title: Oryza sativa RNA-dependent RNA polymerase 6 (OsRDR6) contributes to DSB formation in rice meiosis

city: Fuzhou

first: mao

last: fei

state: Fujian

address: Shangxiadianlu NO.15

department: National Engineering Research Center of JUNCAO

institute: Fujian Agriculture and Forestry University

summary: RNA-dependent RNA polymerase 6 (RDR6) is a core component of the small RNA biogenesis pathway, but its function in meiosis is unclear. Herein we report a new allele of OsRDR6 (Osrdr6-mei), which causes meiosis-specific phenotype in rice. In Osrdr6-mei, meiotic DSB formation was blocked to some extent. We further created a biallelic mutant, Osrdr6-bi, by crossing Osrdr6-mei with a knock out mutant, Osrdr6-edit (Osrdr6-edi). In Osrdr6-bi, 24 univalents were observed at diakinesis, and no histone H2AX phosphorylation (γH2AX) foci was detected in meiocytes, indicating that OsRDR6 is crucial for meiotic DSB formation. Compared with the wild type, the number of 21-nt small RNAs was dramatically reduced, while the number of 24-nt small RNAs was significantly increased in Osrdr6-mei. And thousands of DMRs discovered in Osrdr6-mei, implying that OsRDR6 plays an essential role on DNA methylation, especially CHH methylation. Meanwhile, the transcriptome data showed that 457 genes were down-regulated in the mutant; including three genes related to DSB formation: OsSDS, P31comet and CRC1. Interestingly, the increased 24-nt small RNA level surrounding down-regulated genes was largely associated with the silencing of these genes, while DMRs were rarely related to them. In summary, we speculated that the small RNA levels are disordered in Osrdr6 mutants, which may lead to the defection of DSB formation.

overall_design: We sequenced transcriptome, methylome and small RNA of anthers at the leptotene-like stage between indica rice cultivar Zhongxian 3037 and its mutant.

first: Changzhen

first: Yi

last: Shen

first: Baoxiang

last: Qin

first: Huili

last: Wen

first: Jiawen

last: Cheng

first: Fei

last: Mao

first: Wenqing

first: Ding

last: Tang

first: Guijie

last: Du

first: Yafei

first: Yufeng

last: Wu

first: Zhukuan


title: Effect of lactational high fat diet and metformin on mid-lactation murine mammary gland gene expression

status: Public on Jun 04 2021

city: Ann Arbor

first: Dave

last: Bridges

state: MI

address: 1415 Washington Heights

department: Nutritional Sciences

country: USA

institute: University of Michigan

type: Expression profiling by high throughput sequencing

summary: Maternal health and diet can have important consequences for offspring nutrition and metabolic health. Signals are communicated from the mother to the infant during lactation through milk via macronutrients, hormones and bioactive molecules. In this study we designed experiments to probe the mother-milk-infant triad in the condition of normal maternal health and upon exposure to high fat diet (HFD) with or without concurrent metformin exposure. We examined maternal characteristics, milk composition and offspring metabolic parameters on postnatal day 16, prior to offspring beginning to wean. We found that lactational HFD increased maternal adipose tissue, mammary gland adipocytes, and altered milk lipid composition causing a higher amount of n-6 long chain fatty acids and lower n-3. Offspring of HFD dams were heavier with more body fat during suckling. Metformin exposure decreased maternal glucose and several amino acids. Offspring of met dams were smaller during suckling. Gene expression in the lactating mammary glands was impacted to a greater extent by metformin but both metformin and HFD altered genes related to muscle contraction, indicating that these genes may be more susceptible to lactational stressors. Our study demonstrates the impact of common maternal exposures during lactation on milk composition, mammary gland function and offspring growth with metformin having little capacity to recuse from the effects of a maternal HFD during lactation.

overall_design: n=4 per group from 4 groups

first: Hannah

last: Hafner

first: Noura

last: El Habbal

first: Brigid

last: Gregg


title: Gene expression of human bone marrow mesenchymal stem cell (hBMSCs) during osteogenesis with or without TNF-alpha

city: hangzhou

first: zhijun

last: pan

address: NO. 88, jiefang road

department: orthopeadics

country: China

institute: second affiliated hospital, zhejiang university

summary: In our previous study, we found that TNF-alpha (100ng/mL) different treatment times have opposing effects on BMSC osteogenesis. To investigate the roles of TNF-alpha  in the osteogenic differentiation of hBMSCs, we performed gene microarray to detected the gene expression of hBMSCs with or without  TNF-alpha during osteogenesis on days 3 and 4.

overall_design: we performed an mRNA microarray to determine the comparative transcriptome analysis of four group, 3d TNF-α (100ng/mL)-treated (Os3_T), control (Os3_C), 4d TNF-α (100ng/mL)-treated (Os4_T) and control (Os4_C) osteogenic BMSCs. Triplicates of Os3_T, Os3_C, Os4_T and Os4_C samples were collected and subjected to mRNA microarray analysis to identify differentially expressed genes (DEGs).

first: Kai

last: Hang

first: Zhijun

last: Pan


title: Differential gene expression in a BPs lysogen Mycobacterium chelonae CCUG 47445 compared to wild type

city: Orono

first: Sally

middle: Dixon

last: Molloy

state: Maine

address: 5735 Hitchner Hall, University of Maine

institute: The University of Maine

summary: The goal of this sequencing project was to identify bacterial genes that are differentially expressed in the presence of the BPs prophage.

overall_design: Total RNA was isolated from lysogen and non-lysogen cultures in log phase, depleted of rRNA and prepared for sequencing using a strand-specific libraries.

first: Keith

last: Hutchison


title: RNA-seq in HepG2 cells with YY1 knockdown

city: Uppsala

first: Claes

last: Wadelius

state: Uppsala

address: Husargatan 3 PO BOX 815, BMC B11:4

department: Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala universitet

summary: Dysregulation of YY1 has been observed in many human cancers. Recent studies have shown that overexpression of YY1 plays a pivotal role in the initiation and progression of nonalcoholic fatty liver disease (NAFLD) which may further progress into hepatocellular carcinoma (HCC). To obtain a detailed view of genes and pathways regulated by YY1 in the liver, we carried out global RNA-seq in liver HepG2 cells with YY1 knocked down.

overall_design: The expression of YY1 was knocked down by lentiviral-mediated short-hairpin RNAs (shRNAs) and artificial miRNA (amiRNA). The RNA-seq was carried out in HepG2 cells with YY1 knockdown (n=8) and the HepG2 cells tranduced with the control virus (n=14).

first: Gang


title: Time-course bulk RNA sequencing of endothelial colony forming cells in hypoxic and non-hypoxic hydrogels

city: Baltimore

first: Michael

middle: R

last: Blatchley

state: MD

address: 3400 N Charles St

department: Biomedical Engineering

institute: Johns Hopkins University

summary: With the increased realization of the effect of oxygen (O2) deprivation (hypoxia) on cellular processes, recent efforts have focused on the development of engineered systems to control O2 concentrations and establish biomimetic O2 gradients to study and manipulate cellular behavior. Nonetheless, O2 gradients present in 3D engineered platforms result in diverse cell behavior across the O2 gradient, making it difficult to identify and study O2 sensitive signaling pathways. Using a layer‐by‐layer assembled O2‐controllable hydrogel, the authors precisely control O2 concentrations and study uniform cell behavior in discretized O2 gradients, then recapitulate the dynamics of cluster‐based vasculogenesis, one mechanism for neovessel formation, and show distinctive gene expression patterns remarkably correlate to O2 concentrations. Using RNA sequencing, it is found that time‐dependent regulation of cyclic adenosine monophosphate signaling enables cell survival and clustering in the high stress microenvironments. Various extracellular matrix modulators orchestrate hypoxia‐driven endothelial cell clustering. Finally, clustering is facilitated by regulators of cell–cell interactions, mainly vascular cell adhesion molecule 1. Taken together, novel regulators of hypoxic cluster‐based vasculogenesis are identified, and evidence for the utility of a unique platform is provided to study dynamic cellular responses to 3D hypoxic environments, with broad applicability in development, regeneration, and disease.

overall_design: Use of oxygen-controllable hydrogels for the examination of the role of discretized oxygen gradients on endothelial colony forming cell (ECFC) gene expression at 3 time points (40 minutes, 10 hours, 24 hours), during which ECFC clusters form when cells are exposed to hypoxia, as a first step in cluster-based vasculogenesis.

first: Sharon

last: Gerecht


title: ARID1A deficiency promotes pancreatic tumorigenesis by reducing KRAS-induced senescence

city: Houston

first: Chenghang

last: Zong

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: MBD5 and MBD6 couple DNA methylation to gene silencing through the J-domain protein SILENZIO

city: Los Angeles

first: Lucia

last: Ichino

state: CA

address: 610 Charles E Young Dr East

department: MCDB

institute: University of California, Los Angeles

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is associated with transcriptional repression of eukaryotic genes and transposons, but the downstream mechanism of gene silencing is largely unknown. Here we describe two Arabidopsis methyl-CpG binding domain proteins, MBD5 and MBD6, that are recruited to chromatin by recognition of CG methylation, and redundantly repress a subset of genes and transposons without affecting DNA methylation levels. These methyl-readers recruit a J-domain protein, SILENZIO, that acts as a transcriptional repressor in loss-of-function and gain-of-function experiments. J-domain proteins often serve as co-chaperones with HSP70s. Indeed, we found that SILENZIO?s conserved J-domain motif was required for its interaction with HSP70s and for its silencing function. These results uncover an unprecedented role of a molecular chaperone J-domain protein in gene silencing downstream of DNA methylation.

sample_organism:
Arabidopsis thaliana
Lambdavirus lambda

platform_organism:
Arabidopsis thaliana
Lambdavirus lambda

overall_design:
This study includes 11 DAP-seq samples, 19 ChIP-seq samples, 5 BS-seq samples, 18 BS-PCR samples, 82 RNA-seq samples, 2 GRO-seq samples and 1 EM-seq.
Please note that the MBD5-MYC and MBD6-MYC ChIP-seq data (lib5) is of higher quality than the MBD5-FLAG and MBD6-FLAG ChIP-seq data.
The lists of methylation hypervariable bins and genes have been deposited under the sample GSM5026060 (BSseq_lib1_Col0_rep1). See methods of the paper for details

first: Brandon

middle: A

last: Boone

first: Luke

last: Strauskulage

first: C

middle: J

last: Harris

first: Gundeep

last: Kaur

first: Matthew

last: Gladstone

first: Maverick

last: Tan

first: Suhua

last: Feng

first: Yasaman

last: Jami-Alahmadi

first: Sascha

middle: H

last: Duttke

first: James

last: Wohlschlegel

first: Xiaodong

last: Cheng

first: Sy

last: Redding

first: Steven

middle: E

last: Jacobsen


title: Gene expression profile of primary CAFs exposed to PARPi or not derived from ovarian cancer patients

status: Public on Jun 05 2021

city: Wuhan

first: Tian

last: Fang

state: Hubei

address: Jiefang Avenue

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

summary:
Cancer-associated fibroblasts (CAFs) play significant roles in drug resistance through different ways. Antitumor therapies, including molecular targeted interventions, not only effect tumor cells but also modulate the phenotype and characteristics of CAFs, which can in turn blunt the therapeutic response. Little is known about how stromal fibroblasts respond to poly (ADP-ribose) polymerase
inhibitors (PARPis) in ovarian cancer (OC) and subsequent effects on tumor cells. This is a study to evaluate how CAFs react to PARPis and their potential influence on PARPi resistance in OC. We discovered that OC stromal fibroblasts exhibited intrinsic resistance to PARPis and were further activated after the administration of PARPis. PARPi-challenged fibroblasts displayed a specific secretory profile characterized by increased secretion of CCL5, MIP-3α, MCP3, CCL11, and ENA-78. Mechanistically, increased secretion of CCL5 through activation of the NF-κB signaling pathway was required for PARPi-induced stromal fibroblast activation in
an autocrine manner. Moreover, neutralizing CCL5 partly reversed PARPi-induced fibroblast activation and boosted the tumor inhibitory effect of PARPis in both BRCA1/2-mutant and BRCA1/2-wild type xenograft models. Our study revealed that PARPis could maintain and improve stromal fibroblast activation involving CCL5 autocrine upregulation. Targeting CCL5 might offer a new treatment modality in overcoming the reality of PARPi resistance in OC.

