-quality naive human induced pluripotent stem cells (iPSCs) using a modified Sendai virus (SeV) vector reprogramming system. This reprogramming method realizes the derivation of naive iPSCs from various somatic cells accompanied with fast and robust SeV vector removal at early passages. The established naive iPSCs have superior differentiation ability compared with iPSCs derived from conventional methods.

overall_design: Genomic DNA from the 11 samples were hybridized onto the Infinium OmniExpress24 v1.3 DNA Analysis Kit (Illumina), and intensities were scanned by iScan (Illumina) following the manufacturer’s protocol.

first: Masaki

last: Nomura


title: Mechanisms and function of de novo DNA methylation in placental development [RNA-Seq]

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

summary: DNA methylation is a repressive epigenetic modification that is essential for development, exemplified by the embryonic and perinatal lethality observed in mice lacking de novo DNA methyltransferases (DNMTs). Here we characterise the role for DNMT3A, 3B and 3L in gene regulation and development of the mouse placenta. We demonstrate that each of the DNMTs is required to establish the placental methylome and is distinctly targeted to genome based on underlying chromatin features. Loss of Dnmt3b results in de-repression of germline genes in trophoblast lineages and impaired development of the placental maternal-foetal interface. Critically, loss of DNA methylation in the placenta did not lead to abnormalities in lineage specification or cell identity, but to defective formation and vascularisation of the placental labyrinth. Using Sox2-Cre to delete Dnmt3b in the embryo, leaving expression intact in placental trophoblast cells, we were able to rescue the placental phenotype and, consequently, the embryonic lethality, as Dnmt3b null embryos could now survive to birth. We conclude that the principal function of DNA methylation during embryogenesis is to regulate placental function, which in turn is critical for embryo survival.

overall_design: Using low-input RNA-seq and post bisulphite adaptor tagging (PBAT), we then assayed gene expression and genome-wide DNA methylation in E7.5 ExE and epiblast from Dnmt3a KO, Dnmt3b KO, Dnmt3a/b double KO (DKO), Dnmt3l KO and wildtype (WT) controls.  The de novo DNMT enzymes have been shown to interact with modified histone tails, which modulates their catalytic activity and genome localisation in vitro. Thus, we generated ultra-low input ChIP-seq data for H3K4me1 and H3K27ac to combine with published datasets for H3K4me3, H3K27me3 and H3K36me3 in E6.5 ExE, immediately preceding the completion of de novo DNA methylation.  To investigate the placental phenotype of Dnmt3b KO at the molecular level, we generated single nuclei RNA sequencing data from E12.5 placentas from a Dnmt3b KO and WT control.

first: Courtney

last: Hanna

first: Simon

last: Andrews


title: Mechanisms and function of de novo DNA methylation in placental development

sample_organism:
Mus
Mus musculus

platform_organism:
Mus
Mus musculus


title: Mechanisms and function of de novo DNA methylation in placental development [ChIP-seq]


title: Mechanisms and function of de novo DNA methylation in placental development [PBAT]


title: Expression and role of the receptor tyrosine kinase-like orphan receptor2 (ROR2) in small cell lung cancer

city: Kumamoto

first: Takaaki

last: Ito

address: 325, Izumi-cho, Kita-ku

country: Japan

institute: Kumamoto Health Science University

summary: Heterogeneity of ROR2 was observed in the tumor tissues form patient-derived xenograft (PDX) model of SCLC, in which the cells with high ROR2 expression (ROR2high cell) and those without ROR2 expression (ROR2low cell) were gained and subjected to RNA sequence analysis. Cell proliferation activity was suppressed in ROR2 KO SBC3 cells in vitro and in vivo. Comparison of the downregulated DEG in the ROR2 KO SBC3 cells and the upregulated DEG in ROR2high cells in the PDX model revealed 135 common genes. After Metascape analysis of these genes, we focus on Aurora kinases. These results suggest that ROR2 could regulate cell cycle through AURKA and/or AURKB. This study clarrifies the function of ROR2 in SCLC with heterogeneous expression condition.

overall_design: Examination of RNA-sequencing of 2 conditions: 1) ROR2high and ROR2low cells sorted from small cell lung cancer xenograft. 2) ROR2 knockout or control SBC-3 cells.

first: Mune

last: Sanada

first: Masaya

last: Yamazaki


title: CXCR5 Antagonist in Angioimmunoblastic T-cell Lymphoma

city: New Haven

first: Elias

last: Lolis

state: Connecticut

address: PO Box 208066, 333 Cedar St.

department: Pharmacology

institute: Yale University

summary: We report the differential RNA expression and splicing variants in xenografted AITL cells and the associated mouse stromal cells in the lymph node of 3 CXCR5-antagonist-treated mice and 3 vehicle-treated mice

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Differential mRNA expression in xenografted AITL cells from a mouse lymph node

first: Lolis

last: Elias

first: Katz

last: Samuel

first: Kerr


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type HCT116 and MTF1-KO HCT116 injected tumor Transcriptomes

city: Hefei

first: qiangsheng

last: li

state: Anhui

address: Huangshan Road 443

department: Life Sciences and Medicine

institute: University of Science and Technology of China

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to use RNA-seq to find differences between WT and MTF1-KO tumor in colorectal cancer
Methods: HCT116 cells and MTF1-KO HCT116 cells were injected subcutaneously into the back of NSG mice at 2x106 cells/recipient , At day 24 after injection，Tumor tissue were isolated from infected recipients，and Total RNA was collected. Besides,about 5x106  cultured HCT116 cells and MTF1-KO HCT116 cells were collected for total RNA isolation ,and sent all of them for sequencing.
Conclusions: Our study represents the transcriptome difference between WT HCT116 tumor and MTF1-KO HCT116 tumor  has a very positive significance for the pathological process of colorectal cancer，especially for cell adhension

overall_design: Total RNA were isolated from tumor of 24-day old wild type (WT) and MTF1-KO HCT116 injected mice

first: Qiangsheng

last: Li

first: Chunliang

last: LI

first: Bofeng


title: Mechanisms and function of de novo DNA methylation in placental development [snRNA-seq]


title: Exploring the Pars Tuberalis (PT) and Hypothalamus (HT) transcriptome from Rasa Aragonesa ewes with different estrus and anestrus phases

city: Zaragoza

first: Kenza

last: Lakhssassi

state: Zaragoza

address: Av Montañana, 930,

country: Spain

institute: CITA

summary:
Purpose: High-throughput sequencing technology were used to explore transcriptional changes in the PT and the HT tissues during follicular (F) and luteal (L) phases of estrus cycle, and anestrus phase in seasonal ewes. Real-Time Quantitative PCR Analysis (RT-qPCR) were performed to evaluate the reliability of our RNA-seq results.
Methods: The PT and HT transcriptomes of 21 Rasa Aragonesa ewes (7 for each phase and tissue) were generated by Illumina Hi-Seq 2000 platform. The reads were trimmed with Trimmomatic. HISAT2were used to align lean reads to the ovine reference genome Texel Oar_v3.1 Texel Oar_v3.1  followed by samtools to be converted and sorted to bam files. StringTie was used to assemble transcripts and quantify RNA-seq. Differential gene expression were mesured using DESeq2 package in R. RT-qPCR validation of 5 housekeeping genes and 16 DEGs was performed using SYBR Premix Ex Taq II and an ABI Prism 7500 platform running the samples in triplicate.
Results: RNA sequencing of HT and PT generated pproximately, 834 and 874 million paired-end reads respectively from 42 libraries (21 from each tissue). On average, the overall alignment rate to reference genome was 90%.69% of all the clean reads were uniquely mapped to the reference genome. 18895 and 18960 genes (with nonzero total read count) were expressed in PT and HT, respectively. In HT, 72 and 3 DEGs were found (p_adjusted<0.05) in the comparisons between F vs A and L vs A phases, respectively. In PT, 6, 4 and 14 DE genes were found in the comparisons F vs A, L vs A and L vs F phases, respectively. The RPL19 and RPL32 were the housekeeping genes most stable for the HT whereas the B2M and RPL27  genes were the most stable for PT. With qRT-PCR analysis, Thirteen genes from the twenty analyzed were validated confirming the reliability of our RNA-seq data.
Conclusions: Reliability of RNA-seq results was validated by qRT-PCR suggesting that the results of the RNA-seq experiments were efficient and accurate. These findings showed significant possible roles of these candidate genes in regulation of seasonal reproduction and in the reproductive stages. This study affords a basic data for future research to understand, more in depth, the molecular mechanism that take place during seasonal reproduction.

overall_design: Comparison of the luteal, anestrous and follicular transcriptomes in ewes Hypothalamus and Pars Tuberalis tissues

first: Jorge

middle: H

last: Lacosta


title: Gene expression profiles of human primed and naive pluripotent stem cells

first: Akira

summary: We introduce a method for generating transgene-free and high-quality naive human induced pluripotent stem cells (iPSCs) using a modified Sendai virus (SeV) vector reprogramming system. This reprogramming method realizes the derivation of naive iPSCs from various somatic cells accompanied with fast and robust SeV vector removal at early passages. The established naive iPSCs have superior naive-specific differentiation ability compared with iPSCs derived from conventional methods.

