title: Ultrasound effect on DNA methylation level of the wheat (Triticum aestivum) seedlings

city: Martonvásár

first: Norbert

middle: Tibor

last: Hidvégi

address: Brunszvik street 2.

department: Department of Biological Resources

country: Hungary

institute: HUN-REN Centre for Agricultural Research Agricultural Institute

type: Methylation profiling by high throughput sequencing

summary: In present experiment we evaluated the effects of the utrasonication of winter wheat seeds on seedling growth and development. Effect of treatment on the gene transcription and DNA methylation of seedlings were evaluated.

overall_design: In present experiments, the germination of a breeding line of winter wheat (Triticum aestivum L. cv. SE15) was investigated. The water content of the seeds was 13.6%. Half of the seeds (100 seeds) were ultrasonicated before germination at 30 kHz, 70 W for 5 minutes. The seeds were placed into open Petri dishes 4 cm away from the ultrasound head. The parameters of the ultrasound treatment have been optimized previously in preliminary experiments. The other half of the seeds (100 seeds) served as control and were non-ultrasonicated. Thereafter, winter wheat seeds were germinated at 20 °C in darkness for a week, in accordance with the Hungarian standard of MSZ 6354-3:2008 describing the determination of germination. Seedling samples were collected 7 days after germination. Three independent biological samples were collected both from control and from ultrasonicated plant material and they were stored at -80 °C until DNA and RNA analysis.

first: Andrea

last: Gulyás

first: Judit

last: Dobránszki


title: Ultrasound effect on the wheat (Triticum aestivum) seedlings

status: Public on Sep 14 2022

type: Expression profiling by high throughput sequencing

overall_design: In present experiments, the germination of a breeding line of winter wheat (Triticum aestivum L. cv. SE15) was investigated. The water content of the seeds was 13.6%. Half of the seeds (100 seeds) were ultrasonicated before germination at 30 kHz, 70 W for 5 minutes. The seeds were placed into open Petri dishes 4 cm away from the ultrasound head. The parameters of the ultrasound treatment have been optimized previously in preliminary experiments. The other half of the seeds (100 seeds) served as control and were non-ultrasonicated. Thereafter, winter wheat seeds were germinated at 20 °C in darkness for a week, in accordance with the Hungarian standard of MSZ 6354-3:2008 describing the determination of germination. Seedling samples were collected 7 days after  germination. Three independent biological samples were collected both from control and from ultrasonicated plant material and they were stored at -80 °C until DNA and RNA analysis.


title: Hypoxia promotes an inflammatory phenotype of fibroblasts in pancreatic cancer

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

country: USA

institute: University of Michigan

summary: Pancreatic ductal adenocarcinoma (PDAC) is characterized by an extensive fibroinflammatory stromal reaction, which contributes to its hypovascular and hypoxic microenvironment. To assess the effects of hypoxia on fibroblast phenotype in an unbiased fashion, we performed RNA-sequencing profiling of mouse pancreatic stellate cells (PSCs) cocultured with mT3 PDAC cells exposed to normoxia (21% oxygen) or hypoxia (1% oxygen).

overall_design: mRNA profiles of PSCs cultured in a transwell system with tumor organoids exposed to normoxia (21% oxygen) or hypoxia (1% oxygen) for 48 hours.

first: Kyoung

middle: E

last: Lee

first: Weisheng

last: Wu

first: Dana

middle: M

last: King


title: Liver gene expression profile in mice (C57Bl/6J) lacking ATGL in white adipose tissue in response to feeding, fasting or beta 3 adrenergic stimulation with CL316243

status: Public on Sep 15 2022

city: Toulouse

first: Hervé

last: Guillou

address: 180 Chemin de Tournefeuille

department: ToxAlim

country: France

institute: INRAE

summary: Adipocyte-specific Atgl knockout (Atgladipo-/-) mice were bred at the animal facility of the University of Graz. They were originally generated at the animal facility of the University of Pittsburgh by mating the floxed-Atgl mouse strain with Adiponectin-Cre mice to obtain Cre+/−Atglflox/flox mice (AAKO). Cre-/-Atglflox/flox mice (Atgladipo+/+) were used as controls (CTRL).

overall_design: Mice were either fed ad libitum (Fed), or fasted for 24h (fasted) or treated with a single dose of beta3 adrenergic receptor agonist (fed beta 3).

first: Anne

last: Fougerat

first: Gabriele

last: Schoiswohl

first: Arnaud

last: Polizzi

first: Achim

last: Lass

first: Claire

last: Naylies

first: Yannick

last: Lippi


title: EV-miRome-wide identification of noncoding RNAs for detecting metastatic colorectal cancer and monitoring the therapeutic response

city: Taoyuan City

first: Hsuan

last: Liu

address: No.259, Wenhua 1st Rd., Guishan Dist.

country: Taiwan

institute: Chang Gung University

type: Non-coding RNA profiling by high throughput sequencing

summary: Molecular composition of circulating small extracellular vesicles (EVs) does not merely reflect the cells of origin, but also is enriched in specific biomolecules directly associated with the cellular transformation. Given their functional and clinical relevance, small EVs have emerged as a promising target among the liquid biopsy approaches for cancer detection. However, while most of the currently identified EV-miRs are only geared towards one-dimensional disease detection, their application for long-term tracking and treatment response monitoring has been largely elusive. In this study, we established and optimized a rapid, sensitive and robust liquid biopsy sampling method, and further used small RNA sequencing to comprehensively catalogue EV-miRomes in association with the progression and outcome of metastatic colorectal cancer (mCRC). By cross-comparison of EV-miRomes (n = 290) from multi-stage and longitundial cohorts, we uncovered 28 EV-miRs for detecting mCRC, and 131 EV-miRs for long-term monitoring of tumor size progression. Among these candidates, we further pinpointed a 15-EV-miR signature with dual detection and monitoring functions for mCRC. From this panel, EV-miR-320c was uncovered as a strong clinical marker – aside from its diagnostic power, its high expression has also been linked to lower overall survival and a greater likelihood of disease recurrence. Furthermore, target spectrum of this 15-EV-miR signature of mCRC suggested an involvement of small EVs in programming the mesenchymal–epithelial transition (MET) transition for distant localization of the metastasized cells and also in creating a tumor-favoring metastatic niche. Our clinically-oriented delineation of the mCRC-associated circulating EV-miRomes revealed the functional significance of these liquid biopsy markers and further strengthen their translational potential in tumor therapeutic monitoring.

first: Chan-Keng

last: Yang

first: Hung-Chih

last: Hsu


title: Effect of beta3 adrenergic activation on liver gene expression profile in mice (C57Bl/6J) expressing hepatocyte PPARalpha or not

summary: Pparα hepatocyte-specific knockout (Pparαhep-/-) mice were generated at INRAE’s rodent facility (Toulouse, France) by mating the floxed-Pparα mouse strain with C57BL/6J albumin-Cre transgenic mice to obtain albumin-Cre+/-Pparαflox/flox mice (LKO). Albumin-Cre-/-Pparαflox/flox (Pparαhep+/+) littermates were used as controls (LWT). Twelve week-old mice were transferred in a ventilated cabinet at the specific temperature of 30°C (thermoneutrality) 2 weeks before experiments. Mice were fed ad libitum or fasted at ZT0 and given beta3 adrenergic receptor agonist: CL316243 ((3 mg/kg body weight; Sigma Aldrich) = Beta3) or vehicle (0.5% carboxymethyl cellulose in sterilized water)=vehicle) by gavage at ZT10 and sacrificed at ZT16.

overall_design: Gene expression profile was analyzed in 6 mice of each condition in both genotypes.

first: Franck

last: Soubès


title: RNA-seq analysis after GSK595 treatment in CAL-1 cells

city: Singapore

first: Rui

last: Yokomori

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore, National University of Singapore

summary: RNA-seq analysis was performed in BPDCN patient-derived cell line CAL-1 (WT and METTL3 KO) to analyze gene expression changes after loss of METTL3 concurrent with GSK595 treatment

overall_design: METTL3 KO was induced in CAL-1 cells with Tetracycline and cells were subsequently treated with DMSO (control) or GSK595 (0.31 uM) for 72 hours.  Total RNA was extracted using miRNeasy Mini Kit.  Strand-specific library construction and 150-bp paired-end sequencing with a sequencing depth of 130M reads on the NovaSeq6000 platform were performed at Macrogen.

first: Malini

last: Rethnam

first: Takaomi

last: Sanda

first: Toshio

last: Suda


title: Endogenous transcripts direct microRNA degradation in Drosophila, and this targeted degradation is required for proper embryonic development

city: Cambridge

first: David

last: Bartel

state: MA

address: 455 Main St

institute: Whitehead Institute, MIT

summary: MicroRNAs (miRNAs) typically direct degradation of their mRNA targets. However, five miRNA targets in vertebrate animals are reported to have unusual miRNA-binding sites that direct degradation of cognate miRNAs. Here, we identify six sites, five in mRNAs and one in a non-coding RNA named Marge, that serve this purpose in Drosophila cells or embryos, which shows that target-directed miRNA degradation (TDMD) shapes endogenous miRNA levels in some invertebrate animals. The six sites direct miRNA degradation without collateral target degradation, helping to explain the potency of this miRNA-degradation pathway. Mutations that disrupt this pathway in Drosophila are lethal, with many flies dying as embryos. Derepression of miR-3 and its paralog miR-309 is responsible for some of this lethality, whereas the loss of Marge-directed degradation of miR-310 miRNAs causes defects in embryonic cuticle development. Thus, TDMD is strongly implicated in the viability of an animal and is required for its proper development.

overall_design: Samples analyzed from dora[A], dora[B], and CR43432 fly lines (each with paired wild-type controls), as well as from Drosophila S2 cells. At least two fly lines (or clonal S2 lines) serve as replicates for each dataset. For fly lines, mRNA and sRNA samples were collected at various timepoints throughout embryonic development.

first: Elena

middle: R

last: Kingston

middle: P


title: Sensing of individual stalled 80S ribosomes by Fap1 for non-functional rRNA turnover. Li et al

city: Tokyo

first: Sihan

last: Li

address: Shirokanedai 4-6-1, Minato-ku

department: The Institute of Medical Science

country: Japan

institute: The University of Tokyo

summary: Cells can respond to stalled ribosomes by sensing ribosome collisions and employing quality control pathways. How ribosome stalling is resolved without collisions, however, has remained elusive. Here, focusing on non-colliding stalling exhibited by decoding-defective ribosomes, we identified Fap1 as a stalling sensor triggering 18S non-functional rRNA decay via poly-ubiquitination of uS3. Ribosome profiling revealed an enrichment of Fap1 at the translation initiation site but also association with elongating individual ribosomes. Cryo-EM structures of Fap1-bound ribosomes elucidated Fap1 probing the mRNA simultaneously at both the entry and exit channels suggesting a mRNA stasis sensing activity, and Fap1 sterically hinders formation of canonical collided di-ribosomes. Our findings indicate that individual stalled ribosomes are the potential signal for ribosome dysfunction, leading to accelerated turnover of the ribosome itself.

overall_design: 20 ribosome profiling (ribo-seq) samples are included in the study. Ribo-seq samples were obtained from (1) total cell lysates (input) collected prior to purification, (2) MS2-purified ribosomes carrying exogenously encoded wild type or mutant rRNA, or (3) co-purified ribosomes from pull-downs of proteins of interest (Mag2, Fap1, or Yil161w). Input samples serve as controls that are compared against purified ribosomes. Each sample has a biological replicate.