overall_design: Three strains of primary CAFs were isolated. Each strain of CAF was amplified in nine T75 culture flasks, when the confluence reached 60-70%, one was exposed to DMSO as control, the next one was exposed to 30uM olaparib and another one was exposed to 20uM niraparib; each kind of treatment was conducted in triplicate. After 72 hours, cells from each culture flask were gathered and dissoved in 1ml Trizol and stored in -80℃ for RNA-seq.

first: Xiaoting

last: Li

first: Zongyuan

last: Yang

first: Qinglei

last: Gao


title: The chromatin remodeler Brg1 cooperates with tissue-specific transcription-factors to regulate Sox2 activation via multiple enhancers to establish proneurosensory identity within otic ectoderm

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Specification of Sox2+ proneurosensory progenitors within otic ectoderm is a prerequisite for the production of sensory cells and neurons for hearing. However, the underlying molecular mechanisms driving this lineage specification remain unknown. Here, we show that Brg1-based SWI/SNF chromatin-remodeling complex interacts with the neurosensory-specific transcriptional regulators Eya1/Six1 to induce Sox2 expression and proneurosensory-lineage specification. Ablation of the ATPase-subunit Brg1 or both Eya1/Six1 results in loss of Sox2 expression and lack of neurosensory identity. Brg1 and Six1 co-occupy three distal 3' Sox2 enhancers and Brg1-recruitment to these regions is disrupted in Eya1- or Six1-null otocyst. Eya1 as a coactivator of Six1 synergistically regulates the activity of these enhancers, which drives expression in otic neurosensory cells in response to binding to Six1. Thus, through interaction with Six1/Eya1, the Brg1-based SWI/SNF complex specifies otic proneurosensory lineage. Furthermore, genome-wide and transcriptome analyses reveal that Brg1 also suppresses expression of non-otic genes.

overall_design: We sequenced RNA isolated from otic cells FACS-purified from control and Brg1-cKO otocysts.

first: Jinshu

last: Xu

first: Jun

first: Ting

last: Zhang

first: Li

last: Shen

first: Pin-Xian


title: Epigenetic methylation chip analysis of childhood medulloblastoma patient samples

city: Aurora

first: Andrew

middle: M

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

type: Methylation profiling by genome tiling array

summary: DNA methylation analysis was perfomed using Infinium EPIC Methylation BeadChip platform on 29 patient samples. Resulting .idat files were then uploaded to the molecularneuropathology.org classifier to obtain molecular subgroup and copy number variance. This data was further assigned to medulloblastoma subtypes by Martin Sill (DFKZ, Heidelberg, Germany).

overall_design: Bisulphite converted DNA from the 29 samples were hybridised to the Illumina Infinium EPIC Methylation Beadchip


title: Next Generation Sequencing Facilitates Quantitative Analysis of aged (Day10) and young (L4) C. elegans Transcriptomes

city: Gainesville

first: yi

last: sheng

state: FL

department: Department of Aging & Geriatric Research

institute: uf

summary: survey on the age-related changes in protein homeostasis machineries of Caenorhabditis elegans

overall_design: mRNA profiles of 10-day old wild type (WT) and L4 C. elegans

first: Yi

last: Sheng

first: Rui

last: Xiao


title: Childhood medulloblastoma


title: Hair follicle stem cell progeny heal blisters while pausing skin development

city: Turin

first: Andrea

last: Lauria

address: Via Accademia Albertina, 13

department: Life Sciences and Systems Biology

country: Italy

institute: University of Turin

summary: Injury in adult tissue generally reactivates developmental programs to foster regeneration, but it is not known whether this paradigm applies to growing tissue. Here, by employing blisters, we show that epidermal wounds heal at the expense of skin development. The regenerated epidermis suppresses the expression of tissue morphogenesis genes accompanied by delayed hair follicle (HF) growth. Lineage tracing experiments, cell proliferation dynamics, and mathematical modeling reveal that the progeny of HF junctional zone stem cells, which undergo a morphological transformation, repair the blisters while not promoting HF development. In contrast, the contribution of interfollicular stem cell progeny to blister healing is small. These findings demonstrate that tissue development can be sacrificed for the sake of wound regeneration and suggest that tissue repair does not coincide with the reactivation of developmental programs in all regenerative contexts. Our study elucidates the key cellular mechanism of wound healing in skin blistering diseases.

overall_design: RNA profiles of the blistered (regenerated) and control wild type dorsal skin epidermis at P2.

first: Yu

last: Fujimura

first: Mika

last: Watanabe

first: Kota

last: Ohno

first: Yasuaki

last: Kobayashi

first: Shota

last: Takashima

first: Hideki

last: Nakamura

first: Hideyuki

last: Kosumi

first: Yunan

last: Wang

first: Yosuke

last: Mai

first: Valentina

last: Proserpio

last: Ujiie

first: Hiroaki

last: Iwata

first: Wataru

last: Nishie

first: Masaharu

last: Nagayama

first: Salvatore

last: Oliviero

first: Giacomo

last: Donati

first: Hiroshi

last: Shimizu

first: Ken

last: Natsuga


title: Role of the metabolic sensor AMP-activated protein kinase in T cell function in vivo [TCR-seq]

city: Vienna

first: Katharina

last: Mayer

address: Lazarettgasse 19

department: Institute of Immunology

country: Austria

institute: Medical University of Vienna

summary:
Purpose: To investigate the function of AMPK in T cells during in vivo activation.
Methods: WT (PRKAA1fl/fl) and KO (CD4-Cre PRKAA1fl/fl) T cells were transferred into Rag KO recipients to induce adoptive T cell transfer mediated colitis. Donor WT and KO spleen and mLN T cells were isolated 6 weeks after transfer and gene expression was assessed in WT vs. KO T cells and spleen vs. mLN samples.

overall_design: Comparison of T cell receptor (TCR) clonotypes of in vivo activated WT and KO spleen and mLN T cells.

first: Gerhard

last: Zlabinger


title: Role of the metabolic sensor AMP-activated protein kinase in T cell function in vivo [RNA-seq]

overall_design: Comparison of mRNA profiles of in vivo activated WT and KO spleen and mLN T cells (in quadruplicates).


title: HDAC7 is a major contributor in the pathogenesis of t(4;11)/MLL-AF4+ infant B-cell acute lymphoblastic leukemia

city: Badalona

first: Maribel

last: Parra

state: Barcelona

address: Ctra. de Can Ruti, Camí de les Escoles, s/n

department: Lymphocyte Development and Disease

country: Spain

institute: Josep Carreras Leukaemia Research Institute

summary: Infants diagnosed of precursor B-cell acute lymphoblastic leukemia (iB-ALL) presenting MLL-AF4 chromosomal rearrangement are at high risk of disease progression into fatal outcome. This specific subtype of pediatric leukemia constitutes a tough challenge in leukemia research, given the difficulties found when trying in vivo modelling. However, the understanding of mechanisms leading to proper lymphocyte generation may become of high utility in gaining deep insight on this malignancy. As we report here, the lack of HDAC7, a key transcriptional regulator in B lymphocyte differentiation, worsens the prognosis of iB-ALL patients. In fact, MLL-AF4+ iB-ALL patients with high expression of HDAC7 display an improved survival, partially mediated by the repression of oncogenes, such as c-MYC, and chemoresistance markers, like the ASNS enzyme. Accordingly, HDAC7 drastically reduces leukemic cells proliferation in MLL-AF4+ iB-ALL through the induction of apoptosis. Moreover, RNA sequencing of HDAC7-overexpressing cells has revealed that HDAC7 alters the genomic profiling of MLL-AF4+ iB-ALL cells towards that of healthy B-cell progenitors. In summary, the findings here reported highlight the role of HDAC7 in predicting prognosis of a lethal subtype of iB-ALL and open new clinical perspectives, since MLL-AF4+ iB-ALL infants would highly benefit from therapeutic options eventually restoring HDAC7 expression.

overall_design: SEM-K2 cells (derived from an infant diagnosed of MLL-AF4+ iB-ALL) were transduced with a Tet-On-Tight system, either containing HDAC7 transcription factor or its corresponding empty vector, in order to conditionally overexpress HDAC7. RNA was extracted from SEM-TetOn-Tight-control and SEM-TetOn-Tight-HDAC7 cells. In both cases, both samples treated with doxycycline and untreated ones were obtained. For RNAseq analysis, three replicates for condition were processed. The unspecific effect of doxycycline was removed from that of HDAC7 by removing the DEGs between SEM-TetOn-Tight control + Doxycycline and untreated control cells.

first: Oriol

last: de Barrios

first: Alexandros

last: Galaras

first: Juan

middle: L

last: Trincado

first: Alba

last: Azagra

first: Olga

last: Collazo

first: Ainara

last: Meler

first: Antonio

last: Agraz-Doblas

first: Ignacio

last: Varela

first: Paola

last: de Lorenzo

first: Maria-Grazia

last: Valsecchi

first: Pantellis

last: Hatzis

first: Pablo

last: Menéndez


title: Role of the metabolic sensor AMP-activated protein kinase in T cell function in vivo


title: Single-cell RNA-seq analysis of microglial cells in demyelinated corpus callosum

city: Marseille

first: Daian

last: Fabrice

address: Case 907 - Parc Scientifique de Luminy

country: France

institute: CNRS

summary: CX3CR1-GFP mice were fed with cuprizone for 4 weeks to induce brain demyelination. The central and lateral parts of the corpus callosum (CC) were then separately dissected, dissociated and GFP+ microglial cells were isolated by FACS. 2133 migroglial cells from medial CC and 2304 cells from lateral CC were then processed for single-cell RNA-seq analysis.  Single Cell RNA sequencing library were generated using the 10x Genomics Chromium Platform and sequenced on the Illumina Nextseq 500.

overall_design: FACS sortedmicroglial cells were processed using the Chromium Single Cell Controller  (10X  genomics, Pleasanton).  Libraries were generated and sequenced from the cDNA and the 10x Barcodes are used to associate individual reads back to the individual partitions.  Analysis using molecular indexing information provides an absolute digital measurement of gene expression levels.  Sequencing was performed using a NextSeq 500 Illumina device (2samples) containing transcript lengh of 57 bp.Droplet Based

first: Béatrice

last: Brousse

first: Karine

last: Magalon

first: Fabrice

last: Daian

first: Durbec

last: Pascale


title: Single-cell RNA-seq analysis of subventricular zone-derived neural progenitors mobilized to demyelinated corpus callosum

summary: NestinCreERT2:RosaYFP mice were fed with cuprizone for 4 weeks to induce brain demyelination. Corpus callosum was then dissected, dissociated and YFP+ subventricular zone-derived cells were isolated by FACS. 1931 cells were then processed for single-cell RNA-seq analysis.  Single Cell RNA sequencing library were generated using the 10x Genomics Chromium Platform and sequenced on the Illumina Nextseq 500.