overall_design: RNA-seq analysis for human naive pluripotent stem cell lines (n= 7), human primed pluripotent stem cell lines (n= 6)

first: Tomoaki

middle: M

last: Kato

first: Masaki


title: DNA methylation profiles of human primed and naive pluripotent stem cells

last: Kunitomi

overall_design: Bisulphite converted DNA from the 13 samples were hybridised to the Illumina Infinium Human Methylation 450K or EPIC BeadChip Kit


title: Gene expression profiling of placental villi from intrauterine and tubal ectopic pregnancies

city: Shanghai

first: Xiaoya

last: Zhao

state: shanghai

address: No. 910, Hengshan Rd

department: Department of Obstetrics and Gynecology, International Peace Maternity and Child Health Hospital

institute: School of Medicine, Shanghai Jiaotong University

summary: The tubal ectopic pregnancy (TEP) is a severe pregnancy complication accounted for 10-15% pregnancy-related deaths owing to the implantation and growth of embryos in fallopian tubes. Placental villi from TEP exhibit significant difference compared with that from intrauterine pregnancy (IP) in total volumes, trophoblast differentiation and intravillous vascularization.  To investigate the difference in expression profiles of placental villi from IP and TEP, placental villi were collected from each phenotype, separated from maternal tissues and analyzed by high-throughput sequencing.  generated a mouse model in which p53 is activated in neural crest cells due to the expression of a mutant p53 protein (p53-25,26) that can bind to and stabilize wild-type p53. Here, we performed gene expression profiling on neural crest cells isolated from these embryos, to identify the transcriptional response to p53 activation during embryogenesis.

overall_design: RNA-seq was performed on placental villi from pregnant women at 6-8 gestational weeks. Exclusion criteria for all samples are: IP with EP histories, miscarriage, preeclampsia, and preterm delivery. EP with some risk factors associated with fallopian tubal abnormalities, e.g., smoking, obvious tubal inflammatory adhesions, previous fallopian tubal diseases, and tubal surgery histories, were also excluded for avoiding complications. In each case, gestational days was 40-64 days confirmed from the last menstrual period. n=5 for both IP and TEP.

first: X

middle: Y

first: Z

last: Zhang

first: J

first: C

last: Lin


title: Identification of a novel LysR family transcriptional regulator controlling acquisition of sulfur sources in Acinetobacter baumannii.

city: North Ryde

first: Ian

last: Paulsen

state: New South Wales

address: 14 Eastern Road

department: Molecular Sciences

country: Australia

institute: Macquarie University

summary: RNA sequencing transcriptomics was performed on a highly multidrug resistant A. baumannii strain belonging to international clone I, AB5075_UW and a transposon insertion inactivated mutant of ABUW_1016 (cbl), which encodes a LysR-type transcriptional regulator.Transcriptomics suggests that Cbl controls expression of the genes involved in acquisition and reduction of various sulfur sources in A. baumannii.

overall_design: Global transcriptomic profiles of the cbl mutant and the parental A. baumannii strain were compared. The parental and mutant cells were grown to mid exponential phase at 37°C, with shaking. Cell pellets were harvested and the total RNA was extracted from three biological replicates. Ribosomal RNA was depleted using Ribozero magnetic kit (Bacteria) (Illumina, Inc., USA) and the cDNA library was generated using Truseq stranded RNA preparation kit (Illumina, Inc., USA). RNA libraries were prepared for sequencing using standard Illumina protocols.

first: Alaska

last: Pokhrel

first: Liping


title: Expression profiles of circRNA in HCT-8 cells infected with Cryptosporidium parvum IId subtype

first: Yanling

last: Yin

state: Shaanxi

address: No.22 Xinong Road

department: College of veterinary medicine

summary:
Cryptosporidium parvum is one of the most important opportunistic enteric parasites, causing severe diarrhea in immunocomprised human and animals. However, few effective control agents were available for this parasite. circular RNA (circRNA) was discovered to play key roles in many diseases, and the well-known regulatory mechanism for circRNAs is that act as miRNA sponges competitively binding to miRNAs to block miRNA-mRNA interaction.
Here, using microarray assay, we investigated the expression profiles of circRNAs in HCT-8 cells after the infection of C. parvum IId subtype, the prevalent subtype of China. A total of 178 circRNAs were dysregulated expressed in HCT-8 cells at 24 h post infection (pi) of C. parvum IId subtype.

overall_design: we collected the HCT-8 cell infected with cryptosporidium parvum at 24 hours and analysed the pofiles of circRNAs.

first: Guanghui


title: CRISPR-free Programmable RNA pseudouridylation to suppress premature termination codons

city: BeiJing

first: Kai

address: Yi He Yuan Street No.5

department: School of Life Science

institute: Peking University

summary: We present RESTART, a programmable approach employing engineered artificial guide snoRNA (gsnoRNA) to achieve precise and efficient site-directed pseudouridylation in mammalian cells without changing the coding information. We identified and optimized gsnoRNA scaffolds, which can mediate PTC-readthrough by recruiting endogenous DKC1 (pseudouridine synthase). We also found combining exogenous non-canonical DKC1-isoform3 with gsnoRNA can further improve the efficiency of PTC-readthrough. We applied such strategies to correct disease-relevant nonsense mutations, while maintaining the global Ψ abundance in cellular RNA and gene expression. Collectively, RESTART would become a powerful tool for therapeutics and basic research.

overall_design:
Examination of HEK293T cells co-transfected of 2 μg ALDOB-W148X (or SMN1-W190X) and 2 μg gACA19 / gCtrl / empty vector (Vec) together with or without 500 ng DKC1-isoform3 (iso3) constructs.

Detection of pseudouridine modification by CeU-seq and targeted deep amplicon sequencing

first: Chengqi

last: Yi


title: RNA sequencing to identify immunity-regulated genes in C. elegans defense against pathogen infection

city: Changsha

first: Zhongfan

last: Zheng

address: No. 27 Tianma Road

institute: Hunan university

summary: To understand the molecular mechanism of C. elegans innate immunity, we used RNA sequencing to profile gene expression in wild-type animals with or without P. aeruginosa (PA14) infection. We found that a bZIP transcription factor ZIP-11 is dramatically induced in wild-type worm upon PA14 infection. And ZIP-11 promotes innate immunity through activating PMK-1/p38 pathway and interacting with a CCAAT/enhancer-binding protein CEBP-2.

overall_design: Three replicates of two groups of RNA samples (wild-type L4-stage animals with or without exposure to P. aeruginosa for 24 hrs) were sequenced. Gene expression was compared between groups to identify differentially expressed genes under uninfection or infection conditions.

first: Haijun

last: Tu


title: Transcriptomic and metabolomic analysis reveal that fullerol improves drought tolerance in Brassica napus L.

status: Public on Dec 14 2022

city: Wuhan

first: Jun-Lan

last: Xiong

state: Hubei

address: No. 2 Xudong 2nd Road, Wuchang District, Wuhan

department: Chinese Academy of Agricultural Science

institute: Oilcrops Research Institute

summary: The fullerenes, a kind of carbon nanoparticles, have potential for enhanced stress tolerance in plants. While the positive effects of polyhydroxy fullerene—fullerol on plants in response to drought at the physiological level have been documented, the molecular mechanism in Brassica napus are not entirely understood. In this study, exogenous fullerol was applied to the leaves of B. napus seedlings given drought. The leaves of B. napus seedlings in each treatment (sufficient water condition, drought, and drought combined with fullerol) were used to conduct the molecular mechanism using transcriptomic analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for leaves of Brassica napus seedlings under different treatment (well-watered, drought, drought applied with fullerol).

first: Ni

last: Ma


title: Targeting HDAC6-Mediated Deacetylation of STAT4 Is Critical for T helper Type 1 Cell Differentiation and Capability

city: Suzhou

first: Yanan

state: Jiangsu

address: 199 Renai Road

department: Institutes of Biology and Medical Sciences

institute: Soochow University

summary: We report that inhibition and knockout of HDAC6 enhanced Th1 cell differentiation, and decreased Listeria monocytogenes infection in mice. Mechanistically, HDAC6 directly deacetylated CBP-catalyzed acetylation on STAT4 lysine 667 via its enzymatic activity, which is required for IL-12-induced phosphorylation on STAT4. Stat4K667R mutant mice lost the ability to normally differentiate Th1 cell and developed sever L. monocytogenes infection. Our study identifies the STAT4 acetylation on K667 modified dynamically by CBP and HDAC6, as an essential signaling event for Th1 cell differentiation and defense of intracellular pathogen infections, highlighting the therapeutic potential of HDAC6 inhibition for controlling intracellular pathogen infections.

overall_design: mRNA profiles in CD4+ Th0 and Th1 cells  of  wild type (WT), Stat4-/- and Stat4-K667R mice were generated by deep sequencing, in triplicate, using Illumina HiSeq2500.

first: Y

middle: E

last: Chin


title: scRNAseq analysis of forskolin effect on Th1, Th2 and Th17 differentiation

city: Brno

first: Radim

last: Jaroušek

state: Česká republika

address: Kotlářská 2

department: Immunology and experimental biology

country: Czech Republic

institute: Masaryk university

summary: Adenylate cyclase signaling pathway is suggested to be a key regulator of immune system functions. However, specific effects of cyclic adenosine monophosphate on T helper cell differentiation and functions are unclear. Involvement of cAMP in Th cell differentiation program, in particular development of Th1, Th2, and Th17 subsets, was evaluated employing forskolin (FSK), a labdane diterpene well known as AC activator.

overall_design: We performed scRNA sequencing to understand the distinct effect of forskolin on Th1, Th2 and Th17 differentiation program. We included following samples: non-treated control (NT ctrl, resting cells), activated control (ACT - anti-CD3/anti-CD28 stimulated cells), cells differentiated into distinct subsets: Th1, Th2, TH17, and these subsets treated with 10 µM forskolin: Th1+FSK10, Th2+FSK10, Th17+FSK10.

