title: ZNF384 fusion oncoproteins drive lineage aberrancy in acute leukemia [RNA-seq 2]

status: Public on Aug 31 2022

city: MEMPHIS

first: QINGSONG

last: GAO

state: Tennessee

address: 262 DANNY THOMAS PLACE

country: USA

institute: ST JUDE CHILDREN'S RESEARCH HOSPITAL

type: Expression profiling by high throughput sequencing

summary: To investigate usage of exon 8 in ZNF384 in different myeloid/lymphoid populations from MPAL/BALL PDX and cell lines

overall_design: PDX cells from SJBALL004031_X18-4052 (primary engrafted NSG-SGM3 PDX) and SJMPAL046472_X2-PAVRCX-063S5-1411 (secondary engrafted NSG-SGM3 PDX) and JIH-5 cells  were thawed and stained with the following human specific antibodies (all from BD Biosciences, catalogue number in parentheses): anti-CD45-FITC (345808), anti-CD19-BV605 (562653) and anti-CD33 PE-Cy7 (333946). Cells were then sorted in 2 or more of the following CD45+ tumor populations (PT): PT1: CD33+CD19+; PT2: CD33-CD19-; PT3: CD33-CD19+; PT4: CD33-CD19-. Sorted cells were collected, resuspended in RLT buffer (Qiagen, Cat. No. 79216) and processed for DNA and RNA extraction by the AllPrep DNA/RNA Mini Kit (Qiagen, Cat. No. 80204). RNA samples were sequenced by total stranded RNA-seq (SJMPAL046472_X2-PAVRCX-063S5-1411_PT1 and SJMPAL047180_C2-JIH5_PT1) or low input RNA-seq (SJBALL004031_X16-4052: PT1, PT2, PT3 and PT4; SJMPAL046472_X3-PAVRCX-063S5-1411_PT2 and SJMPAL047180_C4-JIH5_PT3).

first: Kirsten

last: Dickerson

first: Ilaria

last: Iacobucci

first: Charles

last: Mullighan


title: Next Generation Sequencing of  the transcriptomes of prostate cancer cells with or without ectopic expression of microRNA miR-30e

city: Orlando

first: Ratna

last: Chakrabarti

address: 12722 Research Parkway

institute: University of Central Florida

summary: MicroRNAs (miRNAs) function as regulators of cancer progression as they modulate different cellular processes. The objective of this study is to demonstrate a multi-dimensional function of miR-30e through regulating genes involved in various signaling pathways including androgen receptor signaling. miR-30e targets androgen receptor mRNA and functions as a tumor suppressor. We noted loss of miR-30e expression in prostate tumors and restored expression of miR-30e led to cell cycle arrest, induction of apoptosis, improved drug sensitivity in prostate cancer cells, and reduced tumor progression in prostate cancer xenograft models. To understand the tumor suppressor function of miR-30e on a global scale, we performed total RNA-sequence analysis upon overexpression of miR-30e in a prostate cancer cell line 22Rv-1, which expresses a splice variant of androgen receptor and represents an androgen-independent and drug-resistant form of prostate cancer.qRT-PCR validation of RNA-sequencing data  supports our in vitro study showeing differential expression of genes involved in cell cycle progression, apoptosis and ubiquitination upon expression of miR-30e in prostate cancer cells.

overall_design: Prostate cancer cells 22Rv-1 stably  transfected with inducible expression vector containing miR-30e precursor gene were  induced with doxycycline (1µg/ml) or left uninduced and used for RNA- seq analysis


title: The polyaminoisoprenyl compound NV716 re-sensitizes antibiotics against Pseudomonas aeruginosa by perturbing outer membrane permeability and reduces bacterial virulence.

city: Hanover

first: Susanne

last: Häußler

address: Feodor-Lynen-Str. 7

department: Molecular Bacteriology

country: Germany

institute: Twincore

summary:
Objective: to determine the changes in transcriptome induced by exposure during 52 successive passages of PAO1 to membrane-active agents, namely colistin (CST), alexidine (ALE) and NV716, an investigation polyamino-isoprenic compound
Methods:  PAO1 was exposed during 50 passages to each of these agents at 1/2 MIC, after which , cells were harvested, and RNA was purified and analyzed by RNAseq
Results: upregulations of genes involved in lipidA/LPS synthesis as well as downrelgulation of genes involved in virulence were observed with NV716. Changes in genes related to LipidA and LPS synthesis were also observed with the other agents.
Conclusion: Our results provide new insights into the mechanism of action of NV716 and potential targets in P. aeruginosa.

overall_design: Determination of alteration of transcriptomic RNA expression in P. aeruginosa PAO1 treated with CST, ALE and NV716, compared with untreated

first: Gang

last: Wang

first: Jean-Michel

last: Brunel

first: Matthias

last: Preusse

first: Negar

last: Mozaheb

first: Sven

last: Willger

first: Pieter

last: Baatsen

last: Haussler

last: Bolla

first: Françoise

last: Van Bambeke


title: Assay for Transposase Accessible Chromatin (ATAC)-sequencing of the AML cell line U937

city: Freiburg

first: Gabriele

last: Greve

address: Hugstetter Str 55

department: Department of Internal Medicine 1

institute: University of Freiburg Medical Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: All-trans retinoic acid (ATRA, RA) has powerful activity in APL; its efficacy in non-APL AML is still unclear, but may be boosted by epigenetic drugs such azanucleoside DNMT inhibitors (Blagitko-Dorfs et al. PLoS ONE  2013).  In a randomized phase II study (DECIDER trial, NCT00867672) the addition of RA to decitabine (DAC) in newly diagnosed non-fit older AML patients resulted in a clinically meaningful extension of survival. We hypothesize that in vitro, the add-on of RA to DAC results in cooperative transcriptome and chromatin accessibility changes (possibly associated with demethylation), which may explain at least in part this clinical result.

overall_design: The AML cell line U937 was treated with decitabine (DAC) ± ATRA in technical triplicates for 3 consecutive days (with daily change of media and DAC add-on). For ATAC-sequencing (ATAC-seq), 50.000 fresh cells were processed in triplicates as described in the Omni-ATAC protocol by Corces et al. Size selection and purification was performed using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA, USA). Validation of enriched open chromatin sites was determined by qPCR and paired-end libraries were sequenced with 40 million read/sample.

first: Bettina

last: Berberich

first: Dennis

last: Zimmer

first: Michael

last: Lübbert


title: TANK binding kinase 1 induces transcription factor BACH1 to regulate iron metabolism in pancreatic cancer cells

city: Sendai

first: Mitsuyo

last: Matsumoto

address: 2-1 Seiryo-machi Aoba-ku

department: Biochemistry

country: Japan

institute: Tohoku university school of medicine

summary: BTB and CNC homology 1 (BACH1) represses the expression of genes involved in the metabolism of iron, heme and reactive oxygen species and promotes metastasis of various cancers including pancreatic ductal adenocarcinoma (PDAC). Knockdown of Tank binding kinase 1 (TBK1) led to reductions of BACH1 mRNA and protein amounts in AsPC-1 human PDAC cells. Gene expression analysis of PDAC cells with knockdown of TBK1 or BACH1 suggested the involvement of TBK1 and BACH1 in the regulation of iron homeostasis. Ferritin was increased upon BACH1 knockdown in AsPC-1 cells. Cytometry analysis showed that AsPC-1 cells with BACH1 knockout or knockdown contained lower labile iron than control cells, suggesting that BACH1 increased labile iron by repressing the expression of ferritin genes.

overall_design: RNA sequencing of total 4 samples was performed. Each sample is biologically duplicated. There are two different conditions:  Total RNA of stealth RNA and negative control treatment against TBK1 in AsPC-1, the pancreatic cancer cell line.

first: Liang

last: Liu

first: Kazuhiko

last: Igarashi


title: Understanding gene expression profile of human brain primary endohtelial cell (HBMECs) treated with conditioned media (CM)

city: Seatlle

first: Yu Jung

last: Shin

state: WA

address: 850 Republican st, Brotman 419

department: Bioengineering

institute: University of Washington

summary:
To investigate transcriptomic changes in human brain parymary endohtelial cells in response to conditioned media obtained from BNMN (unconditioned media), hiPSC-CN harboring swedish mutation (Swe22) and hiPSC-CN harboring isogneic control background (CVIA2).
Overall, we are tyring to understand how EC transcriptome changes in reponse to Alzheimer's disease mimicking condition.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for primary HBMECs treated with conditioned media (BNMN, CVIA2 (SweWT/WT) and SWE22 (Swe+/+)) two batches of conditioned media (DEC and FEB) was treated.

first: YuJung

first: Kira

middle: M

last: Evitts

first: Jessica

middle: E

last: Young

first: Ying

last: Zheng


title: RNAseq analysis of blood after co-infection with influenza virus and Streptococcus pneumoniae

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

institute: University Münster

summary:
Mouse blood transcriptome after infection with Influenza A virus (H1N1, PR/8/34, mouse-adapted) and Streptococcus pneumoniae (serotype 19F, strain BHN 100)
Results: Differentially expressed genes were observed after single and co-infection
Project: COST_mouse_2021

overall_design: PBS_PBS: treatment with PBS on day0, then PBS on day7, sample collection 8h later; PBS_SPN: treatment with PBS on day0, then S.p. on day7, sample collection 8h later;  IAV_PBS: treatment with IAV on day0, then PBS on day7, sample collection 8h later;  ; IAV_SPN: treatment with IAV on day0, then S.p on day7, sample collection 8h later;

first: Dunja

last: Bruder


title: The association and difference of normal THP-1 cell and H37Rv infected THP-1 cell.

city: DongGuan

first: JiaJun

last: Wang

address: No. 1 Xincheng Road

country: China

institute: Guangdong Medical University

summary: ①Background:Tuberculosis is mainly a respiratory tract infection caused by mycobacterium tuberculosis and one of the leading causes of death worldwide. According to the Global Tuberculosis Report in 2021, About a quarter of the world's population is infected with Mycobacterium tuberculosis and China is the second highest burden of TB. Although TB diagnosis and prevention techniques have become more mature, the number of TB cases is still increasing, mainly due to: the prevalence of drug-resistant tuberculosis bacteria, tuberculosis and HIV co-infection, long incubation time of mycobacterium tuberculosis difficult to early diagnosis and so on. Therefore, it is of great significance to study the pathogenesis of mycobacterium tuberculosis infection.②Method: THP-1 cells were treated with 50ng/ml PMA for 24 hours, so that THP-1 cell can be induced into macrophages. After that THP-1 macrophages were infected with mycobacterium tuberculosis H37Rv(MOI=1), which were collected and applied to RNA-sequencing. The constructed sequencing library was sequenced using an Illumina Novaseq 6000 system.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for normal THP-1 cells and H37Rv infected THP-1 cells.