title: H3.1K27me1 maintains transcriptional silencing and genome stability by preventing GCN5-mediated histone acetylation

city: New Haven

first: Yannick

last: Jacob

state: Connecticut

address: YSB 416 260 Whitney Avenue

department: Department of Molecular, Cellular  & Developmental Biology

institute: Yale university

summary: In plants, genome stability is maintained during DNA replication by the H3K27 methyltransferases ATXR5 and ATXR6, which catalyze the deposition of H3K27me1 on the replication-dependent H3.1 variant. Loss of H3.1K27me1 in atxr5 atxr6 mutants leads to heterochromatin defects, including transcriptional de-repression and genomic instability, but the molecular mechanisms involved remain largely unknown. In this study, we identified the conserved histone acetyltransferase GCN5 as a mediator of transcriptional de-repression and genomic instability in the absence of H3.1K27me1. GCN5 is part of a SAGA-like complex in plants and requires ADA2b and CHR6 to mediate the heterochromatic defects of atxr5 atxr6 mutants. Our results show that GCN5 acetylates multiple lysine residues on H3.1 variants, but that H3.1K27 and H3.1K36 play key roles in inducing genomic instability in the absence of H3.1K27me1. Overall, this work reveals a key molecular role for H3.1K27me1 in maintaining genome stability by preventing GCN5-dependent histone acetylation in plants.

overall_design: Examination of RNA seq and Rx ChiP seq of H3K27ac and H3K36ac in 4 different backgrounds col0, atxr5/6, gcn5. atxr5/6 gcn5

first: Jie

last: Dong

first: Chantal

last: LeBlanc

first: Axel

last: Poulet

first: Benoit

last: Mermaz

first: Gonzalo

last: Villarino

first: Kimberly

last: Webb

first: Valentin

last: Joly

first: Josefina

last: Mendez

first: Philipp

last: Voigt


title: Butterfly wing pattern mimicry radiated via parallel evolution of ancient, pleiotropic enhancers [HiC-seq]

city: Ithaca

first: James

middle: Joseph

last: Lewis

state: NY

address: 215 TOWER ROAD

department: Ecology & Evolutionary Biology

institute: Cornell University

summary: Aposematic color pattern mimicry in Heliconius butterflies provides a well-known example of adaptation via selection on a few genes of large effect. To understand how selection at individual genes can drive the evolution of complex traits, we functionally characterized five novel enhancers of the color pattern gene, optix. In Heliconius erato we found that wing pattern enhancers are largely ancestral, pleiotropic, functionally interdependent, and introgressed between populations. Remarkably, many of these enhancers are also associated with regional pattern variation in the distantly related co-mimics Heliconius melpomene and Heliconius timareta. Our findings provide a case study of how parallel co-evolution of ancient, multifunctional regulatory elements can facilitate the rapid diversification of complex phenotypes, and provide a counterpoint to many widespread assumptions of cis-regulatory evolution.

overall_design: HiC data for day 3 Heliconius erato pupal wings.

first: Robert

middle: D

last: Reed


title: Chromatin remodelers and lineage specific factors interact to target enhancers to establish pro-neurosensory fate within otic ectoderm

first: Jun

last: Li

address: 1425 Madsion Ave, 14th Fl, RM 14-02

department: Department of Genetics and Genomic Sciences

summary: Specification of Sox2+ pro-neurosensory progenitors within otic ectoderm is a prerequisite for the production of sensory cells and neurons for hearing. However, the underlying molecular mechanisms driving this lineage specification remain unknown. Here, we show that Brg1-based SWI/SNF chromatin-remodeling complex interacts with the neurosensory-specific transcriptional regulators Eya1/Six1 to induce Sox2 expression and promote pro-neurosensory-lineage specification. Ablation of the ATPase-subunit Brg1 or both Eya1/Six1 results in loss of Sox2 expression and lack of neurosensory identity, leading to abnormal apoptosis within the otic ectoderm. Brg1 binds to two of three distal 3' Sox2 enhancers occupied by Six1, and Brg1-binding to these regions depends on Eya1-Six1 activity. We demonstrate that the activity of these Sox2 enhancers in otic neurosensory cells specifically depends on binding to Six1. Furthermore, genome-wide and transcriptome profiling indicate that Brg1 may suppress apoptotic factor Map3k5 to inhibit apoptosis. Together, our findings reveal an essential role for Brg1, its downstream pathways, and their interactions with Six1/Eya1, in promoting pro-neurosensory fate induction in the otic ectoderm and subsequent neuronal lineage commitment and survival of otic cells.

overall_design: Genome-wide Brg1/Six1/Histone modification binding feature was characterized in whole embryo and cochlea using ChIP-seq.

first: Aarthi

last: Ramakrishnan

first: Li

last: Shen

first: Pin-Xian

last: Xu


title: Butterfly wing pattern mimicry radiated via parallel evolution of ancient, pleiotropic enhancers

sample_organism:
Heliconius melpomene rosina
Heliconius erato lativitta
Heliconius melpomene aglaope


title: Butterfly wing pattern mimicry radiated via parallel evolution of ancient, pleiotropic enhancers [ChIP-Seq]

overall_design: Examination of optix binding sites in Heliconius erato.


title: Butterfly wing pattern mimicry radiated via parallel evolution of ancient, pleiotropic enhancers [ATAC-Seq]

sample_organism:
Heliconius melpomene rosina
Heliconius melpomene aglaope

overall_design: Examination of chromatin accessibility in wing tissue between populations of H. melpomene.


title: CC-122 versus Lenalidomide

city: Columbus

last: Blachly

state: OH

address: B305 Starling-Loving Hall

institute: The Ohio State University

summary: Gene expression profiles of OSU-CLL cells were tested after exposure to CC-122 (0.1 and 1 micromolar), Lenalidomide (1 micromolar), or DMSO, at 5 and 24 hours

overall_design: Examination of 4 drug conditions at 2 timepoints

middle: S

first: Priscillia

last: Do


title: The peroxiredoxin Asp f3 acts as redox sensor in Aspergillus fumigatus

status: Public on Jun 03 2021

city: Jena

first: Sascha

last: Schäuble

address: Beutenbergstraße 11a

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology

summary: The human pathogenic fungus Aspergillus fumigatus is readily eradicated by the innate immunity of immunocompetent human hosts, but can cause severe infections, such as invasive aspergillosis (IA), in immunocompromised individuals. During infection, the fungal redox homeostasis can be challenged by reactive oxygen (ROS) species, either derived from the oxidative burst of innate immune cells or the action of antifungal drugs. The peroxiredoxin Asp f3 was found to be essential to cause IA in mice, but how Asp f3 integrates to fungal redox homeostasis remains unknown. Here, we show that in vivo, Asp f3 acts as a sensor for ROS. While global transcription in fungal hyphae under minimal growth conditions was fully independent of Asp f3, a robust induction of the oxidative stress response required the presence of the peroxiredoxin. Hyphae devoid of Aspf 3 failed to activate several redox active genes, like members of the gliotoxin biosynthesis gene cluster and integral members of the Afyap1 regulon, the central activator of the ROS defence machinery in fungi. Upon deletion of the asp f3 gene Afyap1 displayed significantly reduced nuclear localization during ROS exposure, indicating that Asp f3 can act as an intracellular redox sensor for several target proteins

overall_design: A total of 12 samples was analyzed. The strains used were the Aspergillus fumigatus wild type D141 and the asp f3 knock out mutant. Both strains were analyzed both with and without treatment (challenge with reactive oxygen species) in three biological replicates

first: Jana

last: Boysen

first: Nauman

last: Saeed

first: Thomas

last: Wolf

first: Gianni

last: Panagiotou

first: Falk

last: Hillmann


title: Reelin and Thrombospondin1 regulate cardiomyocyte proliferation through Vldlr

city: Shanghai

first: Lijuan

last: Pei

address: CHIFENG ROAD 67

institute: Tongji University

summary: We performed RNA-Seq analysis of neoatal rat ventricular cardiomyocytes (NRVCs)which were treated with Reelin,or knocking down Vldlr,Thbs1,or overexpressing Vldlr to investigate the moleclular mechanism of Thbs1/Reelin-Vldlr to regulate cardiomyocyte proliferation.In addition,the day 1mouse cardiomyocytes in Myh6-Cre;Vldlr f/f mice ,Myh6-Cre;Vldlr f/+ mice ,versus Vldlr f/f mice were also performed to explore the fucntion of Vldlr which regulating cardiomyocyte proliferation in vivo.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: RNA-Seq analysis of NRVCs which adminstration of Reelin, koncking down Vldlr ,Thbs1,overexpressing Vldlr,2 replicates per group and RNA-Seq analysis of day 1 mouse cardiomyocytes in Myh6-Cre;Vldlr f/f mice, Myh6-Cre;Vldlr f/+ mice and Vldlr f/f mice,3 replicates per group.

first: Hongjie

last: Zhang

first: Ke

last: Wei


title: Effects of a pyrethroid pesticide deltamethrin on gene expression profiles in mouse neuroblastoma Neuro2a cell

city: Toyama

first: Tetsushi

last: Hirano

state: Toyama

address: 2630 sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

summary:
Pyrethroids are one of the most commonly used classes of synthetic pesticides detected from all individuals in every part of the world; however, the mechanisms underlying the neurotoxicity of pyrethroids were still remain unclear.
To understand  neurotoxic mechanisms of DM, we investigated transcriptome changes by exposure to a pyrethroid pesticide deltamethrin (DM) in the mouse neuroblastoma Neuro2a cell.

overall_design: We compared the gene expression profiles of cells exposed to 30 µM DM or vehicle (0.1%DMSO) dossolved in medium for 24 hours. Quality of the RNA was analyzed using a Bioanalyzer 2100. Gene expression was analyzed by an Affymetrix GeneChip® system with a Clariom S  Mouse array.

first: Yoshiaki

last: Tabuchi


title: Reorganization of chromatin architecture during prenatal development of porcine skeletal muscle

city: Guangzhou

first: Renqiang

last: Yuan

state: Guangdong

address: No. 135, Xingang Xi Road

institute: SUN YAT-SEN UNIVERSITY

summary: Myofibers (primary and secondary myofiber) are the basic structure of muscle and the determinant of muscle mass. To explore the skeletal muscle developmental processes from primary myofibers to secondary myofibers, we conducted an integrative 3D structure of genome and transcriptomic characterization of longissimus dorsi muscle (LDM) of pig from primary myofiber formation stage [embryonic day 35 (E35)] to secondary myofiber formation stage (E80). In the hierarchical genomic structure, we found that 11.43% of genome switched compartment A/B status, 14.53% of topologically associating domains (TADs) are changed intra- domain interactions (D-scores) and 3,166 genes with differential promoter-enhancer interactions (PEIs) and (or) enhancer activation from E35 to E80. The alterations of genome architecture were found to affect expression of genes that play significant roles in neuromuscular junction (NMJ) and embryonic morphogenesis in E35, such as NEFL, BRINP1, NTNG1, and MuSK and that function on skeletal muscle development or metabolism, typically MYL1, SLN, Sox6 and Mef2D.

overall_design: We designed the comparation between E35 and E80 by generating 6 in situ Hi-C libraries (3 vs 3), 6 RNA-seq libraries (3 vs 3),and 3 H3K27ac ChIP-seq data (2 vs1).

first: Delin

last: Mo

first: Mingzhou

last: Li


title: BET Bromodomain Protein Inhibition Reverses Chimeric Antigen Receptor (CAR) Extinction and Reinvigorates Exhausted T cells.

