title: Analysis of ceRNA network reveal potential lncRNA Biomarkers in macrophages resistant to vpr induced apoptosis

city: changsha

first: Huaying

last: Zhou

address: Renming ROAD 139

institute: Central south university

summary: Backgrounds:Macrophages are one of HIV reservoirs. Vpr is essential for infection of macrophages by HIV-1 and has the potential to promote survival of macrophages, which could be a highly significant factor in the development and/or maintenance of macrophage viral reservoirs. However, the impact of vpr on macrophages resistance to apoptosis is yet to be comprehended.  Methods:We determined the expression profiles of lncRNAs in THP1-MAC and THP1-MAC treated with Vpr peptides using microarray analysis. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to explore their function. We also constructed competing endogenous RNA (ceRNA) networks with bioinformatics methods.  Results：We identified 410 lncRNAs that were differentially expressed between THP1-MAC and THP1-MAC after Vpr peptides treatment. Significantly enriched GO terms and pathways were identified, some of which were linked to apoptosis and inflammatory responses. CeRNA analysis showed that lncRNA LINC02249 was paired with the most differentially expressed gene. qRT-PCR results confirmed the reliability of the microarray data.  Conclusions：LINC02249 associated ceRNA network may play a role in macrophages resistant to vpr induced apoptosis. This will provide a new avenue for investigating the pathogenesis of macrophages resistant to vpr-induced apoptosis.

overall_design: analysis the expression profiles of lncRNAs in THP1-MAC and THP1-MAC treated with Vpr peptides using microarray analysis. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to explore their function.

first: Zhen

last: Hu

first: Hongyu

last: Luo


title: Alterations in cell cycle progression caused by S375G and S375E phosphomutants of TDP-43

status: Public on Aug 17 2022

city: Trieste

first: Maurizio

last: Romano

address: Via A. Valerio 28

department: Department of Life Sciences

country: Italy

institute: University of Trieste

type: Expression profiling by high throughput sequencing

summary: An emerging area of TDP-43 is represented by the study of post-translational modifications and the way they are connected to disease-associated mutations. Recently, we described a novel mutation in TDP-43 in an early-onset ALS case that was affecting a potential phosphorylation site in position 375 (S375G). A preliminary characterization showed that both the S375G variant and its phosphomimic mutant, S375E, displayed altered nuclear-cytoplasmic distribution and cellular toxicity. To better investigate these effects, we established cell lines expressing inducible TDP-43 WT, S375G, and S375E variants. No significant changes were reported in splicing of known regulated targets, TDP-43 autoregulation, or aggregation. However, cell-cycle analysis of the stable clones showed that the number of cells in the G2 phase decreased in the two phospho-mutants (S375G and S375E), as compared to WT. Furthermore, experiments showed that Apoptosis-inducing factor 1 (AIF1) appeared to be released from the mitochondria. The involvement of apoptosis and alterations in cell-cycle induced by these variants were further validated using RNAseq analysis. Taken together, these data strongly support the growing evidence that alterations of TDP-43 post-translational modifications can play a potentially important role in disease pathogenesis.

overall_design: Generation of Tet-inducible Hek293 Flp-In T-REx  monoclones expressing Wild-Type, S375G, and S375E variants of human TDP-43.

first: Emanuele

last: Buratti


title: Chiwi KO Neural Folds

city: Pasadena

first: Riley

last: Galton

state: CA

address: 1200 E California Blvd

department: BBE

country: USA

institute: Caltech

summary: RNA-seq of HH9- chick embryo cranial neural folds comparing Chiwi CRISPR KO to control

overall_design: HH4 chick embryos were electroporated with Chiwi (right side) and control (left side) CRISPR/Cas9 plasmids and grown to HH9-. Cranial neural folds were then dissected and Chiwi KO vs control tissue from several embryos was pooled for differential RNA-seq

first: Marianne

last: Bronner

first: Katalin

last: Fejes Toth


title: The mismatch-repair proteins MSH2 and MSH6 interact with the imprinting control regions through the ZFP57-KAP1 complex (ChIP-Seq)

status: Public on Aug 16 2022

city: Caserta

first: Francesco

last: Cecere

state: Caserta

address: Via A. Vivaldi, n. 43

department: DiStABiF

institute: University of Campania "Luigi Vanvitelli"

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Genomic imprinting is controlled by CpG-rich regions (ICRs) acquiring differential methylation in the female and male germline and maintaining it in a parental origin-specific manner in somatic cells. Despite their expected mutation rate due to spontaneous deamination of methylated cytosines, ICRs maintain their CpG-richness and show conservation of CpG-bearing transcription binding sites in mammals. In order to gain further insights into the mechanisms of maintenance of methyl CpGs, we sought to identify the proteins interacting with the methylated allele of the ICRs, by determining the interactors of ZFP57 that recognizes a specific methylated ICR motif in mouse ESCs. Several proteins including factors involved in mRNA processing/splicing, chromatin organization, transcription and DNA repair were identified through a tagged approach coupled to LC–MS/MS analysis. The demonstration of the components of the post-replicative mismatch-repair (MMR) complex as ZFP57 interactors prompted us to investigate the DNA binding profile of MSH2 and MSH6 by chromatin immunoprecipitation and sequencing. We found that these proteins were enriched at the methylated allele of the ICRs and their binding was mediated by the ZFP57/KAP1 complex, suggesting that the MMR complex is recruited to these loci to preserve their genetic integrity.

overall_design: In this study we perfomed Chromatin immunoprecipitation and sequencing (ChIP-seq) of Msh2 and Msh6 and methylation analysis (RRBS) in mESCs.

first: Basilia

last: Acurzio

first: Carlo

last: Giaccari

first: Ankit

last: Verma

first: Claudia

last: Angelini

first: Andrea

last: Riccio


title: RNA sequencing of CSN5 inhibition in prostate cancer cells

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

summary: Human prostate cancer cells treated with shCSN5(sh37) or CSN5 inhibitior (CSN5i-3). Cells were treated with DMSO, 1uM (in C4-2), 5uM (in LNCaP, 22Rv1) or 10 uM  (in PC3) CSN5i-3 for 48 hours. Cells were prepared for RNA-seq.

overall_design: To understand the mechanisms of CSN5 nhibition in Human prostan cencer cells. RNA sequencing were were analysed by Partek  flow

first: Ying

middle: Z

last: Mazzu

first: Philip

last: Kantoff


title: The mismatch-repair proteins MSH2 and MSH6 interact with the imprinting control regions through the ZFP57-KAP1 complex (RRBS)

type: Methylation profiling by high throughput sequencing


title: Comparison profiles of RNA m6A and DNA methylation between mouse female germline stem cells and STO cells

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

country: China

institute: Shanghai Jiao Tong University

summary: In this study, epigenetic differences such as DNA methylation and mRNA m6A modification in STO and FGSCs were comprehensively analyzed and compared, and specific binding of Stella and histone modification in FGSCs was combined to find that DNA methylation and mRNA m6A as well as transcription factor Stella might be related to FGSCs cell characteristics.

overall_design: mRNA m6A and DNA methylation  profiles of FGSCs and STO cells ,and the  ChIP-Seq of Stella and H3K27me3, H3K27ac, H3K4me1,H3K4me3 were generated by deep sequencing, in duplicate.

first: Xinyan

last: Zhao


title: Mammalian RNase H1 directs RNA primer formation for mtDNA replication initiation and is also necessary for precise termination of mtDNA replication [small RNA-seq]

city: Perth

first: Stefan

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

type: Non-coding RNA profiling by high throughput sequencing

summary: The exact in vivo role for RNase H1 in mammalian mitochondria has been much debated and we show here that it is essential for site-specific formation of RNA primers to allow initiation of mtDNA replication.  Without RNase H1, the RNA:DNA hybrids at the replication origins are not processed and mtDNA replication is instead initiated at non-canonical sites and becomes impaired.  Furthermore, RNase H1 is also needed for replication completion and in its absence linear deleted mtDNA molecules extending between the two origins of mtDNA replication are formed.  Finally, we report the first patient with a homozygous pathogenic mutation in the hybrid-binding domain (HBD) of RNase H1 causing impaired mtDNA replication. In contrast to catalytically dead pathological variants of RNase H1, this mutant version has enhanced enzyme activity.  This finding shows that the RNase H1 activity must be strictly controlled to allow proper regulation of mtDNA replication.

overall_design: Differential gene expression analysis of RNase H1-/- mice compared to wild type (n=4)

first: Jelena

last: Misic

first: Dusanka

last: Milenkovic

first: Ali

last: Al-Behadili

first: Xie

last: Xie

first: Min

last: Jiang

first: Shan

first: Roberta

last: Filograna

first: Camilla

last: Koomeister

first: Louise

last: Jenninger

first: Aleksandra

last: Filipovska

first: Anders

middle: R

last: Clausen

first: Valerio

last: Carelli

first: Thomas

last: Nicholls

first: Anna

last: Wedell

first: Maria

last: Falkenberg

first: Nils-Goran

last: Larsson


title: Single-cell RNAseq of mouse ear dermal endothelial cells

city: Uppsala

first: Sofia

last: Nordling

address: Dag Hammarskölds väg 20

country: Sweden

institute: Uppsala University

summary: Single blood vascular endothelial cells were isolated from the ear dermis of adult C57Bl/6 mice and subject to whole transcriptome RNA sequencing by SMART-seq2.

overall_design: The data consists of 2 replicates with each replicate consisting of 2 384-well plates. Replicates are a pool of blood vascular endothelial cells from the ears of 6 female adult C57Bl/6 mice. The transcriptomes of individual cells were sequenced by SmartSeq2.

first: Mark

last: Richards

first: Lena

last: Claesson-Welsh


title: Small RNA sequencing of bone marrow from pediatric patients with acute myeloid leukemia and cord blood controls

city: Ghent

first: Jolien

last: Vanhooren

address: Corneel Heymanslaan 10

country: Belgium

institute: Ghent University

summary: Pediatric acute myeloid leukemia (pedAML) is a heterogeneous blood cancer of childhood age. Although survival rates have significantly improved over the past decades, still 20-30% of children will succumb due to treatment-related toxicity or relapse. Molecular characterization of the leukemic stem cell, shown to be responsible for relapse, is needed to improve treatment options and survival. Recently, it became clear that non-coding RNAs, including long non-coding RNAs (lncRNA) and microRNA (miRNA), play a role in the development of human diseases, including pediatric cancer. Nevertheless, non-coding RNA expression data in pedAML are scarce. Here, we explored lncRNA and miRNA expression in pedAML subpopulations (leukemic stem cells (LSC) and leukemic blasts (L-blast)) and their normal counterparts (hematopoeitic stem cells (HSC) and control myeloblasts (C-blast)). The study provides a catalog of non-coding RNAs with a potential role in the pathogenesis of pedAML, paving the way for further translational research studies.

overall_design: We report the miRNA expression in cellular subpopulations of pedAML. To this end, RNA sequencing identified 2588 microRNAs of which 22 showed to be significantly differentially expressed in the LSC compared to the HSC and 60 in the L-blast to C-blast comparison.