first: Petra

last: Daďová

first: Antónia

last: Mikulová

first: Lukáš

last: Kubala


title: KLF4-PFKFB3-driven glycolysis is essential for phenotypic switching of vascular smooth muscle cells (mRNA microarray)

city: shijiazhuang

first: Xinhua

state: Hebei

address: ZhongshanRoad NO.361

department: Biochemistry and Molecular Biology

institute: Hebei Medical University

summary: Vascular smooth muscle cells (VSMCs) within atherosclerotic lesions undergo a phenotypic switching in a KLF4-dependent manner. Glycolysis plays important roles in transdifferentiation of somatic cells, however, it is unclear whether and how KLF4 mediates the link between glycolytic switch and VSMCs phenotypic transitions. Here, we show that KLF4 upregulation accompanies VSMCs phenotypic switching in atherosclerotic lesions. KLF4 enhances the metabolic switch to glycolysis through increasing PFKFB3 expression. Inhibiting glycolysis suppresses KLF4-induced VSMCs phenotypic switching, demonstrating that glycolytic shift is required for VSMCs phenotypic switching. Mechanistically, KLF4 upregulates expression of circCTDP1 and eEF1A2, both of which cooperatively promote PFKFB3 expression. TMAO induces glycolytic shift and VSMCs phenotypic switching by upregulating KLF4. Our study indicates that KLF4 mediates the link between glycolytic switch and VSMCs phenotypic transitions, suggesting that a previously unrecognized KLF4-eEF1A2/circCTDP1-PFKFB3 axis plays crucial roles in VSMCs phenotypic switching.

overall_design: smooth muscle cells treat by GFP or klf4


title: MCUb upregulation in the type 2 diabetic heart impacts cardiac function by altering mitochondrial metabolic fuel flux and the cardiac myocyte phosphoproteome

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: Mitochondrial Ca2+ (mCa2+) plays an important role in regulating cardiac metabolism and physiology. However, its contribution to metabolic and functional defects in the hearts of type 2 diabetic mice (T2D) is not well understood. Ca2+ is imported into mitochondria by the mitochondrial calcium uniporter complex (MCUC) which is a highly selective multimeric Ca2+ ion channel composed of pore-forming, scaffold, and regulatory subunits. Here, we describe new mechanisms involving the MCUC inhibitory subunit MCUb and its role in determining cardiac dysfunction by linking cardiac mitochondrial metabolism and contractile function. Hearts from T2D mice were analyzed 5 months following a single streptozotocin (STZ) injection (75 mg/kg) and high fat diet (HFD) feeding, and compared to control hearts from mice fed normal chow. Transcriptional and proteomic profiling were employed to characterize these hearts. Regulation of MCUb gene expression was investigated using a recombinant mutant inactive Cas9 (dCas9)-based gene promoter pull down approach coupled with mass spectrometry (MS). A dominant negative MCUb (MCUb W246R/V251E=dnMCUb) was engineered. dnMCUb was biochemically characterized in vitro, tested in neonatal cardiac myocytes exposed to culture media mimicking the diabetic milieu, and expressed in type 2 diabetic mice for 1 month. The impact of dnMCUb on the cardiac physiology was then investigated using omics as well as functional approaches aimed to highlight metabolic and contractile features. RNA-seq and proteomics analysis revealed that T2D hearts relied almost exclusively on fatty acid oxidative metabolism. In parallel we found a significant increase in MCUb mRNA and protein in T2D hearts, which was associated with decreased mCa2+ import rates. MS analysis of proteins co-precipitated with dCas9 revealed the presence of NCOR2 in control but not in T2D MCUb gene promoters. Downregulation of NCOR2 in isolated cardiac myocytes from control mice recapitulated the increase in MCUb gene expression. The dnMCUb mutant increased MCUC Ca2+ affinity by improving the architecture of the complex. Furthermore, when dnMCUb was introduced to cardiac myocytes and T2D mice we observed increased mitochondrial glucose oxidation, mitochondrial ATP production, and enhanced cardiac function. These were linked to the complete restoration of phospholamban (PLN) phosphorylation via Protein Kinase A (PKA) as revealed by both MS analysis of the phosphoproteome and studies dedicated on PLN only followed by PKA pharmacological inhibition. We detail a new pathological axis in which T2D induces global metabolic adaptations and inflexibility in part due to impaired mCa2+ transport into the mitochondrial matrix, resulting from MCUb overexpression. Moreover, we describe a mCa2+-dependent regulation of cytosolic Ca2+ (cCa2+) trafficking in which mCa2+ regulates the activity of SERCA2a via PKA-dependent phosphorylation of PLN.

overall_design: Gene expression profiling of mouse hearts from T2D mice over expressing MCUb and controls

first: Federico

last: Cividini

first: Wolfgang

last: Dillmann


title: KLF4-PFKFB3-driven glycolysis is essential for phenotypic switching of vascular smooth muscle cells (circRNA microarray)

last: Zhang

overall_design: smooth muscle cells treat by GFP,KLF4 or KLF5


title: Histone deacetylase 3: A potential target fight against Helicoverpa armigera

first: Liangling

last: Shen

address: 389 Xincun Road

institute: Tongji Hospital, Tongji University

summary: Insect development requires genes to be expressed in strict spatiotemporal order. The degree of histone acetylation regulates insect development, via histone acetyltransferases (HATs) and histone deacetylases (HDACs). Although HDAC3 is required for early embryonic development, its functions in Helicoverpa armigera remain unclear. We treated H. armigera with HDAC3 siRNA and RGFP966, a specific inhibitor, examining how HDAC3 loss-of-function affects growth and development. HDAC3 siRNA and RGFP966 treatment increased mortality at each growth-stage and altered metamorphosis, hampering pupation and causing abnormal wing development, reduced egg production, and reduced hatching rate. RNA-seq analysis identified 2,788 differentially expressed genes (≥ two-fold change; P ≤ 0.05) between siHDAC3- and siNC-treated larvae. Kr-h1, were differentially expressed in HDAC3 knockdown larvae. Pathway enrichment analysis revealed significant enrichment of genes involved in the Hippo, MAPK, and Wnt signaling pathways following HDAC3 knockdown. Histone H3K9 acetylation was increased in H. armigera after siHDAC3 treatment. In conclusion, HDAC3-knockdown dysregulated 20-hydroxyecdysone hormone-related and apoptosis-related genes in H. armigera, affecting many basic processes, including cell cycle regulation, metabolism, and signal transduction. The Result showed that HDAC3 gene can serve as a potential target for fighting against Helicoverpa armigera.

overall_design: mRNA profiles of siNC and siHDAC3 Helicoverpa armigera

first: Huimin

last: Chang

first: Hujuan

last: Mo

first: Maozhi

last: Ren


title: The RNA Sequencing of B Cells in malignant pleural effusion

city: Beijing

first: Mingming

last: Shao

state: State...

address: 8 Gongren Tiyuchang Nanlu

institute: Beijing Chao-Yang Hospital

summary: By using RNA sequencing plat, we employed malignant pleural effusion as research model to performed RNA sequencing of naïve B cells and Breg cells in the immune microenvironment of MPE.

overall_design: RNA profiles of 3 paired naïve B cells and Breg cells of malignant pleural effusion samples

first: Huangzhong

last: Shi

first: Kan

last: Zhai

first: Zhongyin

last: Huang


title: KLF4-PFKFB3-driven glycolysis is essential for phenotypic switching of vascular smooth muscle cells

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

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

overall_design: Refer to individual Series


title: Improved Sendai Viral System for Reprogramming to Naive Pluripotency

first: Akira

last: Kunitomi

address: 1650 Owens Street

institute: The J. David Gladstone Institutes


title: Enterocyte-specific deletion of metal transporter Zip14 (Slc39a14) alters intestinal homeostasis through epigenetic mechanisms

city: Gainesville

first: Robert

middle: John

last: Cousins

state: FL

address: 572 Newell Drive

department: Food Science/Nutrition

institute: University of Florida

summary: Zinc is an essential micronutrient that is believed to influence gut homeostasis by unclear mechanisms. Jimenez et al. identify that zinc transporter Zip14 is essential to maintain protective systems, lower inflammation, and limit dysbiosis through mechanisms that control histone deacetylase activity and transcription factor occupancy of specific genes in intestinal epithelial cells.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 5 WT and 5 Zip14 KO mice.

middle: J

first: Felix

middle: R

last: Jimenez Rondan

first: Courtney

last: Ruggiero


title: Human Chronic Lymphocytic Leukaemia cells: Untreated vs mithramycin-treated

city: Liverpool

first: Joseph

last: Slupsky

state: Select State

address: Sherrington Building, Dept Molecular and Clinical Cancer Med

department: Molecular and Clinical Cancer Medicine

institute: University of Liverpool

summary: Transcriptional profiling of primary human malignant B cells from patients with chronic lymphocytic leukaemia (CLL), comparing untreated CLL cells with CLL cells that have been treated 24h with 200nM mithramycin. Mithramycin intercalates into GC-rich regions of DNA to inhibit binding of the transcription factor SP1. The goal of this experiment is to gain understanding of the genes regulated by SP1 in primary CLL cells.