city: Philadelphia

first: John

middle: Keller

last: Everett

state: PA

address: 425 Johnson Pavilion

department: Microbio

institute: University of Pennsylvania

summary: Analysis of patient CAR T cells with the pharmacologically active form of JQ1 augmented CAR transgene mRNA levels.

overall_design: T-cell mRNA profiles of infusion product from responder and non-responder subjects.

first: Weimin

last: Kong

first: Joseph

last: Fraietta


title: Transcriptomic landscape and metabolic phenotypization of Polydactylous rat with metabolic syndrome after high fat diet challenge

city: Prague

first: Lukáš

middle: Farhád

last: Mirchi

state: Czech Republic

address: Albertov 4

department: First Faculty of Medicine

country: Czech Republic

institute: Charles University

summary:
Metabolic syndrome, with its ever-rising incidence, is an important cause of worldwide morbidity and mortality. MetS is diagnosed if three or more of the following criteria are met: obesity, high serum triglycerides, low HDL-cholesterol, high blood pressure and high serum glucose. Metabolic syndrome has a complex pathogenesis which includes on one hand sedentary lifestyle and high caloric intake, on the other hand there is clear genetic predisposition with heritability in the range of 0.25-0.8. Polydactylous rat (PD hereafter) is a rodent model of  metabolic syndrome manifesting dyslipidemia, insulin resistance and obesity without hypertension. To unravel the genetic and pathophysiologic background of this phenotype we compared liver transcriptomes as well as morphometric and metabolic parameters (lipidemic profiles and serum markers) among PD, Spontaneously hypertensive rat and Brown Norway rat lines after high fat diet challenge.
We used microarray aproach to unravel gene expression differences between SHR, PD and BN responsible for the different phenotypes in our rat strains.

overall_design: Adult male rats of BN, SHR and PD strain were used. Until the age of 6 months, they were fed a standard chow diet ad libitum. Then, after a one-night fasting period, we recorded a body

first: K

last: Junková

first: L

middle: F


title: Comparative Analysis of 1,152 African-American and European-American Men with Prostate Cancer Identifies Distinct Genomic and Immunological Differences

city: San Diego

first: Elai

last: Davicioni

state: California

address: 9725 Lusk Blvd

institute: Veracyte, Inc

summary: Gene expression characteristics of primary prostate cancer tumors from African-Americans are substantially different as compared to European-American men

overall_design: Multi-institutional retrospective analysis of 1,152 patients (596 African-American men (AAM) and 556 European-American men (EAM)) who underwent radical prostatectomy and had the Decipher whole-transcriptome assay.

first: Walter

last: Rayford

first: Alp

last: Tuna Beksac

first: Jordan

last: Alger

first: Mohammed

last: Alshalalfa

first: Mohsen

last: Ahmed

first: Irtaza

last: Khan

first: Ugo

middle: G

last: Falagario

first: Yang

last: Liu

first: Daniel

last: Spratt

first: Edward

last: Schaeffer

first: Felix

last: Feng

first: Brandon

last: Mahal

first: Paul

last: Nguyen

first: Robert

middle: B

last: Den

first: Mark

last: Greenberger

first: Randy

last: Bradley

first: Justin

last: Watson

first: Matthew

last: Beamer

first: Lambros

last: Stamatakis

first: Darrel

last: Carmen

first: Shivanshu

last: Awasthi

first: Jonathan

last: Hwang

first: Rachel

last: Weil

first: Hari

last: Merisaari

first: Nihal

last: Mohammed

first: Leslie

last: Deane

first: Dimple

last: Chakravarty

first: Kamlesh

middle: K

last: Yadav

first: Kosj

last: Yamoah

first: Sujit

last: Nair

first: Ashutosh

last: Tewari


title: Effects of replacing saturated fat with polyunsaturated fat on whole genome gene expression profiles in peripheral blood mononuclear cells - a randomized controlled dietary intervention study

city: Oslo

first: Stine

middle: Marie

last: Ulven

address: Sognsvannsveien 9

department: Department of Nutrition

country: Norway

institute: University of oslo

summary: To further understand the molecular mechanisms underlying the health effects of replacing saturated fat (SFA) with polyunsaturated fat (PUFA), we aimed to explore the whole transcriptome response of peripheral blood mononuclear cells (PBMCs) in a dietary intervention where SFAs were replaced with PUFAs.

overall_design:
Moderately hypercholesterolaemic subjects (n = 115) were randomly assigned to a control diet group (c-diet group) or an experimental diet group (ex-diet group) receiving commercially available and regularly consumed food items with different fatty acid composition (replacing SFAs with mostly n-6 PUFAs) for eight weeks. Microarray analyses of RNA isolated from PBMCs at baseline and after eight weeks of intervention were performed using illuminaHT-12 v4 Expression BeadChips. A total of 92 subjects (ex-diet group; n=43, c-diet group; n=49) were included in the statistical analyses of this study.
Group A = Ex-diet group
Group B = C-diet group

first: Sunniva

middle: V

last: Larsen

first: Kirsten

last: Holven

first: Jacob

last: Christensen

first: Arnar

last: Flatberg

first: Amanda

last: Rundblad

first: Lena

last: Leder

first: Rune

last: Blomhoff

first: Vibeke

middle: T

last: Hansen

first: Marjukka

last: Kolehmainen

first: Carsten

last: Carlberg

first: Mari

middle: C

last: Myhrstad

first: Magne

last: Thoresen


title: Yin Yang 1 interacts with bromodomain-containing coactivators to promote tumorigenesis of advanced prostate cancer

city: DURHAM

first: Chenxi

last: Xu

state: North Carolina

address: 3 Genome Court

department: Department of Pharmacology and Cancer Biology

institute: Duke university

summary: Castration-resistant prostate cancer (CRPC) is a terminal disease and the molecular underpinnings of CRPC development need to be better understood in order to improve its treatments. Here, we report that a transcription factor Yin Yang 1 (YY1) is significantly overexpressed during prostate cancer progression. Functional and cistrome studies of YY1 uncover its roles in promoting prostate oncogenesis in vitro and in vivo, as well as sustaining tumor metabolism including the Warburg effect and mitochondria respiration. Additionally, our integrated genomics and interactome profiling in prostate tumor show that YY1 and bromodomain-containing proteins (BRD2/4) co-occupy a majority of gene-regulatory elements, coactivating downstream targets. Via gene loss-of-function and rescue studies, as well as mutagenesis of YY1-bound cis-elements, we unveil an oncogenic pathway in which YY1 directly binds and activates PFKP, a gene encoding the rate-limiting enzyme for glycolysis, significantly contributing to YY1-enforced Warburg effect and malignant growth. Altogether, this study supports a master regulator role for YY1 in prostate tumor and reveals a YY1:BRD2/4-PFKP axis operating in advanced prostate cancer with implications for therapy.

overall_design: Examination of the genome-wide binding of YY1 in LNCaP prostate cancer cells .

first: Gang

last: Wang

first: Ling

last: Cai


title: Hi-C Analyses with GENOVA: a case study with cohesin variants

city: Utrecht

first: Robin H.

last: van der Weide

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Conformation capture-approaches like Hi-C can elucidate chromosome structure at a genome-wide scale. Hi-C datasets are large and require specialised software. Here, we present GENOVA: a user-friendly software package to analyse and visualise conformation capture data. GENOVA is an R-package that includes the most common Hi-C analyses, such as compartment and insulation score analysis. It can create annotated heatmaps to visualise the contact frequency at a specific locus and aggregate Hi-C signal over a user-specified genomic regions such as ChIP-seq data. Finally, our package supports output from the major mapping-pipelines. We demonstrate the capabilities of GENOVA by analysing Hi-C data from HAP1 cell lines in which the cohesin-subunits SA1 and SA2 were knocked out. We find that ΔSA1 cells gain intra-TAD interactions and increase compartmentalisation. ΔSA2 cells have longer loops and a less compartmentalised genome. These results suggest that cohesinSA1 forms longer loops, while cohesinSA2 plays a role in forming and maintaining intra-TAD interactions. The differences in loop-forming activity affect whole chromosome organisation consistent with a model where loops and compartments counterbalance each other. We show that GENOVA is an easy to use R-package, that allows researchers to explore Hi-C data in great detail.

overall_design: Hi-C; Hap1 SA1 and SA2 knock-out cells

first: Robin

middle: H

first: Elzo

last: de Wit


title: Mapping the transcriptomics landscape of post-traumatic stress disorder symptom dimensions in World Trade Center responders

city: BUFFALO

first: Eduardo

last: Cortes

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

summary: Gene expression has provided promising insights into the pathophysiology of posttraumatic stress disorder (PTSD), but specific regulatory transcriptomic mechanisms remain unknown. The current study addressed this limitation by analyzing transcriptome-wide RNA-Seq of whole blood samples from N=226 World Trade Center responders. The investigation focused on differential expression (DE) at gene, isoform, and alternative splicing (AS) levels associated with Posttraumatic Stress Disorder symptoms: total burden and its re-experiencing, avoidance, numbing, and hyperarousal subdimensions; and is the first study to characterize the AS landscape in PTSD. These dimensions were associated with 76, 1, 48, 15, and 49 genes, respectively (FDR<0.05). Similarly, they were associated with 103, 11, 0, 43, and 32 AS events. Avoidance differed the most from other dimensions with regard to DE genes, isoforms and AS correlates. Gene set enrichment analysis (GSEA) identified pathways involved in inflammatory and metabolic processes, which may have implications for the treatment of PTSD. Overall, findings shed a novel light on the wide range of transcriptomic alterations associated with PTSD at gene and AS levels. The DE analysis associated with PTSD subdimensions highlights the importance of studying PTSD symptom heterogeneity.

overall_design:
Gene expression profiling of 226 samples using RNAseq; All are male volunteers and caucasian.

The variable of interest in this study is PCL-17 (Posttraumatic Stress Disorder Checklist), which is a PTSD questionnaire score and is provided in the sample characteristics field.

first: Pei

last: Kuan

first: Benjamin

middle: J

last: Luft


title: Gene expression of wild-type and Nix-/-Bnip3-/- memory B cells

city: Houston

first: Jin

state: TX

address: 6670 Bertner Avenue

department: Immunobiology and Transplant Science

institute: Houston Methodist Research Institute

summary: Memory B cells are long-lived lymphocytes essential for humoral immunological memory. Autophagy is required for the long-term survival of memory B cells, however, the molecular mechanisms for the protection by autophagy have not been fully elucidated. Here we show that mitochondrial autophagy mediated by Nix and Bnip3 prevents necroptosis in memory B cells by maintaining mitochondrial homeostasis and normal lipid metabolism. In mice with B cell-specific deletion of Nix and Bnip3, memory B cells showed significant increases in viable mitochondria and de novo fatty acid synthesis, with accumulation of lipid droplets in the cytoplasm and accelerated cell death. Inhibiting the mitochondrial citrate transporter Slc25a1 or silencing the necroptosis gene Ripk3 rescued Nix–/–Bnip3–/– memory B cells in vivo. These data indicate that Nix- and Bnip3-dependent mitochondrial autophagy in memory B cells is important for restricting de novo fatty acid synthesis and preventing necroptosis.  Our results suggest a mechanism for autophagy in the maintenance of mitochondrial homeostasis for the protection of immunological memory.

overall_design: RNA-seq of WT and Nix-/-Bnip3-/- memory B cells

first: Srikanth

last: Kodali

first: Min

last: Chen


title: Genome-wide analysis of retinal transcriptome reveals common genetic network underlying perception of contrast and optical defocus detection

city: New York

first: Andrei

middle: V.