first: Laurens

last: Van Camp

first: Tim

last: Lammens

first: Barbara

last: De Moerloose


title: Expression data of penile carcinomas and normal penis

city: Vejle

first: Silvia

middle: Regina

last: Rogatto

address: Beriderbakken 4

department: Clinical Genetics

country: Denmark

institute: University Hospital of Southern Denmark – Vejle

summary:
Penile carcinoma (PeCa) is a rare cancer with orphan disease designation and a prevalence of 0.1-1 per 100,000 men in high-income countries, but it constitutes up to 10% of malignancies in men in some African, Asian and South American regions . Evidence demonstrated that the tumor microenvironment (TME) plays a crucial role in the tumor progression and therapy response. Two landmarks of TME, extracellular matrix (ECM) remodeling and inflammation have been reported in these tumors. However, the cell types and cellular crosstalk involved in PeCa are widely unexplored.
We used microarrays to identify enriched immune and stromal cells from the secretory profile of penile cancer transcriptomes.

overall_design: Transcriptomic analysis was performed in 16 usual PeCa compared to six histologically normal penile glans using the GeneChip™ Human Transcriptome Assay 2.0 (Affymetrix, USA), following the manufacturer recommendations. RNA was isolated from fresh-frozen samples using the RNeasy mini kit (Qiagen, Valencia, USA), according to the manufacturers’ instructions. RNA integrity was verified in all samples using the Agilent 2100 Bioanalyzer RNA 6000 LabChip kit (Agilent Technologies, Santa Clara, CA, USA). The scanning was performed using Affymetrix GeneChip Scanner 7000 (Affymetrix/ThermoFisher, USA). The CEL files were generated by Affymetrix® GeneChip® Command Console® (AGCC) 4.0. The data normalization was performed with Transcriptome Analysis Console (TAC, ThermoFisher, USA, v.4.0) using ANOVA method ebayes.

first: Sarah

middle: S

last: Cury

first: Hellen

last: Kuasne


title: RNA-sequencing of liver from WT and CRY1 KO mice

city: Seoul

first: Jae Bum

last: Kim

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

department: Biological Sciences

country: South Korea

institute: Seoul National University

summary: We conducted RNA-sequencing from three per group C57BL/6J male mice, ten weeks old. Liver tissue was collected from wild-type (WT) and Cryptochrome1 (CRY1) knockout (KO) mice.

overall_design: Examination of 6 samples derived from liver from WT and CRY1 KO mice

first: Ye

middle: Y

first: Hagoon

last: Jang

first: Gung

last: Lee

first: Jae

middle: B


title: Gene expression data from parental HeLa and Dickkopf-1 (Dkk1) knockout HeLa cells after Cisplatin treatment

city: Heidelberg

first: Prof. Dr. Felix

last: Hoppe-Seyler

address: Im Neuenheimer Feld 242

country: Germany

institute: German Cancer Research Center (DKFZ)

summary: Infection with oncogenic human papillomavirus (HPV) is a major cause for the development of cervical cancer, which is mainly driven by the expression of the HPV E6 and E7 oncoproteins. We uncovered that the concentration levels of the putative tumor suppressor Dickkopf-1 (Dkk1) are restricted in cervical cancer cells by HPV E6 expression due to the E6-mediated proteolytic degradation of p53, which is a transcriptional regulator of Dkk1. Moreover, we found that Dkk1 is critically involved in the pro-apoptotic Cisplatin response of these cells, as Dkk1 repression was associated with an increased resistance towards the chemotherapeutic compound. This could be of high relevance for cervical cancer treatments, which usually involve Cisplatin for standard care. Although Dkk1 is a major antagonist of the canonical Wnt signaling, the differential response towards Cisplatin observed in Dkk1-depleted cells was not associated to an activation of this pathway. To elucidate alternative underlying mechanisms, we performed Affymetrix Gene Expression analyses comparing the transcriptome of Cisplatin-treated parental HeLa to CRISPR/Cas9-generated Dkk1 knockout (KO) HeLa cells. These revealed that Dkk1 depletion is linked to an impairment of the pro-apoptotic JNK/AP-1 pathway in cervical cancer cells, suggesting that Dkk1 drives Cisplatin-mediated apoptosis via activation of this signaling hub.

overall_design: Parental HeLa (HeLa WT) and Dkk1 KO HeLa cells were treated for 16 h with 10 µM Cisplatin or were left untreated. After extracting total RNA from the samples, cRNA was generated and hybridized on Affymetrix® GeneChips. All conditions were performed in three biological replicates.

first: Kristin

last: Frensemeier

first: Karin

first: Felix


title: Mammalian RNase H1 directs RNA primer formation for mtDNA replication initiation and is also necessary for precise termination of mtDNA replication [RNA-seq]

first: Stefan

last: Siira

first: Jelena

last: Misic

first: Dusanka

last: Milenkovic

first: Ali

last: Al-Behadili

first: Xie

last: Xie

first: Min

last: Jiang

first: Shan

first: Roberta

last: Filograna

first: Camilla

last: Koomeister

first: Louise

last: Jenninger

first: Aleksandra

last: Filipovska

first: Anders

last: Clausen

first: Valerio

last: Carelli

first: Thomas

last: Nicholls

first: Anna

last: Wedell

first: Maria

last: Falkenberg

first: Nils-Goran


title: Mammalian RNase H1 directs RNA primer formation for mtDNA replication initiation and is also necessary for precise termination of mtDNA replication

first: Stefan

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

overall_design: Refer to individual Series


title: Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet

city: Toronto

first: Michael

middle: M.

last: Hoffman

state: ON

address: 101 College St PMCRT 11-311

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

summary: As part of our larger study, we validated our predicted methylated and hydroxymethylated binding preferences of OCT4. This represents the first conjoint CUT&RUN experiment across conventional, methylation-, and hydroxymethylation-enriched sequences.

overall_design: We employed cleavage under targets and release using nuclease (CUT&RUN), across an aggregated OCT4 sample, with two replicates, which was then sequenced via 3 different strategies. We also included a single IgG control.

first: Coby

last: Viner

first: Charles

middle: A

last: Ishak

first: Shu-Yi

last: Shen

first: Santana

middle: M

last: Lardo

first: Daniel

middle: D

last: De Carvalho

first: Sarah

last: Hainer


title: Transcriptome Analysis of Pediatric Acute Myeloid Leukemia

city: Hong Kong

first: Kathy

middle: YY

last: Chan

address: Rm84041, 6/F, Clinical Science Building, Prince of Wales Hospital, Shatin, N.T.

department: Paediatrics

country: Hong Kong

institute: The Chinese University of Hong Kong

summary:
Purpose: This study aimed to generate a whole transcriptome dataset for children with acute myeloid leukemia
Methods: RNA-seq data were generated by deep sequencing using Illumina. The sequence reads that passed quality filters were analyzed.
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the human genome (buildhg38) and annotated with ensemble release 100.

overall_design: Gene expression profiles of myeloblasts from 48 cases of pediatric acute myeloid leukemia

first: K

middle: T

last: Leung


title: The impact of neoadjuvant chemotherapy on tumor microenvironment in advanced high-grade serous carcinoma

city: Hangzhou

first: Junfen

last: Xu

state: Other (Non U.S.)

address: No.1 Xueshi Road

department: Department of Gynecologic Oncology

institute: Women’s Hospital, Zhejiang University School of Medicine

summary: High-grade serous ovarian, fallopian tube or peritoneal carcinoma is an aggressive subtype that frequently develops resistance to chemotherapy. It remains controversial whether the resistance is caused by the acquisition of new molecular aberrations or alternatively through the selection of rare preexisting tumor clones. To address this question, we applied single cell RNA sequencing to depict the tumor landscape of a single case of advanced high-grade serous fallopian tube carcinoma during neoadjuvant chemotherapy (NACT).

overall_design: Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3' Reagent Kit v3 (10x Genomics) according to manufacturer's protocol.


title: Prenatal Alcohol Exposure Contributes to Negative Pregnancy Outcomes by Altering Fetal Vascular Dynamics and Placental Transcriptome

city: Bryan

first: Rajesh

last: Miranda

address: 8447 Riverside Parkway

institute: Texas A&M University

summary: Prenatal alcohol exposure (PAE) has previously been shown to alter fetal blood flow in utero and is also associated with placental insufficiency and intrauterine growth restriction (IUGR), suggesting an underlying connection between perturbed circulation and pregnancy outcomes. Here we show that a single exposure to ethanol in pregnant mice on gestational day 10 (GD10) by gavage attenuates umbilical cord blood flow transiently during gestation, explaining the observed IUGR, specifically decreased fetal weight, and morphometric indices of cranial growth. Moreover, RNAseq of the fetal portion of the placenta demonstrated that this single exposure has lasting transcriptomic changes, including upregulation of Tet3, which is associated with spontaneous abortion. Weighted gene co-expression network analysis (WGCNA) identified erythrocyte differentiation and homeostasis as important pathways associated with improved umbilical cord blood flow as gestation progresses. WGCNA also identified sensory perception of chemical stimulus/odorant and receptor activity as important pathways associated with cranial growth. Our data suggest that PAE perturbs the expression of placental genes relevant for placental hematopoiesis and environmental sensing, resulting in transient impairment of umbilical cord blood flow and subsequently, IUGR.

overall_design: There were a total of 22 samples, 12 control and 10 PAE, 11 male and 11 female.

first: Marisa

last: Pinson

first: Alexander

last: Tseng

first: Amy

last: Adams

first: Tenley

middle: E

last: Lehman

first: Karen

last: Chung

first: Jessica

last: Gutierrez

first: Kirill

middle: V

last: Larin

first: Christina

last: Chambers

middle: C


title: RNA-seq analysis of triple negative breast cancer cell lines with knockdown of cytokeratin 5 (CK5)

city: Aurora

last: Finlay-Schultz

state: CO

department: Pathology

institute: University of Colorado Denver Anschutz Medical Campus


title: RNA-seq analysis of triple negative breast cancer cell line BT20 with knockdown of cytokeratin 5 (CK5)

summary: BT20 cells expressing pLK0-shControl or pLK0-shCK5-425222

overall_design: No additional treatments, cells with confirmed expression or knockdown of CK5 protein

first: Kiran

last: Paul

first: Olivia

last: McGinn

first: Peter

last: Kabos

first: Carol

last: Sartorius


title: RNA-seq analysis of triple negative breast cancer cell line MDA-MB-468 with knockdown of cytokeratin 5 (CK5)

summary: MDA-MB-468 cells expressing pLK0-shControl or pLK0-shCK5-425222


title: Time-lapse hippocampal transcriptomic profiling after fear conditioning in Tob WT and KO mice

city: Kunigami-gun

first: Mohieldin

last: Youssef

state: Okinawa

address: 1919-1 Tancha

department: Cell Signal Unit

country: Japan

institute: Okinawa Institute of Science and Technology

summary: Fear conditioning induces immediate changes in the mouse hippocampal transcriptome profile. Here, we performed RNA sequqencing in mice hippocampi at 15 minutes, 1 hour and 3 hours post-fear conditioning in addition to non-conditioned mice. Tob gene has been shown to affect cellular stress and behavior. In order to understand the role of Tob gene in the hippocampal stress and fear machinery, we compared hippocampi of Tob WT and KO mice. This dataset shows the temporal transcriptomic changes in mouse hippocampus induced by fear conditioning. Also, it shows the changes occurred after Tob deletion.

overall_design: HIppocampal RNA profiles of 8-12 weeks old wild type (WT) and Tob knockout (KO) mice without fear conditioning (No), and at 15 min (0hr), 1hr and 3hr after fear conditioning. Each condition had three biological replicates.