overall_design: Two condition experiment. CLL cells purified from 4 patient samples. Untreated vs mithramycin-treated CLL cells. Biological replicates: 4 (untreated (control) vs treated (mithramycin))


title: Multi-omics and machine learning reveal context-specific gene regulatory activities of PML-RARA in Acute Promyelocytic Leukemia [APL PBMCs ATAC-seq]

city: London

first: Cameron

last: Osborne

address: Guy's Hospital Campus

department: Medical and Molecular Genetics

institute: King's College London

summary: The PML-RARA fusion protein is the hallmark driver of Acute Promyelocytic Leukemia (APL) and disrupts retinoic acid signaling, leading to wide-scale gene expression changes and uncontrolled proliferation of myeloid precursor cells. While known to be recruited to binding sites across the genome, its impact on gene regulation and expression is under-explored. Using integrated multi-omics datasets, we characterize the influence of PML-RARA binding on gene expression and regulation in an inducible cell line model and APL patient ex vivo samples. We find that genes whose regulatory elements recruit PML-RARA are not uniformly transcriptionally repressed, as commonly suggested, but also may be upregulated or remain unchanged. We apply a novel computational deep learning strategy to deconvolute the complex, local transcription factor binding site environment at PML-RARA bound positions to reveal distinct signatures that modulate how PML-RARA directs the transcriptional response.

overall_design: Application of ATAC-seq to 2 APL patient sample PBMCs

first: William

last: Villiers

first: Richard

last: Dillon

first: Borbala

last: Mifsud


title: Multi-omics and machine learning reveal context-specific gene regulatory activities of PML-RARA in Acute Promyelocytic Leukemia [Cut&Tag]

summary: The PML-RARA fusion protein is the hallmark driver of Acute Promyelocytic Leukemia (APL) and disrupts retinoic acid signaling, leading to wide-scale gene expression changes and uncontrolled proliferation of myeloid precursor cells. While known to be recruited to binding sites across the genome, its impact on gene regulation and expression is under-explored. Using integrated multi-omics datasets, we characterize the influence of PML-RARA binding on gene expression and regulation in an inducible cell line model and APL patient ex vivo samples. We find that genes whose regulatory elements recruit PML-RARA are not uniformly transcriptionally repressed, as commonly suggested, but also may be upregulated or remain unchanged. We develop a novel, computational machine learning application to deconvolute the complex, local transcription factor binding site environment at PML-RARA bound positions to reveal distinct signatures that modulate how PML-RARA directs the transcriptional response.

overall_design: Application of Cut&Tag to NB4 cells.


title: RNA-seq of NSC11 GSCs in the olfactory bulb (OB) compared to the right hemisphere (RH)

city: Besthesda

first: Charlotte

last: Degorre

state: Maryland

address: 10 Center drive

department: NCI

institute: NIH

summary: RNA-seq analysis of NSC11 GSCs present in the OB compared to the RH to analyse the influence of the brain microenvironment to the tumor cells gene expression.

overall_design: Comparative gene expression analysis between NSC11 GSCs in OB (3 samples-2OB per samples) versus RH (3 samples)

first: Ian

last: Sutton

first: Stacey

middle: L

last: Lehman

first: Uma

last: Shankavaram

first: Kevin

last: Camphausen

first: Philip

last: Tofilon


title: RNA-Seq and genome-wide association analysis were utilized to find potential genes for rice seed shattering

city: 广州市

first: Linxuan

last: Wu

state: 广东省

address: 广东省广州市天河区五山路483号华南农业大学科技楼713

institute: South China Agricultural University

summary: The AZ and NAZ of the materials that were loss of shattering (DZ129) and easy to shattering  (W517) were used to perform RNA-Seq, and high-quality differential expression profiles were obtained.

overall_design: Comparative gene expression analysis of RNA-seq data for AZ and NAZ (W517NAZ, W517AZ, DZ129NAZ, DZ129AZ).


title: Hypertrophic cardiomyopathy: data of transcriptome profiling and epigenome-wide DNA methylation analysis

city: Moscow

first: Ivan

last: Kiselev

address: Ostrovitianov st. 1

country: Russia

institute: Pirogov Russian National Research Medical Universitty

type: Methylation profiling by genome tiling array

summary: Hypertrophic cardiomyopathy (HCM) is the most common inherited heart disease, and its pathogenesis is still being intensively studied to explain the reasons of significant genetic and phenotypic heterogeneity of the disease. To search for possible HCM modifier genes involved in the HCM development we first attempted to analyze gene expression profile coupled with DNA methylation profile in the hypertrophied myocardium of HCM patients; the control group consisted of patients with aortic stenosis. The transcriptome analysis identified significant differences in levels of 193 genes, most of which were underexpressed in HCM. The methylome analysis revealed 1755 nominally significant differentially methylated positions (DMPs), mostly hypomethylated in HCM. The clear differences in DNA methylation profiles between the studied groups indicate the involvement of this process in the formation of primary left ventricle hypertrophy in HCM. Based on gene ontology enrichment analysis, the majority of biological processes, overrepresented by both differentially expressed genes (DEGs) and DMP-containing genes, are involved in the regulation of locomotion and muscle structure development. The intersection of 193 DEGs and 978 DMP-containing genes pinpointed eight genes, expression of which differed between studied groups and correlated with methylation levels of the neighboring DMPs. Half of these genes (AUTS2, GIGYF1, PRRT1, and SLC17A7) were found underexpressed in HCM and involved in neurogenesis and synapse functioning. Our data suggesting the possible involvement of innervation-associated genes in HCM provide additional insights in the disease pathogenesis and expand the field of further research.

overall_design: We performed a genome-wide DNA methylation analysis of the heart left ventricle samples obtained from 8 patients with HCM and 5 samples from patients with AS. Bisulphite converted DNA from all 13 samples were hybridised to the Illumina Infinium MethylationEPIC BeadChip.


title: PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and controls RNA polymerase pause release at select gene targets [PRO-Seq II]

city: Boston

first: Susu

last: Zhang

state: MA

address: 360 Longwood Ave, LC6102

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary: This study aim to in-depth understand the function of a transcription factor fusion protein that drives the development of a highly aggressive pediatric malignancy. After engineered the endogenous PAX3-FOXO1 locus, we use chemical genetics to rapidly degrade the protein. This comprehensive, detailed, and accurate study with deep genomic analyses and deep proteomics provide a detailed mechanism by which PAX3-FOXO1 maintains an oncogenic transcriptional regulatory network.

overall_design: Deep mechanistic analysis including proteomics and 15 parameter genomics.

first: Scott

last: Hiebert

first: Kristy

last: Stengel

first: Jing

last: Wang

first: Qi

last: Liu

first: Hayes

last: McDonald

first: Monica

last: Bomber

first: Hillary

last: Layden

first: Jacob

last: Ellis

middle: C

last: Borinstein


title: PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and controls RNA polymerase pause release at select gene targets [ChIP-Seq II]


title: Arginine methylation of BRD4 by PRMT2/4 governs transcription and DNA repair

city: Charleston

first: Wenjian

last: Gan

state: SC

address: 173 Ashley Ave, BSB507

institute: Medical University of South Carolina

summary: BRD4 functions as an epigenetic reader and plays a crucial role in regulating transcription and genome stability. Dysregulation of BRD4 is frequently observed in various human cancers. However, the molecular details of BRD4 regulation remain largely unknown. Here, we report that PRMT2- and PRMT4-mediated arginine methylation is pivotal for BRD4-dependent transcription, DNA repair, and tumor growth. Specifically, PRMT2/4 interact with and methylates BRD4 at R179, R181, and R183. This arginine methylation selectively controls a transcriptional program by promoting BRD4 enrichment at the hyper-acetylated chromatin regions. Moreover, BRD4 arginine methylation is induced by DNA damage and thereby promotes its binding to chromatin for DNA repair. Deficiency in BRD4 arginine methylation significantly suppresses tumor growth and sensitizes cells to BET inhibitors and DNA damaging agents. Therefore, our findings reveal an arginine methylation-dependent regulatory mechanism of BRD4 function and highlight targeting PRMT2/4 for better anti-tumor effect of BET inhibitors and DNA damaging agents.

overall_design: To identify the co-regulation genes of BRD4 and PRMT2/4, we depleted BRD4 or PRMT2/4 by shRNA in MCF7 cells and then performed RNA-seq.

first: Liu

first: Delaney

last: Joe


title: Transcriptome sequencing of primary human oral keratinocytes co-cultured with Prevotella melaninogenica

city: Shanghai

first: Yiting

last: Guo

address: 399 Middle Yanchang Road

institute: Tongji University

summary: Oral lichen planus (OLP) is a common oral mucosal disease, of which the etiology and pathogenesis are still unclear. Microorganisms may play an essential role in the pathogenesis of OLP. Previous studies of our group found that the composition ratio of Prevotella melaninogenica (Pm) on the buccal mucosa surface of OLP patients increased significantly. In addition, Pm could invade the epithelium of OLP. As the first physical defense of the oral mucosa, oral keratinocytes may interact directly with Pm in OLP. Therefore, this study aimed to explore the impact of Pm on primary human oral keratinocytes' transcriptome.

overall_design: Control group: primary human oral keratinocytes; 4 h group: primary human oral keratinocytes co-cultured with Prevotella melaninogenica in MOI=10 for 4 h; 24 h group: primary human oral keratinocytes co-cultured with Prevotella melaninogenica in MOI=10 for 24 h.Each group had three replications.