first: Ken

last: Ikeuchi

first: Misaki

last: Kato

first: Robert

last: Buschauer

first: Takato

last: Sugiyama

first: Shungo

last: Adachi

first: Hideo

last: Kusano

first: Tohru

last: Natsume

first: Otto

last: Berninghausen

first: Yoshitaka

last: Matsuo

first: Thomas

last: Becker

first: Roland

last: Beckmann

first: Toshifumi

last: Inada


title: Time-course bulk RNAseq and single-cell RNAseq of murine AB1 mesothelioma and Renca renal cancer following immune checkpoint therapy

city: Perth

first: Wee Loong

last: Chin

address: Level 5, Qq Block, Qeii Medical Centre 6 Verdun St, Nedlands

country: Australia

institute: National Centre For Asbestos Related Diseases

summary: The on/off dynamics of IFNβ signalling underlie the therapeutic response to immune checkpoint therapy in cancer in mice

overall_design: 8 samples treated with 2 dissociation protocols

first: Rachael

last: Zemek

first: Willem

middle: J

last: Lesterhuis


title: Developmental and housekeeping transcriptional programs in Drosophila require distinct chromatin remodelers

city: Vienna

first: Alexander

last: Stark

address: Campus-Vienna-Biocenter 1

country: Austria

institute: The Research Institute of Molecular Pathology (IMP)

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Uterine-specific SIRT1 deficiency confers premature uterine aging and impairs invasion and spacing of blastocyst and stromal cell decidualization in mice.

city: Raleigh

first: Xiaoqiu

last: Wang

address: 120 W Broughton Dr.

institute: NC State University

summary: We demonstrate that Sirtuin 1 (SIRT1) is an indispensable age-related regulator of invasion and spacing of blastocysts, as well as decidualization of stromal cells. Here, we report the sequencing of the uterine transcriptome of control and conditional knock-out of the Sirtuin 1 (SIRT1) at day 3.5 of murine pregnancy.

overall_design: Mice with uterine-specific ablation of Sirt1 (Sirt1d/d) and littermate controls (Sirt1f/f) were mated to male mice of proven fertility. Upon the presence of the post-coital plug (Gestational day 0.5, GD0.5), mice were sacrificed 3 days later (GD3.5) and uterine horns (embryo were flushed out) were harvested and frozen. RNA was isolated from the uterus. Six biological samples per genotype were sequenced for differential gene expression analysis.

first: Magdalina

last: Cummings

first: Hongyao

last: Yu

first: Guang

last: Hu


title: Tetracycline-induced mitohormesis mediates disease tolerance against influenza

city: Lausanne

first: Gaby

last: El Alam

state: Vaud

address: Station 15

department: SV LISP

country: Switzerland

institute: École polytechnique fédérale de Lausanne

summary: Mitohormesis defines the increase in fitness mediated by adaptive responses to a mild mitochondrial stress. Tetracyclines inhibit not only bacterial but also mitochondrial translation, thus imposing a low level of mitochondrial stress to eukaryotic cells. We show here that the mitochondrial stress response induced by 2 tetracyclins (Tet1, Tet2)  improves survival and disease tolerance against lethal influenza virus (IFV) infection. Tolerance to IFV infection is associated with the induction of genes involved in lung epithelial cell and cilia function and with the down-regulation of inflammatory and immune related gene sets in the lung, liver, and kidney.

overall_design: Design: We subjected 8 week-old female BALB/cN mice to either mock  or intranasal inoculation with 175 PFU of the IFV H1N1 PR8 strain (3 groups). The 3 infected groups were given vehicle, Tet1 (at 40 mpkd) or Tet2 (at 1 mpkd) by daily intraperitoneal injection (mock group respectively injected with vehicule as well). At day 7 post-inoculation, 5-6 mice were sacrified for organ collection.

first: Adrienne

last: Mottis

first: Johan

last: Auwerx


title: HMCES counterbalances the transcriptional regulation of nodal/activin and BMP signaling in mESCs

city: Beijing

first: Qiaoran

last: Xi

address: Haidian District

country: China

institute: School of Life Sciences, Tsinghua University


title: Developmental and housekeeping transcriptional programs in Drosophila require distinct chromatin remodelers (CUT&RUN)

summary: Determine the localization of chromatin remodelers using CUT&RUN

overall_design: CUT&RUN was performed on ~30-40 million cells using the Anti-FLAG M2 monoclonal antibody and pAG-Mnase. As a control, CUT&RUN was performed in the parental cell line, with no FLAG tag, as a control for accessbility bias of the pAG-Mnase.

first: Oliver

last: Hendy


title: HMCES counterbalances the transcriptional regulation of nodal/activin and BMP signaling in mESCs (RNA-Seq)

summary: Despite the fundamental roles to cell fates determination in all metazoans, the mechanism by which the TGF-β family signaling is interpreted into spatial and temporal manner and multiple cell fates is still elusive. The cell context dependent function of TGF-β signaling largely relies on the transcriptional regulation centered by SMAD proteins. Here, we discovered that the DNA-repair related protein, HMCES contributes to early development by maintaining the nodal/activin or BMP signaling related transcriptome homeostasis. HMCES is a R-SMAD proteins binding partner that co-localizes with R-SMADs at active histone marks. However, HMCES chromatin occupancy is independent of  nodal/activin or BMP signaling. Mechanically, HMCES exerts its transcriptional regulation role by counteracting R-SMAD proteins association with chromatin. In Xenopus embryo, hmces-KD causes dramatic development defects with altered left-right axis asymmetry along with increasing expression of lefty1. In sum, we disclosed the novel transcriptional regulatory function of HMCES integrated in TGF-β family signaling.

overall_design:
ESCs were cultured on gelatin coated plates with 15% serum ESC culture medium. mESCs in serum-culturing (no treatment), or in activin A (50 ng/ml, R&D Systems), SB431542 (10 μM), BMP4 (10ng/ml), LDN193189 (50nM) treated for 2h were harvested for RNA-seq
RNA-seq profiling of ESCs, WT and HMCES-KO.

first: Tao

last: Liang

first: Jianbo

last: Bai

first: Wei

last: Zhou


title: RNA-seq analysis of high nitrogen response (HN) in Arabidopsis roots of Col-0, agb1-2, wrky40, and wrky75

city: Sinagpore

first: Daisuke

last: Urano

address: 1 Research Link

institute: Temasek Life Science Laboratory

summary: Purpose: To understand molecular response of Arabidopsis roots upon high nitrogen

overall_design: One-week-old of Arabidopsis seedling were treated with or without 20 mM NH4NO3 for 2hours, pH5.8 , 2-3  biological replicates. Root were excised for total RNA extraction.

first: Kulaporn

last: Boonyaves


title: Expression data from lung mesenchymal cells in bleomycin-induced lung injury

city: Kyoto

first: Koichi

last: Hasegawa

state: Kyoto

address: Kawahara-cho 54, Sakyo-ku

department: Respiratory medicine

institute: Kyoto University

summary:
Bleomycin-induced acute lung injury is characterized by mesenchymal cell activation, which leads to pulmonary fibrosis. They also have the potential to increase epithelial cells to regenerate alveolar epithelial cell integrity.
We used microarrays to detail the change of global gene expression in lung mesenchymal cells in this process.

overall_design: Lung mesenchymal cells were isolated by flow cytometry on day 10 of bleomycin lungs and control lungs.

first: Atsuyasu

last: Sato


title: Identification of differential gene expression profile in rats showing risk-averse and risk-seeking preferences in rat gambling task (rGT)

city: seoul

first: SeungHyun

last: Jung

state: seoul

address: catholic university, medical college, banpo-dong

department: Department of Biochemistry

country: South Korea

institute: Catholic University of Korea

summary: In the present study, we examined using next-generation sequencing (NGS) whether there are differences in gene expression profiles in the brain when rats make different choices toward risk in rGT.

overall_design: Rats were trained in a touch screen chamber to learn the relationships between 4 different light signals on the window of the screen and accompanied reward outcomes or punishments set up with different magnitudes and probabilities. Once they show a stabilized pattern of preference upon free choice, rats were classified into risk-averse or risk-seeking group. After classification in rGT, rats were decapitated, the prefrontal cortex (PFC) and the nucleus accumbens (NAc) were dissected out from their brains, and NGS was performed with total RNA extracted.

first: Seung-Hyun

first: Yeun-Jun

last: Chung

first: Jeong-Hoon

last: Kim

first: Wha

first: Myung

last: Kwak


title: CLIC4 deficiency alters mitochondrial function and transcriptional profiles in murine breast cancer cells.

city: Bethesda

first: Howard

last: Yang

state: MD

address: 37 CONVENT DR, Room 5120

department: CCR

institute: NCI

summary: We report the different transcriptom of 6DT1 (murine mammary cancer cell line) wildtype cells or CLIC4-KO (by CRISPR cas9) untreated or treated 1uM H2O2 for 24 hours.

overall_design: WT or CLIC4-KO cells were untreated or treated with 1uM H2O2 for 24 hours.

first: Heba

middle: A

last: Khamici

first: Vanesa

middle: C

last: Sanchez

first: Hualong

last: Yan

first: Christophe

last: Cataisson

first: Aleksandra

last: Michalowski

first: Luowei

last: Li

first: Maxwell

last: Lee

first: Jing

last: Huang

first: Stuart

middle: H

last: Yuspa


title: Developmental and housekeeping transcriptional programs in Drosophila require distinct chromatin remodelers (MNase)

first: Alexander

last: Stark

summary: Characterization chromatin landscape before and after depletion of remodelers using Mnase-seq

overall_design: Mnase digest was performed on ~30-40 million cells either with Control treatment (H20) or Auxin treatment (500uM IAA) for 12 hours.

first: Oliver

last: Hendy


title: Next Generation Sequencing of zebrafish V2a  interneurons in spinal segments rostral to the lesion after spinal cord injury

status: Public on Sep 13 2022

city: Shanghai

first: Chun-Xiao

address: 65 Chifeng Road, Yangpu District

department: School of Medcine, Tongji University

summary: The goals of this study is to compare transcriptome profiles (RNA-seq) of zebrafish V2a interneurons with regrown axon and those without regrown axon in the spinal segments rostral to the lesion after spinal cord injury. For purification of V2a interneurons with regrown axon, the fluorescent tracer Rhodamine Dextran (RD) was retrogradely applied to Tg(Chx10:GFP) fish at three or eight weeks post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3- or 8 wpi, and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD- cells were FAC-sorted and subjected to RNA-sequencing. Total RNA was isolated using SMART-SeqTM v4 UltraTM Low Input RNA Kit for Sequencing (Clontech). Sequencing libraries (N=5-6) were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer’s instructions (NEB). We mapped about 40-80 million sequence reads per sample to the zebrafish genome and identified 42,370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without regrown axon in the spinal segments rostral to the lesion after spinal cord injury.

overall_design: For purification of V2a interneurons with regrown axon, the fluorescent tracer Rhodamine Dextran (RD) was retrogradely applied to Tg(Chx10:GFP) fish at three or eight weeks post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3- or 8 wpi, and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD- cells were FAC-sorted and subjected to RNA-sequencing. Total RNA was extracted and cDNA libraries (N=5-6) were subjected to Illumina sequencing according to the manufacturer’s instructions.

first: Jianren

last: Song

last: Guan


title: Sensitizing Resistant Cancer Cells to T cell-secreted Cytokines

city: Boston

first: Kai

middle: W.