first: Tadashi

last: Yamamoto


title: Transcriptomic profiling of Phactr1 overexpression in human endothelial cells

city: Hefei

first: Ma

middle: Xiao

last: xuan

address: 443, Huangshan Rd

institute: University of Science and Technology of China

summary: Phactr-1 is an actin and protein phosphatase 1 (PP1) binding protein which is reported to be highly expressed in brain and controls PP1 activity and F-actin remodelling. Genome-wide association studies (GWASs) implicate the Phactr-1 locus (6p24) as a  risk factor for five vascular diseases, including coronary artery disease, migraine headache, cervical artery dissection, fibromuscular dysplasia, and hypertension, with its mechanism of action being incompletely understood. To depict how Phactr1 regulates endothelial cell function, we performed transcriptomic profiling of human umbilical vein endothelial cells (HUVECs) infected with Phactr1 adenovirus. We documented that Phactr1 overexpression triggers multiple aspects of endothelial dysfunction, thus providing a mechanistic basis for Phactr1 mediated disease-relevant vascular functions.

overall_design: Human umbilical vein endothelial cells (HUVECs) were seeded in 0.1% gelatin-coated dishes the day before experiment.    The next day, cells were treated with Phactr1 Adenovirus (2.5×10E10 pfu/ml, WZ Biosciences) or control adenovirus for 24 hours.    After treatment, total RNA was isolated using the RNA-Easy Mini Plus kit (QIAGEN).    RNA libraries were prepared for sequencing using rRNA Removal Library Construction Protocol.    Briefly, take a certain amount of total RNA samples, and remove rRNA by using RNase H or Ribo-Zero method, then fragment the RNA.    Obtain the first and second strands of cDNA by reverse transcription.    Then add adapters at both ends of the cDNA for PCR amplification to obtain the cDNA library.    The library was amplified with phi29 to make DNA nanoball (DNB) which have more than 300 copies of one molecular.    The DNBs were load into the patterned nanoarray and single end 50 (pair end 100) bases reads were generated in the way of combinatorial Probe-Anchor Synthesis (cPAS).    The sequencing data was filtered with SOAPnuke (v1.5.2), afterwards clean reads were obtained and stored in FASTQ format.    The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).     Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database built by BGI (Beijing Genomic Institute in ShenZhen), then expression level of gene was calculated by RSEM (v1.2.12).

first: X

last: Ma

first: Z

last: Liu

first: J

last: Weng

first: S

last: Xu


title: Differentiation Time Course Analysis of Gene Expression in Primary Osteoblasts from Wild Type and β-Arrestin 2 Knockout Mice

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

summary: Gene expression analysis was performed on differentiating obsteoblasts isolated from calvaria of C57BL/6J wildtype or B-arrestin 2 knockout mice.

overall_design: Mouse osteoblasts were prepared independently for each biological replicate. Three biological replicates were used for each time point. Total RNAs were collected and 100 ng analyzed for gene expression using Affymetrix Mouse Gene 2.0 ST GeneChips.

first: Louis

last: Luttrell

middle: L


title: Single-cell Transcriptome Atlas of the Mus musculus developing testis

status: Public on Aug 15 2022

city: Zhuhai

first: Liangyu

last: Zhao

state: Guangdong

address: 52th Meihua Road, Zhuhai, China

institute: Shanghai Jiao Tong University School of Medicinethe Fifth Affiliated Hospital of Sun Yat-sen University

summary: Single-cell transcriptomes of testis from 3, 6, 8, 11, 14, 17, 21, 25 and 35 days old mice

overall_design: Single-cell transcriptomes of testis tissues were collected from 9 C57 mice those are 3, 6, 8, 11, 14, 17, 21, 25 and 35 days old respectively.

first: Zheng

last: Li


title: Timeseries RNA-Seq analysis of low phosphorus-induced adventitious root formation in Populus ussuriensis

city: Harbin City

first: Chenghao

state: HeiLongJiang Province

address: No. 51 HeXing Road,Xiangfang District

department: College of Forestry

institute: Northeast Forestry University

summary: For RNA-seq, new cuttings from 3-week-old in vivo plants were cultured on the solid Woody Plant Medium (WPM) containing 20 g/L sucrose and 3 g/L Gelrite (Duchefa). After 5 days of culture, the root primordium formed cuttings were transferred to modified liquid WPM containing 10 μM or 200 μM KH2PO4, and harvested the basal ends of stem cuttings containing root primordium with its surrounding tissues using 11# scalpel after 2h, 4h, 8h, 12h and 24h culture. Samples were collected from two biological replicates (50 cuttings each).

overall_design: RNA-seq of the basal ends of stem cuttings

first: Hairong

last: Wei

first: Hanzeng

last: Wang


title: RNA-Seq analysis of differentially expressed genes in UPM-exposed epithelium co-cultivated with macrophages and dendritic cells from patients with asthma and COPD

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

summary: The study aimed at evaluation and comparison of airway epithelium mRNA profile in response to airborne particulate matter presented by macrophages using in vitro triple cell co-culture model.

overall_design: mRNA profile of control, asthmatic and COPD nasal epithelium co-cultivated with monocyte derived macrophages and monocyte derived dendritic cells after UPM exposition.

first: Magdalena

last: Paplinska-Goryca

first: Paulina

last: Misiukiewicz-Stepien

first: Dorota

last: Adamska

first: Michal

last: Szelag


title: Zscan4 mediates ubiquitination and degradation of co-repressor complex to promote chromatin accessibility in two-cell embryos and ESCs

city: Tian jin

first: Jiao

last: Yang

address: 94 Weijin Road

institute: Nankai University

summary: Zscan4 regulates chromatin accessibility and 2C in early embryos or 2C-like state in ESC cultures.

overall_design: 2 repeats of Control and 2 repeats Zscan4 overexpression mouse ESCs.

first: Nannan

first: Linlin

first: Huasong

first: Qiangqiang

last: liu

first: Lingling

first: Jie

first: Yiwei

last: Wu

first: Xinqi

first: Xinyi

last: Lu

first: Quan

last: Chen

first: Xudong

first: Yushan

last: Zhu

first: Jiafu

last: Long

first: Lin


overall_design: 2 repeats of Control and 2 repeats Zscan4 overexpression mouse ESCs, 5 repeats of WT and 6 repeats of Zscan4 RNAi 2-cell embryos

last: Liu


title: Comparative transcriptome analysis of manganese transportation in different leaves in soybean under manganese stress

city: guangzhou

first: ying

address: wushan

institute: SCAU

summary: Manganese (Mn) stress is known to be a major limitation for development of soybean, and legume crop productivity globally. However, very little information is available on the adaptive mechanisms, particularly in the important legume crop soybean (Glycine Max L.), which enable leaves to respond to high-Mn availability. Thus, to elucidate these mechanisms in soybean leaves at molecular level, we used an RNA sequencing approach to investigate transcriptomes of the leaves under Mn-sufficient and Pi-excessive conditions. Our investigation revealed that more genes showed altered expression patterns in old leaf than in young leaf under Mn excess, suggesting that the Mn excess-more-sensitive old leaf required expression change in a larger number of genes to cope with high-Mn stress than the Mn excess-less-sensitive young leaf. The functional classification of differentially expressed genes (DEGs) was examined to gain an understanding of how leaves respond to Mn stress, caused by soil Mn excess. As a result, more DEGs involved in nodulation, detoxification, nutrient/ion transport, transcriptional factors, key metabolic pathways, Mn remobilization and signalling were found in Mn-excessive induced old leaves than in Mn-excessive induced young leaves. Our findings have enabled the identification of molecular processes that play important roles in the acclimation of leaves to Mn excess, ultimately leading to the development of Mn-efficient soybean suitable for Mn-excessive soils.

overall_design: The experiment was started at the onset of the fifth leaf stage when the plants were transferred to solutions with either normal (5 μM) or high (100 μM) Mn (added as MnSO4). The nutrient solutions were renewed every 3 days. There were two treatments that were arranged in a randomized, complete block design with 3 replicates.

first: Ying

first: Yingbin

last: Xue

first: Baoxing

last: Xie

first: Bixian

last: Xiao

first: Shengnan

first: Jiang

last: Tian


title: Potential Role of Inflammation in SARS-CoV-2 Disease Pathology: A multi-omic study in Type II pneumocytes of A/J mice exposed to Lipopolysaccharide

city: Minneapolis

first: Andrew

middle: Traver

last: Rajczewski

state: MN

institute: University of Minnesota

summary: Multi-omic analyses of A/J Type II pneumocytes exposed to lipopolysaccharide were performed to ascertain the similarity of the inflammatory response under these conditions to the inflammatory response seen in SARS-CoV-2 infections.

overall_design: A/J mice were subjected to three weeks of intranasal lipopolysaccharide exposure, after which the Type II pneumocytes were isolated and the mRNA extracted for RNA-Seq analysis

first: Qiyuan

last: Han

first: Jenna

last: Fernandez

first: N

last: Tretyakova


title: Transcriptional analysis of Ceratopteris richardii young sporophyte reveals conservation of stem cell factors in the root apical meristem

city: Irapuato

first: Alejandro

last: Aragon Raygoza

state: Guanajuato

address: Km. 9.6 Libramiento Norte Carretera. Irapuato-León

department: UGA/Langebio

country: Mexico

institute: Cinvestav Unidad Irapuato

summary:
To generate a de novo transcriptome assembly from three different parts of the Ceratopteris richardii young sporophyte (Hn-n cultivar).
We then performed a differential gene expression analysis between the different plant segments, while trying to understand the expressed genes for each Ceratopteris part.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for three different segments of Ceratopteris young sporophyte.

last: Aragon-Raygoza

first: Luis

last: Herrera-Estrella

first: Alfredo

last: Cruz-Ramirez


title: Metabolic adaptations underpin resistance to histone acetyltransferase inhibition [ChIP-seq]

city: La Jolla

first: Michael

last: Erb

address: 10650 N Torrey Pines Rd

department: Department of Chemistry

institute: The Scripps Research Institute

summary: Histone acetyltransferases (HAT) catalyze the acylation of lysine side chains and are implicated in diverse human cancers as both oncogenes and non-oncogene dependencies. Acetyl-CoA-competitive HAT inhibitors have garnered attention as potential cancer therapeutics and the first clinical trial for this class is ongoing (NCT04606446). Despite broad enthusiasm for these targets, notably including CBP/p300 and KAT6A/B, the potential mechanisms of therapeutic response and evolved drug resistance remain poorly understood. Using comparative transcriptional genomics, we found that the direct gene regulatory consequences of CBP/p300 HAT inhibition are indistinguishable in models of intrinsically hypersensitive and insensitive acute myeloid leukemia (AML). We therefore modelled acquired drug resistance using a forward genetic selection and identified dysregulation of coenzyme A (CoA) metabolism as a facile driver of resistance to HAT inhibitors. Specifically, drug resistance selected for mutations in PANK3, a pantothenate kinase that controls the rate limiting step in CoA biosynthesis. These mutations prevent negative feedback inhibition, resulting in drastically elevated concentrations of intracellular acetyl-CoA, which directly outcompetes drug-target engagement. This not only impacts the activity of structurally diverse CBP/p300 HAT inhibitors, but also agents related to an investigational KAT6A/B inhibitor that is currently in Phase-1 clinical trials. We further validated these results using a genome-scale CRISPR/Cas9 loss-of-function genetic modifier screen, which identified additional gene-drug interactions between HAT inhibitors and the CoA biosynthetic pathway. Top hits from the screen included the phosphatase, PANK4, which negatively regulates CoA production and therefore suppresses sensitivity to HAT inhibition upon knockout, as well as the pantothenate transporter, SLC5A6, which enhances sensitivity. Altogether, this work uncovers CoA plasticity as an unexpected but potentially class-wide liability of anti-cancer HAT inhibitors and will therefore buoy future efforts to optimize the efficacy of this new form of targeted therapy.