last: Tkatchenko

department: Edward S. Harkness Eye Institute

institute: Columbia University

summary: Refractive eye development is regulated by optical defocus in a process of emmetropization. Excessive exposure to negative optical defocus often leads to the development of myopia. However, it is still largely unknown how optical defocus is detected by the retina. Here, we used genome-wide RNA-sequencing (RNA-seq) to conduct analysis of the retinal genetic networks underlying contrast perception and refractive eye development. We report that the genetic network subserving contrast perception plays an important role in optical defocus detection and emmetropization. Our results demonstrate an interaction between contrast perception, the retinal circadian clock pathway and the signaling pathway underlying optical defocus detection. We also observe that the relative majority of genes causing human myopia are involved in the processing of optical defocus. Together, our results support the hypothesis that optical defocus is perceived by the retina using contrast as a proxy and provide new insights into molecular signaling underlying refractive eye development.

overall_design: Analysis of RNA expression in the retina of 129S1/svlmj, A/J, C57BL/6J, CAST/EiJ, NOD/ShiLtJ, NZO/HlLtJ, PWK/PhJ, and WSB/EiJ mice

first: Tatiana


title: A regulatory axis of YY1-PFKP promotes aggressive prostate tumorigenesis via potentiating tumor cell metabolism [ChIP-seq]

summary: Yin Yang 1 (YY1) acts as a transcription factor crucially involved in cell proliferation, differentiation and survival. We here report that YY1, through gene expression regulation, plays an important role in prostate tumorigenesis, notably in castration-resistant prostate cancer (CRPC) models. Specifically, we found that YY1 displays a significantly elevated level among primary samples from prostate cancer patients, relative to normal. Depletion of YY1 in multiple independent prostate cancer model systems dramatically reduced tumor cell growth in vitro and significantly delayed oncogenic progression in vivo. Using integrated analyses of chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing (RNA-seq), we further defined YY1-regulated cistrome, among which include a set of metabolism-related genes such as PFKP (Phosphofructokinase, Platelet isoform), a rate-limiting enzyme essential for glycolysis. Via both gene loss-of-function and rescue studies, we demonstrate that PFKP serves as a key downstream direct target of YY1, significantly contributing to YY1-enforced oncogenic phenotypes such as enhanced tumor cell glycolysis and prostate cancer growth. Lastly, we show that BRD4, a cofactor of YY1, is critically involved in YY1-mediated activation of metabolic genes in prostate cancer cells. Altogether, this study unveils an oncogenic axis of YY1/BRD4-PFKP in prostate cancer for potentiating more aggressive tumor characteristics, which shall shed light on targeted therapy.

overall_design: Examination of the genome-wide binding of YY1 in prostate cancer cells .


title: Gene expression data from a pool of the four youngest leaves of Arabidopsis thaliana

city: Campinas

first: Michel

middle: George Alberts

last: Vincentz

state: SP

address: Av. Cândido Rondon, 400

department: Biology

country: Brazil

institute: Unicamp

summary:
●   Adjustment to energy starvation is crucial to ensure growth and survival. In Arabidopsis thaliana (Arabidopsis), this process relies in part on the phosphorylation of the circadian clock regulator bZIP63 by SnRK1, a key mediator of responses to low energy.
●   	We investigated the effects of mutations in bZIP63 on plant carbon (C) metabolism and growth. Results from phenotypic, transcriptomic, and metabolomic analysis of bZIP63 mutants prompted us to investigate the starch accumulation pattern and the expression of genes involved in starch degradation and in the circadian oscillator.
●   	In order to get some clues about the role of transcription factor bZIP type bZIP63 in growth and development, we performed a comparative gene expression analysis of bzip63-2 mutant and wild type Ws, harvested at the end of night (EN = ZT 24), immediately before the onset of the light, to maximize the discovery of genes misregulated in bzip63-2. The resulting gene expression profiles revealed 230 upregulated and 117 downregulated genes in bzip63-2 compared to Ws.
●       bZIP63 mutation impairs growth under light-dark cycles, but not under constant light. The reduced growth likely results from the accentuated C depletion towards the end of the night, which is caused by the accelerated starch degradation of bZIP63 mutants. The diel expression pattern of bZIP63 is dictated by both the circadian clock and energy levels, which could determine the changes in the circadian expression of clock and starch metabolic genes observed in bZIP63 mutants.
●       We conclude that bZIP63 composes a regulatory interface between the metabolic and circadian control of starch breakdown to optimize C usage and plant growth.

overall_design: Three biological replicates of each genotype were used for microarray analysis, each replicate was composed of a pool of the four youngest leaves of five plants. Hybridization on the GeneChip Arabidopsis ATH1 array was done

first: Américo

last: Viana

first: Cleverson

last: Matiolli


title: A regulatory axis of YY1-PFKP promotes aggressive prostate tumorigenesis via potentiating tumor cell metabolism

first: Chenxi

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

overall_design: Refer to individual Series


title: Effects of short-chain fatty acids in inhibiting HDAC and activating p38 MAPK are critical for promoting B10 cell generation and function

first: Fagui

last: Zou

address: No. 74, Zhongshan Er Road, Guangzhou

institute: Sun Yat-sen University

summary:
Purpose:RNA-seq was uesd to identify how sodium butyrate regulated murine Bregs differentiation.
Methods:CD19+ B cells isolated from C57BL/6 mice spleen were were polarized to Bregs differentiation with LPS (10μg/ml) in the absence or presence of sodium butyrate (0.5mM) for 48 hours, and treated with PIM at the last 5 hours following RNA preparation.
Results:Using an optimized data analysis workflow, we identified 1462 differentially expressed genes (DEG), of which 720 genes were up-regulated and 742 genes down-regulated, respectively (fold change >2 and adjust p-value < 0.05).  RT-qPCR wasused to confirm the reliability of RNA-seq data. KEGG and GSEA analysis indicated that MAPK signaling pathway might involve the function of butyrate on Bregs,which had been proved by western blotting.  Using an optimized data analysis workflow, we identified 1462 differentially expressed genes (DEG), of which 720 genes were up-regulated and 742 genes down-regulated, respectively (fold change >2 and adjust p-value < 0.05).  RT-qPCR wasused to confirm the reliability of RNA-seq data. KEGG and GSEA analysis indicated that MAPK signaling pathway might involve the function of butyrate on Bregs,which had been proved by western blotting.  Using an optimized data analysis workflow, we identified 1462 differentially expressed genes (DEG), of which 720 genes were up-regulated and 742 genes down-regulated, respectively (fold change >2 and adjust p-value < 0.05).  RT-qPCR wasused to confirm the reliability of RNA-seq data. KEGG and GSEA analysis indicated that MAPK signaling pathway might involve the function of butyrate on Bregs,which had been proved by western blotting.

overall_design: Bregs were were generated with LPS (10μg/ml) in the absence or presence of sodium butyrate (0.5mM) for 48 hours, and treated with PIM at the last 5 hours.

first: Yi

last: Qiu

first: Yilian

last: Huang

first: Hang

first: Xiao

last: Cheng

first: Qingru

last: Niu

first: Aoxiang

last: Luo

first: Jianbo

last: Sun


title: RNA-sequencing of Drosophila expressing mutant Huntingtin in neurons or glia

first: Juan

last: Botas

address: 1250 Moursund St.

institute: Texas Children's Neurological Research Institute

summary: We performed RNA-seq on head tissue collected from Drosophila expressing N-terminal (UAS-HTTNT231Q128) or full-length (UAS-HTTFL200Q) human mHTT in neurons (elav-GAL4) or glia (repo-GAL4).

overall_design: For each combination of HD model and driver, RNA-seq was performed at three time points to capture the early, middle, and late phases of disease pathogenesis, corresponding to behavioral deficits caused by mHTT-induced neuronal or glial dysfunction. At each timepoint, samples for HD and age-matched controls were collected in triplicate.

first: Tarik

last: Onur

first: Andrew

last: Laitman

first: Alma

last: Perez

first: Ying-Wooi

last: Wan

first: Ismael

last: Al-Ramahi

first: Zhandong

last: Liu


title: Epigenomic Landscape and 3D Genome Structure in Pediatric High-Grade Glioma

city: CHICACO

first: Feng

last: Yue

state: ILLINOIS

address: 303 E. Superior Simpson Querrey 7-400

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

summary: Pediatric high-grade gliomas (pHGGs), including glioblastoma multiforme (GBM) and diffuse intrinsic pontine glioma (DIPG), are highly morbid childhood brain tumors. Even with treatment, overall survival is poor, making pHGG the number one cause of cancer death in children. Up to 80% of DIPGs harbor a somatic missense mutation in genes encoding Histone H3 proteins. To investigate whether this H3K27M mutation is associated with distinct chromatin structure that alters transcription regulation, we generated the first high-resolution Hi-C maps of pHGG cell lines and tumor tissue. By integrating transcriptome (RNA-Seq), enhancer landscape (ChIP-Seq), genome structure (Hi-C), and chromatin accessibility (ATAC-Seq) datasets from H3K27M mutant and wild-type specimens, we identified tumor specific enhancers and regulatory networks for known oncogenes. In addition, we identified distinct genomic structural variations that lead to enhancer hijacking and gene co-amplification, including A2M, JAG2, FLRT1.

overall_design:
RNA-Seq, ChIP-Seq for H3K27ac, H3K27me3, and H3K27M, ATAC-seq and genome-wide chromatin conformation capture (Hi-C) in patient-derived cell lines (DIPG n=6, GBM n=3, normal n=2) and frozen tissue specimens (DIPG n=1 normal brainstem n=1).
Note from submitter: we are unable to upload the A3810-raw data files because of privacy issues with human samples.

last: Wang

first: Tina

first: Ye

last: Hou

first: Elizabeth

last: Bartom

first: Xinyan

last: Lu

first: Ali

last: Shilatifard

first: Amanda

last: Saratsis


title: A regulatory axis of YY1-PFKP promotes aggressive prostate tumorigenesis via potentiating tumor cell metabolism [RNA-seq]

first: Chenxi

last: Xu

overall_design: Examination of transcriptome profiles in 22Rv1, C42 and LNCaP prostate cancer cells post-knockdown (KD) of YY1, relative to mock.

first: Gang


title: Drougt Specfic oligonucleotide array Development for drought response study in Gossypium Species

city: Lahore

first: Muhammad

middle: Bilal

last: Sarwar

state: Punjab

address: 87-west canal bank road, Thokar Niaz baig

department: National Center of Excellence in Molecular Biology

country: Pakistan

institute: University of the Punjab

summary: Drought is one of the primary limiting factors affecting the growth and yield of cotton. Studying the genotypic drought response of plant towards stress stimuli necessitates the development of a standardized, comprehensive and cohesive system that specifically captures information regarding the focal purpose. In-house development of drought specific microarray using drought specific oligonucleotide probes was carried out and the leaf and root tissue of the two-important species Gossypium arboreum and Gossypium hirsutum were tested for genetic traits responses under 10 days’ drought stress. Further the response of these tissue under control and drought stress were studied via inhouse developed oligonucleotide chip.