last: Wucherpfennig

address: 450 Brookline Avenue

department: Department of Cancer Immunology and Virology

institute: Dana-Farber Cancer Institute

summary: Tumor heterogeneity is a major barrier to cancer therapy, including immunotherapy. Activated T cells can efficiently kill tumor cells following recognition of MHC class I (MHC-I) bound peptides, but this selection pressure favors outgrowth of MHC-I deficient tumor cells. We performed a genome-scale screen to discover alternative pathways for T cell-mediated killing of MHC-I deficient tumor cells. Autophagy and TNF signaling emerged as top pathways, and inactivation of Rnf31 (TNF signaling) and Atg5 (autophagy) sensitized MHC-I deficient tumor cells to apoptosis by T cell-derived cytokines. Mechanistic studies demonstrated that inhibition of autophagy amplified pro-apoptotic effects of cytokines in tumor cells. Antigens from apoptotic MHC-I deficient tumor cells were efficiently cross-presented by dendritic cells, resulting in heightened tumor infiltration by IFNg and TNFa-producing T cells. Tumors with a substantial population of MHC-I deficient cancer cells could be controlled by T cells when both pathways were targeted using genetic or pharmacological approaches.

overall_design: B16 ctrl-KO, B16 Rnf31-KO, B16 Atg5-KO, B16 Rnf31/Atg5-dKO tumor cells (5x105/well) were plated in 6-well plates and treated with and without TNFa (2 ng/ml, Peprotech) for 24h. Three biological replicates were used to extract total RNA using the RNeasy Plus Micro Kit (Qiagen #74034) according to the manufacturer’s protocol.

first: Yoshinaga

last: Ito


title: Neonatal necrotizing enterocolitis-associated DNA methylation signatures in the colon are evident in stool samples of affected individuals

city: Pittsburgh

first: David

last: Peters

state: PA

address: 204 Craft Avenue

institute: Magee-Womens Research Institute

summary: Neonatal necrotizing enterocolitis (NEC) is a deadly and unpredictable gastrointestinal disease, for which no biomarkers exist. We aimed to describe the methylation patterns in stool and colon from infants with NEC.

overall_design: We performed high-resolution genome-wide epigenomic analysis using solution-phase hybridization and next-generation sequencing of bisulfite-converted DNA from NEC colon tissue, healed NEC (non-NEC) colon tissue, and stool from infants with NEC or controls.

first: Misty

last: Good

first: Tianjiao

last: Chu

first: Patricia

last: Shaw

first: Lila

middle: S

last: Nolan

first: Lora

last: McClain

first: Austin

last: Chamberlain

first: Carlos

last: Castro

first: Qingqing

last: Gong

first: Krista

last: Cooksey

first: Laura

last: Linneman

first: Olivia

middle: N

last: DeWitt

last: Finegold

middle: G


title: Developmental and housekeeping transcriptional programs in Drosophila require distinct chromatin remodelers (STARRseq)

first: Alexander

last: Stark

summary: Changes in enhancer activity after chromatin remodeler depletion

overall_design: Mixed Housekeeping and Developmental STARRseq libraries were transfected into AID tagged cell lines. Cells were split and one half treated with Auxin and other half with Mock (H2O). Cells harvested and prepared for reporter mRNA sequencing after 24hrs.

first: Oliver

last: Hendy


title: Depletion of Scleraxis-lineage cells during tendon healing transiently impairs multi-scale restoration of tendon structure during early healing

city: Rochester

first: Antonion

last: Korcari

state: NY

address: 142 Westminster Rd, Appartment number 914 9th floor

institute: University of Rochester Medical Center

summary: Tendons are composed of a heterogeneous cell environment, with Scleraxis-lineage (ScxLin) cells being the predominant population. Although ScxLin cells are required for maintenance of tendon homeostasis, their functions during tendon healing are unknown. To this end, we first characterized the spatiotemporal dynamics of ScxLin cells during tendon healing, and identified that the overall ScxLin pool continuously expands up to early remodeling healing phase. To better define the function of ScxLin cells during the late proliferative phase of healing, we inducibly depleted ScxLin cells from day 14-18 post-surgery using the Scx-Cre; Rosa-DTR mouse model, with local administration of diphtheria toxin inducing apoptosis of ScxLin cells in the healing tendon.  At D28 post-surgery, ScxLin cell depleted tendons (DTRScxLin) had substantial impairments in structure and function, relative to WT, demonstrating the importance of ScxLin cells during tendon healing. Next, bulk RNAseq was utilized to identify the underlying mechanisms that were impaired with depletion and revealed that ScxLin depletion induced molecular and morphological stagnation of the healing process at D28. However, this stagnation was transient, such that by D56 tendon mechanics in DTRScxLin were not significantly different than wildtype repairs. Collectively, these data offer fundamental knowledge on the dynamics and roles of ScxLin cells during tendon healing.

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data for D28 after injury DTR vs WT tendons

first: Samantha

last: Muscat

first: Elizabeth

last: McGinn

first: Mark

last: Buckley

first: Alayna

last: Loiselle


title: Tranexamic acid may promote melanocores clustering in keratinocytes through upregulation of Rab5b

city: Hangzhou

first: Yebei

last: Hu

address: West Lake Road 38

institute: Hangzhou Third People's Hospital

summary: To explore the effect of TXA on melanocores in keratinocytes.

overall_design: RNA profiles of melanocore-incorporated normal human epidermal keratinocytes (NHEK) treated by Tranexamic acid (TXA)，and melanocore-incorporated NHEK without TXA treatment

first: Xiuzu

last: Song

first: Yi

last: Chen

first: Yan

last: Zhao


title: Time-regulated transcripts with the potential to modulate human pluripotent stem cell-derived cardiomyocyte differentiation

city: Sao Paulo

first: Jose Eduardo

last: Krieger

state: Sao Paulo

address: 44 Av. Dr. Enéas de Carvalho Aguiar

department: Medical School

country: Brazil

institute: University of Sao Paulo

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

platform_organism:
Homo sapiens
synthetic construct


title: Developmental and housekeeping transcriptional programs in Drosophila require distinct chromatin remodelers (PROseq)

summary: Determine the direct effects of chromatin remodeler on transcription using inducible protein degradation combined with nascent transcriptomics.

overall_design: Nascent RNA transcription measured by PRO-seq upon AID-mediated depletion of chromatin remodelers. All cell lines have OsTir1 expression from the Act5c locus, and AID tagged gene indicated in genotype. All experiments were performed in 2 biological replicates.


title: A coordinated function of lncRNA HOTTIP and miRNA-196b underpinning leukemogenesis by targeting Fas signaling

first: Huacheng

last: Luo

state: Zhejiang

address: No. 150, Fucheng Road, Qiantang District

institute: Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences

summary: MicroRNAs (miRNAs) may modulate more than 60% of human coding genes and act as negative regulators, while long non-coding RNAs (lncRNAs) regulate gene expression on multiple levels by interacting with chromatin, functional proteins, and RNAs such as mRNAs and microRNAs. However, the crosstalk between lncRNA HOTTIP and miRNAs in leukemogenesis remains elusive. Using combined integrated analyses of global miRNA expression profiling and state-of-the-art genomic analyses of chromatin such as ChIRP seq., (genome wide HOTTIP binding analysis), ChIP-seq., and ATAC-seq., we found that miRNA genes are directly controlled by HOTTIP. Specifically, the HOX cluster miRNAs (miR-196a, miR-196b, miR-10a and miR-10b), located cis & trans, were most dramatically regulated and significantly decreased in HOTTIP–/– AML cells. HOTTIP bound to the miR- 196b promoter, and HOTTIP deletion reduced chromatin accessibility and enrichment of active histone modifications at HOX cluster associated miRNAs in AML cells, while reactivation of HOTTIP restored miR gene expression and chromatin accessibility in the CTCF-boundary-attenuated AML cells. Inactivation of HOTTIP or miR-196b promotes apoptosis by altering the chromatin signature at the FAS promoter and increasing FAS expression. Transplantation of miR-196b knockdown MOLM13 cells in NSG mice increased overall survival compared to wild-type cells. Thus, HOTTIP remodels the chromatin architecture around miRNAs to promote their transcription, consequently repressing tumor suppressors and promoting leukemogenesis.

overall_design: We have finished the small RNA-SEQ for WT and HOTTIP-KO MOLM13 leukemia cells

first: Suming

last: Huang


title: An animal model for Pierpont syndrome; a mouse bearing the Tbl1xr1Y446C/Y446C mutation.

city: Amsterdam

first: Aldo

last: Jongejan

address: Meibergdreef 9

department: Epidemiology & Data Science

country: Netherlands

institute: Amsterdam University Medical Centers

summary: Unravelling molecular defects resulting from the missense mutation in TBL1XR1 using targeted mutant mice bearing the Tbl1xr1 Y446C/Y446C mutation. These mice used as an animal model of Pierpont syndrome have disturbed hearing and subtle changes in fat metabolism. RNA seq of white adipose tissue has been performed to establish the transcriptome.

overall_design: mRNA profiles for white adipose tissue (WAT) of wild type and Tbl1xr1Y446C/Y446C mice (6 mice for each genotype, 3 male and 3 female mice per genotype).

first: Yalan

first: Peter

last: Lauffer

first: Anita

last: Boelen


title: Genome-wide maps of Argonaute 2-chromosome interactions in miR-204-3p-overexpressed macrophages [ChIP-Seq]

city: Guangzhou

first: Si-Jia

last: Liang

state: Guangdong

address: 74 Zhongshan 2 Rd

department: Pharmacology

institute: Zhongshan School of Medicine, Sun Yat-Sen University

summary: Ago2, an essential effector for miRNA function, has been reported to be found in the nucleus together with miRNA. The miRNA-Ago complexes in the nucleus play an important role in regulating gene transcription. We previously have demonstrated the nuclear presence of miR-204-3p in macrophages. Here, we investigated and compared the Ago2 occupancy on the chromosomes upon miR-204-3p overexpression.

overall_design: Examination of Ago-DNA interactions in human macrophages


title: RNAseq of control and GFI1-expressing A549

city: Tianjin

first: Hao

last: Wang

address: Tianjin Medical University, 22 Qixiangtai Road, Heping District, Tianjin 300070, China

institute: Tianjin Medical University

summary: To study the effect of transcription factor GFI1 on lung cancer cells,  we overexpressed GFI1 in A549 cells and performed RNA-seq. Moreover, control and  GFI1-expressing A549 cells that were forced into suspension for 48hrs were used performed RNA-seq.

overall_design: mRNA profiles of control and GFI1-expressing A549 cultured on cell culture-treated  and  ultra-low attachment and plates

first: Zhe

last: Liu


title: HMCES counterbalances the transcriptional regulation of nodal/activin and BMP signaling in mESCs (ChIP-Seq)

first: Qiaoran

last: Xi

summary: Despite the fundamental roles to cell fates determination in all metazoans, the mechanism by which the TGF-β family signaling is interpreted into spatial and temporal manner and multiple cell fates is still elusive. The cell context dependent function of TGF-β signaling largely relies on the transcriptional regulation centered by SMAD proteins. Here, we discovered that the DNA-repair related protein, HMCES contributes to early development by maintaining the nodal/activin or BMP signaling related transcriptome homeostasis. HMCES is a R-SMAD proteins binding partner that co-localizes with R-SMADs at active histone marks. However, HMCES chromatin occupancy is independent of  nodal/activin or BMP signaling. Mechanically, HMCES exerts its transcriptional regulation role by counteracting R-SMAD proteins association with chromatin. In Xenopus embryo, hmces-KD causes dramatic development defects with altered left-right axis asymmetry along with increasing expression of lefty1. In sum, we disclosed the novel transcriptional regulatory function of HMCES integrated in TGF-β family signaling.

