title: Topoisomerase IIA in Adult NSCs Regulates SVZ Neurogenesis by Transcriptional Activation of Usp37 (ChIP-Seq)

first: Qin

last: shangyao

address: Xiangyin Road 800

department: Institute of Neuroscience

institute: Second Military Medical University

summary: Topoisomerase IIA (TOP2a) has been traditionally known as an important nuclear enzyme that resolves entanglements and relieves torsional stress of DNA double strands. However, little is known about its function in genomic transcriptional regulation, especially during adult neurogenesis. Here, we show that TOP2a is preferentially expressed in neurogenic niches in the brain of adult mice, such as the subventricular zone (SVZ). Conditional knockout of Top2a in adult neural stem cells (NSCs) in the SVZ significantly inhibits their self-renewal and proliferation and ultimately reduces neurogenesis. To gain insight into the molecular mechanisms by which TOP2a regulates adult NSCs, we perform RNA-sequencing (RNA-Seq) and chromatin immunoprecipitation sequencing (ChIP-Seq) and identify ubiquitin-specific proteases 37 (Usp37) as a direct TOP2a target gene. Importantly, overexpression of Usp37 is sufficient to rescue the impaired self-renewal ability of adult NSCs caused by Top2a knockdown. Taken together, our proof-of-principle study illustrates a TOP2a/Usp37-mediated novel molecular mechanism of adult neurogenesis, which will significantly expand our understanding of the function of topoisomerase in adult brain.

overall_design: Chromatin IP was performed with TOP2a antibodies in adult NSCs followed by high throughput sequencing

first: Shangyao

last: Qin

first: Yimin

last: Yuan

first: Zhida

last: Su

first: Cheng

last: He


title: Purinergic antiplatelet-treated colon cancer cells induce SERPINE1 and MAPK-MMP1 signaling pathways associated with metastasis.

status: Public on Sep 20 2022

city: Yuseong-gu

first: Seung Woo

last: Baek

state: Daejeon

address: Gwahak-ro 125

country: South Korea

institute: Korea Research Institute Biology & Biotechnology

summary: Contrary to many reports that antiplatelet agents inhibit cancer growth and metastasis, reports of increased mortality from the development of new solid tumors in patients receiving long-term antiplatelet therapy raise questions about the effects of antiplatelet agents on cancer. Therefore, we have investigated the direct effects on cancer cells in the absence of platelets, assuming long-term antiplatelet therapy. Treatment of cancer cells with four antiplatelet reagents (aspirin and three P2Y12 inhibitors: clopidogrel, prasugrel, and ticagrelor) inhibited the proliferation of cancer cells, similar to the results of previous studies. Surprisingly, there was no difference in the aspirin-treated group, but the motility of cancer cells was significantly increased when treated with purinergic P2Y12 inhibitors. Therefore, gene expression profiles were examined to investigate the effect of antiplatelet reagents on cancer cell mobility. As a result, SERPINE1 was identified as a common gene associated with cancer cell motility and cell death in three groups. SERPINE1 increased by antiplatelet reagent treatment was found to be involved in cell mobility by activating FAK-p38-MMP1. These results show that purine antiplatelet reagents reduce cancer cell proliferation but increase cell motility by inducing SERPINE1 and MAPK-MMP1 signaling pathways. Therefore, we suggest that SERPINE1 could be used as a new target gene for the development and metastasis of cancer in patients with long-term antiplatelet therapy.

overall_design: Total RNA was dataed 24 hours after administration of antiplatelet agents (Aspirin, Clopidogrel, Prasugrel, Ticagrelor) to colon cancer cell lines (HCT116) alone or with aspirin.

first: Won-Tae

last: Kim

first: Sun-Hee

last: Leem


title: NF-κB encodes history of prior signals to coordinate subsequent cellular responses

city: Chicago

first: Savas

last: Tay

state: IL

address: 5640 South Ellis Avenue, Chicago, IL 60637

department: PME

country: USA

institute: University of Chicago

type: Expression profiling by high throughput sequencing

summary: We use a novel microfluidic device to provide different concentrations of a point source of TNF-α to a population of NIH3T3 mouse embryonic fibroblasts. These cells are then retrieved in a spatially resolved manner (notated as near, mid, and far from point source) and sequenced using a modified version of the Smart-Seq2 protocol. We find that spatially resolved transcriptomes reveal distinct gene regulation patterns based on TNF dose and/or distance from the point source

overall_design: Comparison of triplicate RelA-/- RelA-DsRed NIH3T3 populations exposed to TNF-α at two point concentrations (30 and 100 ng/mL), collected 4 hours after stimulus, and in three positions per sample (near, mid, far).

first: Minjun

last: Son

first: Andrew

middle: G

last: Wang


title: AOS10 could benefit the pig's sperm quantity via improvement of intestinal microbiota.

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

country: China

institute: Qingdao Agricultural University

summary: We reported the effects of AOS10 on the intestinal microbiota, and found that this drug could benefit the pig's sperm quantity via improvement of intestinal microbiota.

overall_design: Exploration of the AOS10 effects on the intestinal microbiota.

first: Yue

last: Jiang


title: Homeostatic cytokines reciprocally modulate the emergence of prenatal effector PLZF+CD4+ T cells in humans [Bulk RNA-seq]

status: Public on Sep 19 2022

first: Veronica

last: Locher

summary: The development of human adaptive immunity progresses faster than previously appreciated, with the emergence of memory CD4+ T cells alongside regulatory T (Treg) cells by the second trimester of pregnancy. We previously identified a prenatal-specific subset of PLZF+ CD4+ T cells with heightened effector potential that accounted for most memory T cells in the developing intestine and accumulated in the cord blood of infants exposed to prenatal inflammatory pathologies. However, the signals that drive their tissue distribution and effector maturation are unknown. Here, we define the transcriptional and functional heterogeneity of prenatal PLZF+ CD4+ T cells and identify compartmentalization of Th-like effector function across the small intestine (SI) and mesenteric lymph nodes (MLN).

overall_design: Prenatal intestine PLZF+CD4+ T cells  were isolated by Fluorescence-activated cell sorting (FACS) using proxy markers  were stimulated by PMA/ionomycin and processed for bulk RNAseq.

first: Daniel

last: Bunis

first: Gabriela

middle: K

last: Fragiadakis

first: Joanna

last: Halkias


title: Programmable RNA base editing with a single engineered protein

city: Shanghai

first: zefeng

last: wang

address: 320 Yueyang Road

institute: CAS-MPG Partner Institute for Computational Biology

summary: Programmable base editing of RNA enables rewriting the genetic codes on specific sites. Current tools for specific RNA editing dependent on the assembly or recruitment of the guide RNA into an RNA/protein complex, which may cause delivery barrier and low editing efficiency. Here we report a new set of tools, RNA editing with individual RNA-binding enzyme (REWIRE), to perform precise base editing with a single engineered protein. The REWIRE system contains a human-originated programmable RNA-binding domain (PUF domain) to specifically recognize target sequence and different deaminase domains to achieve A-to-I or C-to-U editing. By utilizing this system, we have achieved editing efficiencies up to 80% in A-to-I editing and 65% in C-to-U editing, with a few non-specific editing sites in the targeted region and a low level off-target effect globally. We applied the REWIREs to correct disease-associated mutations and modify mitochondrial RNAs, and further optimized the REWIREs to improve the editing efficiency and minimize off-target effects. As a single-component base editing system originated from human proteins, REWIRE presents a precise and efficient RNA-editing platform with broad applicability in basic research and gene therapy.

overall_design: To assess the editing efficiency on target reporters, cells were plated in a 6-well plates (at approximately 70% confluency) and transfected 12 hours later with 2μg REWIRE expression vector and 200ng reporter plasmid, and were harvested 48 hours after transfection for further analyses. For the endogenous transcripts, HEK 293T cells were seeded on a 6-well plate (at approximately 70% confluency) and transfected 12 hours later with 2μg REWIRE expression plasmids using Lipofectamine 3000, then harvested cells 48 hours later. All transfections were performed with Lipofectamine 3000 (Thermo Fisher Scientific) in 6-well plates coated with poly-D-lysine (BD BioCoat).

first: Wenjian

last: Han

first: Wendi

last: Huang

first: Miaowei

last: Mao

first: Zefeng


title: DNA methylation and gene expression changes during acquired resistance to ALK inhibitors

city: Daejeon

first: Jong Hwan

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

institute: Korea Research Institute of Bioscience and Biotechnology

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: DNA methylation and gene expression changes during acquired resistance to ALK inhibitors (450k DNA methylation microarray)

summary: To identify novel mechanisms of acquired resistance to ALK inhibitors, we established in vitro models of acquired resistance to ceritinib using H3122 cell. In this study, we examined genome-wide DNA methylation changes during acquired resistance to ceritinib. We also examined the heterogeneity of parental and resistant cells using single cell RNA--seq.

overall_design: Single cell RNA-seq data of 2 samples, H3122 parental cells and one ceritinib-treated resistant cells, were generated using 10X Genomics Single Cell Solution.  Sequencing was performed in paired end reads (2x100 bp) using NextSeq 500 platform (Illumina).

first: Haejeong

last: Heo

first: Jong-Hwan

first: Jeong-Hwan

first: Eun

last: Choi

first: Dong-Uk

middle: S

first: Byoung

middle: C

last: Cho

first: Seon-Young

first: Mirang


title: Topoisomerase IIA in Adult NSCs Regulates SVZ Neurogenesis by Transcriptional Activation of Usp37 (RNA-Seq)

first: Qin

last: shangyao

overall_design: mRNA profiles of DMSO and PluriSIn#2 treated adult NSCs were generated by deep sequencing in triplicates. PluriSIn#2 is a specific inhibitor of Topoisomerase IIA, hence, we used PluriSIn#2 to the elucidate role of Top2a by genome wide transcription profiling.

first: Shangyao

last: Qin

first: Yimin

last: Yuan

first: Zhida

last: Su

first: Cheng

last: He


title: Primary male adult tail fibroblast cell-state specific response to proteasome inhibition

city: Madison

first: Christopher

last: Morrow

state: Wisconsin

address: 1111 Highlange Ave.

institute: University of Wisconsin - Madison

summary: polyA RNA sequencing data generated from primary tail male adult fibroblasts in 4 cells states: proliferating, senescent, quiescent or immortalized and across two conditions: DMSO or MG132 treated were analyzed by RNA sequencing.

overall_design: Primary tail fibroblasts in 4 cells states: proliferating, senescent, quiescent or immortalized and across two conditions: DMSO or MG132 treated were analyzed by RNA sequencing.

first: Darcie

middle: L

last: Moore


title: Targeting MDM2-induced p53 upregulation to enhance anti-leukemia immunity post allogeneic stem cell transplantation

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

summary: Relapse after allo-HCT is a major cause of death of AML patients and results from immune evasion of AML blasts. Dysfunction of the p53 signaling pathway is frequent in AML and often caused by upregulation of the central p53 negative regulator Murine Double Minute 2 (MDM2). Besides its oncogenic effects p53 also regulates immune function and immune surveillance of solid cancer. We hypothesize that p53 also controls immune-related genes in AML cells and that p53 reactivation via MDM2-inhibition may enhance the immunogenicity of AML cells to allogeneic T cells.

overall_design: In total 18 samples were analyzed, including 6 replicates from DMSO control, 6 replicates from MDM2 inhibitor RG7112 and 6 replictes from MDM2 inhibitor HDM201.