overall_design: ChIP-seq in MOLM-13 and HL-60 following acute CBP/p300 HAT inhibition.

first: Timothy

last: Bishop


title: Metabolic adaptations underpin resistance to histone acetyltransferase inhibition [SLAMseq]

overall_design: SLAM-seq in MOLM-13 and HL-60 following acute CBP/p300 HAT inhibition.


title: Metabolic adaptations underpin resistance to histone acetyltransferase inhibition [QUANTseq]

overall_design: 3'-mRNA sequencing of a panel of AML cell lines following CBP/p300 HAT inhibition.


title: HSF1 activates ANXA11-mediated glutamine metabolism by super enhancer long non-coding RNA LINC00857 in colorectal cancer [ChIP-seq]

city: Weifang City

first: Jiaqiu

last: Li

state: 省/直辖市

address: No. 2428, Yuhe Road, Kuiwen District

institute: weifang medical university

summary: We shed light on a closely cooperative machinery between HSF1 and super enhancer for the first time in CRC. HSF1 could stimulate super enhancer activity by the enrichment of acetyltransferase P300 to LINC00857 promoter region, contributing to LINC00857 transcription.

overall_design: HSF1 and H3K27ac enriched peak was analyzed by CHIP-seq with HSF1 and H3K27ac antibodies.


title: Metabolic adaptations underpin resistance to histone acetyltransferase inhibition [CRISPR]

overall_design: Genome-wide CRISPR screen in MOLM-13 with selective pressure from CBP/p300 HAT inhibition.


title: HSF1 activates ANXA11-mediated glutamine metabolism by super enhancer long non-coding RNA LINC00857 in colorectal cancer [array]

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

overall_design: After knocking down HSF1 via 2 specific siRNA, total lncRNA expression profiles was acquired. HCT116 cell was used to acquire expression profiles of a total of 60495 lncRNA after HSF1 knockdown.


title: Gene expression signature of EpCAMlow/PDPN+ and EpCAMhigh/PDPN- cancer cells in engineered human NSCLC HSAEC_4T53RD mouse xenograft model.

city: Tsukuba-shi

first: Shuntaro

last: Tsukamoto

state: Ibaraki

address: 5-1-3 Tokodai, Tsukuba-shi,

institute: Eisai Co., Ltd.

overall_design: HSAEC_4T53RD cells were subcutaneously inoculated into BALB/cSlc-nu/nu mice. Tumor cells were digested and mouse leukocyte and stromal cells were eliminated by using microbieads. Cancer cells were stained by using anti-EpCAM antibody and anti-PDPN antibody, and EpCAMlow/PDPN+ and EpCAMhigh/PDPN- cells were collected by FACS. Gene expression analysis was conducted using Agilent microarray.

first: Machiko

middle: I

last: Yagi

first: Ken

last: Sasai

first: Tsuyoshi

last: Akagi

first: Toshio

last: Imai

first: Hiroki

last: Muto


title: Metabolic adaptations underpin resistance to histone acetyltransferase inhibition

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

overall_design: Refer to individual Series


title: Suppression of heparan sulfation resensitizes YAP1-driven BRAF mutant melanoma to MAPK pathway inhibitors

city: Amsterdam

first: Pierre-Rene

last: Körner

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute (NKI)

summary: Preclinical and clinical data implicate the transcriptional co-activator YAP1 in resistance to multiple targeted therapies, including BRAF and MEK inhibitors. However, tumor subtypes driven by YAP1 activity and associated vulnerabilities are poorly defined. Here, we show particularly high YAP1 activity in the MITFlow/AXLhigh subset of melanoma cell lines and patient tumors characterized by resistance to MAPK pathway inhibition and broad receptor tyrosine kinase activity. To uncover genetic dependencies of melanoma cells with high YAP1 activity, we used a genome-wide CRISPR/Cas9 functional screen and identified SLC35B2, the 3′-phosphoadenosine-5′-phosphosulfate transporter of the Golgi apparatus, as an essential gene for YAP1-mediated drug resistance. SLC35B2 expression correlates with tumor progression, and its loss decreases heparan sulfate expression, reduces receptor tyrosine kinase activity, and sensitizes resistant melanoma cells to BRAF inhibition in vitro and in vivo. Thus, SLC35B2 is a target in YAP1-driven BRAF mutant melanoma for overcoming drug resistance to MAPK pathway inhibitors.

overall_design: YAP1 vs empty vector control

first: Sebastian

last: Dieter

first: Domenica

last: Lovecchio

first: Abhijeet

last: Pataskar

first: Martina

middle: K

last: Zowada

first: Pierre-René

first: Anna

last: Khalizieva

first: Olaf

last: van Tellingen

first: Dirk

last: Jäger

first: Hanno

last: Glimm

first: Reuven

last: Agami


title: Dual RNA-seq reveals a type 6 secretion system-dependent blockage of TNF-alpha signaling and BicA as a Burkholderia pseudomallei virulence factor important during gastrointestinal infection

city: Galveston

first: Steven

middle: G

last: Widen

state: Texas

address: 301 University Blvd

department: BMB

institute: University of Texas Medical Branch

summary: Melioidosis is a disease caused by the Gram-negative bacillus Burkholderia pseudomallei (Bpm), commonly found in soil and water of endemic areas. Naturally acquired human melioidosis infections can result from either exposure through percutaneous inoculation, inhalation, or ingestion of soil-contaminated food or water. Our prior studies recognized Bpm as an effective enteric pathogen, capable of establishing acute or chronic gastrointestinal infections following oral inoculation (Sanchez-Villamil, Tapia et al. 2020). However, the specific mechanisms and virulence factors involved in the pathogenesis of Bpm during intestinal infection are unknown. In our current study, we standardized an in vitro intestinal infection model using mouse primary intestinal epithelial cells (mIECs) and demonstrated that Bpm requires a functional T6SS for full virulence. Further, we performed dual RNA-seq analysis on Bpm-infected mIECs to evaluate differentially expressed host and bacterial genes in the presence or absence of a T6SS. Our results showed a dysregulation in the TNF- signaling via NF-B pathway in the absence of the T6SS, with some of the genes involved in inflammatory processes and cell death also affected. Analysis of the bacterial transcriptome identified virulence factors and regulatory proteins playing a role during infection, with association to the T6SS. By using a Bpm transposon mutant library and isogenic mutants, we showed that deletion of the bicA gene, encoding a putative T3SS/T6SS regulator, ablated intracellular survival and plaque formation by Bpm and impacted survival and virulence when using murine models of acute and chronic gastrointestinal infection. Overall, these results highlight the importance of the type 6 secretion system in the gastrointestinal pathogenesis of Bpm.

overall_design: Three replicates each of Mock infected or Burkholderia pseudomallei (wild-type or T6SS deleted) infected for 6 and 12 hours.

first: Javier

last: Sanchez-Villamil

first: Daniel

last: Tapia

first: Nittaya

last: Khakum

first: Alfredo

last: Torres


title: A tissue dissociation method optimized for ATAC-Seq and CUT&RUN in Drosophila pupal tissues [ATAC-Seq]

city: Ann Arbor

first: Elizabeth

last: Fogarty

state: MI

address: 1105 N. University Ave

institute: University of Michigan

summary: Chromatin accessibility, histone modifications and transcription factor binding are highly dynamic during Drosophila metamorphosis and drive global changes in gene expression as larval tissues differentiate into adult structures. Unfortunately, the presence of pupa cuticle on many Drosophila tissues during metamorphosis prevents enzyme access to cells and has limited the use of enzymatic in situ methods for assessing chromatin accessibility and histone modifications. Here, we present a dissociation method for cuticle-bound pupal tissues that is optimized for use with ATAC-Seq and CUT&RUN to interrogate chromatin accessibility and histone modifications. We show this method provides comparable chromatin accessibility data to the non-enzymatic approach FAIRE-seq, with only a fraction of the amount of input tissue required. This approach is also compatible with CUT&RUN, which allows genome-wide mapping of histone modifications with less than 1/10th of the tissue input required for more conventional approaches such as Chromatin Immunoprecipitation Sequencing (ChIP-seq). Our protocol makes it possible to use newer, more sensitive enzymatic in situ approaches to interrogate gene regulatory networks during Drosophila metamorphosis.

overall_design: ATAC-Seq data for L3 wing discs, 24h and 44h APF pupal wings; ATAC-Seq data for L3 wing discs with and without dissociation.

first: Elli

last: Buchert

first: Chris

last: Uyehara

middle: J

last: McKay

first: Laura

last: Buttitta


title: HSF1 activates ANXA11-mediated glutamine metabolism by super enhancer long non-coding RNA LINC00857 in colorectal cancer.

first: Jiaqiu

last: Li


title: Novel murine primary and orthotopically nasopharyngeal cancer models reveal LMP1 as a driver of metastasis

city: Chengdu, Cihna

first: zhang

last: lu

state: Sichuan

address: No.17 Renming road section3

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

institute: Sichuan University

summary: Current NPC models cannot reproduce the process of NPC tumorigenesis, which is critical for investigating the functions and mechanisms of the disease-associated factors in this malignancy.So,we aimed to generate primary and orthotopic NPC models from normal nasopharyngeal epithelium with NPC related genetic drivers. For this purpose, we cultured normal mouse nasopharyngeal organoids and induced Trp53 and Cdkn2a mutations by CRISPR/cas9 editing, together with Myc overexpression. We showed that these organoids could initiate primary NPC once transplanted into recipient mice subcutaneously or orthotopically. And we also tested the functions of LMP1 in these models and found that it dramatically promoted NPC metastases.

overall_design: Bulk RNA-seq of Normal nasopharyngeal organoids,Normal lung organoids; Trp53-/-;Myc;sgCdkn2a primary and metastasized tumor organoids, and Trp53-/-;Myc;sgCdkn2a; LMP1 primary and metastasized tumor organoids

first: Xudong

last: Wan

first: Jian

last: Wang

first: Lu

last: Zhang

first: Qian

last: Zhong

first: Musheng

last: Zeng

first: Chong

last: Chen


title: Single-cell RNA-seq of germ-free and specific pathogen-free small intestinal epithelium

city: Toronto

first: Derek

middle: Ka Long

last: Tsang

state: Ontario

address: 1 King's College Circle

department: Immunology

institute: University of Toronto

summary: The small intestinal epithelial barrier inputs signals from the gut microbiota in order to balance physiological inflammation and tolerance, and to promote homeostasis. Understanding the dynamic relationship between microbes and intestinal epithelial cells has been a challenge given the cellular heterogeneity associated with the epithelium and the inherent difficulty of isolating and identifying individual cell types. Here, we used single-cell RNA sequencing of small intestinal epithelial cells from germ-free and specific pathogen-free mice to study microbe-epithelium crosstalk at the single cell resolution.