first: Wenhao

last: Han

first: Yuan

last: He


title: PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and controls RNA polymerase pause release at select gene targets [Cut & Run III]


title: The dynamics of Cryptococcus neoformans cell and transcriptional remodeling during infection

city: Belo Horizonte

first: GUSTAVO JOSE

middle: COTA

last: DE FREITAS

state: MG

address: Av. Presidente Antônio Carlos  6627, Instituo de Ciencias Biológicas

department: MICROBIOLOGIA

country: Brazil

institute: UNIVERSIDADE FEDERAL DE MINAS GERAIS

summary:
Purpose: Investigate the dynamics of cryptococcal cell and transcriptional remodeling during pulmonary infection in a murine model
Methods: Dual-RNA sequencing   Sample preparation - C57BL/6 mice were infected intratracheally with the H99 strain to analyze the transcriptome. After 6h or 240h of infection, BALF obtained from 6 mice of each condition were pooled together, generating two replicates of 6h and 240h (10d). BALF was centrifuged at 1200 x g and resuspended in 1mL TRIzol Reagent (Invitrogen Life Technologies) for RNA isolation, according to the manufactures' protocol. RNA from H99 yeasts grown in YPD was used as control.
Results: Dual RNA-Seq analysis of C. neoformans and mice revealed molecular signatures of early and late events of infection We analyzed the up and downregulated genes after 6h and 10 days of infection, compared to the inoculated yeast (YPD x 6h and YPD x 10d) and the differentially expressed genes (DEGs) between 6h and 10 days of infection (designated BAL6h x BAL10d). These analyses revealed molecular signatures unique to early and late stages of infection.
Conclusions: Our findings support a scenario in which the fungus initially deploys mechanisms aimed at survival, proliferation and tissue invasion. Later, the fungus may focus on mechanisms aimed at resistance to the immune response and colonization, that are crucial for disease development. Overall, our study provides new insights into understanding the biology of C. neoformans during infection and generating perspectives for the survey for new therapeutic and diagnostic targets for cryptococcosis.

sample_organism:
Cryptococcus neoformans
Mus musculus

platform_organism:
Cryptococcus neoformans
Mus musculus

first: Gustavo

last: Freitas

first: Ludmila

last: Gouveia-Eufrasio

first: Eluzia

last: Emidio

first: Hellem

last: Carneiro

last: Baltazar

first: Marliete

last: Costa

first: Susana

last: Frases

first: Glauber

last: de Sousa Araújo

first: Tatiane

middle: A

last: Paixão

first: Brunno

middle: G

last: Sossai

first: Melissa

last: Caza

first: James

last: Kronstad

first: Nalu

last: Peres

first: Daniel

last: Santos


title: Early-life stress impacts the adult microglia transcriptome under basal and inflammatory conditions

city: Amsterdam

first: Aniko

last: Korosi

state: Noord Holland

address: Sciencepark 904

department: Swammerdam Institute for Life Sciences

country: Netherlands

institute: University of Amsterdam

summary: Early-life stress (ELS) leads to increased vulnerability to psychiatric illness including cognitive impairment later in life. Neuroinflammatory processes have been implicated in ELS-induced negative health outcomes, but, how ELS impacts microglia, the macrophages of the central nervous system, is unknown. Here, we determined the effects of ELS induced by limited bedding and nesting material during the first week of life (P2 – P9) on the morphology and gene expression of microglia from young (postnatal day (P)9) and adult (P200) mice. ELS led to a change in the proportion of morphological microglia subtypes in adulthood, associated with immune reactivity. At the transcriptional level, whereas at P9 no ELS mediated changes were detected, at P200 ELS induced transcriptional changes in microglia genes involved in the immune response and protein ubiquitination. Additionally, ELS altered microglia gene expression changes during development from P9 to P200 and in response to LPS at P200, in both cases marked by GO-terms associated with the immune response. Concluding, these data show that ELS has persistent effects on the morphology and gene expression program of microglia and results in an altered transcriptional response to a systemic LPS challenge.

overall_design: To determine acute and long-term effects of ELS on microglia, we exposed three different cohorts of mice to control conditions or ELS from postnatal day (P)2 to P9. The first cohort of CTL and ELS-exposed mice was injected with PBS or LPS (5 mg/kg) by the age of 3-5 months of age and was used for morphological characterization of microglia 24 hours after PBS or LPS injection (CTR-PBS (n=5), ELS-PBS (n=4), CTR-LPS (n=10), ELS-LPS (n=6). The second cohort was sacrificed at P9 and in order to investigate how ELS affects the microglia inflammatory response the third cohort was allowed to mature until P200, at which time they were injected with either PBS or LPS (1 mg/kg) (Figure 1A). To determine microglia transcriptional changes, hippocampal microglia were isolated at P9 and P200, and the P200 animals were injected with either PBS or LPS. Thus, for microglia transcriptomics we have the following experimental groups: P9: CTR (n=12), P9: ELS (n=12), P200: CTR-PBS (n=7), P200: ELS-PBS (n=6), P200: CTR-LPS (n=7), P200: ELS-LPS (n=5).

first: Bart

last: Eggen


title: Next-Generation Sequencing Facilitates Quantitative Analysis of Control and HDAC Inhibitors-treated  Uterine Leiomyosarcoma Cell Transcriptome

city: Chicago

first: Qiwei

last: Yang

address: 5841 S. Maryland Avenue

department: Obstetrics and Gynecology

institute: University of Chicago

summary: We report that HDAC inhibition alters multiple biological pathways in uterine leiomyosarcoma cells

overall_design: Examine the transcriptome alteration in uterine leiomyosarcoma cells with or without HDAC inhibitors

first: Ayman

last: Al-Hendy


title: The kinase PLK1 promotes the development of Kras/Tp53-mutant lung adenocarcinoma through transcriptional activation of the receptor RET

city: Lexington

first: Yifan

last: Kong

state: Kentucky

address: 760 Press Avenue, HKRB, Room 334

institute: University of Kentucky

summary: To investigate the function of PLK1 in the regulation of lung cancer development in mice, we performed genetic crosses to incorporate a Plk1 transgene into the KP mouse model (herein KPP) . We then performed gene expression profiling analysis using data from RNA-seq of  tumors from either cohort respectively.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for KP and KPP tumors.

first: Xiaoqi

last: Liu


title: Cell-type specific alternative splicing in the Arabidopsis germline

city: Lisbon

first: Jörg

middle: Dieter

last: Becker

address: ITQB NOVA Avenida da República

country: Portugal

institute: ITQB

summary:
During sexual reproduction in flowering plants, the two haploid sperm cells embedded within the cytoplasm of a growing pollen tube are carried to the embryo sac for double fertilization. Pollen development in flowering plants is a dynamic process that encompasses changes at transcriptome and epigenome level. While the transcriptome of pollen and sperm cells in Arabidopsis thaliana is well documented, previous analyses were mostly based on expression at gene level. In-depth transcriptome analysis, particularly the extent of alternative splicing at the resolution of sperm cell and vegetative nucleus was still lacking. Therefore, we performed RNA-seq analysis to generate a spliceome map of Arabidopsis sperm cells and vegetative nuclei isolated from mature pollen grains.
Based on our de-novo transcriptome assembly we identified 58039 transcripts, including 9681 novel transcripts, of which 2091were expressed in sperm cells and 3600 in vegetative nuclei. Our data from sperm cell and vegetative nucleus identified 468 genes that were regulated both at gene and splicing level, with many having functions in mRNA splicing, chromatin modification, and protein localization. Moreover, a comparison with egg cell RNA-seq data uncovered sex-specific regulation of transcription and splicing factors. Our study provides novel insights into a gamete specific alternative splicing landscape at unprecedented resolution.

overall_design: Seeds of a transgenic marker line harbouring MGH3p::MGH3-GFP and ACT11p::H2B-mRFP  were sown on soil in short-day conditions (8-h light at 21–23 °C) for 8 weeks and then transferred to long-day conditions (16-h light) to induce flowering. Flowers were collected, pollen cracked and FACS sorting of sperm cells and vegetative nucleus from mature pollen grain (MPG) was performed. 3 Biological replicates for each sperm cell and vegetative nuclei sample were used.

first: Chandra Shekhar

last: Misra

first: António

last: Sousa

first: Pedro

last: Barros

first: Anton

last: Kermanov

last: Becke


title: Transcriptomic analysis of B cells from patients with Sjögren’s Syndrome

city: Utrecht

first: Ana

middle: Pinheiro

last: Lopes

state: Utrecht

address: Heidelberglaan 100

institute: University Medical Center Utrecht

summary: Primary Sjögren’s syndrome (pSS) is a systemic autoimmune disease characterized by lymphocytic infiltration of the exocrine glands and prominent B cell hyperactivity. B cells are crucial in the pathophysiology of pSS through several mechanisms, including cytokine production, exocrine gland destruction, and autoantibody secretion. Considering the central role of B cells we performed RNA-sequencing analysis of circulating CD19+ B cells from patients with pSS, non-Sjögren’s sicca (nSS), and healthy controls (HC).

overall_design: RNA-sequencing of pheripheral blood isolated CD19+ B cells from patients with primary Sjögren’s syndrome (pSS; n=14), non-Sjögren’s sicca (nSS; n=11), and healthy controls (HC; n=13).

first: A

middle: P

first: M

last: Hillen

first: S

last: Blokland

first: C

last: Bekker

last: Pandit

last: Kruize

first: T

last: Radstake

first: J

last: van Roon


title: Deciphering the role of cDC2s in Sjogren’s Syndrome: transcriptomic profile reveals altered antigen processing and uptake associated with IFN-signatures and autoimmunity

summary:
Primary Sjögren’s syndrome (pSS) is a systemic autoimmune disease characterized by lymphocytic infiltration of the exocrine glands. Conventional dendritic cells (cDCs)-2 play a critical role in T and B cell activation, leading to germinal centre formation and autoantibody production. To understand the mechanisms underlying cDC2 dysregulation in pSS we performed RNA-sequencing analysis and functional validation on circulating cDC2s from pSS, non-Sjögren’s sicca (nSS) patients and healthy controls (HC).
Two independent cohorts were established to identify reproducible dysregulated signatures, which included the interferon (IFN), toll-like receptors (TLR) signaling and antigen processing and presentation pathways. We confirm by flow cytometry that pSS-cDC2s were less efficient to degrade BSA but more efficient to uptake BSA both linked with the presence of anti-SSA antibodies. As the majority of the SSA+ pSS patients exhibit an IFN-signature, we tested whether IFNα priming would influence cDC2s antigen-uptake and processing. IFNα priming increased cDC2s uptake capacity, but not antigen processing. Additionally, pSS-cDC2s showed an increased uptake capacity of apoptotic salivary gland epithelial cells. Finally, pSS-cDC2s increased the proliferation of HC CD4+ T cells and the expression of CXCR3 and CXCR5 on the proliferating HC CD4+ T cells, contributing to T cell migration into the inflamed salivary glands.
Here we provide the first in-depth molecular characterization of pSS-cDC2s and show that the transcriptomic and functional alterations observed in pSS-cDC2s are linked to IFN-signature. In view of its role in pSS immunopathology, delineating the molecular networks that drive cDC2s holds promise for targeting these cells in pSS.