overall_design: HMCES-ChIP-seq using GFP-trap experiments profiling HMCES and SMAD2 chromatin association in HMCES-GFP mESCs. And SMAD2-ChIP-seq using cut&tag method experiments profiling SMAD2 chromatin association in HMCES-KO or control mESCs

first: Tao

first: Jianbo

last: Bai

first: Wei

last: Zhou


title: Expression data of B lymphocytes isolated from C57BL/6 Tilcara (Til) mouse mutant compared with wild-type C57BL/6 mouse [microarray]

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

institute: University of Canberra

summary:
Recent studies show that PKCs can have a nuclear function as epigenetic enzymes to directly regulate gene expression in the immune system. Using a PKCβ mutant mice model, C57BL/6 Tilcara (Til) mouse mutant, we examined the role of PKCβ as a histone kinase in regulating inducible gene expression in immune cells.
We investigated if PKCβ is important for the expression of key inducible genes upon B cell activation.

overall_design: 4 biological samples.

first: Chloe

last: Lim

first: Sudha

last: Rao


title: Comparative whole transcriptome analysis of gene expression in three canine soft tissue sarcoma types

city: PULLMAN

first: Eric

middle: Aaron

last: Shelden

state: WA

address: 1770 NE Stadium Way

department: School of Molecular Biosciences

institute: Washington State University

summary: We examined gene expression patterns in canine soft tissue sarcomas using RNA-seq analysis of samples obtained from archived formalin-fixed and paraffin-embedded tumors.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for FFPE samples of canine soft tissue sarcomas


title: RNAseq of wildtype and GFI1-KO H1155

summary: To study the effect of transcription factor GFI1 on lung cancer cells,  we knockouted GFI1 in H1155 cells  by CRISPR/Cas9 and performed RNA-seq.

overall_design: mRNA profiles of wildtype and GFI1-knockout H1155


title: Identification of GFI1 target genes in human lung adenocarcinoma cell line A549 [ChIP-seq]

summary: To investigate the genes regulated by the transcription factor GFI1 in lung cancer cells,  we overexpressed GFI1-Flag in A549 cells and performed ChIP-Seq with anti-Flag affinity gel.

overall_design: ChIP-seq analysis of GFI1-Flag-expressing A549 with anti-Flag affinity gel, two replicates.


title: Investigating the effects on the tumour and tumour environment transcriptome, of inhibiting PKC in conjunction with Docetaxel treatment [RNA-seq]

summary: The breast tumour microenvironment (TME) includes fibroblasts, adipocytes, inflammatory and immune cells. While treatment of tumours with chemotherapeutic agents such as Docetaxel, leads to apoptosis of tumour cells, it can also have consequences for the cellular makeup and transcriptional profile of the TME and these, like increased epithelial mesenchymal transition can promote undesirable consequences, such as Cancer Stem Cell development. PKC-theta may have a role in these undesired effects. To be able to examine the effects of co-treatment of Docetaxel with an inhibitor of PKC-theta, we performed RNA-seq on tumours from mice injected with the human breast cancer cell line MDA-MB-231. We then separated reads mapped to the human and mouse genomes in silico, creating tumour and TME transcriptomes for control, Docetaxel, PKC-theta inhibitor and combination treated mice. Separation of the tumour and TME profiles illustrated a role for PKC-theta in the induction of a more basal-type transcriptome in the tumour, and of EMT in the TME.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 4 different treatments, 3 or 4 replicates, samples mapped to both human and mouse genomes.

first: Abel

last: Tan


title: Reconstruction and analysis genome-scale metabolic model of thermophilic fungus  Myceliophthora thermophila

city: tianjin

first: Defei

state: 天津

address: xiqidao 32

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

summary: Myceliophthora thermophila is a thermophilic fungus with great biotechnological characteristics for industrial applications, which can degrade and utilize all major polysaccharides in plant biomass. Nowadays, it has been developing into a platform for production of enzyme, commodity chemicals and biofuels. Therefore, an accurate genome-scale metabolic model would be an accelerator for this fungus becoming a universal chassis for biomanufacturing. Here we present a genome-scale metabolic model  for M. thermophila constructed using an auto-generating pipeline with consequent thorough manual curation. Temperature plays a basic and critical role for the microbe growth. we are particularly interested in the genome wide response at metabolic layer of M. thermophilia as it is a thermophlic fungus. To study the effects of temperature on metabolic characteristics of M. thermophila growth, the fungus was cultivated under different temperature. The metabolic rearrangement predicted using context-specific GEMs integrating transcriptome data.The developed model provides new insights into thermophilic fungi metabolism and highlights model-driven strain design to improve biotechnological applications of this thermophilic lignocellulosic fungus.

sample_organism: Thermothelomyces thermophilus ATCC 42464

overall_design: The experiments were performed in 50 mL medium inoculated with 1×10^6 spores per milliliter in 250 mL Erlenmeyer flask shaken at 150 rpm. The minimal medium (per liter) contained 30 g glucose, 3 g NaNO3, 1 g K2HPO4, 0.5 g MgSO4•7H2O, 1 mL biotin (0.1 g/L), 1 mL trace elements solution (Vogel's salts) and adjusted to a pH of 6.0. The culture was incubated at 35 °C, 40°C, 45 °C and 50 °C, respectively.

first: Chaoguang

last: Tian


title: A targetable pathway in neutrophils mitigates both arterial and venous thrombosis

status: Public on Sep 12 2022

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

summary: Arterial and venous (A/V) thrombosis constitutes the greatest source of morbidity and mortality worldwide. Long considered as distinct entities, accumulating evidence indicates that A/V thrombosis can occur in the same populations suggesting that common mechanisms are likely operative. Although hyperactivation of the immune system is a common forerunner to the genesis of thrombotic events in both vascular systems, the key molecular control points remain poorly understood. Consequently, anti-thrombotic therapies targeting the immune system for therapeutic gain are lacking. Here we show that neutrophils are key effectors of both A/V thrombosis and can be targeted via novel immunoregulatory nanoparticles. Using antiphopholipid antibody syndrome (APS) as a model for devastating A/V thrombosis, we identified the transcription factor Krüppel-like factor 2 (KLF2) as a key regulator of neutrophil activation. Upon activation via genetic loss of KLF2 or administration of antiphospholipid antibodies, neutrophils cluster P-selectin glycoprotein ligand 1 (PSGL-1) via cortical actin remodeling, thereby increasing adhesion potential at thrombosis sites. Targeting clustered PSGL-1 using designer nanoparticles attenuates neutrophil-mediated A/V thrombosis in APS and KLF2 knockout models, illustrating the importance and feasibility of targeting activated neutrophils to prevent pathological thrombosis. Together, our results demosntrate a role for activated neutrophils to prevent pathological thrombosis. Together, our results demonstrate a role for activated neutorphils in both arterial and venous thrombosis and identify key molecular events that serve as potential targets for therapeutics against diverse causes of immunothrombosis.

overall_design: RNA-sequencing of peripheral blood neutrophils isolated from Lysozyme M cre (LysM) control mice and myeloid specific KLF2 knockout (K2KO) mice (n=3 biological replicates)

first: L

last: Nayak

first: D

last: Sweet

first: A

last: Thomas

first: S

middle: D

last: Lapping

first: K

last: Kalikasingh

last: Madera

first: V

last: Vinayachandran

first: R

last: Padmanabhan

first: N

middle: T

last: Vasudevan

first: J

last: Myers

middle: Y

last: Schmaier

last: Mackman

first: X

last: Liao

last: Maiseyeu

first: M

middle: K

last: Jain

first: B

last: Richardson


title: Mesenchymal stem cells derived from patients with premature ageing syndromes display hallmarks of physiological ageing

city: Marseille

first: Frederique

last: Magdinier

address: 27 Bvd Jean Moulin, Aix-Marseille Université. Faculté de Médecine. Campus La Timone

institute: Aix-Marseille Université - Marseille Medical Genetics

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

overall_design: Refer to individual Series


title: Transcriptome analysis the human amniotic epithelial cell-derived extracellular vesicles

first: Qingjian

last: Ou

address: Siping Rd

department: Medical

institute: Tongji University

summary: We aim to explore the types and expression of miRNA in the human amniotic epithelial cell-derived extracellular vesicles.

overall_design: Two human amniotic epithelial cell-derived extracellular vesicles were analysed with miRNA sequencing.

first: Shuqin

last: Hu


title: ALKBH5 induces retinal pigment epithelium anomalies and choroidal neovascularization in age-related macular degeneration via PIK3C2B/AKT/mTOR pathway

city: Nanjing

first: Ruxu

last: Sun

state: Jiangsu

address: 140 Hanzhong Road

institute: Nanjing medical university

summary: Collectively, the present study demonstrated that ALKBH5 induces RPE dysfunction and CNV progression in AMD.

overall_design: m6A-seq andRNA-seq of  RPE cells with or withoutoverexpressing ALKBH5

first: Xue

last: Chen


title: Self-organized emergence of hyaline cartilage in hiPSC-derived multi-tissue organoids

city: St. Paul

first: Timothy

middle: D.

last: O'Brien

state: MN

address: 1333 Gortner Avenue

department: Veterinary Population Medicine

institute: University of Minnesota

summary: Here, we developed a simple xeno- and feeder-free protocol for human hyaline cartilage production in vitro using hydrogel-cultured multi-tissue organoids (MTO). We investigate gene regulatory networks during spontaneous hiPSC-MTO differentiation using RNA sequencing and bioinformatic analyses. We find the interplays between BMPs and neural FGF pathways are associated with MTO phenotype transition. We recognize TGF-beta/BMP and Wnt signaling likely contribute to the long-term maintenance of cartilage growth and specific increase in articular cartilage development. By comparing MTO cartilage transcription signature with human lower limb chondrocytes, we observe MTO chondrocytes show strong correlation with fetal lower limb cartilage tissues. Collectively, our findings describe self-organized emergence of MTO hyaline cartilage, its associated molecular pathways, and spontaneous adoption of articular cartilage development trajectories by MTO.

overall_design: Multi-tissue organoids were induced from induced pluripotent stem cell line ATCC-BYS0110 (ATCC, Cat. #ACS-1024) and harvested at 8, 11, and 15 weeks in culture (n=2 biological replicates of each).  MTOs were lysed in RLT buffer (Qiagen, Hilden, Germany) and RNA isolated from cell lysates using the RNeasy Plus mini kit (Cat. No. / ID: 74134Qiagen, Hilden, Germany) according to manufacturer’s instructions. Extracted RNA was then quantified by RiboGreen RNA assay (Thermo Fisher Scientific, Waltham, MA) and quality/size analyzed by Agilent BioAnalyzer (Agilent Technologies, Santa Clara, CA). 2 x 50bp FastQ paired-end reads for 6 samples (n=62.4 Million average per sample) were trimmed using Trimmomatic (v0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30. Quality control on raw sequence data for each sample was performed with FastQC. Read mapping was performed via Hisat2 (v2.1.0) using the Human genome (GRCh38) as reference. Gene quantification was done via Feature Counts for raw read counts. Existing RNA-seq data were processed using the same pipeline.