first: Lowinus

last: Theresa

first: Zeiser

last: Robert

first: Andrieux

last: Geoffroy

first: Boerries

last: Melanie


title: Mechanistic divergence of piRNA biogenesis in Drosophila [ChIP-seq]

city: Acton

first: Rippei

last: Hayashi

state: Australian Capital Territory

address: 131 Garran Road

department: John Curtin School of Medical Research

country: Australia

institute: The Australian National University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Organisms require mechanisms to distinguish self and non-self RNA. This distinction is crucial to initiate the biogenesis of piRNAs. In Drosophila ovaries, PIWI-guided slicing and the recognition of piRNA precursor transcripts by the DEAD-box RNA helicase Yb are the two known mechanisms to initiate biogenesis in the germline and the soma, respectively. Both, the PIWI proteins and Yb are highly conserved across most Drosophila species and are thought to be essential to the piRNA pathway and for silencing TEs. However, we find that species closely related to D. melanogaster have lost the yb gene, as well as the PIWI gene Ago3. We show that neither mechanism is required to efficiently produce TE antisense piRNAs in Drosophila. Thus, there are more possible routes through which the piRNA pathway can achieve specificity than previously suggested.

sample_organism:
Drosophila bifasciata
Drosophila pseudoobscura

overall_design: The study aims at understanding the mechanism of Piwi-interacting RNA (piRNA) in a variety of Drosophila species.  We generated small RNA sequencing libraries from freshly collected ovaries and embryos as well as immuno-precipitated samples using antibodies against PIWI proteins.  We also generated RNA sequencing libraries from poly-A plus RNA and ChIP sequencing libraries using antibodies against RNA polymerase II to determine the genomic origin of the piRNA precursor RNA.

first: Shashank

last: Chary


title: RNA-seq analysis about Lx8-SINE B2 knocked down samples

city: Tianjin

first: Xuan

last: Zhao

state: Tianjin

address: No. 38 Tongyan Road, Haihe Education Park, Tianjin

department: State Key Laboratory of Medicinal Chemical Biology

institute: Nankai University

summary: We identified a novel long non-coding RNA Lx8-SINE B2, that is a marker of pluripotency. Depletion of Lx8-SINE B2 impacts embryonic stem cell self-renewal. RNA-seq analysis of Lx8-SINE B2 depletion revealed that a number of glycolytic genes with decreased expression.  Mechanistically, we found that the Lx8-SINE B2 activates the glycolysis pathway by binding to Eno1. Collectively, our data suggest that Lx8-SINE B2 maintains the self-renewal of mESCs through glycolysis.

overall_design: We knocked down Lx8-SINE B2 by shRNAs in E14. We performed RNA-seq analysis in order to exam the transcriptome.

first: Xinyi

last: Lu

first: Fuquan

last: Chen

first: Weiyu

last: Zhang


title: Mechanistic divergence of piRNA biogenesis in Drosophila [RNA-seq]

sample_organism:
Drosophila bifasciata
Drosophila pseudoobscura
Drosophila eugracilis


title: Mechanistic divergence of piRNA biogenesis in Drosophila

type: Non-coding RNA profiling by high throughput sequencing

sample_organism:
Drosophila bifasciata
Drosophila melanogaster
Drosophila mojavensis
Drosophila pseudoobscura
Drosophila eugracilis


title: Mechanistic divergence of piRNA biogenesis in Drosophila [ncRNA-seq]

platform_organism:
Drosophila bifasciata
Drosophila melanogaster
Drosophila mojavensis
Drosophila pseudoobscura
Drosophila eugracilis


title: Analysis of the differential expression of genes in Otub2- knockout mice

city: Beijing

first: Wan

last: Chang

state: China

address: Panjiayuan

department: State Key Laboratory of Molecular Oncology, National Cancer Center

institute: Cancer Hospital Chinese Academy of Medical Sciences

summary: Oral and esophageal squamous cell carcinomas (SCCs) are associated with high mortality, yet molecular mechanisms underlying these malignancies are largely unknown. We demonstrate that epigenetic silencing of otubain 2 (OTUB2), a previously recognized oncogene, drives SSCs initiation and drug resistance.

overall_design: Analyze  the differential expression of genes in Otub2- knockout mice transcriptionally.

first: Qingyu

last: Luo

first: Xiaowei

last: Wu


title: Homeostatic cytokines reciprocally modulate the emergence of prenatal effector PLZF+CD4+ T cells in humans

first: Veronica

last: Locher


city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: RNA-Seq analysis of beta-actin knockout MEFs expressing NLS-tagged beta-actin to study role of actin in transcription

overall_design: RNA-Seq was performed on 3 replicates

first: Syed

last: Raza Mahmood


title: ChIP-Seq of H3K27ac in Actb-/- MEFs expressing NLS-tagged beta-actin

summary: Genome-wide ChIP-Seq of H3K27ac in β-actin KO MEFs expressing NLS-tagged beta-actin to assess the role of nulcear actin in regulating histone acetylation

overall_design: ChIP-Seq was performed for 3 replicates

first: Nadine

last: Hosny ElSaid


title: Mouse_Tbx5_del_CreERT2_bulk_RNAseq

city: San Francisco

first: Benoit

last: Bruneau

state: CA

address: 1650 Owens St

institute: Gladstone Institutes

summary: Haploinsufficiency of transcriptional regulators causes human congenital heart disease (CHD), suggesting that reduced transcription factor dosage causes a gene regulation imbalance. Here, we define transcriptional responses to reduced TBX5 in embryonic mouse hearts.

overall_design: Embryonic heart mRNA profiles at E10.5 of wildtype (WT), Tbx5 CreERT2/+, Tbx5 del/+ and Tbx5 del/CreERT2 were generated by deep sequencing, in quadruplicate.

first: Irfan

last: Kathiriya


title: Error-prone protein synthesis recapitulates early symptoms of Alzheimer disease in aging mice

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

summary: Age-related neurodegenerative diseases (NDDs) and neuronal dysfunction are associated with the aggregation and propagation of specific pathogenic protein species (e.g. Aβ, α-synuclein, tau). However, whether the disruption of synaptic homeostasis results from protein misfolding per se rather than accumulation of a specific rogue protein is an unexplored question. Here, we show that error-prone translation with its frequent outcome of random protein misfolding is sufficient to recapitulate many early features of NDDs, including proteostasis dysregulation, perturbed Ca2+ signalling, neuronal hyperexcitability, and mitochondrial dysfunction. Mice expressing the ribosomal ambiguity mutation Rps9 D95N exhibited disrupted synaptic homeostasis resulting in abnormal behavioral changes reminiscent of early Alzheimer's disease (AD), such as learning and memory deficits, maladaptive responses to novel stimuli, spontaneous epileptiform discharges, suppressed circadian rhythmicity, and sleep fragmentation. Ectopic hippocampal NPY expression and cerebral glucose hypometabolism (18F-fluorodeoxyglucose PET) were further signs of neuronal hyperexcitability. Collectively, our findings strongly suggest that random protein misfolding may contribute to the pathogenesis of age-related NDDs providing an alternative framework for understanding the initiation of Alzheimer’s disease.

overall_design: Transcriptomic profile of total RNA extracted from brain cortex of 7 mutant mice (mutation Rps9 D95N) were compared with the profile of 8 WT littermate control mice. 18 months old female mice were used in the experiment.

first: Erik

last: Böttger

first: Dimitri

last: Shcherbakov

first: Margarita

last: Brilkova


title: Effect of ginkgetin on gene expression of LX2 hepatic stellate cells

status: Public on Sep 18 2022

city: Wuhan

first: Huanzhang

last: Niu

address: Jiefang Avenue 1277#

institute: Wuhan Union Hospital

summary: To investigate the mechanism of anti-fibrotic effect of ginkgetin, we performed gene expression profiling analysis using data obtain from RNA-seq of LX2 cells.

overall_design: LX2 cells were treated by DMSO or ginkgetin(5μM) for 48 hours

first: Chaoyang

last: Wang


title: Deficiency of Irx5 protects mice from obesity and associated metabolic abnormalities

city: Toronto

first: Chi-chung

last: Hui

state: ON

address: 686 Bay street

country: Canada

institute: The Hospital for Sick Children

summary: Here we aim to decipher the actions of Irx5 in the regulation of obesity and metabolic abnormalities. We employed a mouse model homozygous for an Irx5-knockout (Irx5KO) allele and conducted droplet based single-cell RNA sequencing (Drop-seq) in the hypothalamic arcuate-median eminence (ARC-ME), which is the main control center for sensing and integrating feeding regulatory signals.

overall_design: Drop-seq was perfomed on WT and Irx5KO adult mouse hypothalamic arcuate nucleus-median eminence. Micro-dissected tissues from 5-7 mice per each group were pooled together for single cell dissociation, followed by Drop-seq sequencing.

first: Joe

middle: E

last: Son

first: Zhengchao

last: Dou

first: Troy

last: Ketela

first: Chi-Chung


title: Analysis of differentially expressed genes by gene expression values through transcriptome sequencing in kidney cancer tissue

city: Goyang-si

first: Sodam

last: Won

address: 323, Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do, Republic of Korea

institute: national cancer center

summary: The aim of this study was to evaluate genetic differences between renal cell carcinoma (RCC) and normal kidney tissue using NGS-derived transcriptase profiling (RNA-seq) and quantitative reverse transcriptase chain reaction (qRT-PCR) methods in human renal tissue.

overall_design: mRNA expression profile by Illumina platform in RCC and normal kidney tissue

first: Han

last: Hyun-ho

first: Hyung-Ho

last: Lee


title: Homeostatic cytokines reciprocally modulate the emergence of prenatal effector PLZF+CD4+ T cells in humans [scRNA-seq]

first: Veronica

last: Locher

overall_design: Prenatal intestine PLZF+CD4+ T cells  were isolated by Fluorescence-activated cell sorting (FACS) using proxy markers, and analyzed using scRNAseq.

first: Daniel

last: Bunis

first: Gabriela

last: Fragiadakis

first: Joanna

last: Halkias


title: DNA methylation and gene expression changes during acquired resistance to ALK inhibitors (scRNA-seq)

first: Jong Hwan

last: Kim

first: Haejeong

last: Heo

first: Jong-Hwan

first: Jeong-Hwan

first: Eun

last: Choi

first: Dong-Uk

first: Yong

first: Byoung

last: Cho

first: Seon-Young

first: Mirang


title: THE LONG NONCODING RNA PLAYRR REGULATES PITX2 DOSAGE AND PROTECTS AGAINST CARDIAC ARRHYTHMIAS

city: Ithaca

first: Charles

last: Danko

state: NY

address: Hungerford Hill Rd

department: Baker Institute

institute: Cornell University

summary: Rationale: The most significantly associated atrial fibrillation (AF) risk loci in humans map to a noncoding gene desert upstream of the evolutionarily conserved left-right (LR) transcription factor Pitx2, a master regulator of LR asymmetric organ development. Pitx2 dosage is fundamentally linked to the development of sinus node dysfunction (SND) and AF, the most common cardiac arrhythmia affecting adults, but the mechanistic basis for this remains obscure. We identified a conserved long noncoding RNA (lncRNA), Playrr, which is exclusively transcribed on the embryo’s right side, opposite to Pitx2 on the left, that participates in mutually antagonistic transcriptional regulation with Pitx2.    Objective: The objective of this study was to investigate a role of Playrr in regulating Pitx2 transcription and protecting against the development of cardiac rhythm disturbances.   Methods and Results: Playrr expression in the developing heart was analyzed with RNA in situ hybridization. Playrr was expressed asymmetrically (on the right) to Pitx2 (on the left) in developing mouse embryos, including in mouse embryonic sinoatrial node cells. We utilized CRISPR/Cas9 genome editing in mice to target Playrr, generating mice lacking Playrr RNA transcript (PlayrrEx1sj allele). Using qRT-PCR we detected upregulation of the cardiac isoform, Pitx2c, during visceral organ morphogenesis in PlayrrEx1sj mutant embryos.  Surface ECG (AliveCor®) and 24-hour telemetry ECG detected bradycardia and irregular interbeat (R-R) intervals suggestive of SND in PlayrrEx1sj mutant adults. Programmed stimulation of PlayrrEx1sj mutant adults resulted in pacing-induced AF. Within the right atrium of PlayrrEx1sj mutant hearts, Masson’s trichrome stain revealed increased collagen deposition indicative of fibrosis, and immunofluorescence demonstrated mis-localization of Connexin 43 in atrial cardiomyocytes. These findings suggested an altered atrial substrate in PlayrrEx1sj adult mice. Finally, transcriptomic analysis by chromatin run-on and sequencing (ChRO-seq) in atria of PlayrrEx1sj mutant mice compared to wild type controls revealed differential expression of genes involved in cell-cell adhesion and motility, fibrosis, and dysregulation of the key cardiac genes Tbx5 and Hcn1.  Conclusions: Adult mice lacking functional Playrr lncRNA transcript have baseline bradyarrhythmia and increased susceptibility to AF. These cardiac phenotypes are similar to those observed in Pitx2 heterozygous mice. Interactions between Pitx2 and Playrr may provide a genetic mechanism for modulating Pitx2 dosage and susceptibility to SND and AF.