sample_organism:
Gossypium hirsutum
Gossypium arboreum

overall_design: (Two Condition Experiment; Control vs Drought), (studied tissue; Leaf tissue and root tissue),  (studied specie; Gossypium hirsutum and Gossypium arboreum), total Sample studied 12 (6 for control: 6 for drought stressed, one array considered as a replicate, plant grown unnder normal condition

first: Zarnab

last: Ahmad

first: Bushra

last: Rashid

first: Sajjad

last: sadique

first: Sameera

last: Hassan

first: Tayyab

last: Hussnain


title: Gene expression analysis of human CD14+ monocytes after anti-Clever-1 treatment

city: Turku

first: Maija

last: Hollmén

address: Tykistökatu 6A 4th floor

country: Finland

institute: University of Turku

summary: Clever-1 is a scavenger receptor expressed on a subset of immunosuppressive macrophages and monocytes. We analyzed the gene expression profiles of CD14+ monocytes isolated from cancer patients treated with a humanized anti-Clever-1 antibody (FP-1305) in a phase I/II clinical trial (MATINS; NCT03733990) to understand how anti-Clever-1 treatment changes the phenotype and activation of circulating monocytes.

overall_design: Pre-dose (day 0) and post-dose (day 1 and day 7) blood samples were collected from four patients receiving anti-Clever-1 therapy. Peripheral blood CD14+ monocytes were isolated from the samples and monocyte total RNA extracted for mRNA sequencing.

first: Jenna

last: Rannikko


title: Physiomimetic model of the human Gut-Liver axis for studies of inflammatory diseases

city: Cambridge

first: Linda

middle: G.

last: Griffith

state: MA

address: 77 Massachusetts Avenue, Building 16-429

institute: Massachusetts Institute of Technology

summary: Association between the microbiome, IBD and liver diseases are known, yet cause and effect  remain elusive. By connecting human microphysiological systems of the gut, liver and circulating  Treg/Th17 cells, we modeled progression of ulcerative colitis (UC) ex vivo. We show that  microbiome-derived short-chain fatty acids (SCFA) may either improve or worsen disease  severity, depending on the activation state of CD4 T cells. Employing a multiomic approach, we  found SCFA reduced innate activation of the UC gut and increased hepatic metabolism. However,  during acute T cell-mediated inflammation, SCFA exacerbate CD4 T cell effector function leading  to gut barrier disruption and liver damage. These paradoxical findings underscore the emerging  utility of human physiomimetic technology in combination with systems immunology to study  causality and temporal facets of gut-liver axis related diseases where animal models might leave  ambiguity.

overall_design: RNA-Seq analyses of tissues from a physiomimetic model of the human gut-liver axis; samples collected and analyzed in triplicates collected under different connectivity patterns.

first: Martin

last: Trapecar


title: Microarray and differential expression analysis were used to identify the noncoding RNAs (ncRNAs) and mRNAs that were expressed abnormally between the cartilage from KOA patients and healthy controls (miRNA).

status: Public on Jun 02 2021

first: Jun

last: Jing

address: 107 Riverside Road, Guangzhou, Guangdong Province 510120, China

department: Department of Rheumatology

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

summary: miRNA expression, three patients with KOA and three paired healthy controls

overall_design: Three patients with KOA and three paired healthy controls were recruited from the Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University from January 2020 to April 2020, and all of them were all Han Chinese men aged 40-60. Their corresponding clinical parameters was collected. The cartilage of KOA patients and healthy volunteers were collected from tibia plateau. All samples were immediately frozen in liquid nitrogen before RNA isolation.

last: Zeng


title: Microarray and differential expression analysis were used to identify the noncoding RNAs (ncRNAs) and mRNAs that were expressed abnormally between the cartilage from KOA patients and healthy controls


title: Unique transcriptome and gene expression analysis of flag leaves of a super-hybrid rice WFYT025

city: 南昌

first: Jianmin

last: Bian

state: 江西 (Jiāngxī)

address: 志敏大道1101

institute: 江西农业大学

summary: In this study, we focused on a super rice variety, WFYT025, which is widely used in China. Therefore, we took the flag leaves of WFYT025 and its two parents for high-throughput transcriptome sequencing, trying to find some genes related to photosynthesis or transpiration and development of seeds. The aim of our study is (1) we investigated the length, width, and leaf area of flag leaves for WFYT025 and its parents. MPH and HPH were estimated for the heterosis of flag leaf. (2) We selected the flag leaves of hybrid rice WFYT025 and its parents for transcriptome sequencing, the first day and the tenth days after flowering in the environment of early rice and middle rice, respectively. (3) we referred to further investigate the gene regulatory network. Several major sub-networks were found to represents interactions among genes with similar expression profiles via gene regulatory network analysis.

overall_design: we took the flag leaves of WFYT025 and its two parents for high-throughput transcriptome sequencing  under two stages of two enviroment,each group was repeated three times

first: Qin

last: Cheng


title: RNA-seq analysis of isogenic dnaN+ and dnaN-E202K E. coli strains derived from MG1655.

city: Buffalo

first: Mark

middle: D

last: Sutton

state: New York

address: 955 Main Street

department: Biochemistry

institute: University at Buffalo, SUNY

summary: RNA-seq was performed using 2 isogenic strains of E coli bearing either the wild type dnaN allele (strain VB001), or a dnaN allele with a glutamic acid-202 to lysine substitution (dnaN-E202K; strain VB019).

overall_design: Analysis of RNA profiles (following rRNA depletion) for  isogenic dnaN+ and dnaN-E202K E. coli strains.

first: Vignesh

middle: P

last: Babu


title: Microarray and differential expression analysis were used to identify the noncoding RNAs (ncRNAs) and mRNAs that were expressed abnormally between the cartilage from KOA patients and healthy controls (circRNA).

city: Guangzhou

summary: Circular RNA expression, three patients with KOA and three paired healthy controls


title: Microarray and differential expression analysis were used to identify the noncoding RNAs (ncRNAs) and mRNAs that were expressed abnormally between the cartilage from KOA patients and healthy controls (lncRNA).

summary: LncRNA and mRNA expression, three patients with KOA and three paired healthy controls


title: Effects of mixed culture fermentation of Bacillus amyloliquefaciens and Trichoderma longibrachiatum on its constituent strains and the biocontrol of tomato Fusarium wilt

city: Qingdao

first: Kaoshan

last: Chen

address: No. 72 Binhai Road

department: School of Life Science

institute: Shandong University

summary: In this study, an in vitro antifungal growth experiment showed that the inhibitory rate of the MCF broth on pathogenic fungi (Fusarium oxysporum f. sp. lycopersici, Botrytis cinerea, Trichothecium roseum, and Colletotrichum gloeosporioides) was less than that of B. amyloliquefaciens culture fermentation (BCF). Moreover, the content and gene expression of lipopeptide antibiotics was also lower than that in the BCF group. However, the pot experiments based on irrigation with appropriately diluted fermentation broth showed that the biocontrol effect of MCF on tomato Fusarium wilt was significantly higher than that of TCF (T. longibrachiatum culture fermentation) and BCF, and was approximately 15.79% higher than that of the BTF group which made by mixing equivalent amounts of BCF and TCF. In MCF broth, two microorganisms antagonized and coexisted, and the growth of T. longibrachiatum was inhibited. Using transcriptomic methods, we speculated that MCF can up-regulate the expression of genes related to carbon and nitrogen metabolism, oxidation–reduction activity, sporulation, environmental information response and chemotaxis, and biosynthesis of secondary metabolites of B. amyloliquefaciens, which might enhance the nutrient substances metabolism and competitiveness, survival ability, colonisation, and adaptability to the environment to increase its biocontrol potential.

overall_design: In order to explore the possible mechanism of changes in the biocontrol activity of tomato Fusarium wilt of the mixed culture fermentation (MCF) of Bacillus amyloliquefaciens and Trichoderma longibrachiatum compared with that of monoculture fermentation of B. amyloliquefaciens (BCF), the fresh cell-free filtrates of culture fermentation of the BCF and MCF groups were mixed with the sterile fresh medium to a final concentration of 75% (v/v). Each treatment was inoculated with 2% of the activated B. amyloliquefaciens spore suspension. The cultures were incubated at 30 ± 2 ℃ and shaken at 150 rpm for 24 h. Sample cells were harvested by centrifugation (10,000 g, 4 ℃), washed with sterile water, and then centrifuged and stored in liquid nitrogen immediately. The sample cells were sent to Novogene Bioinformatics Technology Co., Ltd. (Tianjin, China) for transcriptome sequencing.

first: Qunfei

last: Ma


title: Identification of miRNAs that regulate tinnitus development

city: Seoul

first: Munyoung

last: Chang

address: 102 Heukseok-ro, Dongjak-gu

department: Otorhinolaryngology-Head and Neck Surgery

country: South Korea

institute: Chung-Ang University College of Medicine

summary: To investigate which miRNAs regulate the development of tinnitus, we have performed microarray for miRNAs as a discovery platform. The changes in dorsal cochlear nucleus after noise exposure have been suggested to play an important role in the development of tinnitus. This study was performed using 12 week-old-male Sprague-Dawley rats. Based on our previous experiment about the development of tinnitus, we set a time point for harvesting dorsal cochlear nuclei: 3 weeks after the exposure of 6-8 kHz narrow-band noise (110 dB SPL for 2 h) at right side. Eight animals were divided into two experimental groups: tinnitus group showing evidence of tinnitus (n = 5); and non-tinnitus group showing no evidence of tinnitus (n = 3) in the gap pre-pulse inhibition of acoustic startle reflex (GPIAS) recordings. Three animals of each group were anesthetized deeply and euthanized at 3 weeks post noise exposure. Dorsal cochlear nucleus at right side was harvested. Microarray for miRNAs was performed using the Affymetrix miRNA 4.0 microarray. Considering the fold change of normalized signal intensities between tinnitus and non-tinnitus groups, miR-375-3p was selected as the candidate miRNA. This result was validated by quantitative reverse transcription-PCR.

overall_design: MiRNAs expression induced by the exposure of noise in dorsal cochlear nucleus of Sprague-Dawley rat was measured at 3 weeks post noise exposure. Comparing these results between tinnitus and non-tinnitus groups, the candidate miRNAs that might regulate tinnitus development were selected.


title: Enterocytes, fibroblasts and myeloid cells synergize in anti-bacterial and anti-viral pathways with IL22 as the central cytokine.

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: IL22 is an important cytokine involved in the intestinal defense mechanisms against microbiome. By using ileum-derived organoids, we show that the expression of anti-microbial peptides (AMPs) and anti-viral peptides (AVPs) can be induced by IL22. In addition, we identified a bacterial and a viral route, both leading to IL22 production by T cells, but via different pathways. Bacterial products, such as LPS, induce enterocyte-secreted SAA1, which triggers the secretion of IL6 in fibroblasts, and subsequently IL22 in T cells. This IL22 induction can then be enhanced by macrophage-derived TNFα in two ways: by enhancing the responsiveness of T cells to IL6 and by increasing the expression of IL6 by fibroblasts. Viral infections of intestinal cells induce IFNβ1 and subsequently IL7. IFNβ1 can induce the expression of IL6 in fibroblasts and the combined activity of IL6 and IL7 can then induce IL22 expression in T cells. We also show that IL22 reduces the expression of viral entry receptors (e.g. ACE2, TMPRSS2, DPP4, CD46 and TNFRSF14), increases the expression of anti-viral proteins (e.g. RSAD2, AOS, ISG20 and Mx1) and, consequently, reduces the viral infection of neighboring cells. Overall, our data indicates that IL22 contributes to the innate responses against both bacteria and viruses.

overall_design: Microarray analysis was performed on ileum organoids (isolated from C57/BL6 mice) that were grown in 3D (matrigel) or 2D (on Collagen I) for 2 days and were subsequently treated with mIL22 (5 ng/ml) or vehicle for 24 hrs.