first: Jia-Jun

first: Jun-Fa

last: Xu

first: Jun-Ai

last: Zhang

last: LI

first: Ji

last: Huang


title: Effects of amiloride in lithium induced kidney interstitial fibrosis

city: Dunedin

first: Paulomi

last: Mehta

state: Otago

address: 56 Hanover street

department: Department of Pathology

country: New Zealand

institute: University of Otago

summary:
Purpose: The goal of this study is to understand the role of co-administred amiloride. This was derived through RNAseq of kidney cortex and determining differential genes in response to lithium, lithium+amiloride and control at 14 days, 28 days and 6 months.
Methods: RNAseq of kidney cortex treated with either lithium alone, lithium+amiloride or control.  Deseq2 was performed using contrast argument with Wald test to identify significant differentially expression genes at each time point individually.
Result & Conclusion: Co-administration with amiloride at all time points contributed in the reduction of inflammation and fibrosis caused by lithium.

overall_design: mRNA profile of rats treated with lithium compared to lithium, lithium-amiloride compared to lithium at 14 days, 28 days and 6 months time points.

first: Gregory

last: Gimenez

first: Tania

middle: L

last: Slatter

first: Robert

middle: J

last: Walker


title: Rubella Virus wildtype and vaccine strains induce transcription of chemokines and components of innate immunity in human embryonic endothelial cells

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

summary: We describe the transcriptional response to infection of human umbilical vein endothelial cells (Huvec) with different rubella virus strains

sample_organism:
Homo sapiens
Rubivirus rubellae

platform_organism:
Homo sapiens
Rubivirus rubellae

overall_design: Bulk RNA-seq was performed from infected cells

first: Esther

last: Behrsing

first: Agnieszka

last: Bauer

first: Jermaine

last: Voß

first: Markus

last: Landthaler

first: Annette

last: Mankertz


title: Transcriptome profiling by RNA-sequencing of the AML cell line MOLM-13.

first: Gabriele

last: Greve

summary: All-trans retinoic acid (ATRA, RA) has powerful activity in APL; its efficacy in non-APL AML is still unclear, but may be boosted by epigenetic drugs such azanucleoside DNMT inhibitors (Blagitko-Dorfs et al. PLoS ONE  2013).  In a randomized phase II study (DECIDER trial, NCT00867672) the addition of RA to decitabine (DAC) in newly diagnosed non-fit older AML patients resulted in a clinically meaningful extension of survival. We hypothesize that in vitro, the add-on of RA to DAC results in cooperative transcriptome changes (possibly associated with demethylation), which may explain at least in part this clinical result.

overall_design: The AML cell line MOLM-13 was treated with decitabine (DAC) ± ATRA in technical triplicates for 3 consecutive days (with daily change of media and DAC add-on). Cells were harvested and RNA was isolated after 72 hours, Fragment analysis by TapeStation confirmed RQN values ≥9.7.  rRNA was removed and strand-specific libraries of each replicate were sequenced on an Illumina HiSeq 2500 with approximately 40 million reads per sample.

first: Ruth

last: Meier

first: Dennis

last: Zimmer

first: Bettina

last: Berberich

first: Christoph

last: Niemöller

first: Daniel

last: Lipka

first: Michael

last: Lübbert


title: Human lung tissue treated with interferons

first: Klaus

last: Schughart

summary:
RNAseq analysis of human lung slices after treatment with different interferons.
Results: Differentially expressed genes were observed after treatment with different interferons.
Methods: Tumor-free human lung explants were obtained from patients undergoing lung surgery at the University Hospital Muenster on the day of surgery. Tissue blocks were individually placed in a 12-well plate in RPMI medium. Tissues were treated with different interferons. RNA was prepared from tissue homogenates.

overall_design: Design: Lung mRNA profiles of lung tissues from three donors after treatment with interferons were compared to mock-treated controls.

first: Linda

last: Brunotte


title: Expression of exosomal microRNAs in bovine serum with clinical or subclinical mastitis

city: Beijing

first: Mengling

last: Wang

address: No. 2 Yuanmingyuan West Road

institute: Institute of Animal Science, Chinese Academy of Agricultural Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: Bovine mastitis causes changes in the serum exosomal miRNAs expression. Serum samples from healthy dairy cows (n = 7) were compared to those of cows with subclinical (n = 7 ) using small RAN sequencing. Three hundred fifty-five miRNAs (341 known and 14 novel ones) were identified. There were 42 miRNAs up-regulated in serum-derived EVs from cows with subclinical mastitis, including bta-miR-1246, bta-miR-2431-3p, bta-miR-126-3p, bta-miR-29a, etc. The MAPK signaling pathway was the most affected pathway by clinical mastitis. Thus, miRNA alterations in mastitis serum-derived EVs support the potential regulator role of specific miRNAs as exosomal cargo in clinical mastitis physiology.

overall_design: EVs of bovine serum  were isolated from healthy cows (n = 7, the control group), and cows with subclinical mastitis (n = 7, the SM group), and cows with clinical mastitis (n = 7, the CM group) .

first: Megnling


title: Characterization of differentially expressed exosomal microRNAs   in bovine milk with clinical or subclinical mastitis

summary: Milk microRNAs (miRNAs) encapsulated in extracellular vesicles (EVs) are a novel class of bioactive food compounds. Milk produced by cows with subclinical mastitis threatens animals healthy and milk safety. However, little is known about the differentially expressed miRNA in milk-derived EVs related to subclinical mastitis. This study profiled miRNAs in milk-derived EVs from healthy cows and cows with subclinical mastitis. The potential targets for differentially expressed (DE) miRNAs were predicted. Milk-derived EVs were isolated from healthy cows (n = 7, the control group) and cows with subclinical (n = 7, the SM group). Two hundred ninety miRNAs (221 known and 69 novel ones) were identified. The top 20 miRNAs were commonly abundant (> 0.1% of the total read counts) in Healthy and SM groups, were regarded as abundant bovine milk-derived EVs miRNAs. MiR-21-5p was the most highly expressed known miRNA. Target genes of the top 20 abundant miRNAs were significantly enriched in Ras signaling pathway. The bta-miR-21-5p, bta-miR-30a-5p and miR-6-1096 were differentially expressed. For DE miRNAs, there was no significantly enriched pathways were found in the KEGG enrichment analysis. The linkage between the validated target genes and diseases suggested that we pay particular attention to exosome miRNAs from mastitic milk in milk safety.

overall_design: Milk-derived EVs were isolated from healthy cows (n = 7, the control group), and cows with subclinical (n = 7, the SM group)，and cows with clinical (n = 7, the CM group).


title: The expression profiles of longissimus dorsi muscle from six Laiwu pigs (three with extremely high and three with extremely low intramuscular fat content).

city: Jinan

first: Tao

last: Su

state: Shandong

address: 440 Jiyan Rd

institute: Shandong Cancer Hospital and Institute

summary:
To understand the role of message RNA (mRNAs, lncRNAs and circRNAs) in regulation of intramuscular fat deposition, the expression profiles of longissimus dorsi muscle from six Laiwu pigs were sequenced based on rRNA-depleted library construction.
We then performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for six Laiwu pigs.

first: Jingxuan

last: Li

first: Jiying


title: SymMap database and TMNP algorithm reveal Huanggui Tongqiao granules for Allergic rhinitis through IFN-mediated neuroimmuno-modulation

first: Aiping

last: Chen

address: No. 11, Bei San Huan Road, Chaoyang District

institute: Beijing University of Chinese Medicine

summary:
The aim of this study is to determine the active components of HTG and to reveal its possible targets and mechanisms of action for the treatment of AR. Through mass spectrometry, six components, including ononin, paeoniflorin, psoralenoside, isoliquiritin apioside, glycyrrhizic acid and arctiin were identified.
Further studies employing SymMap database and TMNP algorithm showed that IFN-γ, which has been demonstrated to be a molecular link between immunity and neural circuits, is a key target involved in the HTG treatment of AR. The enrichment of several immune and virus-related signaling pathways together indicated the neuroimmuno-modulatory potential of HTG.

overall_design: AR mouse model was established by Ovalbumin (OVA) challenge and was used to verify the therapeutic effects of Huanggui Tongqiao Gragunles (HTG)  in vivo. HTG significantly relieved AR symptoms and nasal mucosal inflammation, reduced OVA-specific IgE levels and balanced IFN-γ/IL-4 ratio.

first: Jing

last: Jin

first: Jun

last: Tai


title: RNAseq analysis of CC F2 female mice at day3 after infection with Ebola virus

summary:
F2 female mice were generated from a cross of two collaborative cross (CC) strains, CC011 x CC074. These mice were infected with Ebola virus and liver samples were prepared at day three after infection. RNA from the livers were prepared and subjected to RNAseq analysis. This data set can be combined with data from GSE165142, in which female mice from the same cross were infected with Ebola virus, and liver samples were prepared at day six after infection.
Results: Variations in gene expression levels that may be perdictive for severity

overall_design: Livers were collected from infected mice, RNA was isolated and sequenced.


title: Immune response of TRIM28 KO cells infected with H1N1 IAV

summary:
RNAseq analysis of A549-TRIM28 KO cells that were infected with low pathogenic laboratory strain PR8 (H1N1)
Differentially expressed genes in infected vs. non-infected cells
Project: A549_TRIM28_KO

overall_design: Comparison of the mRNA expression level of control cells (A549) and A549-TRIM28 KO cells infected with H1N1 (PR8 Strain) influenza A viruses


title: Differential expression of cell wall remodeling genes is part of the dynamic phase-specific transcriptional program of conidial germination of Trichoderma asperelloides