overall_design: ChRO-seq experiments in wild-type and PLAYRR mutant adult mice.

first: Shao-Pei

last: Chou

first: Frances

last: Chen

first: Eva

middle: M

last: Oxford

first: Natasza

middle: A

last: Kurpios


title: Integrated multi-omics analysis of adverse cardiac remodeling and metabolic inflexibility upon ErbB2 and ERR⍺ deficiency

city: Montréal

first: Vincent

last: Giguère

state: QC

address: 1160 Pine Ave West, McIntyre Bldg Room 710

department: Goodman Cancer Centre

institute: McGill University

summary: Functional oncogenic links between ErbB2 and ERR⍺ in HER2+ breast cancer patients support a therapeutic benefit of co-targeted therapies. However, ErbB2 and ERR⍺ also play key roles in heart physiology, and this approach could pose a potential liability to cardiovascular health. Using integrated phosphoproteomic, transcriptomic and metabolic profiling, we uncovered molecular mechanisms associated with the adverse remodeling of cardiac functions in mice with combined attenuation of ErbB2 and ERR⍺ activity. Genetic disruption of both effectors results in profound effects on cardiomyocyte architecture, inflammatory response and metabolism, the latter leading to a decrease in fatty acyl-carnitine species further increasing the reliance on glucose as a metabolic fuel, a hallmark of failing hearts. Furthermore, integrated omics signatures of ERR⍺ loss-of-function and doxorubicin treatment exhibit reciprocal features of chemotherapeutic cardiotoxicity. These findings thus reveal potential cardiovascular risks in discrete combination therapies in the treatment of breast and other cancers.

overall_design: Hearts (n=3)  isolated from 15-week old WT, ErbB2 Knock-In (KI), ERR⍺ KO mice, and KI:KO (ErbB2 KI x ERR⍺ KO) mice were used for gene expression studies using Affymetrix Mouse Gene 2.0 ST arrays.

first: Catherine

middle: R

last: Dufour

last: Giguere


title: BGC-823 Cells: Control vs. BGC-823 Cells METTL3 Overexpressed

status: Public on Sep 17 2022

city: 蚌埠

first: 癸森

last: 彭

address: F座

institute: 蚌埠医学院

summary: METTL3-mediated RNA N6-methyladenosine (m6A) is the most prevalent modification participates in tumor initiation and progression via regulating expression of their target genes in cancers.. In this study, we conducted an  analysis of m6A microarray  in gastric cancer cells.

overall_design: The total RNA the control and METTL3 overexpression group were extracted by Trizol for m6A-tagged mRNA quantification. The m6A epitranscriptomic microarrays were performed by Aksomics  +- , Inc. (Shanghai, China).

first: Guisen

last: Peng

first: Shuran


title: Kmt2d deficiency promotes acute myeloid leukemia development and maintenance

city: Chengdu, China

first: Ailing

last: Zhong

state: Sichuan

address: No.17 Renmin road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sichuan University.

institute: Sichuan University

summary: The histone-3 lysine-4 methyltransferase KMT2D is frequently mutated in human cancers. However, knowledge of its role in the initiation and maintenance of acute myeloid leukemia (AML) is incomplete. Here, we show that KMT2D is generally downregulated in human AML. Using shRNA and CRISPR/Cas9 technologies, we show that Kmt2d loss, by cooperating with Trp53 and Nf1 loss, promoted mouse acute myeloid leukemogenesis through a differentiation block of hematopoietic stem and progenitor cells. Furthermore, using a doxycycline-induced shRNA system, we show that restoring Kmt2d impairs AML maintenance. Multi-omics analyses of Kmt2d-deficient and -restored AML cells showed that Kmt2d, via histone methyltransferase activity and chromatin remodeling, epigenetically regulates the expression of genes controlling hematopoietic stem cell differentiation. Lastly, we showed that 3-Deazaneplanocin A, a histone methyltransferase EZH2 inhibitor, could specifically repress Kmt2d-deficient AML cell growth and reverse pro-leukemia programs. Thus, our study indicate Kmt2d is a tumor suppressor, whose downregulation promotes AML development through differentiation blockage.

overall_design: RNAseq, ATACseq and CUT&Tag in Kmt2d knockdown, Kmt2d restoration and Kmt2d wild-type bone marrow or hematopoietic stem and progenitor cells.

first: Jing

last: Xu

first: Shan

last: Zhang


title: Soybean derived phosphatidylserine synthetically targets OTUB2 epigenetic silencing in squamous cell carcinoma

first: Wan

last: Chang

summary: Oral and esophageal squamous cell carcinomas (SCCs) are associated with high mortality, yet molecular mechanisms underlying these malignancies are largely unknown. We demonstrate that epigenetic silencing of otubain 2 (OTUB2), a previously recognized oncogene, drives SSCs initiation and drug resistance. Mechanistically, OTUB2 promotes deubiquitination and phosphorylation of signal transducer and activator of transcription 1 (STAT1), then activates transcriptional regulation of calmodulin-like protein 3 (CALML3). Activation of CALML3-mediated mitochondrial calcium signaling promotes oxidative phosphorylation (OXPHOS) and glycerophospholipid synthesis, among which phosphatidylserine (PS) is the most obviously affected. Orally administered soybean-derived PS dramatically inhibits low-OTUB2-expressed SCC initiation and increased sensitivity to chemotherapy in various mouse models. Our study indicates that the OTUB2/STAT1/CALML3/PS axis plays a critical tumor-suppressive role in SCCs, clarifies the low incidence of oral and esophageal SCCs in Western countries with a high-fat diet and demonstrates the potential of food supplementation with PS as a strategy for treatment and prevention of SCCs.

overall_design: RNA-seq of OTUB2 overexpressed and control KYSE150 cells after administrating phosphatidylserine

first: Qingyu

last: Luo

first: Xiaowei

last: Wu


title: Targeting CDK12-mediated transcription regulation in anaplastic thyroid carcinoma

first: Meijuan

last: Geng

address: No.22 Qixiangtai Road

institute: Tianjin Medical Universuty

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

overall_design: Refer to individual Series


title: Expression data from  Butyroside D treated B16F10 cells

city: Tsukuba,

first: Meriem

last: Bejaoui

state: Ibaraki

address: 1 Chome-1-1 Tennodai

country: Japan

institute: University of Tsukuba


title: RNA-Seq of both undifferentiated and differentiated mouse skeletal muscle cells that have been stretched or not stretched with the goal of discovering the impact of stretching on global gene expression and alternative splicing

city: Chapel Hill

first: Jimena

last: Giudice

state: NC

address: 6340B MBRB, Campus Box 7545

department: Cell Biology and Physiology

institute: UNC - Chapel Hill

overall_design: 48 samples total, 24 myoblast, 24 myotube each with three timepoints (1h, 3h, 6h) with stretch samples and no-stretch control samples

first: Emma

last: Hinkle


title: Targeting CDK12-mediated transcription regulation in anaplastic thyroid carcinoma [RNA-seq]

summary: Anaplastic thyroid carcinoma (ATC) is the most aggressive type of thyroid cancer, with no effective treatment available. Identification of new anti-ATC drugs represents an urgent need. In this study, we find that ATC cells are highly sensitive to THZ531, a potent inhibitor of the transcriptional cyclin-dependent kinase (CDK), CDK12. Cell-based assays demonstrate that CDK12 inhibition significantly impedes cell cycle progression, induces apoptotic cell death, and impairs colony formation in ATC cells. THZ531 causes a loss of elongating RNA polymerase II and suppresses gene expression in ATC cells. An integrative analysis of gene expression profiles and super-enhancer landscape, combining with functional assays, leads to the discovery of two new ATC cancer genes, ZC3H4 and NEMP1. Furthermore, CDK12 inhibition enhances the sensitivity of ATC cells to doxorubicin-mediated chemotherapy. Thus, these findings indicate that CDK12 is a potential therapeutic target for ATC treatment and its inhibition may help to overcome the chemoresistance in patients with ATC

overall_design: mRNA profiles of CAL-62 treated with DMSO or THZ531 for 6 h were generated by deep sequencing, in duplicate, using Illumina NovaSeq.

first: Xinyi

last: Cao

first: Lirong


title: Expression data from  Butyroside D treated B16F10 cells [0.2uM]

summary:
Gene expression profiling reveals a potential role of Butyroside D in melanogenesis inhibition in B16F10 cells.
B16F10 cells were murine melanoma cell line, treated with 0.2 μM Butyroside D for 48 h. Microarray gene expression profiling was conducted for two biological replicates

overall_design: RNA was extracted using Isogen (Nippon Gene Co. Ltd., Toyama, Japan). The integrity of RNA was quantified using NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). RNA samples were prepared for gene expression profiling analysis  using Affymetrix’s GeneChip® System (Affymetrix Inc., Santa Clara, CA, USA) using Mouse Clariom S Array following the manufacturer’s instructions. Complementary RNA (cRNA) was synthesized using IVT PLUS Reagent Kit (Affymetrix Inc., Santa Clara, CA, USA). The prepared samples were fragmented and labeled and prepared for hybridization using GeneChipTM Hybridization, Wash and Strain Kit. Each specific sample was injected into the GeneChip TM cartridge of Clariom S Array and incubated with rotation of 60 rpm for 16 h at 45℃ in the GeneChip®  hybridization oven 645. Arrays were washed and stained with GeneChip® Fluidic station 450 and scanned with GeneChip® Scanner 3000.


title: scRNA-seq of lymph node stromal cells from mouse treated with anti-CD40L

city: BALTIMORE

first: yang

last: song

address: 670 W. Baltimore St.

institute: UNIVERSITY OF MARYLAND IN BALTIMORE

summary: C57BL/6 mouse lymph node stromal cells treated with anti-CD40L were isolated for scRNA-seq, more than 2x104 cells were run on the 10X Chromium Controller (10X Genomics) to partition single cells with uniquely barcoded beads and processed for sequencing library preparation using the Chromium Single Cell 3’ Reagent Kit. cDNA libraries were sequenced on a NovaSeq 6000 sequencing system. 4 x 103 cells per sample were captured on the 10X Chromium chip. 5-10 x 104 reads/cell were obtained with characterization of 2-3 x 103 transcripts/cell.