overall_design: RNA-sequencing of pheripheral blood isolated cDC2s from patients with primary Sjögren’s syndrome (pSS; n=23), non-Sjögren’s sicca (nSS; n=15), and healthy controls (HC; n=18).

last: Hinrichs


title: Transcriptome analysis of CD229 OE (CAG-OE) and WT(CAG-WT) in CAG

city: Nanjing

first: Zigen

last: Lin

address: No.138 Xianlin Avenue, Qixia District, Nanjing city, Jiangsu Province, China

institute: Nanjing University of Chinese Medicine

summary: Transcriptome sequencing was used to analyze changes in related signaling pathways and gene expression in CAG cells when CD229 was overexpressed.

overall_design: Examination  in CAG cells.

first: Ye

last: Yang

first: Chunyang

last: Gu


title: Next Generation Sequencing Facilitates Quantitative Analysis of Control and Slc25a1 plus Idh3α-deficient MLE12 cells

city: Changsha

first: Chaxiang

last: Guan

state: Hunan

address: 87 Xiangya Road

department: Department of Physiology, School of Basic Medical Science

institute: Central South University

summary:
Purpose: To understand the biological function of citratemt accumulation, we performed RNA-seq analysis.
Methods:MLE12 cells were transfected simultaneously with shIdh3α lentivirus (MOI: 50) and shSlc25a1 lentivirus (MOI: 50) and negative control (shCtrl lentivirus, MOI: 50) in the presence of 1HitransG P (Lot: REVG005, GeneChem).Empty construct was used as control for all experiments. The cells were washed with fresh complete medium 16 h later and then cultivated for an additional 80 h.Total RNA was extracted from control and Slc25a1 plus Idh3α-deficient MLE12 cells. The transcriptome library for sequencing was generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following the manufacturer’s recommendations. The index codes were added to attribute sequences to each sample. After the quality of sequencing libraries was confirmed on the Agilent 2100 system, clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia, San Diego, CA, USA) according to the manufacturer’s instructions. The library preparations were then sequenced on an Illumina Hiseq 2500 platform (Illumina, San Diego, CA, USA), and paired-end reads were generated. Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity with min_kmer_cov set to 2 by default and all other parameters set to default.
Results: Using an optimized data analysis workflow,We found that 215 genes were upregulated in MLE12 cells with citratemt accumulation . To determine the functional properties of the top 30 genes upregulated by citratemt, we performed Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. KEGG pathway analysis indicated that the 30 genes were involved in regulating the TNF signaling pathway , one of the critical signaling pathways for triggering necroptosis
Conclusions: These results further suggest that citratemt accumulation specifically drives necroptosis

overall_design: mRNA profiles of control and Slc25a1 plus Idh3α-deficient MLE12 cells

first: Hui-Hui

first: Cha-xiang


title: RNA profiling of PB-020 and anti-PD-1 antibody treated MC38 tumor tissue

city: Hangzhou

first: Yingjie

last: Wang

state: Zhejiang

address: Research Center C701,School of Medicine,Zhejiang University,866 Yuhangtang Road

department: Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine

institute: Zhejiang University

summary: Immune surveillance escaping is essential for survival of original tumor. Considering PB-020’s good pharmacokinetic properties, combined effect of PB-020 and immunotherapy drugs is worth studying. As PB-020 can effectively suppress mouse colorectal cancer cell lines in cell culture, we tested the effect of combining PB-020 with the anti-PD-1 monoclonal antibody RMP1-14 on the growth of subcutaneously implanted MC38 cells to C57BL/6 mice as a syngeneic mouse model of colorectal cancer. To clarify the molecular mechanism underling this anti-cancer therapy, we executed RNA sequencing of tumor sample obtained from the experiment above.

overall_design: MC38 cells were injected subcutaneously to C57BL/6 mice. After tumor formation, mice were randomly divided into four groups and treated with vehicle, PB-020, anti-PD-1 and PB-020+anti-PD-1. When experiment finished, tumor samples were collected for RNA-sequencing.

first: Bo

last: Kang


title: Differential gene set analysis of isolated liver sinusoidal endothelial cells of Lyve-1 deficient (Lyve-1-KO) and control mice

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary: Liver sinusoidal endothelial cells (LSEC) of both Lyve-1-KO (B6.129S1-Lyve1tm1Lhua/J (JAX stock #006221)) and Ctrl mice were isolated and mRNA were comparatively analyzed by a microarray (Affimetryx). Even though there was no single gene significantly dysregulated, an overall representation analysis of HALLMARK pathways revealed regulation of Myc targets as well as immunological pathways involved in TNF-α, Interferon-α or -γ signaling.

first: Philipp-Sebastian

last: Reiners-Koch

first: Anna

middle: S

last: Jauch

first: Sebastian

last: Wohlfeil

first: Cyrill

last: Géraud

first: Carolina

last: Delatorre


title: RT_Immunological Changes_interval

city: Seoul

first: YI NA

last: YOON

address: 75, Nowon-ro, Nowon-gu

country: South Korea

institute: korea institute of radiological and medical sciences

summary: RT upregulated PD-L1 expression levels in tumor cells from the middle to late phase, which subsequently declined to a level comparable to baseline in the progression phase. When compared to 7.5 Gy, the frequency of PD-L1+ myeloid-derived suppressor cells with 2 Gy × 5 was maintained to be higher, showing tumor regression to a lesser extent. The proportion of PD-1+CD8+ and interferon-γ+CD8α T cells continued to increase until the end of the evaluation. The frequency of splenic PD-1+CD8+ T cells was significantly elevated following RT, and the effect was sustained longer with 2 Gy × 5. The transcriptomic data analysis revealed that RT stimulated the transcription of overall immunostimulatory and inhibitory genes, showing sequentially altered patterns.

overall_design: Each time point has 0Gy, 2Gyx5, and 7.5Gy samples. PreRT sample is a non-irradiated control group.

first: Yi

middle: N

last: Yoon


title: Whole blood gene expression to predict susceptibility to nontuberculous mycobacterial pulmonary disease in adults with cystic fibrosis

city: Vancouver

first: Bradley

last: Quon

state: BC

address: 1081 Burrard Street

department: Department of Medicine

country: Canada

institute: Centre for Heart and Lung Innovation

summary: Background: Patients with cystic fibrosis (CF) have an elevated lifetime risk of infection and disease caused by nontuberculous mycobacteria (NTM). Currently, there is no method to predict whether patients with cystic fibrosis will develop disease related to non-tuberculous mycobacteria. In non cystic fibrosis populations, several genetic susceptibility factors have been described. In this study, we examined whether patients with cystic fibrosis demonstrate a similar pattern of genetic susceptibility and explored host immune-related biomarkers predictive of NTM pulmonary disease (NTM-PD).   Methods: We evaluated whole blood gene expression using bulk RNA-seq in a cohort of CF patients at the time of first isolation of NTM. Differential gene expression was compared in patients who did (n = 12) vs. did not (n= 30) develop NTM-PD following first NTM growth.  Results: No differences in demographics or composition of white blood cell sample populations at the time of sample collection were identified between groups. There were no significant differences in the expression of genes previously reported to confer susceptibility to NTM-PD in non-CF populations. However, CF patients who went on to develop NTM-PD had higher expression of genes involved in the interferon ( and ), tumor necrosis factor, and IL6 STAT3 JAK pathways.   Conclusion: Patients with CF who develop NTM-PD have increased expression of genes involved in innate immunity, in contrast to non-CF populations where these responses seem to be suppressed.

overall_design: RNAseq gene expression profiling in whole blood of adult patients with cystic fibrosis and infection with nontuberculous mycobacteria. Compares expression of patients who developed nontuberculous mycobacterial pulmonary disease and those who did not.

first: Miguel

middle: D

last: Prieto

first: Alessandro

last: Franciosi

first: Jiah

last: Jang

first: Avgay

last: Yossef

first: Bach

last: Horacio

first: Tebbut

last: Scott


title: PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and controls RNA polymerase pause release at select gene targets [Cut & Run II]

first: Susu

last: Zhang

first: Scott

middle: W

last: Hiebert

first: Kristy

last: Stengel

first: Jing

last: Wang

first: Qi

last: Liu

first: Hayes

last: McDonald

first: Monica

last: Bomber

first: Hillary

middle: M

last: Layden

first: Jacob

last: Ellis

last: Borinstein


title: RNA-seq analysis of WT and Pim1-/- BMDMs

first: Soo Young

last: Lee

address: 52, Ewhayeodae-gil, Seodaemun-gu

institute: Ewha Womans University

summary: The Pim (proviral integration site for Moloney murine leukemia virus) proteins form a serine threonine kinase family that regulates cell proliferation, migration and cell survival. Here we demonstrate for the first time that a Pim1 kinase plays an essential role in antiviral innate immune responses. Specifically, our in vivo, in vitro and RNA-sequencing analyses showed that Pim1 was quickly upregulated after Toll-like receptor (TLR) stimulation in a NF-kB-dependent manner and then promoted IFN-b production by forming a cell-surface complex composed of TRIF-signaling molecules and IRF3 that promoted IRF3 phosphorylation, nuclear translocation, and IFN-b production. As shown by Pim1 knockdown and knockout, Pim1 was essential for this role but its kinase activity was not involved. Pim1-deficiency increased the susceptibility of mice to poly I:C-induced sepsis. Our study uncovers a previously unrecognized role for Pim1 in antiviral innate immune responses, thus providing a new target for controlling viral infection.