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

summary: The nature of saprophytic and mycoparasitic hyphal growth of Trichoderma spp. has been studied extensively, yet information concerning conidial germination in this genus is lacking. Using near-synchronous germinating cultures of Trichoderma asperelloides, we followed the morphological progression from dormant conidia to initial polar growth, to germling formation and to evidence for first branching. We found that the stage-specific transcriptional profile of T. asperelloides is one of the most dynamic described to date; Transcript abundance of over 5000 genes, comprising approximately half of the annotated genome, was uniquely reduced in the transition from dormancy to polar growth, providing a potentially high degree of flexibility for germination on diverse substrates. Conversely, after the onset of germination, transcript abundance of approximately a quarter of the genome was exclusively elevated during transition from elongation to initial branching. Bayesian network analysis has identified several chitinases (including chi42) and glucanase-encoding genes as hallmarks of transcriptional hubs during germination. Furthermore, the fact that the expression of specific members of the chitin synthase and glucan elongase families was significantly increased during germination in the presence of Rhizoctonia solani, a known host of the mycoparasite, indicates that host recognition can occur during early stages of mycoprasite development.

overall_design: mRNA were sampled from 4 stages of Trichoderma asperelloides conidial germination on PDA and on Rhizoctonia solani living cultures

first: Zheng

last: Lopez-Giraldez

first: Oded

last: Yarden


title: RNA-sequencing assay to Identify changed gene expression in esophageal squamous cell carcinoma (ESCC) cells with RAB23 knockdown

city: Tianjin

first: Gang

last: Ma

email: horsegang@163.com, horsegang@tmu.edu.cn

address: West Huan-Hu Rd, Ti Yuan Bei, Hexi District

department: Department of Gastric Surgery

institute: Tianjin Medical University Cancer Institute and Hospital

summary:
Purpose: To elucidate how RAB23 influenced the expression profile in ESCC cells, RAB23 expression was reduced using two siRNAs in ESCC KYSE30 cells. Then, transcriptional profiling of two populations of cells with RAB23 knockdown (si-RAB23-1 and si-RAB23-9) and the control cells (si-NC) was performed to characterize differentially expressed genes (DEG).
Methods: When si-NC, si-RAB23-1 and si-RAB23-9 cells grew to approximately 80% confluence, these cells were washed twice using pre-chilled PBS. Total RNAs were harvested using Trizol reagents (Thermo Fisher Scientific).  Poly(A) mRNA was isolated and enriched using NEBNext Poly(A) mRNA Magnetic Isolation Module. The mRNA was then recovered for library generation with NEBNext ® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, E7420S) following the manufacturer’s instructions. The cDNA libraries were sequenced at WuXiNextCODE (China). FastQC was used to examine the quality of raw reads. Read alignment was conducted using STAR (v2.5.1b),  and R package edgeR (v3.8.5) was used to determine relative transcript abundances and differentially expressed genes (DEGs) between sample pairs.
Results: Generally, 1041 genes  were increased and 1013 genes decreased in si-RAB23-1 cells, compared with si-NC cells (FDR<0.05, Fold Change>2). Additionally, 1154 genes (FDR<0.05, Fold Change>2) were increased and 958 genes decreased in si-RAB23-9 cells, relative to si-NC cells. GO analysis showed that these changed genes were significantly enriched in signal pathways related to cancer.
Conclusions: Reduced RAB23 expression alters multiple cancer-related signal pathways.

overall_design: Two biological replicates for each group - si-NC, si-RAB23-1 and si-RAB23-9 - were subjected to RNA-sequencing analysis respectively, among which si-NC acted as the reference sample for si-RAB23-1 and si-RAB23-9.

first: Yi

last: Sun

first: Han

last: Liang

first: Rupeng

last: Zhang


title: RNA sequencing of GES-1 cells co-cultured with H.pylori with high and low Trx1 expression

first: Xin

last: Guan

address: Peking University Third Hospital, 49 Huayuan North Road, Haidian District, Beijing

institute: Peking university Third Hospital

summary: GES-1 gastric epithelial cells were used for co-culturing with H.pylori with high and low Trx1 expression, and RNA sequencing was performed on the co-cultured cells to explore transcriptome differences between the two groups, so as to further explore the pathogenic mechanism of Trx1 in H.pylori.

overall_design: Collecting the 12h co-cultured cell precipitation included GES-1 cells without H.pylori infection (NC group), GES-1 cells co-cultured with H.pylori with high Trx1 expression (HP Trx1 high expression group) and GES-1 cells co-cultured with H.pylori with low Trx1 expression (HP Trx1 low expression group)

last: Ning


title: B cell activating factor (BAFF) attenuates immunosuppressive monocytes in the melanoma tumor micro-environment

city: Homburg (Saar)

first: Marc

last: Remke

state: Saarland

address: Kirrberger Straße 100, Gebäude 9

department: Pediatric Translational Oncology Lab

institute: Universitätsklinikum des Saarlandes

summary: Emerging evidence indicates BAFF to be an important cytokine influencing anti-tumoral immunity. We generated a BAFF-overexpressing B16.F10 (BAFF) melanoma cell model and found that a significant survival advantage was conferred to C57BL/6 mice inoculated with BAFF cells. BAFF tumors  had decreased myeloid infiltrates with lower PD-L1 expression. Monocyte depletion and anti-PD-L1 antibody treatment confirmed the functional significance on the phenotype. RNA-Seq analysis confirmed that monocytes isolated from BAFF tumors where characterized by a decreased exhaustive phenotype and enriched for in genes activating adaptive immune responses and NF-𝜅𝛽 signaling. We wondered about the clinical relevance of BAFF plasma levels in melanoma patients. Evaluation of late stage metastatic melanoma patients treated with inhibitors of the PD-1/PD-L1 axis demonstrated a stratification of patients with high and low BAFF plasma levels, the former of which experienced lower responses to anti-PD-1 immunotherapies. In summary, we have shown that BAFF, through effects on tumor infiltrating monocytes not only impacts primary tumor growth but as biomarker can contribute to predicting response to anti-PD1 immunotherapy in later stages of advanced disease.

overall_design: C57BL/6 mice were inoculated subcutaneously with  BAFF or control cells. 13 days post-inoculation, monocytes were sorted from BAFF and control tumors. Isolated monocytes were analyzed using RNA-Seq analysis

first: Daniel

last: Picard

first: Aleksandra

last: Pandyra


title: RNA sequencing of control and dystrophin-mutant engineered heart tissues from human induced pluripotent stem cell-derived cardiomyocytes

city: Seattle

first: Christian

last: Mandrycky

address: 850 Republican St

summary: We report the transcriptomic differences between engineered heart tissues generated from hiPSCs with a dystrophin-truncating mutation and an isogenic control. We find that the dystrophin mutation induces profound differences at the transcriptomic level and illuminates potential disease-causing mechanisms.

overall_design: RNA sequencing of control and dystrophic engineered heart tissues

first: Samantha

middle: B

last: Bremner

first: Nathan

last: Sniadecki

first: David

last: Mack


title: Transcriptome profiling by RNA-sequencing of the AML cell line U937.

first: Gabriele

last: Greve

overall_design: The AML cell line U937 was treated with decitabine (DAC) ± ATRA in technical triplicates for 3 consecutive days (with daily change of media and DAC add-on). Cells were harvested and RNA was isolated after 72 hours, Fragment analysis by TapeStation confirmed RQN values ≥9.7.  rRNA was removed and strand-specific libraries of each replicate were sequenced on an Illumina HiSeq 2500 with approximately 40 million reads per sample.

first: Ruth

last: Meier

first: Dennis

last: Zimmer

first: Bettina

last: Berberich

first: Christoph

last: Niemöller

last: Lipka

first: Michael

last: Lübbert


title: Mouse lung gene expression after co-infection with influenza virus and Streptococcus pneumoniae

first: Klaus

last: Schughart

summary:
Mouse lung RNAseq after infection with Influenza A virus (H1N1, PR/8/34, mouse-adapted) and Streptococcus pneumoniae (serotype 19F, strain BHN 100)
Results: Differentially expressed genes were observed after single and co-infection
Project: COST_mouse_2021_lung

overall_design: PBS_PBS: treatment with PBS on day0, then PBS on day7, sample collection 8h later; PBS_SPN: treatment with PBS on day0, then S.p. on day7, sample collection 8h later;  IAV_PBS: treatment with IAV on day0, then PBS on day7, sample collection 8h later;  ; IAV_SPN: treatment with IAV on day0, then S.p on day7, sample collection 8h later;

first: Dunja

last: Bruder


title: Dose-dependent consequences of sub-chronic fentanyl exposure on neuron and glial co-cultures

city: Livermore

first: Stephen

middle: Patrick

last: Wilson

state: CA

address: 7000 East Ave

department: BBTD

institute: LLNL

summary: It remains poorly understood what and how changes in brain activity from chronic fentanyl use influences the respective behavioral outcome. We examined the functional and molecular changes to cortical neural network activity following sub-chronic exposure to two fentanyl concentrations, a low (0.01 µM) and high (10 µM) dose from primary rat co-cultures, containing cortical neurons, astrocytes, and oligodendrocyte-lineage cell.

overall_design: Primary rat co-cultures, containing cortical neurons, astrocytes, and oligodendrocyte precursor cells, at 24-26 days in vitro were treated with  a low (0.01 µM) or high (10 µM) dose for four days before RNA was extracted.

first: Heather

last: Enright

first: Doris

last: Lam

first: Aimy

last: Sebastian


title: Gene expression profile of RAS/RAF–wild-type colorectal cancer patient-derived spheroids II

city: Kyoto

first: Makoto

middle: Mark

last: Taketo

state: Kyoto

address: Yoshida-Honmachi, Sakyo

department: Kyoto University Hospital

institute: Kyoto University

summary: Fibroblast growth factor receptor inhibitors (FGFRi) were introduced into clinical trials on several cancer types and found to be particularly efficacious on urothelial cancer and cholangiocarcinoma. Although many enrolled patients responded well in clinical trials, there were some patients who did not respond to FGFRi despite that their tumors carried the genomic changes that met the enrollment criteria. As already established, fibroblast growth factor receptor (FGFR) and epidermal growth factor receptor (EGFR) share the downstream signaling pathway of MAPK activation. Accordingly, it is conceivable that chemotherapeutic inhibition of FGFR alone may leave the MAPK signaling unaffected when the signaling through EGFR is relatively strong. To test this hypothesis, we calculated the FGFR to EGFR mRNA ratio (F/E for short) of colorectal cancer stem cell (CRC-SC) spheroid, biliary-tract cancer, and urothelial cancer cell lines. As a result, CRC-SC spheroid and cancer cell lines responsive to FGFRi had higher F/E than non-responsive lines. In conclusion, we propose a novel parameter F/E as a biomarker that helps predict cancer chemosensitivity to FGFRi.