overall_design: C57BL/6 mice received one dose of 250 ug anti-CD40L i.v. for one day. After enzymatic digestion of the lymph nodes (LNs)from  C57BL/6 mice, CD45- cells were purified with the CD45 negative selection beads and were stained with anti-mouse CD45 before sorting for viable CD45- cells. For scRNA-seq, more than 2x104 CD45- LN stromal cells were run on the 10X Chromium Controller (10X Genomics) to partition single cells into nanoliter-scale droplets containing uniquely barcoded beads and processed for sequencing library preparation using the Chromium Single Cell 3’ Reagent Kit (v3 chemistry) (10x Genomics, Pleasanton, CA). Generated cDNA libraries were sequenced on a NovaSeq 6000 sequencing system. 4 x 103 cells per sample were captured on the 10X Chromium chip, 5-10 x 104 reads/cell were obtained with a characterization of 2-3 x 103 transcripts/cell.

first: Li

last: Lushen

first: Song

last: Yang

first: Bromberg

last: Jonathan


title: Sel1L-Hrd1 ERAD is required for the maintainenance of beta cell identity and function

city: Ann Arbor

first: Neha

last: Shrestha

state: MI

address: 1000 Wall Street

institute: University of Michigan

summary: Mice with Sel1L deficient beta cells develop severe hyperglycemia, glucose intolerance and impaired insulin secretion. Using single cell sequencing, we identified that Sel1L plays a major role in maintaining beta cell maturation by suppressing TGF-beta signaling.

overall_design: Islets were isolated from 5 weeks old Sel1Lf/f and Sel1LIns1 mice and following overnight recovery, trypsinized to obtain single cell suspension and processed using 10X Genomics CHROMIUM single cell 3' solution.

first: Ling

last: Qi


title: Dose Response Transcriptional Profiling of Plasmodium falciparum 3D7 and Dd2 strains treated with chloroquine (CQ), MK-4815, and mefloquine (MFQ)

city: Singapore

first: Zbynek

last: Bozdech

state: Singapore

address: 50 Nanyang Avenue

country: Singapore

institute: Nanyang Technological University

summary: Gene expression changes of drug treated trophozoites of P. falciparum 3D7 and Dd2 strains (approx 26-32 HPI)

overall_design: For each antimalarial, trophozoites were treated with 9 different concentrations of CQ, MK-4815, and MFQ (4-fold dilutions) for 6 hours. Three technical replicates of untreated control were included in each bioreplicate experiment

first: Grennady

last: Wirjanata

first: Nur

last: Binte Zulkifli

first: Josephine

last: Boentoro


title: Expression data from  Butyroside D treated B16F10 cells [2uM]

summary:
Gene expression profiling reveals a potential role of Butyroside D in melanogenesis inhibition in B16F10 cells.
B16F10 cells were murine melanoma cell line, treated with 2 μM Butyroside D for 48 h. Microarray gene expression profiling was conducted for two biological replicates


title: KDM6 histone demethylase inhibitor GSK-J4 induces metal and stress responses in multiple myeloma cells [GSK-J4]

status: Public on Sep 16 2022

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

summary: Thioneins are cysteine-rich, evolutionary conserved apoproteins that regulate divalent metal homeostasis by virtue of their metal-chelation properties resulting in the ligand-bound metallothionein state. Previous studies have demonstrated a transient upregulation (102- 103-fold) of a cluster of metallothionein genes as part of a transcriptional response to a class of histone demethylase tool compounds targeting human Fe2+ dependent ketoglutarate oxygenases KDM6A (UTX) and KDM6B (JmjD3). Exposure of multiple myeloma cells to the prototypic bioactive KDM6 inhibitor GSK-J4 induces apoptotic cell death and transcriptomic profiles that are dominated by metal and metabolic stress response signatures. We here investigate the hypothesis that the metal-chelating property of GSK-J4 provides the means for transport and intracellular release of Zn2+ leading to a metallothionein transcriptomic response signature. Live cell imaging upon myeloma cell exposure to GSK-J4 shows a transient increase of intracellular free Zn2+ concentrations upon KDM6 inhibitor treatment consistent with a model of inhibitor mediated metal transport. Comparison of KDM6 inhibitor and ZnSO4 treatments in the presence or absence of metal chelators show that both treatment conditions induce different transcription factor repertoires with an overlapping MTF1 transcriptional regulation responsible for metallothionein and metal ion transport regulation.

overall_design: JJN3 cells were treated with DMSO or GSK-J4 for 3hr, 6hr or 24hr

middle: P

first: Udo

last: Oppermann


title: Targeting CDK12-mediated transcription regulation in anaplastic thyroid carcinoma [ChIP-seq]

city: Tianjin

first: Meijuan

last: Geng

overall_design: We performed a genome-wide analysis of pSer2 signal by chromatin immunoprecipitation coupled with sequencing (ChIP–Seq).

last: Zhang


title: KDM6 histone demethylase inhibitor GSK-J4 induces metal and stress responses in multiple myeloma cells


title: RNA sequences amplified from a HBV-genome-encoding plasmid

city: Basel

first: Jitao David

address: Grenzacherstrasse 124

department: Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel

institute: F. Hoffmann-La Roche

summary: We collected sequences amplified from three HBV-genome-encoding plasmids, one wild type and two with predefined point mutations.

sample_organism:
Hepatitis B virus
blank sample

platform_organism:
Hepatitis B virus
blank sample

overall_design: The data was generated to validate a variant-calling strategy of HBV genomes based on RNA-sequencing data. We cloned part of HBV genome into a commercially available plasmid. We introduced predefined point mutations for benchmarking purposes, and validated them. Wild-type- and mutant-containing plasmids were mixed in pre-defined proportions and amplified to generate HBV transcripts. We applied RNA-sequencing, generated reads, and used the software *HBVouroboros* that we developed to  perform de-novo assembly of the genome and variant calling. The results demonstrate that the RNA-sequencing +  HBVourboros approach recalls HBV genomic variants with high fidelity.

first: Milad

last: Adibi

first: Rui

last: Li

first: Ding

last: Ma

first: Qun

last: Wang

first: Longyu


title: Expression data from human glioma tissues and corresponding adjacent non-tumor tissues

city: Wuhu

first: Xueqin

address: 2 Western Zheshan Road

institute: wannan medical college

summary: We performed microarray expression profiling to analyze the differentially expressed genes between 5 human glioma tissues and corresponding adjacent non-tumor tissues.

overall_design: Glioma tissues and corresponding adjacent non-tumor tissues were selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain highly expressed in glioma tissue.

first: Hui


title: CDK12 regulates co-transcriptional splicing and RNA turnover in human cells

first: Brian

last: Magnuson

address: 1500 East Medical Center Drive

summary: The cyclin-dependent kinase CDK12 promotes transcription completion of long genes by suppressing the utilization of intronic polyadenylation sites that cause premature transcriptional termination. One class of genes that are particularly affected by loss of CDK12 activity are DNA damage response genes and therefore inhibitors of CDK12 have garnered interest as cancer therapeutic amplifiers. In this study, we used the CDK12/13 inhibitor THZ531 to treat HF1 (normal human fibroblasts), K562 and HeLa cells and the adenine analog 1-NM-PP1 to treat analog-sensitive HeLa cells and to assess the acute effects on transcription and RNA processing using Bru-seq and BruChase-seq. While acute transcriptional changes were small and limited to the 3’-ends of genes, RNA turnover was dramatically affected by CDK12 inhibition. Importantly, the downregulation of DNA damage response genes was predominantly due to increased mRNA turnover. Co-transcriptional splicing was suppressed by CDK12 inhibition. Finally, many introns that showed premature transcriptional termination were found to be resistant to degradation following CDK12 inhibition despite showing efficient splicing. We speculate that premature termination and addition of poly(A)s protect these spliced intronic fragments from degradation. These studies reveal previously unknown roles of CDK12 in regulating RNA turnover and co-transcriptional splicing.

overall_design: The nascent RNA sequencing methods Bru-seq and BruChase-seq were used to determine co-transcriptional splicing and turnover in human cells.  HeLa cells expressing anolog-sensitive CDK12 (HeLa-AS) were treated with DMSO (control) or 1NMPP1 and subject to Bru-seq (2 replicates each) or BruChase-seq (3 replicates each, 2h chase).  HF1, K562, and HeLa cells were treated with either DMSO (control) or THZ531 and subject to Bru-seq (1 replicate each) or BruChase-seq (1 replicate each; 6h chase for K562 and HF1 and 2h chase for HeLa).

first: Karan

last: Bedi

first: Ishwarya

last: Venkata Narayanan

first: Bartlomiej

last: Bartkowiak

first: Hailey

last: Blinkiewicz

first: Michelle

middle: T

last: Paulsen

first: Arno

last: Greenleaf

first: Mats

last: Ljungman


title: KDM6 histone demethylase inhibitor GSK-J4 induces metal and stress responses in multiple myeloma cells [ZNSO]

first: Adam

overall_design: Treatment of JJN3 cell lines with GSK-J4 and ZnSO4 for 3hr, 6hr and 24hrs

first: Udo


title: Probing cell identity hierarchies by fate titration and collision during direct reprogramming [scRNA-seq & scATAC-seq]

city: Planegg-Martinsried

first: Bob

last: Hersbach

address: Großhaderner Str. 9

department: Institute of Stem Cell Research

institute: Helmholtz Zentrum Munich

summary: Collide-seq: A systematic comparison of how different reprogramming transcription factors achieve conversion as well as an in-depth analysis of how cells resolve the conflict when more than one fate is instructed.

overall_design: Mouse embryonic fibroblasts were nucleofected with doxycycline inducible constructs for Ascl1, MyoD1 and a DNA binding mutant of Ascl1 (mutAscl1). Cells were expanded for about 10 days and positive cells sorted using FACS. All conditions were pooled and plated together. Transcription factor expression was induced for 72h via the administration of doxycycline. After 72h, cells were collected for scMultiome, i.e., scRNA-seq and scATAC-seq from the same cells

first: David

last: Fischer

first: Giacomo

last: Masserdotti

first: Deeksha

last: Deeksha

first: Karolina

last: Mojžišová

first: Thomas

last: Waltzhöni

first: Diego

last: Rodriques-Terrones

first: Matthias

last: Heinig

first: Fabian

middle: J

last: Theis

first: Magdalena

last: Götz

first: Stefan

middle: H

last: Stricker


title: Reference Long-Read Transcriptomes of Human Peripheral Blood Lymphocytes (PacBio Iso-Seq, Matched to Illumina RNA-Seq Data)

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: Long-read sequencing technologies such as Iso-Seq (PacBio Inc.) generate highly accurate sequences of full-length mRNA transcript isoforms. Long-read transcriptomics may be especially useful in the context of lymphocyte functional plasticity as it relates to human health and disease. However, no long-read isoform-aware reference transcriptomes of human circulating lymphocytes seem to be publicly available despite being valuable as benchmarks in a variety of transcriptomic studies. To begin to fill this gap, we purified four lymphocyte subsets (CD4 T, CD8 T, NK, and Pan B cells) from the peripheral blood of a healthy male donor and obtained high-quality RNA (RIN>8) for PacBio Iso-Seq analysis and parallel RNA-Seq analysis.

overall_design: Four lymphocyte subsets (CD4 T, CD8 T, NK, and Pan B Cells) were purified from peripheral blood mononuclear cells of a healthy male donor. RNA was extracted from each purified subset and used for Pacific Biosciences Iso-Seq long-read sequencing in parallel with Illumina RNA-Seq short-read sequencing. The resulting datasets are offered here as reference transcriptomes for studies of circulating human lymphocytes.