first: Manci

last: Li

first: Juan

middle: E

last: Abrahante

first: Amanda

last: Vegoe

first: Yi

middle: W

last: Chai

first: Beth

last: Lindborg

first: Ferenc

last: Toth

first: Peter

last: Larsen


title: Comparison and functional analysis of odorant-binding proteins and chemosensory proteins in two closely related thrips species, Frankliniella occidentalis and Frankliniella intonsa (Thysanoptera: Thripidae)

city: Hangzhou, Zhejiang, China

first: Xiaowei

address: No. 298 Deshengzhong road

institute: Zhejiang Academy of Agricultural Sciences

summary: The antennal transcriptome analysis was performed for F. occidentalis and F. intonsa, and the putative chemosensory genes (OBPs and CSPs) were identified and compared between the two species

sample_organism:
Frankliniella occidentalis
Frankliniella intonsa

overall_design: Gene expression profiling analysis of RNA-seq data for one-day-old adults' antennae of  F. occidentalis and F. intonsa

first: Yaobin

last: Lu


title: Transcriptional circuitry of NKX2-1 and SOX1 defines a previously unrecognized lineage subtype of small cell lung cancer to maintain neuroendocrine differentiation (Fixed-tissue ChiP-Seq Mouse)

city: New York

first: Hideo

last: Watanabe

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

summary: Molecular classification of small cell lung cancer (SCLC), a lethal and heterogeneous disease, was recently proposed based on expression of four lineage-defining transcription factors SCLC-A (ASCL1), SCLC-N (NEUROD1), SCLC-Y (YAP1), and SCLC-P (POU2F3). In this study, unsupervised clustering of genome-wide histone H3K27 acetylation profiles uncovered previously unappreciated epigenomic heterogeneity of this recalcitrant disease. Specifically, the major SCLC-A subtype, which accounts for approximately 70% of all SCLC cases, was subdivided into two new subtypes SCLC-A1 and SCLC-A2. SCLC-A1 is distinguished by the presence of super-enhancer at the NKX2-1 locus, also observed in a murine SCLC model and human SCLC specimens. We found NKX2-1, a master regulator of lung lineages as well as a critical lineage factor in central nervous system, is uniquely functionally relevant in SCLC-A1, where it maintains neural lineage rather than pulmonary epithelial identity. Through integrative proteomic, transcriptomic and cistromic analyses, we found that maintenance of this neural identity in SCLC-A1 is mediated by collaborative transcriptional activity with another neuronal transcriptional factor SOX1

overall_design: Fixed-tissue ChIP-seq (FiTAc-seq) for H3K27ac profiling and super-enhancer analysis of GEMM RP and RPN tumors

first: Ranran

last: Kong

first: Eric

last: Snyder


title: Transcriptional circuitry of NKX2-1 and SOX1 defines a previously unrecognized lineage subtype of small cell lung cancer to maintain neuroendocrine differentiation


title: Loss of epigenetic regulation disrupts lineage commitment and promotes breast cancer (scATAC-Seq)

city: Toronto

first: Daniel

last: Schramek

state: ON

address: 600 University Ave, Room 1080

country: Canada

institute: Lunenfeld- Tanenbaum Research Institute

summary: Systematically investigating the scores of genes mutated in cancer to discern the real drivers from the inconsequential bystanders is a prerequisite for Precision Medicine but remains challenging. Here, we use CRISPR/Cas9-mediated somatic gene editing in a breast cancer mouse model to assess the transforming potential of 215 recurrent ‘long-tail’ breast cancer genes. Several core and accessory components of the COMPASS-like histone methylase complex, namely KMT2C, KDM6A and ASXL2 cooperated with PIK3CAH1047R mutation to accelerate mammary tumorigenesis in mice and to transform human breast epithelial cells. Mechanistically, mutations of these ‘EpiDrivers’ converged on enhancing the lineage conversion of basal cells to luminal cells prior to tumorigenesis, as well as an aberrant alveolar differentiation program in both luminal and basal cells. Overall, our work suggests that lactation mimicry is associated with the earliest steps of breast cancer.

overall_design: mRNA profiles of mouse mammary tumors modified by either CRISPR-Cas9 (sample 1-19) or conventional Cre-Lox knockout (20-25) with at least 2 tumors per treatment. Controls for each experient are are sgNT (non-targetting) or Kdm6a wildtype respectively.

first: Ellen

last: Langille

first: Ahmad

last: Malik


title: Loss of epigenetic regulation disrupts lineage commitment and promotes breast cancer (scRNA-Seq)

first: Langille

last: Ellen

first: Malik

last: Ahmad

first: Schramek

last: Daniel


title: Genome-widebinding maps of arabidopsis WRKY63

city: New Taipei City

first: FU-YU

last: HUNG

address: Singyi Rd. 17ave. 9s 8th 2F

institute: RIKEN

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of WRKY63 in 10 days old pro::WRKY63:GFP arabidopsis. By obtaining sequence from chromatin immunoprecipitated DNA, we mapped genome-wide binding levels of WRKY63:GFP. ChIP was performed using anti-GFP antibody (ab290), and ChIP DNA were analyzed by Illumina NovoSeq.

overall_design: Chromatin immunoprecipitation was performed with pro::WRKY63:GFP arabidopsis under vernalization or without vernalization. ChIP DNA was analyzed by Illumina NovaSeq.

first: Fu-Yu

last: Hung

first: Keqiang

last: Wu


title: Selective hypermethylation is evident in small intestine samples from infants with necrotizing enterocolitis [targeted_ileum]

city: Pittsburgh

first: David

last: Peters

address: 204 Craft Avenue

institute: Magee-Womens Research Institute

summary: Necrotizing enterocolitis (NEC) is the most common and lethal gastrointestinal disease affecting preterm infants. NEC develops suddenly and is characterized by gut barrier destruction, an inflammatory response, intestinal necrosis and multi-system organ failure. There is currently no method for early NEC detection, and the pathogenesis of NEC remains unclear.

overall_design: We performed high-resolution genome-wide epigenomic analysis using solution-phase hybridization and next-generation sequencing of bisulfite-converted DNA from NEC ileum tissue and healed NEC (non-NEC) ileum tissue.

first: Misty

last: Good

first: Chu

last: Tianjiao

first: Patricia

last: Shaw

first: Lila

last: Nolan

first: Joseph

last: Wrobleski

first: Carlos

last: Castro

first: Qingqing

last: Gong

first: Olivia

last: DeWitt

last: Finegold


title: Loss of epigenetic regulation disrupts lineage commitment and promotes breast cancer (RNA-Seq)

first: Daniel

last: Schramek

first: Ellen

last: Langille

last: Malik


title: Differential gene expression in the lungs of Syrian hamsters infected with Adenoviurs 14 or Adenovirus 14p1

city: Boise

first: Jay

middle: Ryan

last: Radke

state: ID

address: 500 W. Fort St

institute: IVREF

summary: Adenovirus is a frequent cause of mild, usually self-limited infections in infants and young children. Severe infections occur in immunocompromised patients but are rarely observed in healthy, immunocompetent adults. However, there have been outbreaks around the world of infections with different adenoviral (Ad) serotypes that have resulted in acute lung injury (ALI) and acute respiratory distress syndrome (ARDS) in some of those infected. Ad14p1, the predominant circulating strain of Ad14 worldwide is one such serotype. The explanations for the severity of illness caused by Ad14p1 infection in immunocompetent patients is unknown. Previously, we have shown that A549 cells infected with Ad14 repress macrophage pro-inflammatory responses whereas cells infected with Ad14p1 fail to repress macrophages and, instead, can increase pro-inflammatory responses. Micro-RNAs (miRNA) are small noncoding RNAs that regulate gene expression at the posttranscriptional level. Adenoviral infection has been shown to modulate host miRNA expression, and we hypothesized that differences in miRNA expression between Ad14 and Ad14p1 infected cells might impact pathogenesis. A549 cells were infected with either Ad14 or Ad14p1 and total RNA samples were collected at 6, 12, 24, 36 and 48 post infection for miRNA sequencing. Cluster analysis revealed that there were 3 temporal changes in miRNA expression profiles following infection. Differential expression analysis showed 8-23 differentially expressed miRNA between Ad14 and Ad14p1 from 6 to 36hpi. However, at 48hpi there were 98 differentially expressed miRNAs in Ad14p1 infected cells compared to those infected by Ad14. Pathway enrichment analysis showed that the differentially expressed miRNA might explain the increased pathogenesis of Ad14p1caused by strain-related loss of modulation of cytokine expression. Infection with Ad14p1 results in increased expression of pro-inflammatory genes in the lungs of Syrian hamsters than infection with Ad14. Overall, the data suggest a role for viral regulation of host miRNA expression in pathogenesis by regulating host inflammatory responses through the delivery of deregulated miRNAs by virally infected cell corpses to macrophages.

overall_design:
Female Syrian hamsters were infected with Ad14 or Ad14p1 5x10^9 genomes/hamster via intratracheal installation to assess the effect of infection on gene expression in the hamster lung. 5 days post-infection hamsters were euthanized and the left lobe collection. Total RNA was extracted and RNA-seq libraries generated.
Four biological replicates were analyzed for each of 3 conditions

first: Eric

last: McIndoo


title: Gene expression profile of Eggerthella lenta DSM 2243 during growth in defined media EDM1

city: San Francisco

first: Cecilia

last: Noecker

state: CA

address: 513 Parnassus Ave

department: Microbiology and Immunology

institute: University of California San Francisco

summary: We grew E. lenta in chemically defined media, added one of multiple potential nutrients, and collected RNA during late exponential phase to determine both the overall profile of highly expressed metabolic enzymes and the gene expression response to nutrient conditions..

overall_design: Cultures were grown in a base/limited media formulation for 20 hours (early exponential phase), treated with concentrated solutions of either sodium acetate, L-arginine, agmatine sulfate, or vehicle (H2O). Pellets were collected after an additional 18 hours of growth (late exponential).

first: Peter

middle: J

last: Turnbaugh


title: Genome-wide mapping of histone H3 T6 phosphorylation in mouse B lymphocytes [ChIP-seq]

first: Kristine

last: Hardy

summary: The changes in gene expression can be epigenetically regulated by histone modifications. As PKCB is known to phosphorylate H3T6 leading to gene activation, we examined if the changes in gene expression seen in B cell activation were associated with H3T6 phosphorylation. We want to examine how PKCB mutation will affect H3T6 phosphorylation on a genome-wide level and so we performed ChIP-seq with H3T6 phosphorylation in wildtype and C57BL/6 Tilcara (Til) mouse, a PKCβ mutant mice model.

overall_design: 3 biological samples used for chip

first: Chloe

last: Lim

first: Sudha

last: Rao


title: Epithelial Presenilin-1 drives colorectal tumor growth by controlling EGFR-COX2 signalling

city: Erlangen

first: Reyes

last: Gamez-Belmonte

state: Bayern

address: Hartmanstraße, 14

department: Medizin 1

country: Germany

institute: Universitätsklinikum Erlangen

summary: We analyzed the role of Presenilin1 (Psen1) during intestinal tumorigenesis. With this aim, transcriptome comparison of mouse tumor organoids derived from Psen1flox Apcmin/+ and Psen1ΔIEC Apcmin/+  mice was performed. The analysis revealed  alteration in the EGFR pathway and in arachidonic acid metabolism.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Psen1 flox and Psen1 ΔIEC Apc tumor organoids with and without EGF treatment.