overall_design: RNA sequencing data of 47 colorectal cancer spheroid lines, three colorectal cancer whole tissues, and three normal colorectal epithelial spheroid lines

first: Shoichi

last: Kitano

first: Takehito

last: Yamamoto


title: Caulis Polygoni Multiflori accelerates megakaryopoiesis and thrombopoiesis via activating PI3K/Akt and MEK/ERK (MAPK) signaling pathways

city: Luzhou

first: xin

last: yang

address: Longmatan District Xianglin Road 1 section 1, Luzhou city

institute: Southwest Medical University

summary: In vtro and in vivo experiments revealed that Caulis Polygoni Multiflori (CPM) significantly induced megakaryocyte (MK) differentiation and maturation. To investigate the underlying mechanism of action of CPM in promoting MK differentiation, RNA-seq was performed to reveal the gene expression profile in MK differentiation induced by CPM. Our results showed that CPM up-regulated 850 differentially expressed genes (DEGs), down-regulated 1100 DEGs. Disease Ontology (DO) enrichment analysis revealed that CPM could regulate thrombocytopenia, blood platelet disease and blood coagulation disease. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Reactome pathway enrichment analysis suggested that CPM regulated PI3K/Akt and ERK/MEK (MAPK) signaling pathways.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for K562 cells treated with CPM (80 µg/mL) for 3 days and without CPM.

first: Xin

last: Yang

first: Long

last: Wang

first: Anguo

last: Wu


title: Immune response of TRIM28 KO cells infected with H5N1 HPAIV

summary: Differentially expressed genes in infected vs. non-infected cells

overall_design: RNAseq analysis of A549-TRIM28 KO cells that were infected with highly pathogenic avain influenza virus KAN-1 (H5N1); Project: A549_TRIM28_KO

first: Linda

last: Brunotte


title: Canine DH-28  cells persistant infection with CDV, starving and hypoxic treatments

summary:
RNAseq analysis of canine DH-28 tumor cells persistently infected with CDV canine distemper virus, starving and hypoxic conditions. Gene expression changes in infected and control cells were studied.
Results: Many differences between infection and controls and different treatments

overall_design: Cells were collected from infected and treated samples, RNA was isolated and sequenced.

first: Chistina

last: Puff


title: Bulk RNA sequencing of WT (Batf fl/fl) and Batf-/- (Batf fl/fl PLZFcre+)  ILC3s sorted from small intestine [bulk RNA-seq]

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

summary: Group 3 innate lymphoid cells (ILC3s) are crucial for the maintenance of host-microbiota homeostasis in gastrointestinal mucosal tissues. The mechanisms that maintain lineage identity of intestinal ILC3s, and ILC3s-mediated orchestration of microbiota and mucosal T cell immunity are elusive. Here, we identified BATF as a gatekeeper of ILC3s homeostasis in the gut. Depletion of BATF in ILC3s resulted in excessive interferon-γ production, dysbiosis, aberrant T cell immune responses and spontaneous inflammatory bowel disease (IBD), which was considerably ameliorated by removal of adaptive immunity or antibiotic treatment. Mechanistically, BATF directly regulates ILC3s identity by globally shapes chromatin landscape of ILC3s. BATF directly binds to the cis-regulatory elements of type 1 effector genes, restrains their chromatin accessibility and inhibits their expression. Conversely, BATF promotes chromatin accessibility of genes involved in MHCII antigen processing and presentation pathways. Collectively, our findings reveal BATF is a promising candidate to maintain ILC3s stability and coordinate ILC3s–mediated control of intestinal homeostasis.

overall_design: Bulk RNA sequencing, 2 samples (WT and Batf-/- ILC3s), 3 biological replicates per sample, from small intestine.

first: Xiaopeng


title: Eukaryotic translation initiation factor 2A protects pancreatic beta cells during endoplasmic reticulum stress while rescuing translation inhibition

city: Vancouver

first: Howard

last: Cen

state: BC

address: 2350 Health Sciences Mall

country: Canada

institute: University of British Columbia

summary: Endoplasmic reticulum (ER) stress-induced unfolded protein response (UPR) helps decide b cell survival in diabetes. The alternative eukaryotic initiation factor 2A (EIF2A) has been proposed to mediate EIF2S1-independent translation during cellular stress and viral infection, but its role in b cells is unknown. EIF2A abundance is high in human and mouse islets relative to other tissues, and both thapsigargin and palmitate significantly increased EIF2A mRNA and EIF2A protein levels in MIN6 cells, mouse islets and human islets. Knockdowns of EIF2A, the related factor EIF2D, or both EIF2A and EIF2D, were not sufficient to cause apoptosis. On the other hand, transient or stable EIF2A over-expression protected MIN6 cells, primary mouse islets, and human islets from ER stress-induced, caspase-3-dependent apoptosis. Mechanistically, EIF2A overexpression decreased ERN1 (also known as IRE1a) expression in thapsigargin-treated MIN6 cells or human islets. In vivo, b cell specific EIF2A viral overexpression reduced ER stress, improved insulin signaling, and abrogated hyperglycemia in Ins2Akita/WT mice. EIF2A overexpression significantly increased expression of genes involved protein translation and reduced expression of pro-apoptotic genes (e.g. ALDH1A3). Remarkably, the decrease in global protein synthesis during UPR was prevented by EIF2A, despite ER stress-induced EIF2S1 phosphorylation. The protective effects of EIF2A were additive to those of ISRIB, a drug that counteracts the effects of EIF2S1 phosphorylation. Cells overexpressing EIF2A showed higher expression of translation factor EIF2B5, which may contribute to the lack of translational inhibition in these cells. We conclude that EIF2A is a novel target for b cell protection and the circumvention of EIF2S1-mediated translational repression.

overall_design: Transcriptome wide profiling of MIN6 cells transfected with a plasmid expressing GFP (control) or EIF2A-GFP and treated with thapsigargin for 0, 1 or 3 hours to induce ER stress.

first: James

middle: D

last: Johnson

first: Evgeniy

last: Panzhinskiy

first: Haoning

middle: H


title: Digital Gene Expression data of a group 1 Trypanosoma brucei gambiense vs a Trypanosoma brucei brucei

city: Glasgow

first: Nicola

last: Veitch

address: Bearsden Rd

country: United Kingdom

institute: University of Glasgow

summary: Trypanosoma brucei gambiense is the causative agent of the fatal human disease African sleeping sickness. Using Digital Gene Expression we have compared the transcriptome of a group 1 T.b.gambiense (Eliane) and a T.b.brucei (STIB 247).

sample_organism:
Trypanosoma brucei brucei
Trypanosoma brucei gambiense

overall_design: RNA was extracted from 2 T.b.gambiense cultures and 1 T.b.brucei culture. Digital Gene Expression libraries were created and were sequenced using Illumina next generation sequencing technology.

first: Annette

last: MacLeod

first: Paul

last: Johnston


title: Digital Gene Expression data of two Trypanosoma brucei hybrids (T.b.brucei crossed with T.b.gambiense (group 2))

summary: Trypanosoma brucei gambiense is the causative agent of the fatal human disease African sleeping sickness. Using Digital Gene Expression we have compared the transcriptome of two T.b.brucei (STIB 247)xT.b.gambiense (STIB386) hybrids.

sample_organism: Trypanosoma brucei brucei x Trypanosoma gambiense 414

sample_organism: Trypanosoma brucei brucei x Trypanosoma gambiense 181

overall_design: RNA was extracted from 2 T.b.brucei/T.b.gambiense hybrids. Digital Gene Expression libraries were created and were sequenced using Illumina next generation sequencing technology.


title: Analysis of m6A modification-related regulators in Ara-C-resistant cells and parental cells in AML cells

status: Public on Aug 30 2022

city: Hangzhou

first: Weina

last: Yun

address: yuhangtang road

institute: Zhejiang University

summary: Despite the current rapid development of targeted therapy and immunotherapy, chemotherapy is still the most common treatment for AML. However, relapse after chemotherapy remains a major obstacle to curative treatment of AML. Here, we found that the methyltransferase METTL14 was upregulated in drug-resistant AML cells, but overall m6A level was not significantly changed. Overexpression of METTL14 in AML cells increased resistance to chemotherapeutics, whereas downregulation of METTL14 increased sensitivity to chemotherapeutics.

overall_design: Analysis of gene expression differences between parental cells and Ara-C-resistant THP1 cells

first: Xi

last: Jiang


title: RNAseq analysis of CC F2 female mice after infection with Ebola virus

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

institute: University Münster

summary:
Gene expression changes in the liver was studied by RNAseq
Results: Strong differences in the immune response between mice with high body weight loss and mice with moderate body weight loss

overall_design: Livers were collected from infected and mock-treated control mice, RNA was isolated and sequenced.


title: Telomere Shortening Impairs PGC Fate Decision [RNA-seq]

city: Munich

first: Chenglei

last: Tian

address: Ingolstädter Landstraße 1

institute: Helmholtz Munich

summary: We asked whether telomere shortening impairs differentiation of ESCs into germ cell lineage. Terc-/- ESCs were used to investigate the effects of short telomeres on germ cell specification by in vitro differentiation. Short telomeres greatly reduced induction of PGCLCs from ESCs. Mechanistically, short telomeres resulted in excessive chromatin accessibility, which in turn activated the genes regulated by chromatin. Notably, Fst overexpression reduced BMP-Smad signaling and thus induction of PGCLCs, meanwhile upregulation of MAPK signaling pathway increase somatic lineage differentiation in short telomeres sampels. Moreover, knockin of Terc gene by CRISPR/Cas9 in Terc-/- ESCs restored telomere length and normal gene expression profile, and rescued PGCLC induction, revealing important roles of telomeres in PGC fate decision.

overall_design: We used long telomere (LT), short telomere (LT) and telomere length rescued (RT) EpiLCs, 1dEBs, PGCLCs and 1dMeiLCs differention from ESCs to do RNA-seq for analysis the gene expression of PGC genes, somatic lineage genes, proliferation related gene and meiosis-related genes.