first: Cassandra

last: Woolley

first: Julia

last: Chariker

first: Easton

last: Ford

first: Elizabeth

last: Hudson

first: Vennila

last: Arumugam

first: Sabine

last: Waigel

first: Melissa

last: Smith

last: Mitchell


title: Differential transpiration of pods during stress combination in soybean

city: Columbia

first: Ron

last: Mittler

state: Missouri

address: University of Missouri,1201 Rollins St

department: Christopher S. Bond Life Sciences Center

institute: The Division of Plant Sciences and Technology

summary: Soybean plants were subjected to water deficit, heat stress, and combination of water deficit and heat stress along with control condition and pods were analysed for temperature, water potential, transpiration, yield and differential gene expression compared to control.

overall_design: Soybean plants (16-18 days old) were subjected to water deficit, heat stress, and combination of water deficit and heat stress and pods were collected in liquid nitrogen. Total RNA was isolated and mRNA profile were generated by deep sequencing using NovaSeq 6000 PE150.

first: Ranjita

last: Sinha

first: Benjamin

last: Shostak

first: Sai

last: Induri

first: Sidharth

last: Sen

first: Sara

middle: I

last: Zandalinas

first: Trupti

last: Joshi

first: Felix

middle: B

last: Fritschi


title: IMMUNE SENESCENCE PHENOTYPES PREDICT CHEMOTHERAPY RESISTANCE IN ACUTE MYELOID LEUKAEMIA

city: Nottingham

first: Sergio

last: Rutella

address: Clifton Campus

department: John van Geest Cancer Research Centre

institute: Nottingham Trent University

summary: Immunological classifiers that predict patient outcome and therapeutic responses have been constructed through targeted immune gene expression profiling of diagnostic bone marrow samples from patients with acute myeloid leukaemia.

overall_design: In the study presented here, well annotated cohorts of adults with newly diagnosed acute myeloid leukaemia were used to acquire immune gene expression data. An immune effector senescence-related gene set was shown to correlate with stemness and with poor response to induction chemotherapy.


title: MicroRNA and mRNA expression profiles of hepatobiliary tumor patients' tissue together with those of non-tumor part tissues and serum exosomes. (mRNA)

city: Kanagawa

first: Satoko

last: Takizawa

state: Kamakura

institute: Toray Industries, Inc.

summary: 10 cholangiocarcinoma (including 4 younger cases) and 14 control (10 hepatocellular carcinomas and 4 benigns) patients' tumor and non-tumor parts were obtained and then devided into 8 groups. Total RNA were extracted and purified from tissues and microRNA signal intensities are measured using Toray 3D gene microarrays designed for expression profiles.  mRNA signal intensities were measured using agilent one color microarrays designed for expression profiles.

overall_design: Tumor and non-tumor parts were obtained from surgically resected tissue.

first: Y-h

last: Taguchi

first: Etsushi

last: Kawamura


title: Genome-wide expression analysis in murine liver after Nbs1 induced knockout

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

summary: NBS1 (Nbn in Mus musculus) is a critical component of the MRN (MRE11/RAD50/NBS1) complex, which regulates ATM- and ATR-mediated DNA damage response (DDR) pathways. NBS1 mutations cause the human genomic instability syndrome Nijmegen Breakage Syndrome (NBS), in which microcephaly and intellectual disability are marked neuronal deficits. NBS1 is essential for life, because of its function in the DDR to ensure proliferation and preventing the cell death of replicating cells. However, the function of NBS1 in postmitotic cells is unclear. To explore the possible role of Nbs1 in non-dividing cells and the effection of its deletion on gene expression, RNA-seq was carried out with Nbs1 induced knockout liver samples, in which most cells are postmitotic.

overall_design: In total, samples of murin left lateral liver were analysed of which 3 are control (Ctr) and 3 are Nbs1 induced knockout (Nbs1-iKO).

first: Zhongwei

last: Zhou


title: Probing cell identity hierarchies by fate titration and collision during direct reprogramming

first: Bob

last: Hersbach

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

overall_design: Refer to individual Series


title: Probing cell identity hierarchies by fate titration and collision during direct reprogramming [scRNA-Seq]

overall_design: Mouse embryonic fibroblasts were nucleofected with doxycycline inducible constructs for the indicated reprogramming transcription factors. Cells were expanded for about 10 days and positive cells sorted using FACS. All experimental conditions were pooled and transcription factor expression induced for the indicated time points before scRNA-seq.

first: David

last: Fischer

first: Giacomo

last: Masserdotti

first: Deeksha

last: Deeksha

first: Karolina

last: Mojžišová

first: Thomas

last: Waltzhöni

first: Diego

last: Rodriques-Terrones

first: Matthias

last: Heinig

first: Fabian

last: Theis

first: Magdalena

last: Götz

first: Stefan

last: Stricker


title: Long primed germinal centers with enduring affinity maturation and clonal migration

status: Public on Sep 15 2022

city: La Jolla

first: Shane

last: Crotty

state: California

address: 9420 Athena

institute: La Jolla Institute For Immunology

summary: Germinal centers (GCs) are the engines of antibody evolution. Using HIV Env protein immunogen priming in rhesus monkeys (RM) followed by a long period without further immunization, we demonstrate GC B cells (BGC) lasted at least 6 months. A 186-fold BGC cell increase was present by week 10 compared to a conventional immunization. Single cell transcriptional profiling revealed both light and dark zone GC states were sustained. Antibody somatic hypermutation (SHM) of BGC cells continued to accumulate throughout the 29-week priming period, with evidence of selective pressure. Env-binding BGC cells were still 49-fold above baseline at 29 weeks, suggesting they could be active for even longer periods of time. High HIV neutralizing antibody titers were generated after a single booster immunization. Fully glycosylated HIV trimer protein is a complex antigen, posing significant immunodominance challenges for B cells. Memory B cells (BMem) generated under these long priming conditions had higher levels of SHM, and both BMem cells and antibodies were more likely to recognize non-immunodominant epitopes. Numerous BGC cell lineage phylogenies spanning the >6-month GC period were identified, demonstrating continuous GC activity and selection for at least 191 days with no additional antigen exposure. A long prime, slow delivery (12-day) immunization approach holds promise for difficult vaccine targets, and suggests that patience can have great value for tuning GCs to maximize antibody responses.

overall_design: Lymph node fine needle aspirations were used to collect samples from the left and right inguinal lymph nodes of Indian rhesus macaques (RMs). HIV Env+ and Env- BGC cells were then isolated via Fluorescence-activated cell sorting (FACS) and sequenced using the Chromium Next GEM Single Cell V(D)J Reagent Kit v1.1. PBMCs were collected from the same RMs and HIV Env+ BMem cells were isolated via FACS and sequenced using the Chromium Next GEM Single Cell 5’ Reagent Kit v2 (Dual Index)

first: Jeong Hyun

last: Lee

first: Henry

last: Sutton


title: The amyloid precursor protein regulates synaptic transmission at medial perforant path synapses

city: Hannover

first: Maximilian

last: Lenz

address: Carl-Neuberg-Straße 1

department: Institute of Neuroanatomy and Cell Biology

institute: Hannover Medical School

summary: The perforant path provides the main cortical excitatory input to the hippocampus. Due to its important role in information processing and coding, entorhinal projections to the dentate gyrus have been studied in considerable detail. Nevertheless, a characterization of synaptic transmission between individual connected pairs of entorhinal stellate cells and dentate granule cells is still pending. Here, we have used organotypic entorhino-hippocampal tissue cultures, in which the entorhino-dentate (EC-GC) projection is present and EC-GC pairs can be studied using whole-cell patch clamp recordings. Using cultures of wildtype mice, the properties of EC-GC synapses formed by afferents from the lateral and medial entorhinal cortex were compared and differences in short-term plasticity were revealed. Since the perforant path is severely affected in Alzheimer´s disease, we used cultures of APP-deficient mice to address the role of the amyloid-precursor protein (APP) at this synapse. APP-deficiency caused alterations in excitatory neurotransmission at medial perforant path synapses that were accompanied by transcriptomic and ultrastructural changes. Moreover, the deletion of pre- but not postsynaptic APP through the local injection of Cre-expressing AAVs in conditional APPflox/flox tissue cultures increased the efficacy of neurotransmission at perforant path synapses. Together, these data suggest a physiological role for presynaptic APP at medial perforant path synapses, which may be adversely affected under conditions of altered APP processing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for dentate gyrus samples from APP-deficient and wildtype animals.

first: Amelie

last: Eichler

first: Pia

last: Kruse

first: Christos

last: Galanis

first: Dimitrios

last: Kleidonas

first: Peter

last: Jedlicka

first: Ulrike

last: Müller

last: Deller

first: Andreas

last: Vlachos


title: Probing cell identity hierarchies by fate titration and collision during direct reprogramming [Cut & Tag]

first: Bob

last: Hersbach

overall_design: Mouse embryonic fibroblasts were nucleofected with doxycycline inducible constructs for the indicated reprogramming transcription factors. Cells were expanded for about 10 days and positive cells sorted using FACS. Transcription factor expression was induced for 72h via the administration of doxycycline. After 72h, cells were collected for CUT&RUN.

first: David

last: Fischer

first: Giacomo

last: Masserdotti

first: Deeksha

last: Deeksha

first: Karolina

last: Mojžišová

first: Thomas

last: Waltzhöni

last: Rodriques-Terrones


title: Effects of plantain on transcriptional profile of liver in obese rats

city: Guangzhou

first: jinfeng

last: fu

state: Guangdong

address: Wushan Street

department: School of Food Science and Engineering

institute: South China University of Technology

summary: We explored the mechanisms underlying the anti-obesity effect of plantain. Plantain flour was used to feed obese rats fed a high-fat diet. Six groups were set, viz., the normal control (NC), obese control (OC), low-dose (LD), middle-dose (MD), high-dose (HD), and positive control (PC). The differentially expressed genes in the liver, as well as the lipid and glucose metabolic pathways were investigated. Transcriptome analyses showed that the expression of the PPARα, CPT1A, AMPK, and PGC1α genes was upregulated in the plantain intervention groups. Conclusion: Some key genes in fatty acid and sugar metabolic pathways were regulated by the plantain diet, which probably led to the observed fat and weight loss effects.

overall_design: liver mRNA profiles of obese rats and obese rats treated with plantain were generated by deep sequencing, in triplicate, using Illumina NovaSeq 6000

first: Jinfeng

last: Fu

first: Junxiu

last: Xiao

first: Juan

last: Wang

first: Ou

last: Sheng


title: IMMUNE CORRELATES OF RESPONSE TO IMMUNE CHECKPOINT BLOCKADE IN ACUTE MYELOID LEUKAEMIA

first: Sergio

last: Rutella

summary: Immunological classifiers that predict patient outcome and therapeutic responses have been constructed through targeted immune gene expression profiling of pre-treatment bone marrow samples from patients with acute myeloid leukaemia treated with pembrolizumab and hypomethylating agent azacytidine (clinicaltrials.gov identifier: NCT02845297).

overall_design: In the study presented here, a well annotated cohort of adults with relapsed/refractory acute myeloid leukaemia was used to acquire immune gene expression data. An immune exhaustion and senescence-related gene set was shown to correlate with poor response to immune checkpoint blockade.


title: MicroRNA and mRNA expression profiles of hepatobiliary tumor patients' tissue together with those of non-tumor part tissues and serum exosomes.

first: Satoko

last: Takizawa

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


title: MicroRNA and mRNA expression profiles of hepatobiliary tumor patients' tissue together with those of non-tumor part tissues and serum exosomes. (miRNA)

overall_design: Tumor and non-tumor parts were obtained from surgically resected tissue. Exosomes were obtained from serum.