first: R

first: M

last: Mahapatro

first: L

last: Erkert

last: Gonzalez-Acera

first: E

last: Naschberger

first: Y

last: Yu

last: Tena-Garitaonaindia

first: JV

last: Patankar

last: Wagner

last: Podstawa

last: Schödel

first: B

last: Bubeck

middle: F

last: Neurath

last: Stürzl

first: C

last: Becker


title: Enteric glial cells favor accumulation of anti-inflammatory macrophages during the resolution of muscularis inflammation

city: Leuven

first: Gianluca

last: Matteoli

address: Herestraat 49

country: Belgium

institute: KU Leuven

summary: Monocyte-derived macrophages (Mφs) are crucial regulators during muscularis inflammation. However, it is unclear which micro-environmental factors are responsible for monocyte recruitment and anti-inflammatory Mφ differentiation in this paradigm. Here, we investigate Mφ heterogeneity at different stages of muscularis inflammation and determine how environmental cues can attract and activate tissue-protective Mφs. Results showed that muscularis inflammation induced marked alterations in mononuclear phagocyte populations associated with a rapid infiltration of Ly6c+ monocytes that locally acquired unique transcriptional states. Trajectory inference analysis revealed two main pro-resolving Mφ subpopulations during the resolution of muscularis inflammation, i.e. Cd206+ MhcIIhi and Timp2+ MhcIIlo Mφs. Interestingly, we found that damage to the micro-environment upon muscularis inflammation resulted in EGC activation, which in turn stimulated monocyte infiltration and the consequent differentiation in anti-inflammatory CD206+ Mφs via CCL2 and CSF1, respectively. In addition, CSF1-CSF1R signaling was shown to be essential for the differentiation of monocytes into CD206+ Mφs and EGC proliferation during muscularis inflammation. Our study provides a comprehensive insight into pro-resolving Mφ differentiation and their regulators during muscularis inflammation. We deepened our understanding in the interaction between EGCs and Mφs, thereby highlighting pro-resolving Mφ differentiation as a potential novel therapeutic strategy for the treatment of intestinal inflammation.

overall_design: Neurosphere-derived glial cells were obtained as previously described in John K Mich et al., (Elife, 2014). Briefly, total intestines from E14.5 C57BL/6J mice were digested with collagenase D (0.5 mg/ml; Roche) and DNase I (0.1mg/ml; Roche) in DMEM/F-12, GlutaMAX, supplemented with 1% HEPES, streptomycin/penicillin and 0.1% β-mercaptoethanol (Gibco) for approximately 30 min at 37°C under gentle agitation. Cells were cultured for 1 week in a CO2 incubator at 37°C in DMEM/F-12, GlutaMAX, streptomycin and penicillin and 0.1% β-mercaptoethanol (Gibco) supplemented with B27 (Gibco), 40 ng/ml EGF (Gibco) and 20 ng/ml FGF (Gibco). After 1 week of culture, cells were treated with 0.05% trypsin (Gibco), transferred into PDL (Sigma-Aldrich) coated plates and cultured in DMEM supplemented with 10% FBS, 1% HEPES, glutamine, streptomycin and penicillin and 0.1% β-mercaptoethanol (Gibco) until confluence. EGCs were activated with LPS (100ng/ml; Sigma) for 12 hours. RNA was isolated using RNeasy Micro Kit according to manufacturer’s instructions. cDNA indexed library was prepared the Illumina TruSeq RNA library Kit and sequencing was performed on the Illumina NextSeq500 platform at the nucleomics core at VIB, Leuven. The reads were preprocessed by trimming for quality and to remove adapters (cutadapt 1.15 and FastX 0.0.14) followed by filtering for quality (FastX 0.0.14 and ShortRead 1.40.0) and removal of contaminants (bowtie 2.3.31). The reads were then mapped against the reference genome GRCm3882 using STAR (2.5.2b). Further filtering, sorting and indexing was done using samtools 1.5 and counts file is prepared and differential expression analysis is performed using EdgeR.

first: Michelle

last: Stakenborg

first: Saeed

last: Abdurahiman

first: Veronica

last: De Simone

first: Gera

last: Goverse

first: Nathalie

first: Lies

last: Van Baarle

first: Qin

last: Wu

first: Dimitri

last: Pirottin

first: Jung-Seok

last: Kim

first: Louise

last: Maor

first: Isabel

last: Pintelon

first: Sofie

last: Thys

first: Emilie

last: Pollenus

first: Louis

last: Boon

first: Philippe

last: Van den Steen

first: Marlene

last: Hao

first: Jo

last: Van Ginderachter

first: Guy

last: Boeckxstaens

first: Jean-Pierre

last: Timmermans

first: Steffen

last: Jung

first: Thomas

last: Marichal

first: Sales

last: Ibiza


title: Glioma MYC gene signature

first: Daniel

last: Schramek

summary: There is little overlap on publicily avaiable gene signatures and it is unclear how relevant these are to glioma biology. MYC is a very dynamically regulated gene, and it's gene signature will vary with respect to cell context. To determine what genes fall within the MYC signature of glioma, we performed ChIP-SEQ upon 4 different glioma PDX with two different MYC antibodies. The overlapping enriched genes will provide context of a MYC signature within the context of glioma.

overall_design: ChIP sequencing of 4 glioma PDX with 2 MYC antibodies

first: Ahmad

last: Malik

first: Connor

last: Yanchus


title: Mesenchymal stem cells derived from patients with premature ageing syndromes display hallmarks of physiological ageing [RNA-Seq]

first: Frederique

last: Magdinier

summary: Progeroid syndromes are rare genetic diseases with a majority of autosomal dominant transmission, the prevalence of which is less than 1 / 10,000,000. These syndromes caused by mutations in the LMNA gene encoding A-type Lamins belong to the group of disorders called laminopathies. Lamins are implicated in the architecture and function of the nucleus and  chromatin. Patients affected with progeroid laminopathies display accelerated ageing of mesenchymal stem cells (MSCs)-derived tissues associated with nuclear morphological abnormalities. In order to identify pathways altered in progeroid patients’ MSCs, we used induced pluripotent stem cells (hiPSCs) from patients affected with classical Hutchinson-Gilford Progeria Syndrome (HGPS, c.1824C>T - p.G608G), HGPS-Like Syndrome (HGPS-L; c.1868C>G - p.T623S) associated with farnesylated prelamin A accumulation, or Atypical Progeroid Syndromes (APS; homozygous c.1583C> T - p.T528M; heterozygous c.1762T>C - p.C588R; compound heterozygous c.1583C>T and c.1619T>C - p.T528M and p.M540T) without progerin accumulation. By comparative analysis of the transcriptome and methylome of hiPSC-derived MSCs, we found that patient’s MSCs display specific DNA methylation patterns and modulated transcription at early stages of differentiation. We further explored selected biological processes deregulated in the presence of LMNA variants and confirmed alterations of age-related pathways during MSC differentiation. In particular, we report the presence of an altered mitochondrial pattern, an increased response to double-strand DNA damage and telomere erosion in HGPS, HGPS-L and APS MSCs, suggesting converging pathways, independent of progerin accumulation, but a distinct DNA methylation profile in HGPS and HGPS-L compared to APS cells.

overall_design: Transcriptomic analysis of hIPSc and  hIPSc derived MSC in HGPS, HGPS-l and APS

first: Jérôme

last: Robin

first: Frédérique

first: Jean-Philipe

last: Trani

first: Raphael

last: Chevalier


title: Mesenchymal stem cells derived from patients with premature ageing syndromes display hallmarks of physiological ageing [array]

overall_design: DNA methylation profiling of hIPSc and  hIPSc derived MSC in HGPS, HGPS-l and APS

first: Magdinier

last: Frédérique

first: Chevalier

last: Raphaël


title: Blood transcriptome of human sepsis in an Indian cohort

city: Kalyani

first: SAMANWOY

last: MUKHOPADHYAY

state: West Bengal, INDIA

country: India

institute: NATIONAL INSTITUTE OF BIOMEDICAL GENOMICS

overall_design: Refer to individual Series


title: Hippocampus-specific loss of intellectual disability-related gene Brpf1 impaired spatial and contextual learning

city: Shanghai

first: Hang

last: Zhang

address: 130 Dongan Road

institute: Medical College, Fudan University

summary: To help explain the dominant symptom-intellectual disability found in those patients with BRPF1 mutations, we used a genetically modified mouse model and used several methods to study the effect caused by BRPF1 knockout. We then performed gene expression profiling analysis using data obtained from RNA-seq of two genotypes of mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT mice and cKO mice

first: Baicheng

last: Zhao

first: Ying

last: Liu

first: Gaoyu

last: Zu

first: Shuai

first: Linya

last: You


title: RNA sequencing of blood-brain barrier (BBB) microvessels from mice with hematogenous pneumococcal meningtis

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: Bacterial meningitis is a deadly disease most commonly caused by Streptococcus pneumoniae that leads to severe neurological sequelae including cerebral edema, seizures, stroke, and mortality when untreated. Meningitis is initiated by the transfer of S. pneumoniae from hematogenous source into the brain across the blood-brain barrier (BBB); the mechanisms however are still poorly understood. Current treatment strategies include adjuvant dexamethasone therapy for cerebral edema, the prime reason for neurological complications and mortality, which is followed up by antibiotics. The success of corticosteroids is however inconclusive, necessitating the development of new therapies for controlling cerebral edema. We have previously shown a general activation of hypoxia inducible factor (HIF-1α) in bacterial infections, we therefore hypothesized that HIF-1α, via induction of vascular endothelial growth factor (VEGF) is critically involved in the transmigration of pathogens across the BBB. In human and murine meningitis brain samples, HIF-1 activation was observed by immunohistochemistry. HIF-1α/VEGF expression and permeability was therefore analyzed in vitro in infected brain endothelial cells (ECs). Localization of S. pneumoniae in brain ECs from mouse/human sources was visualized in vitro and in vivo by confocal, super-resolution, and electron microscopy. S. pneumoniae infection in brain ECs resulted in upregulation of HIF-1α/VEGF by Western blotting and qRT-PCR that was associated with increased paracellular permeability, which was supported by bacterial localization at cell-cell junctions. RNA sequencing of brain microvessels from hematogenously infected mice with increased permeability and S. pneumoniae deposition in the brain showed upregulation of genes in HIF-1α/VEGF pathway. Inhibition of HIF-1α with echinomycin, siRNA in bEnd5 cells and by using primary brain ECs from HIF-1α KO mice revealed a reduced endothelial permeability and transmigration of S. pneumoniae. We thus demonstrate a critical role for HIF-1α/VEGF in transmigration of S. pneumoniae across the BBB and propose targeting this pathway to prevent BBB dysfunction in infections.

overall_design: 4 samples from hematogenously S. pneumoniae infected mice 18h post infection and 4 samples from healthy mice were used for the analysis. Each sample was pooled from 2 mice brains and comprised both male and female adult mice belonging to the C57BL/6 strain. All the animals were throroughly perfused with PBS transcardially followed by isolation of brain microvessels that were lysed in RLT buffer (Qiagen) containing 40mM DTT followed by RNA quality anaylsis and RNA sequencing.

first: Gayatri

last: Devraj

first: Kavi

first: Volkhard

last: Kempf


title: ERBB2b mRNA isoform encodes a nuclear variant of the ERBB2 oncogene in breast cancer

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

summary: The presence of nuclear ERBB2 receptor-type tyrosine kinase is one of the causes of the resistance to membrane ERBB2-targeted therapy in breast cancers. It has been previously reported that this nuclear location arises through at least two different mechanisms: proteolytic shedding of the extracellular domain of the full-length receptor and translation of the messenger RNA (mRNA)-encoding ERBB2 from internal initiation codons. Here, we report a new mechanism and function where a significant portion of nuclear ERBB2 results from the translation of the variant ERBB2 mRNA under the transcriptional control of a distal promoter that is actively used in breast cancer cells. We show that both membrane ERBB2a and nuclear ERBB2b isoforms are prevalently expressed in breast cancer cell lines and carcinoma samples. The ERBB2b isoform, which is translated from mRNA variant 2, can directly translocate into the nucleus due to the lack of the signal peptide which is required for an intermediate membrane location. Small interfering RNA-mediated gene silencing showed that ERBB2b can repress ERBB2a expression, encoded by variant 1, whereas ERBB2a activates ERBB2b. Nuclear ERBB2 binding to its own promoter was revealed by chromatin immunoprecipitation assay. Altogether, our results provide new insights into the origin and function of nuclear ERBB2 where it can participate at the same time in a positive or a negative feedback autoregulatory loop, dependent on which of its promoters this bona fide transcription factor is acting. They also provide a new understanding for the resistance to therapies targeting the membrane-anchored ERBB2 in breast cancer.