title: Effect of depletion of NLRC3 on glycolytic genes of macrophage with LPS  treatment

city: Wuhan

first: You

last: Shang

state: Hubei

address: Jianghan district

department: Critical Care Medicine

institute: Wuhan Union Hospital

summary: The impaired aerobic glycolysis of monocyte/macrophage are the main features in sepsis that encountered immunosuppression. NLRC3, an inhibitory sensor, can diminish the Toll-like receptor 4 pathways of macrophages which is associated with sepsis-induced immunosuppression, but whether NLRC3 plays key role in regulating the immunosuppression of macrophage via interfering glycolysis still unclear. The aim of this study was to characterize the transcriptome alterations by which NLRC3 loss, and further investigate the role of the glycolysis in the macrophage with the development of sepsis. Bone marrow-derived macrophages (BMDMs) was isolated from the femurs and tibias of the NLRC3 WT (LysM-Cre-NLRC3fl/fl) and NLRC3ΔMac (LysM-Cre+ NLRC3fl/fl) mice and then was treated with or without LPS for 12 hours, and the macrophages mRNA profiles of five-weeks-old NLRC3 WT mice (WT macrophages) and of five-weeks-old NLRC3ΔMac mice (NLRC3-/- macrophages) were generated by deep sequencing, in triplicate, using Illumina 6000.

overall_design: Bone marrow-derived macrophages (BMDMs) was isolated from the femurs and tibias of the NLRC3 WT (LysM-Cre-NLRC3fl/fl) and NLRC3ΔMac (LysM-Cre+ NLRC3fl/fl) mice and then treated with or without LPS for 12 hours.

first: Jiqian

last: Xu

first: Chenggang

last: Gao

first: Yajun

last: He

first: Xiangzhi

last: Fang

first: Deyi

last: Sun

first: Zhekang

last: Peng

first: Hairong

last: Xiao

first: Miaomiao

first: Pei

last: Zhang

first: Ting

last: Zhou

first: Xiaobo

first: Yuan

last: Yu

first: Ruiting

last: Li

first: Xiaojing

last: Zou

first: Huaqing

last: Shu

first: Yang

last: Qiu

first: Shiying

last: Yuan

first: Shanglong

last: Yao


title: LncRNA affects epigenetic reprogramming of porcine embryo development by regulating global epigenetic modification

city: Changchun

first: Daoyu

address: Xinzhu street 1977

institute: Jilin University

summary: The key lncRNAs that regulate embryo development were screened through analyzing expression pattern of lncRNA in porcine in vivo fertilization (IVV) embryos. By knocking down lncRNA expression in in vitro fertilization (IVF) embryos, we investigated its function and mechanism of regulating embryonic development.  The RNAseq was curry out to explore the genes influenced by lncT(LOC102165808).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control and LncT KD porcine embryos

first: Ziyi


title: Systematic identification of tumor-intrinsic resistance mechanisms and combinatorial therapy targets for immunotherapy

city: Bethesda

first: Suman Kumar

last: Vodnala

state: MD

address: 10 Center Drive

department: Surgery Branch

institute: NCI

summary: A number of reports have demonstrated that tumor-intrinsic mechanisms of resistance, such as the loss of genes critical for antigen presentation and inflammatory responses, along with the activation of various cellular signaling cascades, can limit the efficacy of immunotherapy. Strategies to sensitize tumor cells to immunotherapy may overcome some resistance mechanisms, but identifying therapeutic targets has remained challenging. Here, we integrate a two-cell type (2CT) whole-genome CRISPR-Cas9 screen with dynamic transcriptional profiling of the tumor/T cell interaction to comprehensively identify tumor genes that are induced to promote tumor survival. We assessed the therapeutic potential of pharmacological inhibition of these and other top CRISPR identified targets as combinatorial targets to improve the efficacy of tumor destruction by T cells.

overall_design: RNA expression was measured by RNAseq on sorted Mel624 tumor and primary human NY-ESO TCR T cell samples after 0 or 6 hours of coculture.  Additional experiments measured RNA expression by RNAseq when A375 tumor cells with non-targeting of BIRC2 targeting sgRNAs and Cas9 expression were treated with vehicle or 100 ng TNFa for 16 hrs

first: Rigel

last: Kishton

first: Suman

middle: K


title: Intestinal epithelial c-Maf expression determines enterocyte differentiation and nutrient uptake

city: Berlin

first: Christian

last: Neumann

address: Hindenburgdamm 30

institute: Charité-Universitätsmedizin Berlin

summary: We performed RNA-Seq analysis of small intestinal epithelial cells (IEC) of Vil.Cre Maf.flox and Maf.flox control mice.

overall_design: CD45- EpCAM+ IEC were isolated from the small intestine of Vil.Cre Maf.flox and Maf.flox control mice and subjected to RNA-Seq.

first: Catalina

last: Cosovanu

first: Philipp

last: Resch

first: Stefan

last: Jordan

first: Andrea

last: Lehmann

first: Markus

last: Ralser

first: Vadim

last: Farztdinov

first: Joachim

last: Spranger

first: Michael

last: Mülleder

first: Sebastian

last: Brachs


title: MANIO: Mechanism of wild-type and mutant p53 activation and therapeutic potential in colorectal cancer

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

country: Italy

institute: ICGEB

summary: In an attempt to find new effective p53-activating agents with antitumor activity, the anti-proliferative activity of a small chemical library of 6,7-bis(hydroxymethyl)-1H,3H-pyrrolo[1,2-c]thiazoles was investigated in a panel of human cancer cells with different p53 status. The (3S)-6,7-bis(hydroxymethyl)-5-methyl-3-phenyl-1H,3H-pyrrolo[1,2-c]thiazole (MANIO) was selected due to its noticeable selectivity to cancer cells expressing p53. The IC50 values of MANIO ranged from 0.20 – 0.97 µM or 0.088 – 2.90 µM in wtp53- or mutp53-expressing cells, respectively, to 26.20 – 48.25 µM in p53-null cells.

overall_design: To gain more evidence of the potential to engage the p53 response pathway at the transcriptional level, HCT116 p53+/+ cells were treated with 1 µM MANIO or DMSO control for 24 hours followed by RNA-sequencing. Four biological replicates were performed.

first: Helena

last: Ramos

first: Isabel

last: Soares

first: Liliana

last: Raimundo

first: Joana

last: Silva

first: Célia

last: Gomes

first: Flávio

last: Reis

first: Filipe

last: Monteiro

first: Cláudia

last: Nunes

first: Salette

first: Petr

last: Chlapek

first: Renata

last: Veselska

first: Lucília

last: Domingues

first: Bartolomeo

last: Bosco

first: Alberto

last: Inga

first: Teresa

last: Pinho e Melo

last: Saraiva


title: Overexpression of long noncoding RNA 4933425B07Rik leads to renal hypoplasia by inactivating the Wnt/β-catenin signaling pathway

city: Shanghai

first: Shanshan

last: Xue

address: 399 Wanyuan Road

institute: Children's Hospital of Fudan University

summary:
Background
Congenital anomalies of the kidney and urinary tract (CAKUT) refer to a diverse group of developmental malformations, which are the leading cause of chronic kidney disease and end-stage renal disease in children. The etiology and pathogenesis of CAKUT are complex. In recent years, the relationship between long noncoding RNAs and renal development and disease has attracted much attention. Our previous study established a long noncoding RNA 4933425B07Rik (Rik) overexpression mouse model by inserting the PB transposon and found that overexpression of Rik led to renal hypoplasia. This study aimed to explore the molecular mechanism of renal hypoplasia induced by Rik overexpression in vitro.
Results
In this study, by constructing Rik overexpression cell models and a Rik knockout cell model to accompany previously developed RikPB/PB;Hoxb7 mice and by applying RNA-seq, RT‒PCR and other experimental methods, it was found that when Rik was highly expressed, the expression of Wnt10b, Fzd8 and β-catenin decreased, while Rik was knock down, the expression of these genes increased.
Conclusions
The findings suggest that overexpression of Rik leads to renal hypoplasia by inactivating the Wnt/β-catenin signaling pathway. This research perspective may provide a basis for exploring new causes and mechanisms of CAKUT and provide new targets for the prevention and treatment of CAKUT.

overall_design: The study had two cell lines, MPTC cells and MK3 cells, each divided into two groups, the Rik overexpression experiment group (LV-Rik-MPTC/MK3) and the empty vector control group (con238-Rik-MPTC/MK3), each with 3 repetitive samples. Comparative gene expression profiling analysis of RNA-seq data for LV-Rik-MPTC/MK3 cells and its control group con238-Rik-MPTC/MK3.

first: Qian

last: Shen


title: Transcriptomic profiling of MCF-7 breast cancer cells treated with Karanjin

city: Guwahati

first: Anil

middle: Mukund

last: Limaye

state: Assam

address: IIT Guwahati

department: Department of Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology Guwahati

summary: Application of next generation sequencing (NGS) technology to identify karanjin-modulated genes in MCF-7 breast cancer cells

overall_design: MCF-7 breast cancer cells treated with 10 μM karanjin (n=3) or vehicle (0.1% DMSO, n=3) for 24 h.

first: Gaurav

last: Bhatt

first: Akshita

last: Gupta

first: Latha

last: Rangan


title: Effects of the glucagon-like 1 receptor agonist exendin-4 on activated gut intraepithelial lymphocytes

status: Public on Aug 29 2022

city: Toronto

first: Chi Kin

last: Wong

address: 600 University Avenue

institute: LTRI

summary: Gut intraepithelial lymphocytes (IELs) are one of the few immune cell populations in the body that expresses glucagon-like 1 receptors (GLP-1R). To test the potential effects of GLP-1 on gut IEL function, we performed bulk RNA-seq on gut IELs isolated from C57BL/6J mice treated with anti-CD3 and with or without exendin-4 for 3 hours.

overall_design: 4 anti-CD3- and PBS-treated and 4 anti-CD3- and exendin-4-treated C57BL/6J mice. Total RNA isolated from sorted gut IELs was prepared into stranded mRNA library using TruSeq stranded mRNA library preparation kit (Illumina) and sequenced on a NovaSeq (Illumina) with a read length of 2 x 200 bp.

first: Daniel

last: Drucker


title: Transcriptome changes in chlorsulfuron-treated plants are caused by acetolactate synthase inhibition and not induction of a herbicide detoxification system in Marchantia polymorpha

city: Vienna

first: Alexandra

last: Casey

address: Dr.-Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute

summary:
We set out to test the hypothesis that there is a sensing system in plants that perceives herbicides resulting in transcriptome changes that lead to the expression of genes encoding proteins that detoxify these molecules.
We show that chlorsulfuron-treatment induces changes in the Marchantia polymorpha transcriptome. However, these transcriptome changes do not occur in target site resistant mutants treated with chlorsulfuron.  Instead, we show that inactivation of the chlorsulfuron target, acetolactate synthase (ALS) (also known as acetohydroxyacid synthase (AHAS)), is required for the transcriptome response.