first: Y-h

last: Taguchi

first: Etsushi

last: Kawamura


title: RNA sequencing of human meniscal fibrochondrocytes treated with 17beta-estradiol

city: Lawrence

first: Jennifer

last: Robinson

state: Kansas

department: Department of Chemical and Petroleum Engineering

institute: University of Kansas

summary: Meniscal tears are the most prevalent intra-articular knee injury and pose significant risk in the development of knee osteoarthritis, a progressive disease that affects around 250 million people worldwide. Meniscus tissue, especially the avascular inner third, heals poorly and the only treatment option is surgery. Epidemiological data and the vital role of estrogen in tissue repair and homeostasis indicate that estrogen could be fundamental for knee joint health and could be useful for tissue regeneration. However, the specific cell response to estrogen and the differences in response of cells from different donors is unknown. In this study, RNA sequencing was used to characterize the mRNA transcriptome of human meniscal cells from male (47-year-old) and female (16-, 17-, and 47-year-old) donors treated with 17beta-estradiol. The goal is to provide data valuable to the design and implementation of estrogen replacement therapies for meniscal health and osteoarthritis reduction.

overall_design: 2 separate experiments, each with cells isolated from 2 different donors each split into 5 different treatment groups run in triplicate for a total of 30 samples per experiment

first: Kelsey

last: Knewtson

first: Adam

last: Podgorny

first: Jesus

last: Gonzalez Flores

first: Cuncong

last: Zhong

first: Donna

last: Pacicca


title: Reference Long and Short-Read Transcriptomes of Human Peripheral Blood Lymphocytes

first: Eric

last: Rouchka


title: mRNA expression quantitative Analysis of Kasumi-1 treated with I3 compared with control

city: Weifang

first: Liuya

last: Wei

address: 7166 number, Baotong West Street

institute: Weifang Medical University

summary: The goals of this study are toevaluate the mRNA expressions of genes in Kasumi-1 cell lines treated with I13

overall_design: There are 6 samples for Kasumi-1 cell line ( control and I3-treated).

first: M

last: Zhao


title: ZMYND8 Suppresses MAPT213 LncRNA Transcription To Promote Neuronal Differentiation

city: kolkata

first: Chandrima

last: Das

state: West Bengal

address: 1/AF Bidhan nagar, Sector-III, Salt Lake

department: Biophysics & Structural Genomics

country: India

institute: Saha Institute of Nuclear Physics

summary: In this study,  we have shown how ZMYND8, a putative chromatin reader, role in neuronal differentiation.

overall_design: Non-coding RNA in MAPT regulation during neuronal differentiation

first: Santanu

last: Adhikary

first: Vipin

last: Singh

first: Ramesh

last: Choudhari

first: Barbara

last: Yang

first: Swagata

last: Adhikari

first: Enrique

last: Ramos

first: Soumi

last: Chaudhuri

first: Siddhartha

last: Roy

first: Shrikanth

last: Gadad


title: Coordinated metabolic transitions and gene expression by NAD+ during adipogenesis.

city: MEXICO CITY

first: LORENA

last: AGUILAR ARNAL

address: TERCER CIRCUITO EXTERIOR, CU

department: BIOLOGIA CELULAR Y FISIOLOGIA

country: Mexico

institute: INSTITUTO DE INVESTIGACIONES BIOMEDICAS- UNIVERSIDAD NACIONAL AUTONOMA DE MEXICO

summary: Adipocytes are the main cell type in adipose tissue, a critical regulator of metabolism, highly specialized in storing energy as fat. Adipocytes differentiate from multipotent mesenchymal stromal cells through adipogenesis. Using RNA-seq we explored the effect of manipulating NAD+ bioavailability during adipogenic differentiation from human mesenchymal stem cells. Cells were harvested either undifferentiated (hMSC) or after days 8 and 16 of adipogenic induction. During adipogenesis, cells were treated with either NAD+ (5 mM), or FK866 (1 nM) or EX527 (50 μM).

overall_design: mRNA was obtained from human mesenchymal stem cells (hMSC) either undifferentiatiated or at days 8 and 16 after adipogenic induction. During differentation, cells were trated with NAD+ (5 mM), FK866 (1 nM) or EX527 (50 μM). Each condition was analyzed per triplicate.

first: Lorena

last: Aguilar-Arnal

first: Egar

last: Sánchez-Ramírez


title: HaCaT cells treated with bleogen pB1 or eGF

city: Singapore

first: Antony

last: Kam

address: 03S-74, 60 Nanyang Drive

institute: Nanyang Technological University

summary: Transcriptome profiling by using RNA-seq was performed on bleogen pB1-treated, EGF-treated, and untreated HaCaT keratinocytes to gain further insights into the wound healing effects of bleogen pB1 and EGF

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HaCaT keratinocytes were treated with/without bleogen pB1 (1 µM; 24 h) or epidermal growth factor (EGF) (10 nM; 24 h).

first: Shining

last: Loo

first: James

last: Tam


title: Effects of corosolic acid on gene expression of in Bel-7402 and Bel-7404 cells

city: Shanghai

first: Yanfeng

last: Xu

address: No.274, Zhijiang Middle Road

institute: Shanghai Hospital of Traditional Chinese Medicine

summary: The purpose of this study was to investigate gene expression in corosolic acid-treated liver cancer cells (Bel-7402 and Bel-7404)

overall_design: We treated Bel-7402 and Bel-7404 cells with corosolic acid, and then used RNA-seq to analyze gene expression in both cell lines after treatment with corosolic acid.

first: Yingxiu

last: Peng


title: Targeting IRAK2 in triple-negative breast cancer cells decreases cellular growth in vitro and delays tumor progression in murine models

city: Aachen

first: Jochen

last: Maurer

state: NRW

address: Pauwelsstraße 30

institute: RWTH Uniklinik Aachen

summary: Breast cancer stem cells (BCSCs) are responsible for tumor recurrence and therapy resistance. We have established primary BCSC cultures from human tumors of triple-negative breast cancer (TNBC), a subgroup of breast cancer likely driven by BCSCs. Primary BCSCs generate xenografts phenocopying the tumors of origin, representing a suitable model to investigate breast cancer targeting strategies. In the TNBC cell line MDA-MB-468, we previously screened kinases whose depletion elicited a differentiation response, among which IRAK2 was identified. Since IRAK2 is highly enriched in primary BCSCs we wondered if its depletion could affect their growth. Primary BCSCs and MDA-MB-468 presenting IRAK2 downregulation exhibited decreased proliferation and sphere-forming capacity, evidencing the role of IRAK2 in cellular growth and self-renewal. When transplanted orthotopically into immunocompromised mice, IRAK2 knockdown cells originated smaller xenografts in comparison with control cells, suggesting that IRAK2 downregulation may delay tumor development. Investigating the molecular pathways affected by the knockdown, NF-κB and ERK phosphorylation, IL-6 and cyclin D1 expression, ERN1 signaling and autophagy were decreased in a cell line-dependent way. Transcriptome analysis confirmed that the cells were to some extent differently affected by the knockdown, indicating that their heterogeneity, different mutations, genetic background, expression of IRAK2 and level of its downregulation could influence the outcome of the knockdown. Given that overall IRAK2 downregulation decreased cellular ability to sustain aggressive growth and to endure cellular stress, IRAK2 may be considered an interesting target to compromise TNBC progression, positively contributing to TNBC clinical outcome.

overall_design: IRAK2 was downregulated in BCSC1, BCSC3 and MDA-MB-468 through lentiviral delivery of shRNA. In particular, the knockdown was induced in cells with the control vector (CV) or the IRAK2 knockdown (shIRAK2) vector treating them for five days with 100 ng/ml Doxycycline. Afterwards, transcriptome analysis comparing CV cells with shIRAK2 cells was performed through RNA-seq (n=3).

first: Francesca

last: Ferraro

first: Anja

last: Steinle

first: Harini

last: Narasimhan

first: Paula-Marie

last: Stolzenberg

first: Andreas

last: Bleilevens

first: Till

last: Braunschweig

first: Elmar

last: Stickeler


title: Identification of chemically-induced osteogenic cells (ciOG) through single cell RNA-seq

city: Cheonansi

first: Ji-Young

last: Yoon

state: Chungnam

address: Dandaero 119

department: Nanbiomedical science

institute: Dankook University

summary: Here we report the reprogramming of human fibroblasts to produce chemically-induced osteogenic cells (ciOG), and explore the potential uses of ciOG in bone repair and disease treatment. A chemical cocktail of RepSox, forskolin, and phenamil was used for osteogenic induction of fibroblasts by activation of RUNX2 expression. Following a maturation, the cells differentiated toward an osteoblast phenotype that produced mineralized tissue. Single-cell RNA sequencing analysis of ciOG identified unique clusters of cells, among which the cluster of active cells related to osteogenic cells was ~49% of the cells, or ~80% of active cells; another cluster of active cells (~12% of the cells) was related to fibroblasts. The reprogramming trajectory over time revealed the transition from fibroblasts to mainly osteogenic cells or to an inactive state.

overall_design: ciOG identification through single cell RNA-seq

first: Jung-Hwan

last: Lee

first: Hae-Won

last: Kim


title: Chemically-induced osteogenic cells (ciOG)


title: Transcriptome-module phenotype association study implicates extracellular vesicles biogenesis in Plasmodium falciparum artemisinin resistance

city: Accra

first: Kwesi

middle: Zandoh

last: Tandoh

state: Greater Accra Region

address: WACCBIP, Volta Road, University Of Ghana

department: Department of Biochemistry, Cell and Molecular Biology

country: Ghana

institute: West African Centre for Cell Biology of Infectious Diseases, University of Ghana

summary: The role of extracellular vesicles in developing artemisinin resistance in Plasmodium falciparum is not known. We have posited a role for EVs in the development of ARTr (EVs export hypothesis) (Tandoh et al.,2022).The objective of this study was to test a prediction of the EVs export hypothesis to gain insight into a putative role for EVs in the expression of the artemisinin resistant phenotype. We compared the gene expression profile of two artemisinin resistant parasites (C580R and R539T) generated by CRISPR based editing of an artemisinin susceptible parasite (Dd2) for enrichment with an EVs module of interest using gene set enrichment analysis.

overall_design:
We leveraged high throughput next generation sequencing technology to determine the global gene expression profiles of three parasite line (Dd2,R539T, C580R) in unsynchronised cultures. Samples were collected for three conditions: untreated, treated with 0.1% DMSO for six hours and treated with dihydroartemisinin for six hours. At least three independent experiments were conducted for each parasite strain and condition, except for the untreated condition ( which was done in duplicates). The TRIzol method was used to extract total RNA from TRIzol-preserved parasites after thawing at room temperature (Invitrogen). The extracted RNA was dissolved in 100µl RNase-free water and DNA removed by DNase I digestion, after which the purified DNA was eluted into 50µl RNase-free water. Qubit High Sensitivity RNA assay (Thermo Fisher Scientific) was used to quantify the purified RNA, and RNA integrity was determined on an Agilent Bioanalyzer (Agilent Genomics, Waldbronn, Germany). Library preparation and next-generation sequencing for whole mRNA transcriptome were done as per Single Cell Discoveries (The Netherlands) protocols.
-----------------------
Single Cell Discovery, Netherlands.

middle: Z

first: Nancy

middle: O

last: Duah-Quashie

first: Michael

middle: D

last: Wilson

first: Neils

last: Quashie


title: Single cell RNA sequencing of bone marrow from ground or running mice

summary: We report the use of single cell RNA sequencing to identify differentially-expressed genes in bone marrow from ground or running mouse and highlight specific subpopulation clusters that may contribute to the associated skeletal and immune phenotype.