overall_design: Expression profiling of small intestinal epithelial cells from germ-free mice and specific pathogen free mice by highthroughput sequencing

first: Dana

last: Philpott


title: Prolonged FOS Activity Disrupts A Global Myogenic Transcriptional Program By Altering 3D Chromatin Architecture in Primary Muscle Progenitor Cells

city: Durham

first: Rasim

last: Barutcu

state: NC

address: 6 Davis Drive

institute: ScitoVation

summary: Background  Quiescent (non-dividing) muscle satellite cells (SCs) transition into proliferating progenitor cells that differentiate to repair skeletal muscle after injury. Recently, the AP-1 family member, FOS, was found to be rapidly and transiently induced in SCs in response to muscle damage, and its activity is required for effective SC activation and muscle repair. However, why FOS is rapidly down-regulated before SCs enter the cell cycle as progenitor cells remains unclear. In addition, whether boosting FOS expression in primary cycling muscle progenitor cells can enhance their myogenic properties needs to be evaluated.     Methods  In this study, we established a lentiviral, doxycycline-inducible system to explore the molecular and functional consequences of continued FOS expression in SC-derived, cycling muscle progenitor cells ex vivo. Specifically, we performed cell growth and EdU incorporation assays to measure cellular proliferation; myotube formation assays to evaluate terminal differentiation potential; and RNA-Sequencing (RNA-Seq) in conjunction with high-throughput chromosome conformation capture (Hi-C) to uncover changes in gene expression and long-range chromatin interactions.   Results  Persistent FOS activity in cycling muscle progenitor cells modestly enhances progenitor cell proliferation, but severely antagonizes their ability to differentiate and form myotubes. Genome-wide RNA-Seq analysis revealed that ectopic FOS activity in cycling muscle progenitor cells suppresses a global pro-myogenic gene expression program, while activating a stress-induced Mitogen-Activated Protein Kinase (MAPK) transcriptional signature. Importantly, we found various chromosomal re-organization events in A/B compartments, TADs, and long-range genomic loops near FOS-regulated differentially expressed genes in cycling muscle progenitor cells ectopically expressing FOS.     Conclusions  Altogether, our results suggest that elevated FOS activity in proliferating muscle progenitor cells perturbs cellular differentiation by altering the 3-dimensional (3D) chromosome organization near critical pro-myogenic genes. This work highlights the crucial importance of tightly controlling FOS expression in the muscle lineage, and raises the possibility that in states of chronic stress or disease, persistent FOS activity in muscle stem and/or progenitor cells may actually disrupt the muscle forming process.

overall_design: RNA-seq and Hi-C  on FOS and GFP expressing muscle satellite cells

first: A

middle: R

first: Gabriel

last: Elizalde

last: Gonzalez

first: Kartik

last: Soni

first: John

last: Rinn

first: Amy

last: Wagers

first: Albert

last: Almada


title: Single-cell RNA sequencing of C3(1)-Tag cancer cells during invasion and colony formation.

city: Baltimore

first: Elana

middle: Judith

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

summary:
Purpose: Assess the cellular heterogeneity during the transition through partial EMT and MET in the spontaneous C3(1)-Tag breast cancer model.
Methods: We performed MULTI-seq single cell RNA sequencing analysis in two different ex vivo assays: the collagen assay that models invasion and the colony formation assay that models metastatic outgrowth. Briefly, organoids were isolated from 4 different mice and either plated directly into collagen I matrix or further dissociated into clusters and plated into Matrigel. Cells were removed from the matrix and dissociated into single cells at day 0 (12h in matrix), day 3 and day 5. For each day, cells were barcoded by mouse and matrix and flow sorted for live cells before being processed on the 10X Genomics platform for barcoding and library construction. As a control for batch effect during library construction for the different time point, we added a cell line control (4T1) at each day. Finally, the libraries were sequenced together using the NOVAseq.
Results: We sequenced 8,908 cells. After correction for batch effect, we performed a pseudotime analysis. We observed a temporal progression of the cells during invasion and colony formation. This transition is associated with a decrease in E-cadherin and an increase in vimentin expressions as well as other EMT genes during invasion and the opposite during colony formation. These results demonstrated at the single cell resolution that there is a temporal progression associated with EMT and MET during invasion and colony formation, respectively.

overall_design: single-cell RNA sequencing profile of C3(1)-Tag cancer cells during invasion and colony formation ex vivo.

first: Eloise

last: Grasset

first: Andrew

last: Ewald

first: Gaurav

last: Sharma


title: Quantitative analysis of standard diet and high fat diet-fed wild type and Sirt3 knockout mouse pancreatic islets transcriptomes.

city: Shanghai

first: Xing

last: Ming

state: Shanghai

address: Huangpu

department: Department of Endocrine and Metabolic Diseases

institute: Shanghai Jiaotong University School of Medicine

summary: To explore the underlying mechanism for the regulatory role of SIRT3 in pancreatic islets under standard and high fat diet feeding, we conducted RNA sequencing on the isolated islets from standard diet and high fat diet-fed wild type and pancreatic beta cell selective Sirt3 knockout mice (four groups in total). Three biological replicates were performed for each group.

overall_design: Examination of Sirt3 knockout in two different diet fed mice in pancreatic islets.

first: Alice

middle: S

last: Kong


title: Genome-wide localization profile (ChIP-seq) and differential expression profile upon RNAi treatment (RNA-seq) of L(3)mbt and its interactor in ovarian somatic cells[OSCs] in Drosophila

city: Yayoi, Bunkyo-ku

first: Hitomi

last: Yamamoto-Matsuda

state: Tokyo

department: Dept. Biol. Sci.

institute: the University of Tokyo

summary: L(3)mbt regulate the transcription of germ-specific genes in somatic cells but the detailed mechanism remains unclear. We performed ChIP-seq of L(3)mbt and a newly identified interactor in OSCs to elucidate the genome-wide localization. Then we performed RNA-seq of OSCs before and after RNAi treatment of L(3)mbt and its interactors and performed differential expression analysis.

overall_design: ChIP-seq of OSCs were performed in duplicate and RNA-seq of OSCs before and after RNAi treatment of L(3)mbt and its interactor were performed in triplicate.

first: Mikiko

last: Siomi


title: A tissue dissociation method optimized for ATAC-seq and CUT&RUN in Drosophila pupal tissues [CUT&RUN]

status: Public on Aug 14 2022

first: Elizabeth

last: Fogarty

overall_design: CUT&RUN for H3K27me3 in 24h APF Drosphila wings

first: Elli

middle: M

last: Buchert

middle: A

first: Chris

last: Uyehara

first: Daniel

last: McKay

first: Laura

last: Buttitta


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and CCAR2-/-  MDA-MB-231 cells Transcriptomes

city: tianjin

first: Qiangqiang

last: Liu

state: State...

address: weijin road94

summary: CCAR2 has been characterized as a key regulator of physiological and pathophysiological activities, such as DNA damage, senescence and tumorigenesis. However, the mechanism by which the functional stability of CCAR2 is regulated has yet to be elucidated.  We performed Next Generation Sequencing analysis in wild-type and CCAR2 knockout MDA-MB-231 cells to investigate global gene expression changes under normal or hypoxic condition.

overall_design: Here, we performed RNA-seq of CCAR2 deficient and WT MDA-MB-231 cells to further study the molecular changed between KO and WT.

first: Yanping

last: Zhao

first: Yushan

last: Zhu


title: Effect of supplementation of M9 0.4% glucose with root exudates of either tomato or maize on gene expression in WT Pseudomonas donghuensis P482

city: Gdansk

first: Dorota

middle: Magdalena

last: Krzyzanowska

state: Pomeranian

address: Abrahama 58

department: Intercollegiate Faculty of Biotechnology UG&MUG

institute: University of Gdansk

summary:
To investigate and compare the influence of root exudates of tomato and maize on Pseudomonas donghuensis P482, we have grown the strain up to a stationary phase in M9 0.4% glucose medium supplemented with maize exudates (Maize), tomato exudates (Tomato) or without supplementation (Control).
We then performed differential gene expression analysis, identifying changes in transcriptome profiles between each treatment (Tomato, Maize) and the Control as reference conditions, and between the two treatments.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for P482 cells grown in an unsupplemented medium (Control) and in medium supplemented with either tomato exudates (Tomato) or maize exudates (Maize).

first: Sylwia

last: Jafra


title: Combined single-cell tracking and omics improves blood stem cell fate regulator identification

city: Basel

first: Arne

last: Wehling

state: Basel-Stadt

address: Mattenstrasse 24

department: Department of Biosystems Science and Engineering

country: Switzerland

institute: ETH Zurich

summary:
HSCs can undergo asymmetric lysosomal division, marking the daughter receiving less lysosomes for metabolic activation and its corresponding sister for quiescence (Loeffler et al. 2019, Nature). We use scRNA-Seq to trace the earliest fate regulators controlling this fate divergence in HSC daughter cells.
Methods: We use quantitative time-lapse imaging of murine HSCs to detect their first in-vitro division. Cells are isolated with a micromanipulator and submitted to Smart-Seq2 RNA sequencing. Single-end reads were mapped to the M 21 release mouse genome using STAR aligner. Raw Counts are extracted with featureCounts.
Results: We successfully isolated 474 high-quality single cell transcriptomes from HSC daughter cells and mapped their transcriptional profiles to the observed inheritance.

overall_design: Single-cell mRNA profiles of HSC daughters isolated from 12–19 week old, male C57BL/6JRj mice. We use quantitative time-lapse imaging of murine HSCs to detect their first in-vitro division. Cells are isolated with a micromanipulator and submitted to Smart-Seq2 RNA sequencing with their inheritance and relationship recorded. To match raw read files to paired daughter cells, use the metadata .csv files provided. Daughter cells share the same 'Movie', 'Experiment', 'Position' and 'Colony'. The column 'LysosomeInheritanceLabel' identifies each daughter cell in the pair as either having received less or more lysosomes than the corresponding other sister. Fastq names can be retrieved from the column 'FastQNames'.

first: Dirk

last: Loeffler

first: Tobias

last: Kull

first: Cinzia

last: Donato

first: Barbara

last: Szczerba

first: Yang

last: Zhang

first: Berthold

last: Göttgens

first: Nicola

last: Aceto

first: Timm

last: Schroeder

first: German

last: Ortega Camargo

first: Andreas

last: Moor

first: Minkyoung

last: Lee


title: Transcriptome of yw fly, L(3)mbt mutant fly and Lint-O mutant fly were performed in triplicate in Drosophila melanogaster

city: Bunkyo-ku

first: Soichiro

last: Yamanaka

institute: The University of Tokyo

summary: L(3)mbt regulates the transcription of germ-specific genes in somatic cells but the detailed mechanism remains unclear. We performed ChIP-seq of L(3)mbt and a newly identified interactor in OSCs to elucidate the genome-wide localization. Then we performed RNA-seq of OSCs before and after RNAi treatment of L(3)mbt and its interactors and performed differential expression analysis.

overall_design: RNA-seq of yw fly, L(3)mbt mutant fly and Lint-O mutant fly were performed in triplicate.

first: Mikiko

last: Siomi


title: Effect of depletion of TET3 on gene expression of HTR8-SVneo trophoblast cells.

city: Nanjing

first: Shuwen

last: Cheng

state: Jiangsu

address: 22 Hankou Road

institute: Nanjing University

summary: To investigate the function TET3 in the regulation of DNA methylation, we established HTR8-SVneo cell lines in which target gene has been knocked down by siRNA. We then performed gene expression profiling analysis using data obtained from RNA-seq for three replicates.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HTR8-SVneo cells and its KD derivatives (siTET3).