overall_design: Differential expression analysis of RNA-Seq data for 8 day-old gemmalings of Marchantia polymorpha Tak-2 accession and MpalsP197L_7 and MpalsP197L_10 mutant lines

first: Liam

last: Dolan


title: RNA transcriptome sequencing analysis of primary human keratinocytes transfected with shRNA-NR037661 or control shRNA

city: shanghai

first: Ming

middle: zhe

last: Ma

email: mmz666@163.com, mmz666@shca.org.cn

address: Dongan Road 270

department: Department of gastric surgery

institute: Fudan university shanghai cancer center

summary: a RNA transcriptome sequencing analysis was performed in primary human keratinocytes that were transfected with  shRNA-NR037661 or control shRNA

overall_design: mRNA profiles of   primary human keratinocytes transfected with shRNA-NR037661 or control shRNA

first: Chunxiao

last: Li

first: Mingzhe


title: Development and characteristics of an apetalous nullisomic in Brassica juncea through interspecific hybridization

city: Guiyang

first: jie

last: yu

address: 116 Baoshan North Road

institute: Guizhou Normal Universuty

summary: The aim of this study was to compare apetalous nullisomic with its parent. Transcriptome analysis (RNA-SEQ) and quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) of parent "YLC" andapetalous nullisomic were performed, and the best high-throughput data analysis protocol was evaluated

overall_design: Comparative gene expression profiling analysis of RNA-seq data for apetalous nullisomic "AN" and its parent "YLC"

first: Zhu

last: Bin

first: Yu

last: Jie


title: RNA-Seq analysis of cSCC cells followed by siRNA-induced gene knockdown of lncRNA LINC00094 (SERLOC)

city: Turku

first: Liisa

last: Nissinen

address: Medisiina D, 5th floor; Kiinamyllynkatu 10

department: Dermatology

country: Finland

institute: University of Turku

summary: Keratinocyte-derived cutaneous squamous cell carcinoma (cSCC) is the most common metastatic skin cancer, and its incidence is increasing globally. Long non-coding RNAs (lncRNAs) are involved in various biological processes, and their role in cancer progression is emerging. Whole transcriptome analysis of cSCC cells (n=8) and normal human epidermal keratinocytes (NHEKs, n=4) revealed overexpression of long intergenic ncRNA (LINC00094) in cSCC cells (GSE66412). We wanted to futher study the RNA expression profile of LINC00094 knockdown cSCC cells.

overall_design: Total RNAs from negative control and LINC00094 siRNA-treated cSCC cell lines (n=3) were extracted. The samples were sequenced using Illumina HiSeq3000.

first: Minna

last: Piipponen

first: Veli-Matti

last: Kähäri


title: Short-term tamoxifen administration improves hepatic steatosis and glucose intolerance through JNK/MAPK in mice

city: Xi'an

first: Zhiqiang

last: Fang

state: Shaanxi

address: No.169,Changle West Road

institute: Xijing Hospital

summary: Nonalcoholic fatty liver disease (NAFLD) which is a leading cause of chronic liver diseases lacks effective treatment. Tamoxifen has been proved to be the first-line chemotherapy for several solid tumors in clinics, however its therapeutic role in NAFLD has never been elucidated before. In vitro experiments, tamoxifen protected hepatocytes against sodium palmitate-induced lipotoxicity. In male and female mice fed with normal diets, continuous tamoxifen administration inhibited lipid accumulation in liver and in blood, and improved glucose and insulin intolerance. Short-term tamoxifen administration largely improved hepatic steatosis and insulin resistance, however the phenotypes manifesting inflammation and fibrosis remained unchanged in abovementioned models. In addition, mRNA expressions of genes related to lipogenesis, inflammation and fibrosis were downregulated by tamoxifen treatment. Moreover, the therapeutic effect of tamoxifen on NAFLD was not gender or ER dependent, as male and female mice with metabolic disorders shared no difference in response to tamoxifen and ER antagonist (fulvestrant) didn’t abolish its therapeutic effect as well. Mechanistically, RNA-sequence of hepatocytes isolated from fatty liver revealed that JNK/MAPK signaling pathway was inactivated by tamoxifen. Pharmacological JNK activator (anisomycin) partially deprived the therapeutic role of tamoxifen in treating hepatic steatosis, proving tamoxifen improved NAFLD in a JNK/MAPK signaling dependent manner.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for primary hepatocytes isolated from MCD diet-induced NASH mice administrated with tamoxifen or vehicle for consecutive 5 days

first: Lin

last: Wang


title: LncRNA LINC00839 promotes colorectal cancer progression by RUVBL1/Tip60-NRF1 signaling pathway

city: Guangzhou

first: Xiaoting

last: Liu

address: Baiyun District

institute: Southern Medical University

summary:
Purpose: we focused on the biological roles and mechanism of the lncRNA LINC00839 in CRC.
Methods:   In situ hybridization (ISH), and quantitative real-time PCR (qPCR) were used to detect the expression of LINC00839 in paired CRC specimen. Biological function of LINC00839 was determined in vitro and in vivo. Western blot, bioinformatics analysis, RNA pull-down, RNA immunoprecipitation (RIP) and chromatin immunoprecipitation assays (ChIP) were performed to identify the mechanisms underlying the functions of LINC00839 in CRC.
Results: We found that LINC00839 was located in the nucleus of CRC cells and that LINC00839 was upregulated in CRC. High expression of LINC00839 was associated with poor outcome in CRC patients. Functionally, upregulation of LINC00839 promoted CRC cell proliferation, invasion, and metastasis in vitro and in vivo. Mechanistic investigations revealed that LINC00839 can promote the acetylation of histones H4K5 and H4K8 at the promoter of NRF1 after recruiting the RUVBL1/Tip60 complex, thereby upregulating the expression of NRF1. Subsequently, NRF1 served as an activator in mitochondrial metabolism and biogenesis, which, in turn, promoted CRC progression.

overall_design: overexpressing LINCRNA CRC compared with control cell Transcriptomes

first: Jun

last: Zhou


title: Digital Gene Expression data of human serum sensitive and resistant group 2 Trypanosoma brucei gambiense

city: Glasgow

first: Nicola

last: Veitch

address: Bearsden Rd

institute: University of Glasgow

summary: Trypanosoma brucei gambiense is the causative agent of the fatal human disease African sleeping sickness. Using Digital Gene Expression we have compared the transcriptome of two isogenic T.b.gambiense lines that are either sensitive or resistant to human serum.

platform_organism:
Trypanosoma brucei brucei
Trypanosoma brucei gambiense

overall_design: RNA was extracted from 3 human serum sensitive and 3 human serum resistant T.b. gambiense cultures (from human serum). Digital Gene Expression libraries were created and were sequenced using Illumina next generation sequencing technology. 2 additional  human serum resistant T.b. gambiense cultures in 20% fetal bovine serum.

first: Annette

last: MacLeod

first: Paul

last: Johnston


title: Alternative splicing analysis of SRRM1 or SRRM2 targets in THP-1 cells

city: Singapore

first: Xavier

last: ROCA

state: Singapore

address: 60 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

summary: We reported the joint SRRM1/2 regulation is not the major mechanism of SRRM2-mediated alternative splicing, and that maintenance of splicing condensates by SRRM2 is important for proper alternative splicing. We knocked SRRM1/2 down with three different shRNAs, performed RNA-seq and derived the differential alternative splicing events (DASEs) using rMATS. DASEs of SRRM1/2 were largely different with little overlap, and displayed a different splicing pattern. SRRM2 deficiency induces skipping of cassette exons with short introns and weak 5’ splice. Nearly 25% of the skipped events upon SRRM2 knockdown were unannotated. More than 40% of validated DASEs upon SRRM2 suppression were associated with protein domain change (>50% domain removed by splicing). Domain changes, and especially large region removal by multiple exon skipping is a significant mechanism for protein dysfunction. Thus, alternative splicing is the major mechanism for the maintenance of protein function and cell homeostasis by SRRM2.

overall_design: Transcriptome profiles and alternative splicing analysis of THP-1 cell lines with either SRRM1 or SRRM2 knockdown, by three different shRNAs respectively

first: Shaohai

last: XU


title: Saracatinib inhibits TGF-β–induced phenotypic changes in human lung fibroblasts

city: New York

first: Christine

last: Becker

state: NY

address: 1470 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

summary: Idiopathic Pulmonary Fibrosis (IPF) is a chronic, progressive, and often fatal disorder. Using an in-silico data-driven approach, we identified a robust connection between the transcriptomic perturbations in IPF disease and those induced by saracatinib, a selective Src kinase inhibitor, originally developed for oncological indications.We investigated the anti-fibrotic efficacy of saracatinib relative to nintedanib and pirfenidone in in vitro modele using normal human lung fibroblasts (NHLFs).

overall_design: To investigate the effects of saracatinib in pulmonary fibrosis we used a  disease-relevant in vitro model. We generated transcriptomic drug signatures by performing bulk RNA sequencing (RNAseq) on Normal Human Lung Fibroblast (NHLF) cells treated with saracatinib, nintedanib, pirfenidone, or vehicle control in the presence or absence of TGF-β stimulation.

first: Farida

last: Ahangari

first: Loukia

last: Lilli

first: Carly

last: Meador

first: Kelly

last: Correll

first: Helen

last: Roybal

first: Joel

middle: T

last: Dudley

first: Naftali

last: Kaminski

first: Gregory

middle: P

last: Downey


title: Production of MHCII-expressing classical monocytes increases during aging in mice and humans

city: Los Angeles

middle: S

last: Goodridge

address: 8700 Beverly Boulevard

institute: Cedars-Sinai Medical Center

summary: Aging is associated with increased monocyte production and altered monocyte function. Classical monocytes are heterogenous and a shift in their subset composition may underlie some of their apparent functional changes during aging. We have previously shown that mouse granulocyte-monocyte progenitors (GMPs) produce “neutrophil-like” monocytes (NeuMo), whereas monocyte-dendritic cell progenitors (MDPs) produce monocyte-derived dendritic cell (moDC)-producing monocytes (DCMo). Here, we demonstrate that classical monocytes from the bone marrow of old male and female mice have higher expression of DCMo signature genes (H2-Aa, H2-Ab1, H2-Eb1, Cd74), and that more classical monocytes express MHCII and CD74 protein. Moreover, we show that bone marrow MDPs and classical monocytes from old mice yield more moDC. We also demonstrate higher expression of Aw112010 in old monocytes and that Aw112010 lncRNA activity regulates MHCII induction in macrophages, which suggests that elevated Aw112010 levels may underlie increased MHCII expression during monocyte aging. Finally, we show that classical monocyte expression of MHCII is also elevated during healthy aging in humans. Thus, aging-associated changes in monocyte production may underlie altered monocyte function and have implications for aging-associated disorders.

overall_design:
mRNA profiles (scRNAseq) of bone marrow Ly6Chi monocytes from young (14-15 week) and old (26.5-27 month) male and female mice (4 groups, 5 mice per group).