overall_design: Bone marrow from ground or running mice

first: Xianghang

last: Luo

first: Hui


title: Inhibition of the m6A Reader IGF2BP2 as a Strategy against T-cell Acute Lymphoblastic Leukemia

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: N6-methyladenosine (m6A) reader Insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) participates in the initiation and growth of cancers by communicating with various targets. Here, we found IGF2BP2 is highly expressed in T-ALL. Gain and loss of IGF2BP2 demonstrated IGF2BP2 was essential for T-ALL cell proliferation in vitro and loss of IGF2BP2 prolonged animal survival in a human T-ALL xenograft model. Mechanistically, IGF2BP2 directly bound to T-ALL oncogene NOTCH1 via an m6A dependent manner.

overall_design: Decoding the RNA Composition of Jurkat Cells with IGF2BP2 Protein

first: Chunyan

last: Ji

first: Jingxin

last: Li

first: Baobing

last: Zhao

first: Panpan

last: Feng


title: Single cell analysis uncovers novel populations of CD4+ T cells associated with antifungal vaccine efficacy

city: Madison

first: Colin

last: Dewey

address: 425 Henry Mall, 5420 Genetics/Biotechnology Center

institute: University of Wisconsin-Madison

summary: Memory T cells underpin vaccine-induced immunity but are not yet fully understood. To distinguish features of memory cells that confer protective immunity, we used single cell transcriptome analysis to compare antigen-specific CD4+ T cells recalled to lungs of mice that received a protective or nonprotective subunit vaccine followed by challenge with a fungal pathogen. We unexpectedly found populations specific to protection that expressed a strong type I interferon response signature, whose distinctive transcriptional signature appeared unconventionally dependent on IFNγ receptor. We also detected a unique population enriched in protection that highly expressed genes for chemokine CCL5 and natural killer cell marker NKG7. Lastly, we detected differences in TCR gene use and in Th1- and Th17-skewed responses after protective and nonprotective vaccine, respectively, reflecting heterogeneous Ifng- and Il17a-expressing populations. Our findings highlight key features of transcriptionally diverse and distinctive antigen-specific T cells associated with protective vaccine-induced immunity.

overall_design: Mice were inoculated either intranasally (IN) or subcutaneously (SC) with Blastomyces dermatitidis endoglucanase-2 (Bl-Eng2) six weeks prior to pathogen challenge. Tetramer-positive CD4+ T cells were FACS sorted and sequenced 3 days after the pulmonary challenge with B. dermatitidis

first: Therese

last: Woodring

middle: N

first: Lucas

last: Dos Santos Dias

first: Xin

last: He

first: Hannah

last: Dobson

first: Marcel

last: Wüthrich

first: Bruce

last: Klein


title: Chemically-induced osteogenic cells (ciOG) in PCL (polycarprolactone) film and NF (nanofiber)

first: Ji-Young

last: Yoon

summary: Here we report the reprogramming of human fibroblasts to produce chemically-induced osteogenic cells (ciOG), and explore the potential uses of ciOG in bone repair and disease treatment. A chemical cocktail of RepSox, forskolin, and phenamil was used for osteogenic induction of fibroblasts by activation of RUNX2 expression. Following a maturation, the cells differentiated toward an osteoblast phenotype that produced mineralized tissue. When generated on a nanofiber substrate ciOG accelerated osteogenic gene expressions and mineralization compared to PCL film followed by bone matrix formation in a calvarial defect, indicating that the engineered biomaterial promotes the osteogenic capacity of ciOG in vivo.

overall_design: The transcriptome comparisons of ciOG and ciOG (M7p) in PCL film and NF

first: Jung-Hwan

last: Lee

first: Hae-Won

last: Kim


title: Chemically-induced osteogenic cells (ciOG) from fibroblasts

summary: Here we report the reprogramming of human fibroblasts to produce chemically-induced osteogenic cells (ciOG), and explore the potential uses of ciOG in bone repair and disease treatment. A chemical cocktail of RepSox, forskolin, and phenamil was used for osteogenic induction of fibroblasts by activation of RUNX2 expression. Following a maturation, the cells differentiated toward an osteoblast phenotype that produced mineralized tissue. Bulk RNA sequencing revealed that up- and down-regulated genes in ciOG relative to aHDF resembled those in hOB during maturation.

overall_design: The comparisons of global transcriptome among ciOG, ciOG(M7p) (maturated ciOG with phenamil for further 7 days), HDF (human dermal fibroblasts), and hOB (human osteoblasts)


title: The crosstalk between MYC and mTOR during osteoclastogenesis

city: NEW YORK CITY

first: Kyung-Hyun

last: Park-min

state: NY

address: 535 E 70th st

institute: Hospital for Special Surgery

summary: Osteoclasts are bone-resorbing cells that undergo extensive changes in morphology throughout their differentiation. Altered osteoclast differentiation and activity lead to changes in pathological bone resorption. The mammalian target of rapamycin (mTOR) is a kinase, and aberrant mTOR complex 1 (mTORC1) signaling is associated with altered bone homeostasis. The activation of mTORC1 is biphasically regulated during osteoclastogenesis; however, the mechanism behind mTORC1-mediated regulation of osteoclastogenesis and bone resorption is incompletely understood. Here, we found that MYC coordinates the dynamic regulation of mTORC1 activation during osteoclastogenesis. MYC-deficiency blocked the early activation of mTORC1 and also reversed the decreased activity of mTORC1 at the late stage of osteoclastogenesis. The suppression of mTORC1 activity by rapamycin in mature osteoclasts enhances bone resorption activity despite the indispensable role of high mTORC1 activation in osteoclast formation in both mouse and human cells. Mechanistically, MYC induces Growth arrest and DNA damage-inducible protein (GADD34) expression and suppresses mTORC1 activity at the late phase of osteoclastogenesis. Taken together, our findings identify a MYC-GADD34 axis as an upstream regulator of dynamic mTORC1 activation in osteoclastogenesis and highlight the interplay between MYC and mTORC1 pathways in determining osteoclast activity.

overall_design: Each condition has two biological replicates.

last: Park-Min


title: Transcriptomic profiling of fibro/adipogenic progenitors treated by Musclin in vitro

city: Chengdu

first: Xia

last: Kang

address: Rongdu Avenue, #270

institute: General Hospital of Western Theater Command

summary: The aim of this study is to explore the molecular mechanism on how Musclin regulates the biological process of fibro/adipogenic progenitors.

overall_design: RNA-Seq of fibro/adipogenic progenitors treated by Musclin or vehicle for 72 hours in vitro

first: Kang-lai

last: Tang

first: Hong-ming

last: Miao

first: Jin

last: Qian


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

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

summary: Human pluripotent stem cell-derived cardiomyocytes (hPSC-CM) are a promising disease model, although hPSC-CMs are not fully mature cardiomyocytes. We examined exponential differentially expressed miRNA/gene to identify critical time-regulated transcripts associated with hPSC-CM differentiation. We uncovered 324 interactions among 29 differentially expressed genes and 51 miRNAs from 20.543 transcripts during the 120 days of hPSC-CM differentiation. We found 16 genes and 26 miRNAs with an inverse pattern of expression (Pearson R-values < -0.5) validated using several human and mouse databases. We further validated these findings using two hPSC-CM lines and seven sampling times over a 30-day protocol and observed 16 inverse interactions among eight genes and 12 miRNAs (Person R-values < -0.5) changing over time. Finally, we tested the top eight miRNAs by adding miRNA mimics to differentiating hPSC-CMs and found that they influenced proliferation and maturation phenotypes. These time-regulated transcripts appear to regulate single or multiple pathways affecting cardiac differentiation.

overall_design:
Gene expression array of human pluripotent stem cells (hPSCs), hPSCs progenitor cardiomyocytes, and hiPSC early cardiomyocytes at different time-points of differentiation were analyzed in duplicates at 0, 2, 4, 6, 8, 15 and 30 days of maturation
Total RNA extracted from hPSC commited to cardiomyocytes differentiation protocol in different time points of development

first: Juan

last: Munõz

first: Rafael

last: Dariolli

first: Caio

last: Silva

first: Elida

last: Neri

first: Lauro

last: Turaça

first: Mariana

middle: L

last: Carvalho

first: Mariliza

last: Velho

first: Eric

last: Sobie

first: José


title: RNA-seq analysis after PIK75 treatment in T-ALL cells

first: Rui

last: Yokomori

address: 14 Medical Drive

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

summary: RNA-seq analysis was performed in two T-cell acute lymphoblastic leukemia (T-ALL) cell lines (Jurkat and DND-41) to analyze gene expression changes after the treatment with PIK-75.

overall_design: Two T-ALL cell lines (Jurkat and DND-41) were treated with DMSO (control) or PIK-75 (120nM) for 4 hours.  Synthesized RNAs (spike-in) was added to the samples based on the cell number.  Total RNA was extracted using QIAzol lysis reagent, miRNeasy Mini Kit, and DNase I (Qiagen). Strand-specific library construction and 100-bp paired-end sequencing with a sequencing depth of 20 M reads on the DNBSEQ platform were performed at BGI Genomics.

first: Fang

middle: Q

last: Lim

first: Takaomi

last: Sanda


title: Transcriptional analysis of primary astrocytes from human fœtal brain inflamed or not with IL-1 beta and subsequently exposed to IL-27

city: Montréal

first: Nathalie

last: Arbour

state: Quebec

address: 900 Saint Denis Street

department: Neuroscience

institute: CHUM-University of Montreal

summary:
To examine the broad impact of IL-27 on human astrocytes, we performed a microarray analysis assessing >20,000 well annotated genes on primary astrocytes culture from four fetal brain donors. Astrocytes were inflamed or not using human recombinant IL-1 beta (20 ng/mL) befor being exposed or not to human recombinant IL-27 (100 ng/mL).
Our goal was to investigate the impact of interleukin-27 on the gene expression profil of human astrocytes

overall_design: Human astrocytes from 4 donors were isolated and then inflamed or not  with IL-1 beta for 48h before adding or not of IL-27 (100 ng/mL) in the media. RNA was purified and transcriptome-wide analysis of gene expression was performed by Genome Québec using the Clariom S HT array.

first: F

last: Lemaître

first: N


title: The epigenetic reader PHF21B modulates social memory and synaptic plasticity-related genes in mice

city: SYRACUSE

first: Mira

last: Krendel

state: New York

address: 505 Irving Ave

institute: Upstate Medical University

summary: Plant homeodomain (PHD) finger proteins are epigenetic readers whose dysfunctions are implicated in neurological conditions, but the molecular mechanisms linking PHD protein deficits to disease remain unclear. Here we generated a PHD finger protein 21B (Phf21b)-depleted mutant CRISPR mouse model (Phf21bΔ4/Δ4) to examine its roles in the brain. KO animals exhibited impaired social memory. Reduced expression of synaptic proteins and impaired long-term potentiation were observed in the KO hippocampi. Transcriptome profiling revealed differential expression of genes involved in synaptic plasticity processes. Furthermore, we characterized a novel interaction of PHF21B to H3K36me3 (histone H3 tri-methylated lysine 36), a histone modification associated with transcriptional activation, and the transcriptional factor CREB. These results establish PHF21B as an important upstream regulator of synaptic plasticity-related genes, and a candidate therapeutic target for murine neurobehavioral dysfunction, with potential applications in human neurological and psychiatric disorders.