first: Xu

last: Yetao


title: T cell differentiation, lineage commitment and plasticity in cancer: a  multi-dimensional approach from the molecular mechanism to the patients

city: Paris

first: Sebastian

last: Amigorena

address: 26 rue D'ulm

country: France

institute: Institut Curie

summary: Cancer immunotherapy (including by checkpoint inhibitors) aims to “re-program” cells of the immune system, and most importantly CD8+ T lymphocytes, but also CD4+ T helper and regulatory cells, to reject tumors. Understanding this re-programing is both a major fundamental and translational research goal, relevant to the fundamental mechanisms of fate decision / lineage commitment, and to immunotherapy and vaccination in general. Differentiation is driven by gene expression programs that are themselves controlled epigenetically.

overall_design: RNA-seq from FFPE tissue blocks from resected from NSCLC tumors

first: Agathe

last: Givelet

first: Marine

last: Lefevre

first: Simon

last: Lefranc

first: Sarah

last: Lagha

first: Anne-Sophie

last: Tedesco

first: Nicolas

last: Girard

first: Audrey

last: Rapinat

first: David

last: Gentien

first: Sylvain

last: Baulande

first: Antonela

last: Merlotti

first: Benjamin

last: Sadacca

first: Joshua

last: Waterfall


title: Dll1 dependent heterogeneity of tumor and cancer fibroblasts

city: St. Louis

first: MALAY

last: HALDAR

state: MO

address: 7751 charing square lane

department: Pathology and Immunology

institute: Washington University in St. Louis

summary: To survey the diverse  tumor cell populations of aggressive luminal breast cancer (non-TNBC) at a cellular level, we utilized Dll1+ and Dll1- tumors from a recently published PyMT-Dll1mCherry reporter breast cancer mouse model.

overall_design: Dll1+ and Dll1- tumors  were harvested to generate single cell suspensions and CD45- live cells were FACS sorted.

first: Ajeya

last: Nandi

first: Tsun

last: To

first: Malay

last: Haldar

first: Rumela

last: Chakrabarti


title: RNA-Seq Exploration of the Influence of Stress on Meat Quality in Spanish Goats

city: fort valley

first: phaneendra

last: batchu

state: georgia

address: 1005 State univerity drive

department: Animal Science

institute: fort valley state university

summary: Studies exploring the transcriptome of stress and its effects on meat quality are very limited, particularly in goats.  Fifty-four male Spanish goats (8-mo old; BW = 29.7 ± 2.03 kg) were randomly subjected to one of three treatments (TRT; n = 18 goats / treatment): (i) transported for 180 min, (ii) transported for 30 min, or (iii) held in pens (control) to analyze the transcriptome of stress and meat quality in goats using RNA-seq technology. Blood samples were collected before and after treatment, and meat samples were collected after humane slaughter for stress hormone, meat quality (Longissimus dorsi), and transcriptomic analysis. Plasma epinephrine concentrations were higher (P < 0.01) in 180 min and 30 min groups compared to the control group; however, norepinephrine concentrations were not affected by the treatment. Muscle glycogen concentrations (15 min postmortem) were lower (P < 0.01) in both 30 min and 180 min groups compared to the control group. Calpastatin levels were higher (P < 0.01) in 180 min and 30 min groups than the control group. Warner-Bratzler shear force values of loin chops were the highest in the 180 min group (4 ± 0.15, kg), lowest in the control group (3.51 ± 0.10, kg), and intermediate in the 30 min group (3.78 ± 0.09, kg; P < 0.01) both at day 1 and day 6 aging time.  Additionally, desmin levels of day 6 samples were lowest in the control group, highest in 180 min group, and intermediate in 30 min group (P < 0.05).  RNA-seq results showed that a total of 10,633 genes were differentially expressed (5,194 up regulated; 5,439 down regulated) among all comparisons (blood and day 1 and day 6 muscle samples). Among these differentially expressed genes (DEGs), KLF9, AMPK, FOXO3, PTX3, GADD45, PTPN1, CASP7, MAPK4, HSPA12A, and JAK-STAT were probably associated with the effects of stress on skeletal muscle proteins and involved in biological process such as cellular response to corticosteroid stimulus, endoplasmic reticulum stress, insulin resistance, DNA repair, apoptosis, MAPK cascade and regulation of proteolysis.  The KEGG analysis revealed that AMPK and JAK-SAT signaling pathways and autophagy were among the top 20 enriched pathways in our treatment comparisons. The results provide an understanding of the genes and pathways involved in stress responses and related changes in postmortem muscle metabolism and meat quality characteristics in goats.

overall_design: Prior to beginning of the experiment, the protocols for this research were duly reviewed and approved by the Animal Care and Use Committee at Fort Valley State University.  Fifty-four intact male Spanish goats (8-mo old; BW = 29.7 ± 2.03 kg), raised primarily on free range pasture with a grain supplement and with ad libitum access to hay and water, were used in this experiment.  The animals were randomly subjected to one of three stress treatments (TRT; n = 18 goats/treatment): (i) transported for 30 min (approx. 50 km), (ii) transported for 180 min (approx. 200 km), or (iii) held in pens (control), on two different days. A livestock trailer was used to transport the goats and the ambient temperatures were -3.0 ± 1.0 ºC and 1.0 ± 1.0 ºC on day 1 and 2, respectively. Feed was withheld overnight prior to the day of the experiment. Goats were slaughtered using humane procedures.

first: Aditya

last: Naldurtiker

first: Phaneendra

last: Batchu

first: Brou

last: Kouakou

first: Thomas

middle: H

last: Terrill

first: Arshad

last: Shaik

first: Govind

last: Kannan


title: RNA-seq transcriptome analysis of HCMV (AD169) and mock infected MRC5 fibroblasts

city: Rochester

last: Munger

state: New York

address: 601 Elmwood Ave, Room 3-8828

department: Biochemistry & Biophysics

institute: University of Rochester

summary: We employed RNA-seq to map the transcriptome of human MRC5 fibroblasts during HCMV infection with AD169. These data will highlight the ways in which the HCMV infection alters RNA levels during infection.

overall_design: Infect quiescent MRC5 fibroblasts in 15-cm dishes at MOI = 3 and harvest samples for RNA-seq at 48 hpi.

first: Xenia

last: Schafer


title: Fibroblast growth factor receptor 3 overexpression mediates ALK inhibitor resistance in ALK-rearranged non-small cell lung cancer

city: Koto-ku

first: Ryohei

last: Katayama

department: The Cancer Chemotherapy Center

institute: Japanese Foundation for Cancer Research

summary: The rearrangement of anaplastic lymphoma kinase (ALK) occurs in 3%-5% of patients with non-small cell lung cancer (NSCLC) and confers sensitivity to ALK-tyrosine kinase inhibitors (TKIs). For the treatment of patients with ALK-rearranged NSCLC, various additional ALK-TKIs have been developed. Ceritinib is a second-generation ALK-TKI and has shown great efficacy in the treatment of patients with both newly diagnosed and crizotinib, a first-generation ALK-TKI, refractory ALK-rearranged NSCLC. However, tumors can also develop ceritinib resistance. This may result from secondary ALK mutations, but other mechanisms responsible for this have not been fully elucidated. In this study, we explored the mechanisms of ceritinib resistance by establishing ceritinib-resistant, echinoderm microtubule-associated protein-like 4 (EML4)-ALK-positive H3122 cells and ceritinib-resistant patient-derived cells. We identified a mechanism of ceritinib resistance induced by bypass signals that is mediated by the overexpression and activation of fibroblast growth factor receptor 3 (FGFR3). FGFR3 knockdown by small hairpin RNA or treatment with FGFR inhibitors was found to resensitize the resistant cells to ceritinib in vitro and in vivo. FGFR ligands from either human serum or fetal bovine serum were able to activate FGFR3 and induce ceritinib resistance. A detailed analysis of ceritinib-resistant patient-derived specimens confirmed that tyrosine-protein kinase Met (cMET) amplification induces ceritinib resistance. Amplified cMET counter-activated EGFR and/or Her3, and induced ceritinib resistance. These results reveal multiple ceritinib resistance mechanisms and suggest that ceritinib resistance might be able to overcome by identifying precise resistance mechanisms.

overall_design: comparison of the gene expression between H3122 parental cells and ceritinib, ALK inhibitor, resistant H3122-LR2 or H3122-LR3 cells

first: Takuya

last: Sakashita

first: Noriko

last: Yanagitani

first: Sumie

last: Koike

first: Siew-Kee

last: Low

first: Satoshi

last: Takagi

first: Satoko

last: Baba

first: Kengo

last: Takeuchi

first: Makoto

last: Nishio

first: Naoya

last: Fujita


title: Hypolipidemic effects of Zexie Decoction on the lipid profile in hyperlipidemia rats by RNA-sequencing

status: Public on Aug 13 2022

city: Fuzhou

first: wenjin

last: Lin

address: Road 54

institute: Fujian Academy of Medical Sciences

summary: RNA sequencing and transcriptome analysis were performed collaboratively, including analysis of differentially expressed genes (DEGs), GO functions and KEGG pathway analysis. The results showed that 1981 (1370 upregulated and 611 downregulated) DEGs were identified in the HFD group compared to those in the CON group. 474 DEGs (350 upregulated and 124 downregulated) were detected in the ZXD group compared to those in the HFD group. Furthermore, GO analysis revealed that DEGs were mainly involved in the following functions: developmental process, response to external stimulus, ion transport, alcohol binding and plasma membrane part. Pathway analysis suggested that these DEGs were significantly enriched in bile secretion, malaria, cell adhesion molecules, retinol metabolism, the sphingolipid signaling pathway, chemical carcinogenesis, and the T cell receptor signaling pathway. In conclusion, our study demonstrated that ZXD alleviated the lipid metabolism disorder caused by hyperlipidemia through multiple mechanisms, which provided vital scientific evidence for further pharmacological studies of ZXD.

overall_design: In this study, we aimed to investigate the hyperlipidemic activity and the potential molecular mechanisms of ZXD in hyperlipidemia rats at the transcriptional level.

first: Xiaomei

last: Xu

first: Wenjin


title: Effect of Combinatorial Extracellular Matrix and Substrate Stiffness on Gene Expression of Activated Hepatic Stellate Cells

city: Urbana

first: Dr. Gregory

last: Underhill

address: 1406 West Green Street

institute: University of Illinois at Urbana Champaign

summary: Understand mechanisms of NAFLD related liver fibrosis

overall_design: Gene expression of Human Hepatic Stellate Cells  as a function underlying Extracellular Matrix Composition and Substarte Stiffness

first: Ishita

last: Jain

first: Gregory


title: Genomic survey of NPF and NRT2 transporter gene families in five inbred maize lines and their responses to pathogens infection

city: Beijing

first: Xinyao

last: Xia

address: West Yuanmingyuan Road, Haidian District, Beijing

institute: caas

summary: To further confirm whether the expression of NRT genes were influenced by pathogen infection, maize leaves were sampled at 0h, 24h, 40h, 60h and 96h post inoculation with wild-type strain Colletotrichum graminicola, the causing agent of maize anthracnose disease.

overall_design: Maize leaves were sampled at 0h, 24h, 40h, 60h and 96h post inoculation with wild-type strain Colletotrichum graminicola, the causing agent of maize anthracnose disease.

first: Wende

last: Liu

first: Hanxiang

last: Wu


title: Effect of FOXA2 knockout (KO) on transcriptome wide gene expression in hepatic progenitors (HP) and mature hepatocytes (MH)

city: Mölndal

first: Ramy

last: Elgendy

state: Göteborg

address: Pepparedsleden 1

institute: AstraZeneca

summary: iPSC generated from healthy controls and FOXA2 knockout (KO) were allowed to undergo hepatic differentiation, and RNA was collected from hepatic progenitors (DAY 10) and mature hepatocytes (DAY21) for next-generation sequencing.