Grant ID: R01 AI134987
Grant title: Monocyte Production by Bone Marrow Progenitors
Grantee: Helen Goodridge
Funding source: NIH (NIAID)

first: Pijus

last: Barman

first: Juliana

last: Shin


title: Comparison of transcriptional changes in IPF mouse models (Bleomycin and Ad-TGFb)

summary: Idiopathic Pulmonary Fibrosis (IPF) is a chronic, progressive, and often fatal disorder. Using an in-silico data-driven approach, we identified a robust connection between the transcriptomic perturbations in IPF disease and those induced by saracatinib, a selective Src kinase inhibitor, originally developed for oncological indications.We investigated the anti-fibrotic efficacy of saracatinib in two in vivo modeles (bleomycin and recombinant adenovirus transforming growth factor-beta (Ad-TGF-β) murine models of pulmonary fibrosis).

overall_design: To investigate the effects of saracatinib in pulmonary fibrosis we used two animal models pulmonary fibrosis. In the first model, fibrosis was induced using a single dose of bleomycin (1.5U/Kg) administered into the lung by oropharyngeal aspiration (OPA) and mice received saracatinib or vehicle control once daily via oral gavages on days 10-27 post-bleomycin administration. A second model of pulmonary fibrosis was established using expression of recombinant murine TGF-β using adenoviral-mediated gene delivery (Ad-TGF-β) administered to the lung intranasally. As in the bleomycin model, drug or vehicle  were given to mice once daily via oral gavages from days 10-27 after TGF-β administration. On day 28, all the mice were euthanized, lungs were harvested for further analysis.

first: Xing

last: Wang

first: Daniel

last: Foster

first: Keriann

last: Beke


title: Reversibility of etomidate-induced contractile arrest through activation of myocardial autophagy

first: Yangyang

last: liu

address: Jin zun 115

institute: Shanghai Jiao Tong University School of Medicine

summary:
Anesthetic management of heart failure patients undergoing noncardiac surgery remains challenging due to cardiac suppressive properties of anesthetics. Due to varying electrophysiological properties, small and large animals are not good models for studying human myocardial anesthetic responses. Here we use hypertrophic (HCM), dilated (DCM) and healthy human induced pluripotent stem cells derived cardiomyocytes (hiPSC-CMs) to evaluate the cardiac suppression of propofol and etomidate. We demonstrate that propofol and etomidate act through GABAA receptors and contractile inhibition can occur without cell-cell junction. At supraphysiological dosage (100mM), we discovered that cardiac suppression induced by etomidate is reversible while propofol is not. Using transcriptome profiling, we uncover that etomidate was capable of inducing autophagy, likely through induction of cytosolic calcium. Lack of autophagy induction in propofol treated cardiomyocytes were associated with increased apoptosis. Together, we provide the robustness of using hiPSC-CMs as an in vitro cardiotoxicity platform for anesthetics.
To delineate how etomidate confers cardioprotection during contraction inhibition, we performed transcriptome profiling on DCM hiPSC-CMs treated with either 10 μM propofol, 10 μM etomidate or DMSO control.

overall_design: Yangyang, Liu


title: Curcuma longa and Boswellia serrata extracts modulate different and complementary pathways on human chondrocytes in vitro: deciphering of a transcriptomic study

city: Liège

first: Christelle

last: Sanchez

address: Quai G. Kurth 45

country: Belgium

institute: ULiege

summary: Objectives: Curcuma longa (CL) and Boswellia serrata (BS) extracts are used to relieve osteoarthritis symptoms. The aim of this in vitro study was to investigate their mechanisms of action at therapeutic plasmatic concentrations on primary human osteoarthritic (OA) chondrocytes.Methods: BS (10-50 µg/mL) and CL (0.4-2 µg/mL corresponding to 1-5 µM of curcumin) were evaluated separately or in combination on primary chondrocytes isolated from 17 OA patients and cultured in alginate beads. 10 patients were used for RNA-sequencing analysis. Proteomic confirmation was performed either by immunoassays in the culture supernatant or by flow cytometry for cell surface markers after 72h of treatment. Results: Significant gene expression modifications were already observed after 6 hours of treatment at the highest dose of CL (2 µg/ml) while BS was significantly effective only after 24h of treatment whatever the concentration tested. The most over-expressed genes by CL were anti-oxidative, detoxifying, and cytoprotective genes involved in the Nrf2 pathway. Down-regulated genes were principally pro-inflammatory cytokines and chemokines. Inversely, BS anti-oxidant/detoxifying activities were related to the activation of Nrf1 and PPARα pathways. BS anti-inflammatory effects were associated with the increase of GDF15, a decrease in cholesterol cell intake and fatty acid metabolism involved genes, and a down-regulation of Toll-like receptors (TLRs) activation. As CL, BS down-regulated ADAMTS1, 5 and MMP3, 13 genes expression. The combination of both CL and BS was significantly more effective than CL or BS alone on many genes such as IL-6, CCL2, ADAMTS1, and 5. Conclusion: BS and CL have anti-oxidative, anti-inflammatory, and anti-catabolic activities suggesting a protective effect of these extracts on cartilage. Even if they share some mechanism of action, the two extracts act mainly on distinct pathways, and with different time courses, justifying their association to treat osteoarthritis.

overall_design: RNA-Seq on primary human OA chondrocytes mRNA cultured in alginate beads in the presence or not of C. longa, B. serrata or the combination

first: Jeremie

last: Zappia

first: Cecile

last: Lambert

first: Jacques

last: Foguenne

first: Yvan

last: Dierckxsens

first: Jean-Emile

last: Dubuc

first: Jean-Pierre

last: Delcour

first: André

last: Gothot

first: Yves

last: Henrotin


title: Effects of semaglutide on the gut microbiota of high-fat diet-fed mice lacking GLP-1Rs in T cells

first: Chi Kin

last: Wong

summary: Gut intraepithelial lymphocytes (IELs) are one of the few immune cell populations in the body that expresses glucagon-like 1 receptors (GLP-1R). To test the potential effects of GLP-1 on the gut microbiota through the gut IEL GLP-1R, we performed 16s rRNA seq on the DNA isolated from the fecal pellet of Lck-Cre; Glp1rfl/fl mice (Glp1rTcell-/-) or controls (Glp1rTcell+/+) fed a high-fat diet (HFD) for 12 weeks followed by 1 week of HFD plus semaglutide (10 ug/kg) or vehicle treatment. Fecal pellets from a group of age-matched, sex-matched control mice were included as a chow control group.

overall_design: 6 chow-fed control,  9 vehicle-treated Glp1rTcell+/+, 9 semaglutide-treated Glp1rTcell+/+, 11 vehicle-treated Glp1rTcell-/-, and 9 semaglutide-treated Glp1rTcell-/- mice. DNA isolated from fecal pellets was amplified for the V3 and V4 regions of the 16s rRNA gene, prepared into sequencing libraries, and sequenced on a MiSeq (Illumina) with a read length of 2 x 300 bp.

last: Drucker


title: DNA methylation profiling in cord blood neonatal monocytes from women with pre-gestational obesity

city: Rancagua

first: Bernardo

middle: J.

last: Krause

state: VI Region

address: Alameda 611

country: Chile

institute: Universidad de O'Higgins

type: Methylation profiling by genome tiling array

summary: Obesity represents a global burden with an increasing worldwide prevalence, especially in women of reproductive age. Obesity in women, defined as a body mass index (BMI) > 30 kg/m2, has a worldwide prevalence ~21%, however, it exceeds 30% in countries such as Chile, Mexico, United States, and the United Kingdom. Growing evidence support the notion that pre-gestational obesity confers an increased risk for the development of diabetes, obesity and chronic inflammatory diseases in the offspring later in life. In fact, maternal obesity during gestation is associated with an increased risk of asthma and wheezing during early or late infancy, in terms of medication and need for hospital admission. Here we report changes in DNA methylation at a genomic level in monocytes isolated by adherence from cord blood of neonates born to women with obesity and integrate these changes to reveal the epigenetic programming of immune signaling pathways resulting from maternal obesity.

overall_design: The group of newborn-mother dyads included in this study is a subset selected from our prospective cohort according to a series of criteria: healthy pregnant women receiving care in the 12 public health care centers in La Florida and Puente Alto; singleton pregnancies of ≤ 14 weeks of gestation at first antenatal visit; 18 years or older. The pregnant women were classified as normal weight or with obesity according to their BMI at the first clinical pregnancy control (< 14 weeks of gestation). Exclusion criteria were women with overweight (25 ≤ BMI < 30) at ≤ 14 weeks of gestation, macrosomia, premature birth, cardio-respiratory disorder, genetic and/or neurological defects of the neonate. Secondary exclusion criterion (applied during analysis) was inadequate gestational weight gain according to the recommendations of the Institute of Medicine. All the biological samples and clinical data were coded and anonymized after written consent was obtained. Complete details about the study can be found at ClinicalTrials.gov ID: NCT02903134

first: Jose

middle: A

last: Castro-Rodriguez


title: Identification and analysis of circRNAs in the prefrontal cortex of wild boar and domestic pig

city: Chengdu

first: hengkuan

last: li

state: Sichuan

address: Hui ming

institute: Sichuan Agricultural University

summary: Domestication caused significant differences in morphology and behavior between wild and domestic animals, and gene expression changes played an important role in this event. circRNA is a class of non-coding RNA that exerts a wide range of functions in biological processes through the regulation of gene expression. However, the regulatory role of circRNA in the process of domestication is still unclear. Here, we analyzed circRNA expression patterns in the prefrontal cortices of wild boar and domestic pig to determine the potential role of circRNAs in domestication. We identified a total of 11,375 circRNAs and found that 349 and 354 circRNAs were up-regulated in wild boar and Rongchang pig, respectively. This study lays the groundwork for exploring the regulatory role of circRNA in the process of domestication and provides new insights that contribute to further investigation of the molecular mechanism of pig domestication.