overall_design: RNAP2 ChIP-Seq in BT474 cells

first: Guoqiang

last: Hua

first: Aurélie

last: Bergon

first: Brigitte

last: Kahn-Perlès

first: François

last: Bertucci

first: Daniel

last: Birnbaum

first: Nadia

last: Benkirane-Jessel

first: Jean

last: Imbert


title: Gene expression signature of DHTKD1 gene knock-out spinal cord

first: Houbao

last: Zhu

address: 197 Ruijin Road Ⅱ

institute: Shanghai Jiao Tong University School of Medicine

summary:
We employed whole genome microarray expression profiling as a discovery platform to identify gene expression changes after DHTKD1 knock-out
RNAs of spinal cords of 8-weeks-old wild-type (n=3) and DHTKD1 knock-out mice (n=3) were used to identify gene expression.

overall_design: Spinal cords were dissected and frozen into liquid nitrogen immediately. Total RNA was extracted and checked for a RIN number to inspect RNA integration. Qualified total RNA was further purified, amplified and labeled. Labeled cRNA were further purified. Each slide was hybridized with 1.65μg Cy3-labeled cRNA for 17 hours at 65°C in rolling hybridization oven. Then, slides were washed and scanned by Agilent Microarray Scanner with default settings.

first: Wang-yang

last: Xu


title: Transcriptional circuitry of NKX2-1 and SOX1 defines a previously unrecognized lineage subtype of small cell lung cancer to maintain neuroendocrine differentiation (RNA-Seq H187)

first: Hideo

last: Watanabe

overall_design: Transcriptomic profile of NCI-H187 cells genetically engineered to deplete the expression of SOX1 or NKX2-1 with control

first: Ranran

last: Kong


title: Transcriptional circuitry of NKX2-1 and SOX1 defines a previously unrecognized lineage subtype of small cell lung cancer to maintain neuroendocrine differentiation (Fixed-tissue ChiP-Seq Human)

overall_design: Fixed-tissue ChIP-seq (FiTAc-seq) for H3K27ac profiling and super-enhancer analysis of FFPE human SCLC tumors


title: S100A8 Enhances IL-1β Production from Nasal Epithelial Cells in Eosinophilic Chronic Rhinosinusitis

status: Public on Sep 11 2022

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Chronic rhinosinusitis is classified into eosinophilic chronic rhinosinusitis (ECRS) and non-eosinophilic chronic rhinosinusitis (NECRS). ECRS is a refractory allergic disease involving a variety of immune and epithelial cells. S100A8 is a damage-associated molecular pattern that is closely related to allergic inflammation. However, the pathological implications of S100A8 in ECRS have not been clarified. We evaluated the role of S100A8 in the pathogenesis of ECRS. Gene expression profiles of nasal polyps obtained from patients with ECRS or NECRS were evaluated using RNA sequencing. S100A8 was identified as a significantly upregulated gene in nasal polyps associated with ECRS. Consistently, immunohistochemistry revealed that S100A8 stained intensely in nasal polyps from patients with ECRS. Human nasal epithelial cells expressed the receptor for advanced glycation end products and Toll-like receptor 4. Recombinant S100A8 protein induced interleukin-1β secretion in human nasal epithelial cells. Our data demonstrate that S100A8 induces production of interleukin-1β in the nasal epithelium, which may be involved in the pathogenesis of ECRS.

overall_design: Total RNA extracted from nasal polyps from two patients with ECRS and two patients with NECRS were evaluated using RNA sequencing.

first: Ayaka

last: Nakatani

first: Takeshi

last: Tsuda


title: Transcriptional circuitry of NKX2-1 and SOX1 defines a previously unrecognized lineage subtype of small cell lung cancer to maintain neuroendocrine differentiation (ChIP-Seq TF)

state: NY

overall_design: Genomic occupancy of NKX2-1 in SCLC-A1 and 2 LADC cell lines. Genomic occupancy of SOX1 in SCLC-A1 cell lines. Genome-wide profiles of histone H3K27 acetylation in NCI-H187 cells genetically engineered to deplete the expression of SOX1 with control


title: Transcriptional circuitry of NKX2-1 and SOX1 defines a previously unrecognized lineage subtype of small cell lung cancer to maintain neuroendocrine differentiation (RNA-Seq Mouse)

overall_design: Transcriptomic profile of 4 RP and 4 RPN tumors

first: Eric

last: Snyder


title: Bulk RNA sequecning of control and Dimethyloxalylglycine (DMOG) treated Human Primary Pulmonary artery endothelial cells (ATCC: PCS-100-022)

city: Chicago

first: Pinelopi

last: Kapitsinou

state: Il

address: 303 East Superior Street

department: Medicine/Nephrology

institute: Northwestern University, Feinberg School of Medicine

summary: We assessed the role of prolyl hydroxylase inhibiton using DMOG on angiogenic competance and metabolic reprogramming of endothelial cells.

overall_design: Examination of DMOG treated vs untreated  endothelial cells.

last: Kapitisnou

first: Ratnakar

last: Tiwari


title: Transcriptional circuitry of NKX2-1 and SOX1 defines a previously unrecognized lineage subtype of small cell lung cancer to maintain neuroendocrine differentiation (ChIP-Seq K27ac)

summary: Molecular classification of small cell lung cancer (SCLC), a lethal and heterogeneous disease, was recently proposed based on expression of four lineage-defining transcription factors SCLC-A (ASCL1), SCLC-N (NEUROD1), SCLC-Y (YAP1), and SCLC-P (POU2F3). In this study, unsupervised clustering of genome-wide histone H3K27 acetylation profiles uncovered previously unappreciated epigenomic heterogeneity of this recalcitrant disease. Specifically, the major SCLC-A subtype, which accounts for approximately 70% of all SCLC cases, was subdivided into two new subtypes SCLC-A1 and SCLC-A2. SCLC-A1 is distinguished by the presence of super-enhancer at the NKX2-1 locus, also observed in a murine SCLC model and human SCLC specimens. We found NKX2-1, a master regulator of lung lineages as well as a critical lineage factor in central nervous system, is uniquely functionally relevant in SCLC-A1, where it maintains neural lineage rather than pulmonary epithelial identity. Through integrative proteomic, transcriptomic and cistromic analyses, we found that maintenance of this neural identity in SCLC-A1 is mediated by collaborative transcriptional activity with another neuronal transcriptional factor SOX1

overall_design: Genome-wide profiles of histone H3K27 acetylation in SCLC cell lines.


title: Loss of epigenetic regulation disrupts lineage commitment and promotes breast cancer

last: Schramek

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


title: The role of H3K4me3 of low temperature memory in Arabidopsis [ChIP-Seq]

city: Lanzhou

first: Zezhong

last: Su

address: YuZhong

institute: Lanzhou University

summary:
Plants experience a wide array of environmental stimuli to form a memory of adversity. Histone modification plays roles in plant stress memory, of which the mechanisms of H3K4me3 of low temperature memory in plants are poorly understood although H3K4me3 is a key histone modification. Combined with phenotypic analysis, chip-seq, and transcriptome analyses were performed to investigate the potential H3K4me3 contributions for different phases of recurring cold stresses Arabidopsis plants.
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K4me3 in different low temperature stress.

overall_design: Yuan, Song

first: Yuan

last: Song

first: Tianyi

last: Zhang

first: Jianxiong


title: An RNA-based precision oncology platform for patient-therapy alignment in a diverse set of treatment resistant malignancies

status: Public on Sep 10 2022

first: Prabhjot

middle: Singh

last: Mundi

address: 1130 St. Nicholas Avenue

department: Medicine; Systems Biology

institute: COLUMBIA UNIVERSITY HEALTH SCIENCES

summary:
We use a Master Regular-based precision cancer medicine framework to predict drug sensitivity. The network based analysis uses RNASeq profiles of patient tumors, in conjunction with de novo drug mechanism analysis from high throughput drug screens with post-perturbation RNASeq profiles performed in cognate cell line models. The analysis aims to predict available antineoplastic drugs most likely to invert the aberrant protein activity state of individual tumors.
Validation of predictions was performed in corresponding patient-derived xenograft (PDX) mice. Pharmacodynamic samples were obtained from PDX mice after the third dose for RNASeq and downstream analysis.

overall_design: RNASeq profiles of patient tumors and their respective xenografts for which drugs were predicted using the PCM tools OncoTarget and OncoTreat; RNASeq profiles of cognate cell line models; drug perturbational (DMSO controls and post-perturbation) profiles in these cell lines; RNASeq of on-treatment pharmacodynamic PDX samples.

first: Mariano

last: Alvarez

first: Andrea

last: Califano


title: Enteric glial cells favor accumulation of anti-inflammatory macrophages during the resolution of muscularis inflammation

first: Gianluca

last: Matteoli


overall_design: Cells isolated from the muscularis of naïve mice or of WT mice at 24 hours or 72 hours after subjecting to intestinal manipulation were sorted for cd45+ cells. Cells were loaded onto 10x chip targeting the recovery of 1000 cells. Single cell RNA sequencing libraries were prepared using 10x genomics platform according to manufacturer’s instructions (Single cell 3’ solution). Sequencing libraries were loaded at 1.4 pM on an Illumina NextSeq500 with NextSeq 500/550 Mid Output v2 kit (150 cycles) (Illumina). Cell Ranger software (v3.0.2) (10x Genomics) was used to demultiplex Illumina BCL files to FASTQ files (cellranger mkfastq) to perform alignment (to mouse GRCm38/mm10 genome), filtering, UMI counting and to produce gene-barcode matrices. Library preparation, sequencing and sample demultiplexing was done at the Genomics Platform of the GIGA Institute (Liège University, Belgium). Counts from the data of naive mice, 24 hour post intestinal manipulation and 72 hour post intestinal manipulation were concatenated and analysed using Seurat R package. Cells with less than 200 gene and 10% percent of mitochondrial genes were removed from the analysis.

first: Michelle

last: Stakenborg

first: Saeed

last: Abdurahiman

first: Veronica

last: De Simone

first: Gera

last: Goverse

first: Nathalie

first: Lies

last: Van Baarle

first: Qin

last: Wu

first: Dimitri

last: Pirottin

first: Jung-Seok

last: Kim

first: Louise

last: Maor

first: Isabel

last: Pintelon

first: Sofie

last: Thys

first: Emilie

last: Pollenus

first: Louis

last: Boon

first: Philippe

last: Van den Steen

first: Marlene

last: Hao

first: Jo

last: Van Ginderachter

first: Guy

last: Boeckxstaens

first: Jean-Pierre

last: Timmermans

first: Steffen

last: Jung

first: Thomas

last: Marichal

first: Sales

last: Ibiza


title: Transcriptome profiling of gingival fibroblasts treated by vitamin D3

status: Public on Sep 09 2022

city: Xiamen

first: Churen

last: Zhang

state: Fujian

address: 55 Zhenhai Avenue, Siming District.