first: Jean

last: ten Klooster

first: Marianne

last: Bol-Schoenmakers

first: Ingrid

middle: W

last: Bijsmans

first: Kitty

last: van Summeren

first: Arno

middle: L

last: van Vliet

first: Cornelis

middle: A

last: de Haan

first: Frank

last: van Kuppeveld

first: Saertje

last: Verkoeijen

first: Raymond

last: Pieters


title: Natolen128 enhanced salinity stress response

city: Nara

first: Kaori

last: Sako

state: Nara

address: 3327-204, Nakamachi

department: Department of Advanced Bioscience

institute: Kindai University

summary: To identify salt-resistant related genes by Natolen128, which identified from ITbM chenical library, expression profiles between plants treated with or without Natolen128 under salt stress were analyzed using the custom microarray (GPL19830).

overall_design: Wild-type plants (Arabidopsis thaliana ecotype Columbia) were grown on 1/2 MS 0.1 % Agar medium for four days. Then, the plants were administrated to Natolen128 for 24 hours and then treated 100 mM NaCl for two hours. Expression profiles were analyzed using the custom array (GPL19830).

first: Akihiro

last: Matsui

first: Maho

last: Tanaka

first: Motoaki

last: Seki


title: Gene expression data of BASQ-type bladder cancer cells under ITIH5 over-expression

city: Aachen

first: Lin

last: Gan

address: Pauwelsstr. 30

department: IZKF

institute: University Hospital Aachen

summary:
This study aims at characterizing the role of the putative tumor suppressor ITIH5 in basal-type bladder cancers (BLCA). Stable ITIH5 overexpression in SCaBER cell lines.
This study aims at characterizing the role of the putative tumor suppressor ITIH5 in basal-type bladder cancers (BLCA). By sub-classifying TCGA BLCA data, we revealed predominant loss of ITIH5 expression in the BASQ subtype. ITIH5 expression inversely correlated with basal-type makers such as KRT6A and CD44. Interestingly, Kaplan-Meier analyses revealed longer recurrence-free survival in combination with strong CD44 expression, which is thought to mediate ITIH-hyaluronan (HA) binding functions. In vitro, stable ITIH5 overexpression in two basal-type BLCA cell lines, i.e. with (SCaBER, high CD44 expression) and without squamous features (HT1376, low CD44 expression), demonstrated clear inhibition of cell and colony growth of BASQ-type SCaBER cells. ITIH5 further enhanced HA-associated cell-matrix attachment, indicated by altered size and number of focal adhesion sites resulting in reduced cell migration capacities. Transcriptomic analyses revealed enrichment of pathways and processes involved in ECM organization, differentiation and cell signaling. Finally, we provided evidence that ITIH5 increase sensitivity of SCaBER cells to chemotherapeutical treatment (cisplatin and gemcitabine), whereas responsiveness of HT1376 cells was not affected by ITIH5 expression. Thus, we gain further insights into the putative role of ITIH5 as tumor suppressor highlighting

overall_design: Gene expression analysis of BASQ-type bladder cancer cells with stable mock clones or ITIH5 over-expression were performed by applying Gene Chip® HTA 2.0 arrays.

first: Michael

last: Rose


title: RNAsequencing analysis of WT and RhoA-deficient mouse aveolar type 2 cells

city: Baltimore

first: Danh

middle: Cong

last: Do

state: MD

address: 5501 Hopkins Bayview Circle, 3A.4

department: Medicine

institute: Johns Hopkins University

summary: The goal of this study is to identify potential mechanism in which RhoA regulates aveolar type 2 activation and influences airway inflammation and asthma

overall_design: We examined the mRNA transcriptome of primary mouse aveolar type 2 cells isolated from WT or RhoA-deficient mice after cockroach allergen treatment

first: Peisong

last: Gao

first: Haiping

last: Hao


title: Expression data from CD73 positive adipose derived mesenchymal stem cells (CD73+ AD-MSCs) and CD73 negative adipose derived mesenchymal stem cells (CD73- AD-MSCs)  of mouse

city: Xinxiang

first: Huifang

last: Hou

address: 601 Jinsui Avenue

institute: Xinxiang Medical University

summary:
MSCs are a heterogeneous population and the specific population of MSCs may exhibit a selective ability for tissue repair. The aim of our research was to adapt the CD73+ subgroup of adipose derived MSCs (AD-MSCs) for the therapy of myocardial infarction (MI). Our results revealed that CD73+ AD-MSCs played more effective role in the acceleration function of cardiac recovery by promoting angiogenesis in a rat model of MI compared to mixed AD-MSCs and CD73- AD-MSCs.
Microarray analysis shows differences between CD73+ and CD73- AD-MSCs when transcription profile of these two subgroups were compared, especially in VEGF pathway.

overall_design: AD-MSCs were isolated from adipose tissues surrounding the groin of mice and CD73+ AD-MSCs and CD73- AD-MSCs were sorted using flow cytometry. To investigate the therapeutic effects of CD73+ AD-MSCs, CD73+ AD-MSCs were transplanted into rat model of MI, and CD73- AD-MSCs, normal AD-MSCs transplantation served as control. Microarray analysis detected differences between CD73+ and CD73- AD-MSCs.

first: Qiong

last: Li


title: Interleukin-17A causes osteoarthritis-like transcriptional changes in human osteoarthritis-derived chondrocytes and synovial fibroblasts in vitro

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

summary: Increased interleukin (IL)-17A has been identified in joints affected by osteoarthritis (OA), but it is unclear how IL-17A, and its family members IL-17AF and IL-17F, can contribute to human OA pathophysiology. Therefore, we aimed to evaluate the gene expression and signalling pathway activation effects of the different IL-17 family members in chondrocytes and fibroblasts derived from cartilage and synovium of patients with end-stage knee OA. Chondrocytes and synovial fibroblasts derived from end-stage OA patients were treated with IL-17A, IL-17AF, or IL-17F, and gene expression was assessed with bulk RNA-Seq. Hallmark pathway analysis showed that IL-17 cytokines regulated several OA pathophysiology-related pathways including immune-, angiogenesis-, and complement-pathways in both chondrocytes and synovial fibroblasts derived from end-stage OA patients. While overall IL-17A induced the strongest transcriptional response, followed by IL-17AF and IL-17F, not all genes followed this pattern. Disease-Gene Network analysis revealed that IL-17A-related changes in gene expression in these cells are associated with experimental arthritis, knee arthritis, and musculoskeletal disease gene-sets. In conclusion, the association of IL-17-induced transcriptional changes with arthritic gene-sets supports a role for IL-17A in OA pathophysiology.

overall_design: In total 48 samples were analysed, 24 human articular chondrocytes samples and 24 synovial fibroblasts samples. For each cell type, cells from 6 different osteoarthritis patients were used that were treated with either control media, 10ng/ml IL-17A, 10ng/ml IL-17AF, or 10ng/ml IL-17F.

first: Jolet

middle: Y

last: Mimpen

first: Mathew

last: Baldwin

first: Martin

last: Philpott

first: Andrew

last: Carr

first: Stephanie

middle: G

last: Dakin

first: Sarah

middle: B

last: Snelling


title: Maternal Nicotine Exposure Alters Hippocampal Microglia Polarization and Promotes Anti-Inflammatory Signaling in Juvenile Offspring in Mice

city: Huainan

first: Li

last: Zhou

state: AnHui

address: 168 Taifeng Road

department: School of Medicine

country: Zimbabwe

institute: Anhui University of Science and Technology

summary: To further detect possible developmental neurotoxic effects of nicotine in offspring and underlying mechanism, whole genome microarray analysis of the expression profile of hippocampus was performed on PND 20. Significant alterations in the expression of genes related to inflammatory, neurotransmitter and synapsis were observed in the hippocampus after maternal nicotine exposure, as compared to the vehicle control.

overall_design: Hippocampal mRNA profiles of 20-day old offspring mice

first: Xinrong

last: Tao


title: Phytogenics from sage and lemon verbena promote innate immunity and barrier function in the gut of gilthead seabream (Sparus aurata)

city: Santiago

first: Felipe

middle: E.

last: Reyes-López

state: Santiago

address: Av. Libertador Bernado O'Higgins 3363

country: Chile

institute: Universidad de Santiago de Chile

summary: Deciphering the dietary immunomodulatory effects of a medicinal plant leaf extract (MPLE) obateined from sage (Salvia officinalis, Lamiaceae) and lemon verbena (Lippia citriodora, Verbenaceae) upon the gut-associated lymphoid tissue (GALT) of gilthead seabream (Sparus aurata).

overall_design: Transcriptomic analysis was conducted in order to determine the differences on gene expression level between these two dietary strategies at gut-specific level. The experimental design included two conditions: (1) fish fed basal diet with no medicinal plant leaf extract (MPLE) added and low fishmeal (FM) content (7%) (control); (2) fish fed 0.1% inclusion of MPLE (10%, ursolic acid, 3% other triterpenic compounds; 2% verbascoside and < 1% polyphenols) from sage (Salvia officinalis, Lamiaceae) and lemon verbena (Lippia citriodora, Verbenaceae). After 92 days of feeding trial, total RNA were extracted invidually from gilthead sea bream (S. aurata) gut fed basal diet or an experimental diet containing 0.1% inclusion. Total RNA samples were grouped into 3 pools (n= 4 fish for each condition). The transcriptomic analysis was done following a reference design using the control diet group as reference.

first: Ricardo

last: Salomón

middle: E

first: Eva

last: Vallejos-Vidal

first: Enric

last: Gisbert


title: Genomic DNA copy number alterations of neutron-induced medulloblastoma in Ptch heterozygous mice

city: Chiba

first: Kazuhiro

last: DAINO

address: 4-9-1 Anagawa, Inage-ku

institute: National Institutes for Quantum and Radiological Science and Technology

type: Genome variation profiling by genome tiling array

summary: To investigate DNA copy number changes in mouse medulloblastomas induced by neutrons.

overall_design: DNA copy number changes in neutron-induced mouse medulloblastomas were analyzed using array-CGH microarray.

first: Chizuru

last: Tsuruoka

first: Shizuko

last: Kakinuma


title: Spatially-Resolved Live Cell Tagging and Isolation Using Protected Photoactivatable Cell Dyes: KP Tumor

first: Alex

middle: S

last: Genshaft

state: Massachusetts

address: 77 Massachusetts Ave

country: USA

institute: MIT

summary: Cell phenotypes and functions are influenced by dynamic interactions with their microenvironment. To examine cellular spatiotemporal activity, we developed SPACECAT—Spatially PhotoActivatable Color Encoded Cell Address Tags—to annotate, track, and isolate cells while preserving viability. In SPACECAT, samples are stained with photocaged fluorescent molecules and cells are labeled by uncaging those molecules with user-patterned near-UV light. SPACECAT offers single-cell precision and temporal stability across diverse cell and tissue types. Illustratively, we target crypt-like regions in patient-derived intestinal organoids to enrich for stem-like and actively mitotic cells, matching literature expectations. Moreover, we apply SPACECAT to ex vivo tissue sections from four healthy organs and an autochthonous lung tumor model. Lastly, we provide a computational framework to identify spatially-biased transcriptome patterns and enriched phenotypes. This minimally perturbative and broadly applicable method links cellular spatiotemporal and/or behavioral phenotypes with diverse downstream assays, enabling insights into the connections between tissue microenvironments and (dys)function.