overall_design: Untreated WT BMDMs (n=3), LPS-treated WT BMDMs (n=3), untreated Pim1-/- BMDMs (n=3) and LPS-treated Pim1-/- BMDMs (n=3) were subjected to RNA-seq analysis

first: Soo

middle: Y

first: Ryeojin

last: Ko


title: PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and controls RNA polymerase pause release at select gene targets [ATAC-Seq II]

summary: This study aim to in-depth understand the function of a transcription factor fusion protein that drives the development of a highly aggressive pediatric malignancy. After engineered the endogenous PAX3-FOXO1 locus, we use chemical genetics to rapidly degrade the protein. This comprehensive, detailed, and accurate study with deep genomic analyses and deep proteomics provide a detailed mechanism by which PAX3-FOXO1 maintains an oncogenic transcriptional regulatory network.


title: PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and controls RNA polymerase pause release at select gene targets [RNA-Seq]


title: PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and controls RNA polymerase pause release at select gene targets [ChIP-Seq]


title: PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and controls RNA polymerase pause release at select gene targets [Cut & Run]


title: Macrophages induce inflammation by efferocytosis of apoptotic prostate cancer cells via HIF-1α stabilization

city: ANN ARBOR

first: Hernan

last: Roca

state: MI

address: 1011 N. University Ave.

department: Periodontics and Oral Medicine

institute: University of Michigan

summary: Clearance of apoptotic cancer cells by macrophages, known as efferocytosis, fuels the bone-metastatic growth of prostate cancer cells via pro-inflammatory and immunosuppressive mechanisms that are still unclear. In this study, single-cell transcriptomics of bone marrow macrophages undergoing efferocytosis of apoptotic prostate cancer cells revealed a significant enrichment of a cellular response to hypoxia. Here we show that efferocytic macrophages promote HIF-1α stabilization under normoxic conditions through interaction with phosphorylated STAT3. Inflammatory cytokine gene expression analysis of efferocytic HIF-1α-mutant macrophages revealed a reduced expression of the pro-tumorigenic Mif. Furthermore, stabilization of HIF-1α using the HIF-prolyl-hydroxylase inhibitor, Roxadustat, enhanced MIF expression in macrophages. Finally, macrophages treated with recombinant MIF protein activated NF-κB (p65) signaling increased the expression of pro-inflammatory cytokines.  Altogether, these findings suggest that the clearance of apoptotic cancer cell by tumor-associated macrophages triggers p-STAT3/HIF-1α/MIF signaling to enhance tumor-promoting inflammation in bone, suggesting this axis as a target for metastatic prostate cancer.

overall_design: Single cell sequencing of macrophages following efferocytosis

first: Veronic

last: Mendoza-Reinoso

first: Patricia

last: Schenpp

first: Dah

last: Baek

first: John

last: Rubin

first: Ernestina

last: Schipani

first: Evan

middle: T

last: Keller

first: Laurie

middle: K

last: McCauley


title: Expression profiling of a cellular exercise model based on the electrical pulse stimulation.

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

institute: Korea Research Institutue of Bioscience & Biotechnology

summary: Appropriate amount of exercise is the best way to prevent various diseases and have a healthy life. Skeletal muscles communicate with other organs through myokines, which are secreted by muscle itself during exercise and elicit various effects in the body. However, despite the years of efforts to understand molecular mechanisms of crosstalk between muscle and other organs that mediate the beneficial effects of exercise are not completely understood. To identify novel myokines, we used an in vitro exercise model in C2C12 cells using the electrical pulse stimulation (EPS) that can mimic muscle contraction. We generated RNA-seq data of seven in vitro samples to costruct a prediction model based on differentially expressed genes, showing significantly mimicking in vivo exercise.

overall_design: We generated a RNA-seq dataset of seven samples including three control and four EPS-treated samples. Total RNA was extracted from C2C12 myotubes using easy-BLUETM total RNA extraction kit according to the manufacturer’s instructions (iNtRON). RNA quality was assessed by Agilent 2100 bioanalyzer (Agilent Technologies, Amstelveen, The Netherlands), and RNA quantification was performed using ND-2000 Spectrophotometer (Thermo Inc., DE, USA). High-throughput sequencing was performed paired-end reads (2 × 100 bp) using HiSeq 2500 (Illumina, Inc., USA).

first: Bora

first: Yeo

middle: J

last: Shin

first: Ki-Sun

last: Kwon


title: PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and controls RNA polymerase pause release at select gene targets [ATAC-Seq]

city: Boston

first: Susu

last: Zhang

address: 360 Longwood Ave, LC6102

institute: Dana-Farber Cancer Institute

overall_design: Deep mechanistic analysis including proteomics and 15 parameter genomics.

first: Scott

last: Hiebert

first: Kristy

middle: R

last: Stengel

first: Jing

last: Wang

first: Qi

last: Liu

first: Hayes

last: McDonald

first: Monica

middle: L

last: Bomber

first: Hillary


title: Multi-omics and machine learning reveal context-specific gene regulatory activities of PML-RARA in Acute Promyelocytic Leukemia [RNA-seq]

city: London

first: Cameron

last: Osborne

address: Guy's Hospital Campus

institute: King's College London

summary: The PML-RARA fusion protein is the hallmark driver of Acute Promyelocytic Leukemia (APL) and disrupts retinoic acid signaling, leading to wide-scale gene expression changes and uncontrolled proliferation of myeloid precursor cells. While known to be recruited to binding sites across the genome, its impact on gene regulation and expression is under-explored. Using integrated multi-omics datasets, we characterize the influence of PML-RARA binding on gene expression and regulation in an inducible cell line model and APL patient ex vivo samples. We find that genes whose regulatory elements recruit PML-RARA are not uniformly transcriptionally repressed, as commonly suggested, but also may be upregulated or remain unchanged. We develop a novel, computational machine learning application to deconvolute the complex, local transcription factor binding site environment at PML-RARA bound positions to reveal distinct signatures that modulate how PML-RARA directs the transcriptional response.

overall_design: Application of RNA-seq to the U937-PR9 cell line system, before and after PML-RARA inuction. Application of RNA-seq to two ex vivo APL patient samples

first: William

last: Villiers

first: Richard

last: Dillon

first: Borbala

last: Mifsud


title: Identification of Mblk-1-binding DNA regions in honey bee brains by ChIP-seq.

city: Bunkyo-ku

first: Yasuhiro

last: Matsumura

state: Tokyo

department: Department of Biological Sciences

institute: The University of Tokyo

summary: Examination of Mblk-1-binding DNA regions in honey bee adult mushroom bodies(MBs) and pupal whole brains

first: Taiko

last: Kim To


title: Multi-omics and machine learning reveal context-specific gene regulatory activities of PML-RARA in Acute Promyelocytic Leukemia [Capture Hi-C]

overall_design: Application of Capture Hi-C to the U937-PR9 cell line system, before and after PML-RARA inuction. Application of Capture Hi-C to two ex vivo APL patient samples


title: PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and controls RNA polymerase pause release at select gene targets

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

overall_design: Refer to individual Series

last: Layden

first: Jacob

last: Ellis

middle: C

last: Borinstein


title: Multi-omics and machine learning reveal context-specific gene regulatory activities of PML-RARA in Acute Promyelocytic Leukemia [Cut&Run]

overall_design: Application of Cut&Run to the U937-PR9 cell line system, before and after PML-RARA induction. Application of Cut&Run to two ex vivo APL patient samples


title: Compendium of functional regulatory variants in human neuropsychiatric disease (HiChIP)

city: Stanford

first: Margaret

last: Guo

state: CA

address: 269 Campus Dr. CCSR Room 2150

institute: Stanford University

summary:
Abstract: Noncoding variants of presumed regulatory function contribute to neuropsychiatric disease heritability. 4442 noncoding variants connected to risk for 10 neuropsychiatric disorders, including autism spectrum disorder, attention deficit hyperactivity disorder, bipolar disorder, borderline personality disorder, major depression, generalized anxiety disorder, panic disorder, post-traumatic stress disorder, obsessive-compulsive disorder, and schizophrenia, were studied within developing human neural cells. Integrating epigenomic and transcriptomic data with massively parallel reporter assays identified 637 disease-associated single-nucleotide variants (daSNVs) with altered transcription-regulating activity. Expression-gene mapping, network analyses, and chromatin looping identified 619 candidate disease-relevant target genes modulated by these daSNVs. Specific daSNV-associated molecular pathways mapped to prevalent mental health symptoms. These data provide a framework resource to study inherited pathogenic risk for human neuropsychiatric disorders.
Purpose: To place disease-associated single nucleotide variants (daSNVs) in genomic context within human neural cells, matched RNA-seq, chromatin accessibility profiling via ATAC-seq, and enhancer-promoter looping via H3K27ac HiChIP was performed in ES cells and at day 2 (N-D2), 10 (N-D10), and 28 (N-D28) of neuronal differentiation. Additionally, anterior (A-NPC) and posterior (P-NPC) neuronal stem cells were generated and studied. Matched sequencing was also performed on primary human astrocytes from adult brains. Processed and raw data for all neural cell types can be found in this repository. Astrocyte raw data can be found at Donohue, et al. "The combinatorial cis-regulatory vocabulary of cell type-specific gene regulation in homeostasis and disease". All biological replicates (n=2) are merged using the ENCODE pipeline.