institute: The First Affiliated Hospital of Xiamen University

summary: In humans, vitamin D3 is a secosteroid, a prohormonal precursor of biologically active hydroxyforms. Vitamin D3 is related to periodontitis. The third American Health and Nutrition Survey found that plasma 25(OH)D3 levels are negatively correlated with attachment loss in people aged >50 years. The relationship between vitamin D3 and periodontitis remains to be investigated. We sent human gingival fibroblasts treated by vitamin D3 for transcriptome sequencing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human gingival fibroblasts.The cells from one participant were split into two groups; one group received vitamin D3 as stimulation for 48 hours, while the other group received 0.1% ethanol as a control. Each group included three biological repetitions.

first: Ye

last: Han

first: Kaining

last: Liu

first: Jianxia

last: Hou


title: Cancer cells cocultured with macrophage

city: Kumamoto

first: Yoshihiro

last: Komohara

address: Honjo 1‐1‐1, Chuouku

department: Department of Cell Pathology

institute: Graduate School of Medical Sciences, Kumamoto University

summary: Huh6 and Hep-G2 were co-cultured with macrophages directly. NCI-H23 was co-cultured with conditional medium of macrophages and SPP1(osteopontin).

overall_design: Cells were seeded into 6-well plate (200,000 cells per well), and then human monocyte-derived macrophages were added into each well (100,000 cells) for 24 hours. NCI-H23 cells were stimulated with 30% of conditional medium of macrophages or 10ng/mL SPP1(osteopontin) for 24 hours. Based culture madium was DMEM/HamF12 medium supplemented with 10% FBS.


title: Extracellular Vesicle miRNAs in Breast Milk and Maternal Obesity

city: Iowa City

first: Michael

last: Chimenti

state: IA

address: 431 Newton Road

department: Iowa Institute of Human Genetics

institute: University of Iowa

summary: Background: Maternal pre-pregnancy BMI is a critical factor influencing the composition of breast milk. Breast milk has abundant extracellular vesicles (EVs) containing various biological molecules (cargo), including miRNAs. EVs are not degraded in the gastrointestinal system and circulation; thus, breast milk EVs (bEVs) interact with other organs in breastfed infants and modify the gene expression of recipient cells using miRNAs. In maternal obesity, miRNAs in bEVs are deregulated, which might be associated with adverse health outcomes in infants. In this study, we examined 798 miRNAs to determine which miRNAs are altered in the bEVs of obese mothers and their potential impact on breastfed infants.    Methods: We recruited healthy nursing mothers who were either obese (BMI≥30) or lean (BMI<25) based on their pre-pregnancy BMI, and delivered a singleton baby in the prior six months. EVs were isolated from breast milk with ultracentrifugation. bEV characteristics were examined by flow cytometry and fluorescence imaging of EV markers. A total of 798 miRNAs were screened using a NanoString human miRNA panel to find deregulated miRNAs in bEVs of obese mothers compared to lean mothers.  Results: We included 65 nursing mothers: 47 lean and 18 obese mothers based on pre-pregnancy BMI. After bEV isolation, we confirmed the expression of general EV markers. Out of 37 EV markers, CD326 was the most highly expressed marker in bEVs. From miRNA analysis using NanoString, we found that the most abundant miRNAs include miR-30b-5p, miR-494-3p, and let-7 families, and the list of top 10 miRNAs was not different between lean and obese mothers. Target genes of the top 10 miRNAs were associated with the EGFR, ErbB, and FoxO signaling pathway. Nineteen miRNAs were deregulated in bEVs of obese mothers (adjusted p < 0.05 cut-off), including miR-575, miR-548g-3p, miR-582-3p, and miR-652-5p. The target genes of these miRNAs are associated with lipid metabolism, inflammatory diseases, and nervous/cardiovascular system development.   Conclusion: In this study, we demonstrated altered miRNAs in bEVs of obese mothers and identified the pathways of their potential target genes. Our findings will provide insight for future studies investigating the role of bEVs in breastfed infants.

overall_design: We have collected 80 samples in total. Among them, we analyzed 65 samples that are from mothers of normal pre-pregnancy BMI and obese pre-pregnancy BMI.

first: Young

last: Cho


first: Gianluca

last: Matteoli

overall_design:
To induce gene recombination of Rpl22HA in PLP1CreERT2 Rpl22HA transgenic mice at 10-12 weeks of age were injected twice intraperitoneally with 100 µl of 15 mg/ml tamoxifen (Sigma) dissolved in Miglyol 812 (Caesar & Loretz, Hilden, Germany). All animals were sacrificed 3-4 weeks after the first injection. The whole small intestine of each mouse was peeled by removing the mucosa and submucosa in order to obtain preparations of circular and longitudinal smooth muscle layer and adherent myenteric plexus. Next, samples were flash frozen until processing.

Immunoprecipitated samples were processed and analyzed according to published protocols4, 5. In brief, mRNA was captured with Dynabeads oligo(dT) (Life Technologies) according to manufacturer’s guidelines. A bulk variation of MARSseq6 was used to prepare libraries for RNA-seq. RNA was reversed transcribed with MARSseq barcoded RT primer in a 10 mL volume with the Affinity Script kit (Agilent). Reverse transcription was analyzed by qRT-PCR and samples with a similar CT were pooled (up to eight samples per pool). Each pool was treated with Exonuclease I (NEB) for 30 min at 37°C and subsequently cleaned by 1.2 x volumes of SPRI beads (Beckman Coulter). Subsequently, the cDNA was converted to double-stranded DNA with a second strand synthesis kit (NEB) in a 20mL reaction, incubating for 2 h at 16°C. The product was purified with 1.4 x volumes of SPRI beads, eluted in 8 mL and in vitro transcribed (with the beads) at 37°C overnight for linear amplification using the T7 High Yield RNA polymerase IVT kit (NEB). Following IVT, the DNA template was removed with Turbo DNase I (Ambion) 15 min at 37°C and the amplified RNA (aRNA) purified with 1.2 volumes of SPRI beads. The aRNA was fragmented by incubating 3 min at 70°C in Zn2+ RNA fragmentation reagents (Ambion) and purified with 2 x volumes of SPRI beads. The aRNA was ligated to the MARS-seq ligation adaptor with T4 RNA Ligase I (NEB). The reaction was incubated at 22°C for 2 h. After 1.5 x SPRI cleanup, the ligated product was reverse transcribed using Affinity Script RT enzyme (Agilent) and a primer complementary to the ligated adaptor. The reaction was incubated for 2 min at 42°C, 45 min at 50°C, and 5 min at 85°C. The cDNA was purified with 1.5 x volumes of SPRI beads. The library was completed and amplified through a nested PCR reaction with 0.5mM of P5_Rd1 and P7_Rd2 primers and PCR ready mix (Kappa Biosystems). The amplified pooled library was purified with 0.7 x volumes of SPRI beads to remove primer leftovers. Library concentration was measured with a Qubit fluorometer (Life Technologies) and mean molecule size was determined with a 2200 TapeStation instrument.
RNaseq libraries were sequenced using the Illumina NextSeq 2000.
Data analysis was performed by using the UTAP transcriptome analysis pipeline (Kohen et al., 2019). Raw reads were trimmed using cutadapt with the parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A–times 2 -u 3 -u −3 -q 20 -m 25). Reads were mapped to the genome (mm10, Gencode annotation version 10.0) using STAR (v2.4.2a) with the parameters –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No. The pipeline quantifies the 3′ of Gencode annotated genes (The 3′ region contains 1,000 bases upstream of the 3′ end and 100 bases downstream). UMI counting was done after marking duplicates (in-house script) using HTSeq-count in union mode. Only reads with unique mapping were considered for further analysis, and genes having minimum 5 reads in at least one sample were considered. Gene expression levels were calculated and normalized using DESeq2 (1.26.0)

first: Michelle

last: Stakenborg

first: Saeed

last: Abdurahiman

first: Veronica

last: De Simone

first: Gera

last: Goverse

first: Nathalie

first: Lies

last: Van Baarle

first: Qin

last: Wu

first: Dimitri

last: Pirottin

first: Jung-Seok

last: Kim

first: Louise

last: Maor

first: Isabel

last: Pintelon

first: Sofie

last: Thys

first: Emilie

last: Pollenus


title: Effect of depletion of OsMFT1 on gene expression in the absence and presence of salt stress during seed germination.

city: nanjing

first: Jiajun

last: Liu

address: Weigang no.1, Xuanwu District, Nanjing City, Jiangsu Province

institute: Nanjing Agricultural University

summary: To explore the molecular mechanisms of rice seed germination under salt stress mediated by OsMFT1, we established osmft1 mutant lines, and then examined the gene expression profiles in seeds of WT and osmft1.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Zhonghua 11 (WT) and osmft1 mutant lines.

first: Kunxun

last: Lu

first: Ziyu

last: Guo

first: Yuyang

first: Chengqiang

last: Ding


title: Intestinal CD103- Trm cells are first responders to secondary infection

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

summary: To address both the plasticity of intestinal Trm subsets and their unique contributions to tissue and systemic immunity, we have generated mice to fate map CD103+ Trm cells after primary infection and follow their location and functionality during secondary infection. We found that the intestinal CD103– Trm subset are the primary responders to secondary infection and observed limited expansion of the CD103+ Trm subset. To understand the unique features of CD103– Trm cells that allow this population to respond more quickly to secondary infection and to understand the gene expression changes that accompany Trm reactivation, we performed RNA-sequencing on CD103+Tomato+ and CD103–Tomato– LP Trm cells.

overall_design: Examination of gene expression profiles of CD103+ and CD103- intestinal tissue-resident memory T cells before and after secondary infection.

first: Bergsbaken

last: Tessa


title: 3D organization profiling of human hepatocellular carcinoma cell line PLC/PRF/5 in comparison with normal human liver cell line L02 by in situ Hi-C

first: Hu

last: Haolin

state: Shanghai

address: Fenglin Road

institute: Zhongshan Hospital

summary: Genetic and epigenetic alterations accumulate in the process of hepatocellular carcinogenesis, but the role of genomic spatial organization in HCC is still unknown.

overall_design: We performed in situ Hi-C in HCC cell line PLC/PRF/5 compared with normal liver cell line L02, together with RNA-seq and ChIP-seq of SMC3/CTCF/H3K27ac.

first: Haolin

last: Hu

first: Xiaoqiang

last: Chai

first: Liyong

last: Wang


title: Genomic interactions of Myc and rs55705857 in primary mouse derived neural stem cells

city: Toronto

first: Daniel

last: Schramek

address: 600 University Ave, Room 1080

institute: Lunenfeld- Tanenbaum Research Institute

summary: 4C sequencing to determine genomic interactions of Myc and rs55705857 locus in mouse neural stem cells

overall_design: 4C sequencing to determine of genomic interactions between two loci in mouse neural stem cells

first: Connor

last: Yanchus

first: Minggao

last: Liang

first: Ahmad

last: Malik

first: Michael

last: Wilson


title: Epigenetic crosstalk

city: Guangzhou

first: shuang

last: deng

state: Guangdong

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

summary: We report a direct interaction between RNA epigenome and  DNA epigenome. We demonstrate that m6A methyltransferase METTL3 regulates DNA methylation levels co-transcriptionally. We observed a genome-wide correlation between m6A / METTL3 and occupancy by the DNA demethylase TET1, and m6A reader physically interacts and recruits TET1 to m6A-associated chromatin regions. Our results demonstrates an original but unheeded feed-back regulatory mechanism from RNA epigenome to DNA epigenome and detect a new aspect of epigenetic crosstalk to regulate gene expression.

overall_design: Examination of m6A methylation and DNA methylation levels

first: Jian

last: Zheng

first: Shuang

last: Deng