overall_design: Transcriptomic profile of FOXA2 KO iPSCs - derived progenitors and mature hepatocytes was compared with healthy control from two biological replicates.

first: Maryam

last: Aghadi

first: Essam

last: Abdelalim


title: Tfam-deficiency mediated mitochondrial disorder affects Langerhans cell maintenance and function

city: Guangzhou

first: Jun

last: Zhang

address: No.2 Lujing road

department: Dermatology Hospital

institute: Southern Medical University

summary: Langerhans cells (LCs) are skin-resident professional antigen-presenting dendritic cells (DCs) to maintain skin homeostasis. The number and function of LCs are significantly reduced during the skin aging processes, which is closely related to the aging-associated skin disorders. However, the reasons underlying the changes of LC features with age are uncertain. Mitochondria are well known to be the main powerhouse to regulate cell fitness and function, and a decline in mitochondrial quality and activity was associated with normal aging and correlated with the development of a wide range of age-related diseases. So far, it is unknown if mitochondrial abnormality is involved in skin disorders by regulating LC homeostasis. The mitochondrial transcription factor A (Tfam) acts as a nuclear-encoded transcription factor and plays a critical role in mitochondrial stabilization. To explore the role of mitochondrial quality in LC homeostasis, we generated the mice with conditional deletion of Tfam in LC lineage. We found that Tfam-deficient LCs exhibits mitochondrial abnormality including morphology and membrane permeability of mitochondria, decreased cell number as well as maturation, whereas increased phagocytosis and inflammatory response of LCs. Interestingly, age-LCs from human skin have lower Tfam expression compared to young-LCs, and have the similar features with Tfam-deficient LCs analyzed by scRNA sequence (HRA000395). Thus, our data highlight that Tfam-mediated mitochondrial stability is essential for epidermal LC maintenance and function, which might be explain the states of increased susceptible to skin infections and rising incidence of cutaneous tumor in the elder. This is the first time to investigate the effect of mitochondria abnormality on LC homeostasis, which might be helpful for therapeutic interventions in aging-associated skin pathologies.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Epidermal LCs from 4-week old wild type (WT) and CD11cCreTfamfl/fl mice

first: Yingping


title: Secreted fungal effector triggers allergic inflammation via Toll-like receptor 4 to enable lethal infection

status: Public on Aug 12 2022

city: San Francisco

first: Eric

middle: V

last: Dang

state: CA

address: 600 16th Street

institute: UCSF

summary: Invasive fungal pathogens are major causes of human mortality and morbidity1,2.  While numerous secreted effector proteins that reprogram innate immunity to promote virulence have been identified in pathogenic bacteria, there are no examples of analogous secreted effector proteins produced by human fungal pathogens.  Cryptococcus neoformans, the most common cause of fungal meningitis and a major AIDS pathogen, induces a pathogenic type 2 response characterized by pulmonary eosinophilia and alternatively activated macrophages3-8. Here, we identify Cpl1 as an effector protein secreted by C. neoformans that drives alternative activation (also known as M2 polarization) of macrophages to enable pulmonary infection. We observed that Cpl1-enhanced macrophage polarization requires Toll-like receptor 4, best known as a receptor for bacterial endotoxin, but is also a poorly understood mediator of allergen-induced type 2 responses9-12. We show that this effect is due to Cpl1 itself and not contamination by lipopolysaccharide. Cpl1 is essential for virulence, drives polarization of interstitial macrophages in vivo, and requires type 2 cytokine signaling for its impact on infectivity. Strikingly, C. neoformans selectively associates with polarized interstitial macrophages during infection, suggesting a mechanism by which C. neoformans generates its own intracellular replication niche within the host.  This work identifies a novel circuit whereby a secreted effector protein produced by a human fungal pathogen reprograms innate immunity, revealing an unexpected role for Toll-like receptor 4 in pathogenesis of infectious disease.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for murine bone marrow-derived macrophages stimulated under different conditions with three replicates in each condition

first: Susan

last: Lei

first: Hiten

last: Madhani


title: Integrative Analysis Defines Distinct Prognostic Subgroups of Intrahepatic Cholangiocarcinoma

city: Heidelberg

first: Stephanie

last: Roessler

address: Im Neuenheimer Feld 224

institute: Heidelberg University Hospital

summary: Intrahepatic cholangiocarcinoma (iCCA) is the second most common primary liver cancer. It is defined by cholangiocytic differentiation and has poor prognosis. Recently, epigenetic processes have been shown to play an important role in cholangiocarcinogenesis. We performed an integrative analysis on 52 iCCAs using both genetic and epigenetic data with a specific focus on DNA methylation components. We identified four major iCCA subgroups with widespread genomic and epigenomic differences and prognostic implications. Furthermore, our data suggest differences in the cell-of-origin of the iCCA subtypes.

overall_design: We conducted genome wide DNA methylation analyses of intrahepatic cholangiocarcinoma (iCCA) and non-neoplastic bile duct.

first: Reka

last: Toth


title: scRNA-seq analysis of patient-derived luminal breast cancer xenografts

city: Aurora

first: Jessica

last: Finlay-Schultz

state: CO

department: Pathology

institute: University of Colorado Denver Anschutz Medical Campus

summary: Primary breast cancer xenografts

overall_design: Primary breast cancer xenografts, no treatments, dissociated and used for scRNA-seq

first: Kiran

last: Paul

first: Olivia

last: McGinn

first: Peter

last: Kabos

first: Carol

last: Sartorius


title: Induction of senescence upon loss of the Ash2l subunit of histone H3K4 methyltransferase complexes (RNA-Seq)

city: Aachen

first: Chao-Chung

last: Kuo

state: NRW

address: Pauwelsstrasse 30

department: IZKF Genomics Facility

institute: RWTH Aachen University Hospital

summary: Post-translational modifications of core histones participate in controlling the expression of genes. Methylation of lysine 4 of histone H3 (H3K4) is associated with open chromatin and gene transcription. This histone mark is catalyzed by type 2 lysine methyltransferase (KMT2) complexes. In mammals, these consist of one of 6 different KMT2 enzymes, each associated with 4 core subunits, WDR5, RBBP5, ASH2L and DPY30, which are necessary for catalytic activity. The knockout of Ash2l is embryonically lethal in mice as well as in adult animals when hepatocytes or hematopoietic cells are targeted. To expand on the mechanistic understanding of Ash2l, we have used mouse embryo fibroblasts (MEFs). The knockout of Ash2l resulted in the downregulation of H3K4me3 at a large number of promoters, preferentially those associated with CpG islands, accompanied with broad repression of gene expression. The consequence in MEFs was induction of senescence concomitant with a set of down-regulated signature genes. Thus, although the loss of Ash2l in MEFs has broad and complex consequences on the transcriptional program, the biological consequences were distinct, culminating in senescence.

overall_design: Two independently generated mouse embryo fibroblast lines (from two different litters) with floxed exon 4 of Ash2l. These express Cre-ER and were immortalized using shArf. RNA samples were collected from both lines -/+ 4-hydroxytamoxifen at day 5.

first: Agnieszka

last: Bochyńska

first: Alexander

middle: T

last: Stenzel

first: Roksaneh

last: Sayadi Boroujeni

first: Mirna

last: Barsoum

first: Weili

last: Liang

first: Philip

last: Bussmann

first: Ivan

last: Costa

first: Juliane

last: Lüscher-Firzlaff

first: Bernhard

last: Lüscher


title: The matricellular protein SPARC induces inflammatory interferon-response in macrophages during aging

city: New Haven

first: Vishwa Deep

last: Dixit

state: CT

address: 310 Cedar St

department: Comparative Medicine

institute: Yale University

summary: SPARC is a member of matricellular protein, and emerging evidence suggests that it plays a critical role in integrated metabolic and inflammatory responses. However, the mechanism how SPARC activates inflammation is still unanswered. Here we showed that excess SPARC induced sterile inflammation, and converted anti-inflammatory macrophage to pro-inflammatory macrophage. RNA-sequencing analysis revealed that SPARC elicits interferon-stimulated genes (ISGs) by transcription factor IRF7. SPARC also dampened mitochondrial respiration that induced pro-glycolytic inflammatory macrophage. Altogether, we discovered a mechanism how SPARC triggers sterile inflammatory response in anti-inflammatory macrophage, and this implicates the potential role of SPARC as a modulator of anti-inflammatory macrophages to maintain tissue homeostasis.

overall_design: Examination of RNA expression changes in mouse peritoneal macrophages from thioglycollate (TG) injected or IL-4 complex (IL4) injected mice, with or without treatment of SPARC ex vivo.

first: Seungjin

last: Ryu


title: ER, mitochondria and ISR regulation by mt-HSP70 and ATF5 upon procollagen misfolding (primary cells)

city: Bethesda

first: Sergey

last: Leikin

state: Maryland

department: NICHD

institute: National Institutes of Health

summary: We used bulk RNA sequencing (bulk RNAseq) in primary osteoblast cultures to validate scRNASeq and srRNASeq findings on osteoblast cell stress response pathway to misfolding of type I procollagen with Gly610->Cys substitution in the triple helical region of alpha2(I) chain.

overall_design: Primary parietal bone cells were isolated, cultured, and differentiated as described in Gorrell et al, Adv Sci, 2022

first: Laura

last: Gorrell


title: Liver transcriptome analysis after DF-006 treatment in an HBV mouse model

status: Public on Aug 11 2022

city: Shanghai

first: Tony

last: Xu

address: 69 Yuanfeng Road, Baoshan District

institute: Shanghai Drug Farm Biotechnology Co.

summary: A new chemical entity, DF-006, has been shown to suppress HBV replication in an AAV-HBV mouse model. DF-006 activates NF-kB signaling. In order to elucidate the mechanism of action of DF-006, specifically the genes expression stimulated in the liver that mediated its anti-HBV efficacy, we perform deep sequencing of RNA samples taken from AAV-HBV mice 4 hours after 10 μg/kg DF-006 oral administration or vehicle control.  AAV-HBV mouse models were established by injecting male C57B6/J mice with 1011 vg/mouse AAV-HBV (genotype D, serotype ayw, GenBank accession number: KX449554). Dosing with DF-006 resulted in a statistically significant increase of gene expression for 1,685 genes in the liver. We performed an over-representation analysis for Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment and found 53 pathways were significantly enriched. The top 10 pathways included those that involved viral infection (e.g., herpes, influenza, Epstein-Barr, hepatitis B, measles) and those that involved host innate responses (TNF, osteoclast differentiation, NF-κB, toll-like receptor, RIG-I -like receptor). qPCR analysis confirmed genes that are directly or indirectly induced through NF-kB pathway and are reported before to play a role in HBV suppression.

overall_design: Liver mRNA profiles of AAV-HBV mice 4 hours after vehicle or 10 μg/kg DF-006 oral administration

first: Jieqing

last: Fan

first: Yuning

last: Wei


title: Transcriptome analysis of siVCP and siNC in ARP1 cells

city: Nanjing

first: Rong

middle: Fang

address: 138 Xianlin Road

institute: Nanjing Unveristy of Chinese Medicine

summary: Transcriptome sequencing was used to analyze changes in related signaling pathways and gene expression in ARP1 cells when VCP was knocked down.