overall_design: ES-derived neuronal and primary astrocyte HiChIP profiles in vitro


title: Determination of Shavenbaby binding behaviour on  S2 cells [chipseq_svb]

city: Toulouse

first: Cedric

last: Polesello

address: 118 Route de Narbonne

country: France

institute: Centre de Biologie Intégrative de Toulouse

summary:
Shavenbaby (Svb) transcription factor is involved in the differenciation  of epidermal cells, the homeostasis of intestinal stem cell. Svb is first synthetized as a long repressor protein called SvbRepressor (SvbREP). In presence of Pri peptides Svb Repressor is clived by the proteasoome into a shorter activator protein called Svb Activator (SvbACT).
We want in this study determine the binding behaviour of the two Svb forms on S2 cells. We performed ChIPseq Svb experiment in S2 cell lines which present Svb REP  or SvbACT or S2 cell without Svb.

overall_design:
The experiment was performed in cells that either did not show Svb (Ctrl) or showed either the SvbACT or SvbREP form. 2 independent replicates were done for each condition.
Cells are cross-linked with 0.8% of formaldehyde for 10 min at room temperature. Cross-linking was stopped by adding glycine (2M) and cells were washed twice in cold with 1X PBS 1 mM NaBu . Cells were resuspended in 500 μL of ChIP permeation buffer (1X PBS, 0.2% Triton, 10mM NaBu), and incubated for 20 min at room temperature.
Lysis Buffer no SDS (140 mM NaCl, 15 mM HEPES pH 7.6, 1 mM EDTA, 1% Triton, 0.1% NaDOC, 0.5 mM DTT, 10mM NaBU, 25X protease inhibitor) during 5min with gentle rotation at 4°C , then cells are lysed on Lysis Buffer 1% SDS (Lysis Buffer no SDS + 1% SDS, 0.5% N-lauroylsarcosine) during 30min at 4°C with gentle rotation. Chromatin was sonicated in Bioruptor (Diagenode) using high-power settings, intervals of 30s burst/pause for six cycles to obtain fragments of ≈ 250 pb.
The sonicated chromatin was diluted 10 times with Lysis Buffer (no SDS) on protein low bind tubes (Eppendorf). The chromatin fraction was cleared by centrifugation (16000 g, 10 °C, 5 min), then pre-clarified (incubed with empty beads) O/N at 4° C. Beads were washed and blocked with 0.1 mg/mL BSA in Lysis Buffer 0.1% SDS, 0.5% N- lauroylsarcosyl during 2hours at 4°C with gentle rotation.
Beads are then bound to the antibody O/N at 4°C with gentle rotation. For one immunoprecipitation 20μL of blocked beads, 5μL of antibody and 400μL of Lysis Buffer 0.1% SDS (Lysis Buffer no SDS + 0.1% SDS, 0.5% N- lauroylsarcosine). Immunoprecipitation was performed for 4 hours at 4°C with gentle rotation with 5μl antibody, by adding 100μL pre-washed beads to 500μL cleared chromatin in protein low bind tubes. 2% of each sample was kept as input. Chromatin-bead complexes were eluted twice in the same tube by incubating the beads for 20 minutes at 70 °C first in 10 mM EDTA, 1% SDS, 50 mM Tris-Cl ph8, and then with TE, 0.67% SDS.
Samples were incubated overnight at 65°C to reverse the cross-link. Decrosslinked samples were treated with 1μL RNAse A during 45min at 37°C then with proteinase K solution (35mg/sample glycogen,100μg/sample proteinase K) during 2h at 55°C. DNA fragments were purified by phenol- chloroform protocol and resuspended in TE.)
ChIPseq of Control, SvbREP and SvbACT S2 cells (single-end 50 nt) were performed with HiSeq 200 (Illumina) at BGI.

first: Alexandra

last: Mancheno-Ferris


title: Comparing gene-expression profiles between control and CHD6 knock-down HCT116 cells

city: Guangzhou

first: Boyu

last: zhang

state: Guangdong

address: Yuancun Road

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

summary: Colorectal cancer is one of the most common cancers. Cancer cells are highly dependent on dysregulated gene expression to support their uncontrolled growth and high energy needs.  The expression of  gene encoding chromodomain helicase DNA binding protein 6 (CHD6) is frequently altered in tumor tissues of colorectal cancer patients.We performed transcriptomic analysis to identify the differentially expressed genes between control and CHD6 KD HCT116.

overall_design: Colorectal cancer cell line HCT116  with Tet-on inducible CHD6 KD construct was treated with doxycycline or vehicle for 48h. And cells were collected for RNA extraction. The RNA samples were hybridized on Affymetrix microarrays.

last: Zhang

first: Monghong

last: Lee


title: PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and controls RNA polymerase pause release at select gene targets [PRO-Seq]

first: Susu

country: USA

first: Scott

last: Hiebert

first: Kristy

last: Stengel

first: Jing

last: Wang

last: Liu

last: McDonald


title: Regulation of the alveolar regenerative niche by amphiregulin-producing Treg cells (MesSTIM)

city: New York

first: Nicholas

last: Arpaia

state: NY

address: 701 W 168TH ST HHSC 910C

department: Microbiology & Immunology

institute: Columbia University Irving Medical Center

summary: This study investigates the role of regulatory T cell–derived Areg in driving epithelial repair following influenza infection. We use RNA sequencing to probe the gene expression changes within distinct mesenchymal cell subsets of the lung upon stimulation with EGF (50ng/mL), AREG (200ng/mL), or mock. n = 2 wells / group.

overall_design: All populations of mesenchymal cells were extracted from lungs by enzymatic digestion. Cells were enriched by negative selection using magnetic biotinylated beads for depletion of CD45+, CD31+, Epcam+ and Ter119+ cells, then sorted by FACs. Cells were plated overnight in vitro before ex vivo stimulation.

first: Katherine

last: Kaiser

first: Lucas

last: Loffredo

first: Kenia

last: de los Santos


title: Regulation of the alveolar regenerative niche by amphiregulin-producing Treg cells (AT2-AEC)

summary: This study investigates the role of regulatory T cell–derived Areg in driving epithelial repair following influenza infection. We use RNA sequencing to probe the gene expression changes within epithelial cells in wildtype mice and in mice that conditionally lack Areg from T cell sources (CD4-cre Areg-flox). Further, we identify a population of damage-associated intermediate alveolar epithelial cells (AECint) that are induced in reponse to acute injury and exhibit gene expression changes reflective of AT2 transdifferentiation to AT1.

overall_design: All populations of alveolar epithelial cells were isolated by FACs prior to RNA extraction and RNA sequencing.Intermediate alveolar epithelial cells isolated at day 5 post infection with PR8/H1N1 influenza from CD4-cre Areg-fl/fl and Areg-fl/fl controls; n=4 per group.


title: Differential expression of keratin and keratin associated proteins in spontaneously mutated mice

status: Public on Dec 13 2022

city: hyderabad

first: Sivapriya

last: Pavuluri

address: uppal

country: India

institute: cdfd

summary: To find the differential expression of genes at different post natal stages of skin development in spontaneously mutated mice in comparison to the wildtype mice skin.

overall_design: Differential expression of gene analysis was performed using data obtained from RNA-seq of skin samples collected at post-natal days P0, P16, P19 and P28 of wildtype and spontaneously mutated mice.

first: Neeraja

last: Chilukoti

first: Satish

last: Kumar


title: Regulation of the alveolar regenerative niche by amphiregulin-producing Treg cells (10X)

summary: This study investigates the role of regulatory T cell–derived Areg on lung regeneration following influenza infection. We use single-cell RNA sequencing to capture the heterogeneity of lung mesenchymal populations during influenza infection. Here, we probe the gene expression changes within stromal cells from wildtype mice and in mice that conditionally lack Areg from T cell sources (CD4-cre Areg-flox) at day 8 post infection with PR8/H1N1. n = 1 per genotype.

overall_design: Areg-flox and CD4cre Areg-flox mice were infected with H1N1/PR8 influenza and harvested at day 8 post infection. Mesenchymal cells were enriched by negative depletion of CD45+, Epcam+, Ter119+, and CD31+. Enriched cells were delivered to Columbia University Genome Center for 10X bead emulsification.


title: Dual Roles for CND1 in Maintenances of Nuclear and Chloroplast Genome Stability in Plants [ChIP-seq]

city: 广州市

first: 柳

last: 洪

address: 番禺区

department: 中药学院

country: China

institute: 广州中医药大学

summary: The coordination of chloroplast and nuclear genome status are critical for plant cell function, but the mechanism remain largely unclear. In this study, we report that Arabidopsis thaliana CHLOROPLAST AND NUCLEUS DUAL-LOCALIZED PROTEIN 1 (CND1) maintains genome stability in both the chloroplast and the nucleus.

overall_design: The amount of ChIP-DNA coprecipitated by anti-FLAG M2 affinity gel was first normalized by comparing to the total input DNA used for each immunoprecipitation CT = CT (ChIP) -CT (input). Then, these normalized ChIP signals were compared to the input protein. The DNA binding of all the plastid gene in Col-0 was set to 1, these normalized ChIP signals in cnd1-3 were compared to Col-0.

first: Sujuan

last: Duan

first: Ziyue

last: Yang

first: Yunping

last: Zeng