overall_design: Tissue samples from lung tumor were sliced into ~1 mm sections using an acrylic tissue slicer (Braintree Scientific, Inc.). After sectioning, tissue was stained with calcein NVOC as described in “SPACECAT Staining” for at least 30 min prior to imaging and photoactivation. Tissue sections were then imaged and photoactivated as described in “SPACECAT Photoactivation of In Vitro Cell Lines,” using 12 s pulses of 405 nm light at 4X magnification.   After photoactivating the lung tumor sections, samples were dissociated by mechanical and enzymatic methods using the gentleMACS Tissue Dissociation Kit (Miltenyi Biotec). Resultant cell suspensions were stained with calcein violet (ThermoFisher, 1:1,000 dilution in PBS0) as an orthogonal indicator of viability. For lung tumor sections, cells were sorted by gating on positive for both calcein violet (viability following dissociation) and calcein NVOC (presence in the region of interest). All experiments leveraged calcein NVOC stained without photoactivation negative control for determining proper gating. Tumor samples were sorted into 500 µL RPMI + 10% FBS and kept on ice for subsequent single-cell RNA-seq.

first: Carly

last: Ziegler

first: Constantine

middle: N

last: Tzouanas

first: Benjamin

last: Mead

middle: M

last: Jaeger

last: Navia

first: Ryan

last: King

first: Tyler

last: Jacks

first: Jeffrey

middle: F

last: Van Humbeck

middle: K

last: Shalek


title: Long non-coding RNA lnc-TSSK2-8 activates canonical Wnt/β-catenin signaling through small shock proteins HSPA6 and CRYAB

city: Shanghai

first: Bo

last: Wang

address: 1678 Dongfang Road

country: China

institute: Shanghai Children's Medical Center

summary: Congenital heart defect (CHD) is the most common birth defect worldwide. Copy number variations (CNVs) have been revealed as an important source of pathogenic factor of CHD. 22q11.2 deletion syndrome is the most common microdeletion disorder which has been frequently associated with conotruncal malformations. By now, the dosage sensitive geneTBX1 has been adopted as the major pathogenic gene responsible for 22q11.2 deletion-related heart defects. Here we report the lncRNA lnc-TSSK2-8, which is encompassed in the 22q11.2 region, could activate the canonical Wnt/𝛃-catenin signaling by protecting 𝛃-catenin from ubiquitination and degradation. Such effects were mediated by two short heat shock proteins HSPA6 and CRYAB, whose expression were regulated by lnc-TSSK2-8 through the ceRNA mechanism. In clinical practice, pathogenesis of CNV were always attributed to haploinsufficiency of protein coding genes. Here we report the 22q11.2 lncRNA lnc-TSSK2-8 significantly activate canonical Wnt/ 𝛃-catenin signaling, which has major roles in cardiac out flow tract development and should act upstream of TBX1. Our results suggested that lncRNAs should contribute to the etiology of CNV related CHD.

overall_design: TSSK2-8 overexpression

first: Jingjing

last: Fa


title: Evaluation of RNA quality and functional transcriptome of beef longissimus thoracis et lumborum muscle tissue over time post-mortem

city: Davis

first: Payam

last: Vahmani

address: One Shields Avenue

department: Department of Animal Science

institute: University of California Davis

summary: Evaluating RNA quality and transcriptomic profile of beef muscle tissue over time post-mortem may provide insight on RNA degradation and underlying biological and functional mechanisms influencing the biochemical changes occurring post-mortem that transform muscle tissue to meat. RNA-sequencing was performed on longissimus thoracis et lumborum (LTL) muscle samples collected at 5 time points [0 h (45 min post-mortem), 6 h, 24 h, 48 h, and 72 h (drip cooler)] post-mortem from British Continental crossbred beef heifers (n=7). Processed mRNA reads were aligned to the ARS-UCD1.2 bovine genome assembly. Differential expression (DE) analysis identified from 51 to 1434 upregulated and 27 to 2256 downregulated DE genes at individual time points compared to time 0 h, showing a trend of both up and downregulated genes increasing over time . Gene ontology and KEGG pathway term enrichment analyses revealed significant enrichment of biological and molecular functions relating to cellular energy, oxidative stress and NADH activity specific to early time points, as well as cellular signaling and transport and ribosome activity at specific to late time points. This study also revealed that LTL muscle tissue samples, collected as late as 72 h post-mortem remained at a high RNA integrity, suggesting opportunities for late sampling regimes for RNA-Seq analysis of post-mortem muscle tissue and the potential for larger studies to associate desirable meat quality traits with post-mortem transcriptome activity. Additionally, this study highlights the need to evaluate non-coding genetic features involved with epigenetic regulation in post-mortem muscle tissue, as indicated by non-coding RNA transcripts detected post-mortem, including small nucleolar RNA, mitochondrial DNA genes, and long non-coding RNA.

overall_design: Post-mortem beef muscle tissue RNA profiles over 5 times points

first: Stephanie

last: Lam

first: Arun

last: Kommadath

first: Óscar

last: López-Campos

first: Nuria

last: Prieto

first: Jennifer

last: Aalhus

first: Manuel

last: Juárez

first: Michael

last: Dugan


title: Transcriptome Analysis of Wild Type and FGD5-AS1 knockdown CCC-HEH-2 cells

first: Xingyu

last: Zhang

address: No.1678, Dong Fang Road

institute: Shanghai Jiaotong University School of Medicine

summary: Purpose: According to the previous analysis results of gene regulation in fetal heart tissues with tetralogy of Fallot (ToF), we constructed the ceRNA mediated network driven by lncRNAs using a causal inference framework based on the expression correlations and validated miRNA-lncRNA/mRNA evidences. Totally 4 lncRNAs were identified as hub lncRNAs in the network, and FGD5-AS1 was focused for further loss-of-function investigation.   Methods: The specific shRNAs against FGD5-AS1 (sh-FGD5-AS1) as well as the corresponding negative control (sh-NC) were constructed along with lentiviral vector respectively. Then the CCC-HEH-2 human cardiac myocytes cell lines were infected with lentivirus and followed puromycin treatment for several days. The  knockdown efficiencies of the FGD5-AS1 expression were validated by qPCR. Genome-wide RNA expression of control and knockdown CCC-HEH-2 cell lines were observed using RNA-Seq.  Conclusions: Knockdown of this lncRNA interferes with glutamate receptor activity and metalloendopeptidase inhibitor activity. The expression of abundant CHD genes with |fold change| ≥ 2 was validated with qPCR. These results indicate that FGD5-AS1 plays an important role in CHD genes regulation networks.

overall_design: For CCC-HEH-2 cell line, 3 sh-NC cells and 3 sh-FGD5-AS1 cells were used and analyzed. To identify FGD5-AS1 signatures, paired t-test was performed between control shRNA and FGD5-AS1 shRNA samples.


title: HDAC1 paces the temporal expression of morphogenic genes during axolotl limb regeneration

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

summary: These data provide an important, detailed molecular resource that outlines and defines injury repair and regeneration stage-dependent genes and cellular composition orchestrated by wound healing and blastema stage-associated HDAC activity, which enhances our understanding of this complex limb regeneration process.

overall_design: RNA were extracted from axotol tissues (wound epidermis and soft tissues) after amputation with DMSO and MS-275, respectively.

first: M

middle: H

first: H

last: Lee

first: S

last: Lin


title: The gene expression of MZ B cells and neutrophils after Staphylococcus aureus infection in B6 mice

first: Li-Wen

last: Lo

address: 128 Academia Road, Section 2, Nankang, Taipei

institute: Academia sinica

summary: Marginal zone B cells can quickly respond to the bacterial invasion by providing the first-line of antibodies. Neutrophil can help marginal zone B cells activation and differentiation. We investigated the specific gene expression that interacts between the MZ B cells and neutrophils at the initial stage after Staphylococcus aureus infection.

overall_design: We compared the gene profiles of MZ B cells and neutrophils before and 4 hours after S. aureus infection.


title: Chromatin accessibility data in  Wild Type and FGD5-AS1 knockdown CCC-HEH-2 cells (ATAC-Seq)

summary: Purpose: According to the previous analysis results of gene regulation in fetal heart tissues with tetralogy of Fallot (ToF), we constructed the ceRNA mediated network driven by lncRNAs using a causal inference framework based on the expression correlations and validated miRNA-lncRNA/mRNA evidences. Totally 4 lncRNAs were identified as hub lncRNAs in the network, and FGD5-AS1 was focused for further loss-of-function investigation.   Methods: The specific shRNAs against FGD5-AS1 (sh-FGD5-AS1) as well as the corresponding negative control (sh-NC) were constructed along with lentiviral vector respectively. Then the CCC-HEH-2 human cardiac myocytes cell lines were infected with lentivirus and followed puromycin treatment for several days. The  knockdown efficiencies of the FGD5-AS1 expression were validated by qPCR.  The landscape of accessible chromatin in control and knockdown CCC-HEH-2 cell lines were observed using ATAC-Seq.  Conclusions:  Our data reveal a unique different chromatin state between wild type and FGD5-AS1 knockdown CCC-HEH-2 cells.

overall_design: For CCC-HEH-2 cell line, 3 sh-NC cells and 3 sh-FGD5-AS1 cells were used and analyzed.


title: Tubacin mediates the synthetic lethality of cysteine in breast cancer independent on HDAC6

city: HOUGHTON

first: TAHIYAT

last: ALOTHAIM

state: MI

address: DOW 514,1400 Townsend Dr

department: Department of Biological Sciences

institute: Michigan Technological University

summary: Triple-negative breast cancer (TNBC) has a highly aggressive nature and distinct molecular characteristics from other subtypes of breast cancer and lacks effective targeted therapy. The molecular and genetic basis of cysteine/cystine dependency in TNBC is complex. We found that cysteine addiction associates with the expression of a set of Claudin genes in TNBC. The Claudin-high TNBCs are independent on cystine, while the Claudin-low TNBCs undergo rapid ferroptosis upon cystine deprivation or inhibition of cystine transport by erastin. To overcome the resistance of Claudin-high TNBC and luminal breast cancer to the potential targeted cystine-addiction therapy, we explored the synthetic lethality of cysteine by an epigenetic compound library screen. Several potent HDAC6 inhibitors were identified and rendered the Claudin-high TNBCs and luminal cancer cells dependent on extracellular cystine and undergoing ferroptosis upon cystine deprivation. The transcriptomic profiling showed that the HDAC6 inhibitor tubacin in combination with erastin activates a synthetic-lethal transcriptional program. Together, we have identified the HDAC6 inhibitors as potent therapy-sensitizers to revive the targeted cysteine-addiction therapy for various subtypes of breast cancer, not limit in the Claudin-low TNBC.

overall_design: RNA was extracted by RNAeasy kits (Qiagen) from the HCC38 cells that were exposed to the control, 5 µM erastin, 5 µM tubacin, or the combination of erastin and tubacin for 18 hours (three replicates in each condition).

first: Tahiyat

last: Alothaim

first: Xiaohu

last: Tang


title: m6A modification regulates lung fibroblast-to-myofibroblast transition through modulating KCNH6 mRNA translation

city: shanghai

first: jiaxiang

last: zhang

state: shanghai

address: 650 Xinsongjiang Rd

department: Department of Critical Care Medicine

institute: Shanghai Jiaotong University

summary: In summary, we characterized the role of m6A modification in pulmonary fibrosis. We reveal that m6A modification is increased in bleomycin induced pulmonary fibrosis mice model, FMT-derived myofibroblasts and idiopathic pulmonary fibrosis patient lung samples. Lowering m6A level through silencing METTL3 suppress FMT process in vitro and vivo. Fundamentally, m6A modification regulates FMT by modulating the translation of KCNH6 mRNA in a YTHDF1 dependent manner. This study provides novel insights into the mechanism of FMT process and suggests m6A modification intervention may be a promising therapeutic strategy for pulmonary fibrosis.

overall_design: To investigate the variations of m6A modification in specific gene expression, we mapped the m6A site of normal and IPF lung samples by MeRIP-seq.

first: Jia-xiang

first: Rui-lan

last: Wang