overall_design: Examination of  two cell types

first: Rongfang


title: The lncRNA RUNX1-IT1 promotes pancreatic cancer progression by inducing C-FOS expression

city: Chongqing

first: Junfeng

last: Zhang

address: Gaotan Yanzheng Street, Shapingba District

institute: First Affiliated Hospital of Army Medical University

summary: The functional analysis of RUNX1-IT1 in tumors is relatively lacking, and its role and mechanism in pancreatic have not been reported. RUNX1-IT1 is transcribed from the intron of the RUNX1 gene, which plays an important role in solid tumors, and its abnormal expression is closely associated with cancer progression. However, due to the lack of systematic research, the regulatory mechanism and important downstream targets of RUNX1-IT1 and RUNX1 in PC are unclear. To investigate the downstream pathway of RUNX1-IT1 and RUNX1, we performed RNA-seq using two PANC-1 cell groups: RUNX1-IT1 knockdown and control, and RUNX1 knockdown and control.

overall_design: PANC-1 cells were transfected with RUNX1-IT1 Smart Silencer and control Smart Silencer, and sh-RUNX1 and control lentiviral vectors. Total RNA was extracted from the samples using the TRIzol method. The total RNA extracted from the samples was tested by a NanoDrop 2000 and denaturing gel electrophoresis. RNA Sequencing Analysis were performed after the sample quality control.

first: H

last: Wang

first: Songsong

last: Liu


title: Translational efficiency in mock- and heat-treated N.benthamiana leaves

city: Daejeon

first: Hyo-Jun

last: Lee

address: Gwahak-ro

department: Plant Systems Engineering Research Center

institute: Korea Research Institute of Bioscience and Biotechnology

summary: Nicotiana benthamiana is a widely used organism for expression of foreign proteins. To increase protein abundance, overexpression promoters have been developed. However, several proteins cause negative effects on plant growth and development when they are overexpressed. Therefore, overexpression promoters cannot be widely used to generate transgenic plants that produce foreign proteins. In this study, we tried to find stress-inducible promoters which specifically express downstream genes when plants were exposed to stress conditions. By RNA-sequencing analysis of heat- and wound-treated plants, we found that NbHSP20 promoters can be used as a heat-inducible promoters to express foreign proteins in N. benthamiana. The RNA-sequencing data were deposited in GSE210621. In addition to finding mRNA sequencing, we performed polysome RNA sequencing to find genes showing high translational efficiency at high temperature.

overall_design: Three biological replicates of mock- and heat-treated N.benthamiana total RNA and polysome RNA were analyzed

first: Seung

middle: Y

last: Shin

first: Ah

first: Suk

last: Kwon

first: Ki-Beom

last: Moon

first: Hyun-Soon

last: Kim

first: Jae

last: Jeon


title: Differential Expression Profiles and Bioinformatics Analysis of tRNA-derived Small RNAs in Epicardial Adipose Tissue of Patients with Atrial Fibrillation

first: Lei

last: Zhao

state: Beijing

address: Gongti Nanlu No.8

institute: Beijing Chaoyang Hospital

summary: Atrial fibrillation (AF) is the most common sustained arrythmia, but the potential molecular indicators involved in structural and electronical remodeling remains to be clarified. Epicardial adipose tissue (EAT), a visceral fat depot surrounding the heart, is increasingly recognized to be metabolically active and has been proposed with an arrthymogenicity nature. It is able to secret a myriad of bioactive molecules, including exosomes carrying tRNA derived small RNAs (tsRNAs). Accumulating findings have suggested that these specific tsRNAs dynamically impact fundamental cellular processes, but there are no studies discovering the association between tsRNAs of EAT and AF, and their interactions and potential signaling pathways remain to be elucidated.

overall_design:
Epicardial adipose samples collected from patients with persistent non-valvular AF (n=6) and sinus rhythm (n=6) were profiled using RNA-sequencing on the  Illumina NextSeq 500 system using NextSeq 500/550 V2 kit (#FC-404-2205, Illumina).
Please note that SSF and SYL are patients with sinus rhythm and heart failure, ZYQ is a patient with atrial fibrillation and heart failure.


title: Expression profiles of tRNA-derived small RNAs in epicardial adipose tissue of patients with heart failure

summary: Recent studies have reported tRNA-derived small RNAs (tsRNAs) expression profiles in various tissue types; however, tsRNAs expression profile in human epicardial adipose tissue (EAT) remains undefined. This work aimed to compare tsRNAs expression patterns in EAT between the heart failure (HF) and non-HF groups.

overall_design:
Epicardial adipose samples collected from patients with heart failure  (n=5) and control (n=5) were profiled using RNA-sequencing on the  Illumina NextSeq 500 system using NextSeq 500/550 V2 kit (#FC-404-2205, Illumina).
Please note that SSF and SYL are patients with sinus rhythm and heart failure, ZYQ is a patient with atrial fibrillation and heart failure.


title: The cAMP-PKA signaling pathway regulates hyphal growth, conidiation, trap morphogenesis, stress tolerance and autophagy in Arthrobotrys oligospora

city: kunming

first: Meichen

last: Zhu

state: Yunnan

address: kunmingshi

department: School of Life Sciences

institute: yunnandaxue

summary: Signal transduction plays a crucial role in defending against external environmental challenges, which can modulate the cellular response to external stimuli. cAMP/PKA signaling pathway is one of the most important signaling circuits and is evolutionarily conserved in eukaryotes. A. oligospora is a typical nematode-trapping fungi that can specialize adhesive network traps to kill nematodes after sensing the signals. To elucidate the biological roles of cAMP-PKA signaling pathway, we characterized an adenylate cyclase orthologous protein, AoAcy, a cAMP-dependent protein kinase regulator, AoPKaR, and two cAMP-dependent protein kinase catalytic subunits, AoPKaCs in A. oligospora. Furthermore, phenotypic analysis of the gene disruption strains showed that the deletion of AoAcy resulted in a significant decrease in the content of cAMP and arthrobotrisins, and the results indicated that AoAcy, AoPKaR and AoPKaC1 were involved in the hyphae growth, trap morphogenesis, sporulation, stress resistance and autophagy. In addition, AoAcy and AoPKaC1 were also participated in the regulation of mitochondria, thereby affecting energy metabolism. While AoPKaC2 only affected sporulation, the number of nuclei and autophagy. Collectively, these findings highlight the essential role of cAMP/PKA signaling pathway in A. oligospora and provide insights into the regulation mechanisms of signaling pathways in trap formation and sporulation.

overall_design: RNA-seq analysis between six wild-type samples and six ΔAorlmA mutant samples, with three biological replicates per sample, and prediction of multiple cytological processes that may affect trap formation in Arthrobotrys oligospora.

first: Xuemei

last: Li

first: Yankun

first: Zhengyi

last: Zhen

first: Yaqing

last: Zheng

first: Jinkui

last: Yang


title: Alzheimer’s disease-associated U1 snRNP splicing dysfunction causes neuronal hyperexcitability and cognitive impairment

city: Memphis

first: Yingxue

last: Fu

state: Tennessee

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

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

overall_design: Refer to individual Series


title: Changes in bone marrow tumor and immune cells correlate with durability of remissions following BCMA CAR T therapy in myeloma

city: Decatur

first: Akhilesh

last: Kaushal

state: GA

address: 1760 Haygood street

institute: Emory University

summary: Chimeric antigen-receptor (CAR) T cells targeting B-cell maturation antigen (BCMA) lead to high response rates in myeloma, but most patients experience recurrent disease. We combined several high-dimensional approaches to study tumor/immune cells in the tumor microenvironment of myeloma patients pre- and post-BCMA-specific CAR T therapy. A lower diversity of pre-therapy T-cell-receptor (TCR) repertoire, presence of hyperexpanded clones with an exhaustion phenotype, and BAFF+PD-L1+ myeloid cells in the marrow correlated with shorter progression-free survival (PFS) following CAR T therapy. In contrast, longer PFS was associated with increased proportion of CLEC9A+ dendritic cells (DCs), and CD27+TCF1+ T cells with diverse T-cell receptors, followed by emergence of T cells expressing marrow-residence genes. Residual tumor cells at initial response express stem-like genes and tumor recurrence in patients with long PFS was associated with emergence of new dominant clones. These data illustrate dynamic interplay between endogenous T, infused CAR T, myeloid/DC and tumor compartments that impacts durability of response following CAR T therapy in myeloma.

overall_design: Bone marrow mononuclear cells (BMMNCs) were obtained from Multiple Myeloma (MM) patients before and after therapy with BCMA CAR T therapy. Bone marrow mononuclear cells (BMMNCs) were isolated using density gradient centrifugation followed by cryopreservation. Thawed BMMNCs were stained with custom panels of metal-conjugated antibodies at manufacturer-suggested concentrations (Fluidigm). Viable cells and doublets were excluded using cisplatin intercalator and DNA content with iridium intercalator. Equal numbers of cells from each donor were utilized when data were concatenated prior to analysis. Gene expression, cell surface, and TCR libraries were prepared according to the protocol from 10X Genomics. The quality of the prepared libraries was assessed using the Agilent HS Bioanalyzer 2100 and sequencing was conducted on an Illumina NovaSeq 6000.

first: Kavita

last: Dhodapkar

first: Adam

middle: D

last: Cohen

first: Alfred

middle: L

last: Garfall

first: Julia

last: Manalo

first: Allison

last: Carr

first: Samuel

last: McCachren

first: Edward

last: Stadtmauer

first: Simon

middle: F

last: Lacey

first: J. Joseph

last: Melenhorst

first: Carl

last: June

first: Michael

middle: C

last: Milone

first: Madhav


title: Real-time quantitative PCR analysis of miRNAs in HIV patients who did (cases) or did not (controls) experience Type 1 MI

city: LOS ANGELES

first: Neal

last: Yuan

address: 8700 Beverly Blvd, Davis 1015

institute: Cedars-Sinai

summary: RT-PCR of platelet-poor plasma samples per Freedman JE, Gerstein M, Mick E, Rozowsky J, Levy D, Kitchen R, et al. Diverse human extracellular RNAs are widely detected in human plasma. Nat Commun 2016; 7. doi:10.1038/ncomms11106

overall_design: miRNA expression profiling from platelet poor plasma samples

first: Kahraman

last: Tanriverdi


title: RNA-seq comprehensive analysis reveals the long non-coding RNA expression profile and co-expressed mRNA in adult degenerative scoliosis

city: Kunming

first: Xin

last: Shi

address: Dianmian Road No.374

institute: The Second Affiliated Hospital of Kunming Medical University, Kunming

summary: Owing to the intensification of the aging process worldwide, the prevalence of adult degenerative scoliosis (ADS) is increasing at an alarming rate. However, genomic research related to the etiology of ADS is rarely reported worldwide. Since long non-coding RNAs (lncRNAs) play a pivotal role in the progression of human diseases, this study aimed to investigate ADS-associated messenger RNAs (mRNAs) and lncRNAs by RNA sequencing (RNA-seq), as well as performed comprehensive bioinformatics analysis.

overall_design: Six whole blood (WB) samples were obtained from 3 ADS patients and 3 non-degenerative lumbar adult volunteers for RNA-seq exploration to construct differential mRNA and lncRNA expression profiles.

first: Panpan

last: Li

first: Jun

last: Shu

first: Xiang

last: Wu

first: Zhihua

last: Wang

first: Gang

last: Zhao