overall_design: Hippocampal tissues of Phf21b-depleted mutant CRISPR mouse model (Phf21bΔ4/Δ4) and controls (WT) were used for RNAseq experiments

first: Ma-Li

last: Wong

first: Julio

last: Licinio


title: Identification of Nucleolin-binding targets and sequences in LPS-stimulated RAW 264.7 cells by PAR-CLIP

city: Seoul

first: Taeyun

middle: Andrew

last: Lee

address: 262 Seongsan-no, Seodaemun-gu

department: Systems Biology

institute: Yonsei University

summary: To investigate the consensus RNA-binding motifs of Nucleoli, we performed photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) analysis in nucleolar fractions from unstimulated or 12 h LPS-stimulated RAW 264.7 cells

overall_design: We obtained NCL-bound RNAs from the nucleolar fractions of 12 h LPS-stimulated RAW264.7 cells and analyzed PAR-CLIP data using PARpipe analysis.

first: Kyung-Won

last: Min

first: Ahsan

last: Polash


title: Characterization of B-cell receptor repertoire associated with asymptomatic and symptomatic infections of SARS-CoV-2

city: Xian

first: chengsheng

last: zhang

state: Shaanxi

address: 277 West Yanta Road, Xi'an, Shaanxi, P.R.China

department: precision medicine center

institute: First Affiliated Hospital of Xi 'an Jiaotong University

summary: The immune responses to SARS-CoV-2 infections are very complex and remain to be further characterized. In this study, we performed the single-cell B-cell receptor (BCR) sequencing (scBCR-seq) of the PBMC samples from the healthy controls and SARS-CoV-2 infected individuals with various clinical presentations, and subsequently analyzed the abundance, diversity and difference of BCR repertoire in different groups of COVID-19 patients and the healthy controls, respectively. We identified a number of unique heavy or light chain VDJ genes pairs and combinational preference in each group, such as IGKV3-7 enriched in the asymptomatic subjects, whereas IGHV3-23-IGHJ4, IGHV1-18–IGLV3-19, IGHV1-18–IGLV3-21, and IGHV1-1–IGLV3-25 enriched in the recovery patients from the severe diseases. These findings may advance our understanding of the B-cell mediated immune responses to SARS-CoV-2 infections and help develop novel vaccine candidates and therapeutic antibodies against COVID-19.

overall_design: 53 peripheral blood mono-nuclear cell (PBMC) samples including 42 COVID-19 patients derived samples and 11 healthy controls (HCs) derived samples

first: Chengsheng

last: Zhang


title: Next generation sequencing in SETD5-depleted Huh7 cells.

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

institute: Korea Research Institute of Bioscience and Biotechnology

summary: To analyze transcriptomic changes in SETD5-deficient Huh7 cells, we performed RNA-sequencing.

overall_design: Gene expression profiling of Huh7 cell line under transfected with siSETD5.

first: Mijin

last: Park

first: Jung-Ae

first: Jong-Hwan

first: Seon-Young


title: Modeling exercise using optogenetically contractible Drosophila larvae

city: Boston

first: Yifang

last: Liu

state: MA

address: 77 Avenue Louis Pasteur, NRB 336

institute: Harvard Medical School

summary: The pathophysiological effects of a number of metabolic and age-related disorders can be prevented to some extent by exercise and increased physical activity. However, the molecular mechanisms that contribute to the beneficial effects of muscle activity remain poorly explored. Availability of a fast, inexpensive, and genetically tractable model for muscle activity and exercise will allow rapid identification and characterization of the molecular mechanisms that mediate the beneficial effects of muscle activity. Here, we report the development and characterization of an optogenetically-inducible muscle contraction (OMC) model in Drosophila larvae that we used to model acute exercise-like physiological responses. To characterize muscle-specific transcriptional responses to acute exercise, we performed bulk mRNA-sequencing, revealing striking similarities between acute exercise-induced genes in flies and those previously identified in humans. Our larval muscle contraction model opens a path for rapid identification and characterization of exercise-induced factors.

overall_design: Total RNA was extracted from larval cuticle preparations using a Qiagen RNAeasy mini prep kit as per the manufacturer’s instructions. RNAseq on mRNA-selected samples were performed by the Sulzberger Columbia Genome Center, Columbia University, using an Illumina HISEQ 2500 instrument.

first: Arpan

middle: C

last: Ghosh

first: Sudhir

middle: G

last: Tattikota

first: Yanhui

last: Hu

first: Norbert

last: Perrimon


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

first: Jose Eduardo

last: Krieger

overall_design:
microRNA expression array of human pluripotent stem cells (hPSCs), hPSCs progenitor cardiomyocytes, and hiPSC early cardiomyocytes at different time-points of differentiation were analyzed in duplicates at 0, 2, 4, 6, 8, 15 and 30 days of maturation
microRNA extracted from hPSC commited to cardiomyocytes differentiation protocol in different time points of development

first: Juan

last: Munõz

first: Rafael

last: Dariolli

first: Caio

middle: M

last: Silva

first: Elida

middle: A

last: Neri

first: Lauro

last: Turaça

first: Mariana

last: Carvalho

first: Mariliza

middle: R

last: Velho

first: Eric

last: Sobie

first: José

middle: E


title: Gene expression profiling of age-related changes in coronary arterioles following intravenous stromal vascular fraction using RNA-seq

city: Louisville

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: The goal of this study is to examine age-related changes in the beta-1 adrenergic receptor dependent vasodilaiton in coronary microvessels from young, old, and old rats treated intravenously with stromal cells isolated from adipose tissue (SVF). We have shown that an aged coronary microvasculature has impaired vasodilation to adrenergic agonists and that a single treatment of SVF cells ameliorates the impaired vasodilation but the therapeutic mechanism is unknown.

overall_design: Female Fischer-344 rats aged 3 months (young) 24 months (old), and old injected with a single intravenous injection of 10^7 adipose-derived stromal vascular fraction cells four weeks prior to sacrifice were used. Coronary arterioles less than 150 um were isolated for isolated vessel pressure myography experiments or stored at -80 degrees for RNA isolation. RNA was isolated from ≥ 5 microvessels from pooled within the group using RNAeasy Micro plus kit (Qiagen). RNA sequencing will be performed and data analyzed for age-related and cell treatment related changes in the intracellular proteins of the beta-adrenergic vasodilatory signaling cascade as well as proteins for receptor modification, internalization, recycling, and proteins involved in oxidative stress.

first: Amanda

middle: J

last: LeBlanc

first: Gabrielle

last: Rowe

first: Evan

middle: P

last: Tracy

first: Xiaohong

last: Li


title: 2-Guanidino-quinazoline promotes efficient translational suppression of nonsense mutations responsible of Human genetic diseases

city: Orsay

first: Olivier

last: Namy

address: Rue Gregor Mendel, bat 400

country: France

institute: CNRS, Université Paris-Sud

summary: Premature translation termination (PTC) codons account for 10%-20% of genetic diseases in humans. To counteract the gene inactivation by a PTC, it is possible to use drugs to stimulate PTC readthrough, restoring the expression of the full-length protein. To broaden the medical applications of this therapeutic strategy it is important to increase the chemical variety of readthrough-inducers. In the present study we have developed a new reporter cell-line and performed a High Throughput Screening (HTS). Using a workflow of three successive assays we have isolated the 2-Guanidino-quinazoline (TLN468) as a potent readthrough inducer. We tested the clinical potential of the drug onto the 40 most frequent PTC responsible for Duchenne muscular dystrophy and show that TLN468 is more efficient and acts on a broader range of sequences than gentamicin without inducing readthrough of natural stop codons.

overall_design: RiboSeq of three replicates of Hela cells in presence of DMSO, G418 or TLN468, to identify potential stop codon readthrough induced by TLN468. RNASeq of three replicates of Hela cells in presence of DMSO, G418 or TLN468, to identify potential stop codon readthrough induced by TLN468.

first: Laure

last: Bidou

last: Bugaud

first: Goulven

last: Merer

first: Matthieu

last: Coupet

first: Isabelle

last: Hatin

first: Egor

last: Chrikin

first: Pauline

last: François

first: Jean-Christophe

last: Cintrat


title: Effect of doxycycline treatment on germ-free mice

status: Public on Sep 14 2022

city: Lausanne

first: Gaby

last: El Alam

state: Vaud

address: Station 15

department: SV LISP

institute: École polytechnique fédérale de Lausanne

summary: To characterize the mitochondrial stress response induced by Doxycycline in vivo in liver and kidneys, we administered doxycycline (Dox) at 500 mg/kg/day (mpkd) in the drinking water to 9 weeks-old germ-free C57BL/6J mice for 16 days, hence eliminating the potential confounding impacts of Doxycycline on the microbiome.

overall_design: Male 9 weeks-old C57BL/6J mice were treated for 16 days with 500 mg/kg/day doxycycline hyclate (Sigma) in drinking water and sacrified afterwards. All animals used in the experiments were randomly assigned to experimental or control groups. Mice were housed with ad libitum access to water and food and kept under a 12-hour dark/12-hour light cycle. As doxycycline is bitter, we supplemented the water for both conditions (treatments and controls) with 50 g/L sucrose. Drinking water was changed every 48 hours. Germ-free C57BL/6J mice were obtained from the Clean Mouse Facility, University of Bern (Bern, Switzerland). All animal experiments were carried out according to the institutional, national Swiss and EU ethical guidelines and were approved by the local animal experimentation committee of the Canton de Vaud.

first: Adrienne

last: Mottis

first: Nicola

last: Harris

first: Johan

last: Auwerx


title: Crosstalk between AML and stromal cells triggers acetate secretion through the metabolic rewiring of stromal cells

city: BIRMINGHAM

first: Paloma

last: GARCIA

address: INSTITUTE OF BIOMEDICAL RESEARCH, THE MEDICAL SCHOOL,, UNIVERSITY OF BIRMINGHAM

institute: University of Birmingham

summary: Genome wide data investigating the transcriptome of stromal cells alone versus coculture with leukemic cells

overall_design: 3  replicates of RNA-seq in stromal cells (MS5) cultured alone or in co-culture with leukemic cells (SKM1)

first: Nuria

last: Vilaplana-Lopera

last: Garcia

first: Grigorios

last: Papatzikas

first: Jean-Baptiste

last: Cazier


title: Exosomal MicroRNAs Signature Acts as Efficient Biomarker for Non-Invasive Diagnosis of Gallbladder Carcinoma

city: Shanghai

first: Liang

last: Li

state: Shanghai

address: 225 Changhai Road

institute: Eastern Hepatobiliary Surgery Hospital

summary: Gallbladder carcinoma (GBC) is the most common biliary tract malignant tumor. However, few diagnostic and prognostic biomarkers are available. Although the potential role of exosomes in the diagnosis of several tumor types has been repeatedly explored, the use of exosomal microRNAs (miRNAs) as specific biomarkers for GBC has not been systematically conducted. In this study, we identified a 5-exosomal miRNAs set that can be used to evaluate the risk of GBC through a three-step study that relies on biomarker discovery, training and validation. This biomarker set including the exosomal miR-552-3p, miR-581, miR-4433a-3p, miR-496, and miR-203b-3p.

overall_design: Small RNA high throughput sequencing was performed to identify plasma exosomal miRNAs expression between 8 Gallbladder carcinoma (GBC) and 8 chronic cholecystitis (CC) patients. GBC and CC patients were matched according to the enrollment date, specimen collection protocol, age, and sex . A total of 22 types of miRNAs in plasma exosomes of GBC patients were down-regulated and 24 types of up-regulation when compared with CC.

first: Pinghua

last: Yang

first: Fengliang

last: Song

first: Xinwei

first: Xinzhou

last: Yan

first: Baohua

last: Zhang

first: Hongyang

last: Wang