overall_design: We generated RNA sequencing (RNA-seq) data of wild boar of 1-3 replicates.

first: Hengkuan

last: Li

first: Long

last: Jin

first: Mingzhou


title: FOXA1 inhibits prostate cancer hypoxia program through transcriptional repression of HIF1A

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

summary: We and others have previously shown FOXA1 is frequently mutated or downregulated in castration resistant prostate cancer (CRPC). Here we report a novel role for transcription factor FOXA1 in directly repressing HIF1A expression in prostate cancer cells. FOXA1 knockdown induced the expression of HIF1A and hypoxia signature genes, which were reduced by concomitant HIF1A knockdown or treatment with HIF1A inhibitor KC7F2. Thus, our data suggest FOXA1 loss induces aberrant hypoxia signaling and tumor progression in part via HIF1A.

overall_design: Examination of transcriptional reprogramming in human prostate cancer LNCaP cells following FOXA1 knockdown with or without concomitant genetic/pharmacological inhibition of HIF1A. Cells were treated with 100µM CoCl2 to mimic tumor hypoxia and stabilize HIF1A protein when expressed. There are 18 RNA-seq samples with pGIPZ as control. Each condition was performed in triplicate.

first: Lourdes

last: Brea

first: Xiaohai

last: Wang


title: BRD4 inhibitor MZ1 exerts anti-cancer effects in Neuroblastoma

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

summary: MZ1 is a newly designed pan-BET-targeting PROTAC that binds to target proteins (BET proteins such as BRD2, BRD3, and BRD4) and recruits them to the ubiquitin/protease pathway for selective destruction. However, the role of MZ1 in NB models has yet to be determined. The effect of MZ1 on NB cells was investigated using RNA-seq analysis in this work.  MZ1 is a newly designed pan-BET-targeting PROTAC that binds to target proteins (BET proteins such as BRD2, BRD3, and BRD4) and recruits them to the ubiquitin/protease pathway for selective destruction. However, the role of MZ1 in NB models has yet to be determined. The effect of MZ1 on NB cells was investigated using RNA-seq analysis in this work.

overall_design: mRNA profiles of SK-N-BE(2) cells treated with 750nM MZ1 or same volume DMSO for 36 h were generated by RNA sequencing, in double, using Illumina NovaSeq6000.

first: Xianbing

first: Jian


title: Visium Analysis of head and neck squamous carcinoma (HNSCC) spatial transcriptome evolution

city: Taipei

first: Chih-Hung

last: Chung

address: No.155, Sec.2, Linong Street, Taipei, 112 Taiwan (ROC)

department: Institute of Clinical Medicine

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary: We collected HNSCC primary tumor sections from head and neck squamous cell carcinoma patients at the Taipei Veterans General Hospital (TVGH) for 10x Genomics Visium analysis.

overall_design: 10X Visium Spatial transcriptome Sequencing of HNSCC pateint tumor in different part

first: Muh-Hwa

last: Yang

first: Shyh-Kuan

last: Tai


title: Single cell sequence of tumor infiltrated immune cells after cisplatin treatment in control or miR-21 KO in mouse oral cancer model

city: Taipei City

first: han-ying

last: cheng

address: No. 155, Sec. 2, Linong St., Beitou Dist.

department: Institute of clincal medicine

summary: Single cell sequence (SC-seq) has been used to explore the effect of miR-21-modulated chemotherapy-induced tumor microenvironment change. MTC-Q1 WT or MTC-Q1 miR-21 KO cells were subcutaneously injected into C57BL/6 mice. CD45+ immune cells has been isolated after cisplatin injection. The isolated immune cell were sequenced by dropped based scRNA-seq, cDNA were sequenced by Illumina Novaseq 6000.

overall_design: SC-seq of CD45+ immune infiltrated cell in MTC-Q1 WT or MTC-Q1 miR21 KO subcutaneous tumor after 72 hr of cisplain (5mg/kg) injection.

first: Han-Ying

last: Cheng


title: PHOX2B promotes the occurrence and development of neuroblastoma by activating the MAPK signaling pathway

summary: Studies have shown that PHOX2B is the first predisposition gene identified in neuroblastoma.To explore PHOX2B-dependent gene regulation, RNA-seq analysis was performed. Compared with the control group, PHOX2B knockdown SK-N-BE(2) cells showed differently expressed genes. We found that PHOX2B activates the MAPK signaling pathway to promote the occurrence and development of neuroblastoma.

overall_design: mRNA profiles of SK-N-BE(2) cells transfected with scramble shRNA (sh-Scb) or sh-PHOX2B were generated by RNA sequencing, in double, using Illumina NovaSeq6000.

first: Ran

last: Zhuo

last: Pan


title: Super-enhancer-associated TTC8 promotes neuroblastoma progression

summary: We report a previously unrecognized role of super-enhancer-associated TTC8 in neuroblastoma. To explore TTC8-dependent gene regulation, RNA-seq analysis was conducted and the differently expressed genes were revealed in the TTC8-knockdown SK-N-BE(2) cells in comparison to control group. We find that TTC8 activate the MAPK signaling pathway to promote the occurrence and development of neuroblastoma.

overall_design: mRNA profiles of SK-N-BE(2) cells transfected with scramble shRNA (sh-Scb) or sh-TTC8 were generated by RNA sequencing, in double, using Illumina NovaSeq6000.


title: RNA-Seq analysis of the Fzd1 mutant mice

city: Kansas City

first: Congrong

middle: Ron

state: Missouri

institute: Stowers Insitute for Medical Research

summary: We performed RNA-Seq of the total RNA from olfactory epithelia of the Fzd1 knockout, Fzd1 ectopic expression mice, and mice with Fzd1 ectopic expression only at P0 to study the gene expression change associated with Fzd1. The samples include several time points between P0 to P14 and allow the time course study of gene expression.

overall_design: P0, P3, P7, P10, P14 olfactory epithelia samples from Fzd1 knockout and Fzd1 ectopic expression mice with replicates were analyzed. P1, P3, P7, P10, P14 olfactory epithelia samples from Fzd1 ectopic expression mice given DOX at P0 with replicates were analyzed

first: Yunming

last: Wu

first: Limei

last: Ma

first: Jillian

last: Blanck

first: Allison

last: Scott

first: Shiyuan

middle: C

last: Chen

first: Huzaifa

last: Hassan

first: Kate

last: Hall

first: Anoja

last: Perera

middle: R


title: MiRnome profiling of Human bladder cancer line invalidated for the MUC4 gene by ShRNA.

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

overall_design: Comparisons of miRNA in 647-V bladder cancer cell line following stable MUC4 knocked down by ShRNA transfection and MOCK corresponding control cells.

first: Nicolas

last: Jonckheere


title: Effect of overexpression of wildtype (WT), triple acetylation-deficient mutant (K3R), or triple acetylation-mimetic mutant (K3Q) SIRT6 on gene expression in human non-small cell lung cancer cells

status: Public on Aug 28 2022

city: Hong Kong

first: Zezhuo

last: Su

address: No. 21 Sasson Rd, Pokfulam

institute: The University of Hong Kong

summary:
To investigate how the acetylation state of SIRT6 affects its tumor suppressive function in non-small cell lung cancer (NSCLC) cells, we established A549 and H1299 NSCLC cell lines stably expressing either control vector, FLAG-SIRT6 WT, K3R, or K3Q mutants.
We then performed gene expression profiling analysis using data obtained from RNA-seq of established A549 and H1299 cells.

overall_design: Comparison of the gene expression profiles in empty vector, WT, K3R, and K3Q SIRT6 overexpressing A549 and H1299 cells.

first: Kaiqiang

last: Zhao


title: RNA-seq of fluorescence activated cell sorting purified mature olfactory sensory neurons and progenitor cells

last: Yu

summary: This experiment studies the gene expression in the mature olfactory sensory neurons and the intermidiate neuronal progenitors in the olfactory epithelia during the critical period. Mature olfactory sensory neurons from OMP-GFP mice and intermediate neuronal progenitors in the olfactory epithelia from Neurog1-GFP mice were FACS purified. PolyA RNA profiles at P2, P3, P7, P9, and P16 were generated by RNA-Seq.

overall_design: Mature olfactory sensory neuron mRNA profiles from pooled purified cells at P2, P7, P16 were generated by RNA-Seq. Neurog1 expressing progenitor cell mRNA profiles from pooled purified cells at P3, P7, P9, and P16.


title: Single cell analysis of the olfactory epithelia

summary: Single cell RNA-Seq experiment was conducted using mouse olfactory epithelia at E18.5, P14, and adult stage to study the gene expression in different cell types, including olfactory sensory neurons and their progenitor cells.

overall_design: 3 single cell libraries from E18.5, P14, and adult.


title: A Novel Composite Hydrogel for Treating Periodontitis and Hypertension

city: Shanghai

first: Shuo

last: Xu

address: Zhizaoju Road

institute: Shanghai ninth people's hospital

summary:
Periodontitis and hypertension often occur as comorbidities. In the face of severe periodontitis patients with hypertension, periodontists often have to give priority to control the patient's blood pressure before surgical treatment, and how to use drugs also brings a lot of inconvenience for clinical treatment. In the stage of periodontal basic treatment, it is a problem that needs to be solved to treat periodontal inflammation and control blood pressure at the same time, so as to achieve “co-treatment of comorbidities”.
To this issue, we proposed a controlled-release composite hydrogel approach with dual antibacterial and anti-inflammatory activities as a resolution for pathogen-originated periodontitis. Specifically, chitosan (CS) with inherent antibacterial properties was crosslinked with antimicrobial peptide (AMP) modified polyethylene glycol (PEG) to form the dual antibacterial hydrogel (CS-PA). Subsequently, curcumin nanoparticles (CNP) were encapsulated in the hydrogel to impart anti-inflammatory activities.
In the mouse model of periodontitis complicated with hypertension, CS-PA/CNP was applied to gingival sulcus, found that it produced a perfect therapeutic effect on periodontitis and hypertension at the same time. The antibacterial experiments showed that CS-PA/CNP had an excellent inhibitory effect on a variety of periodontal pathogens, demonstrated the potential regulatory ability of the microbiota. In addition, cytological studies revealed the molecular mechanism that CS-PA/CNP enhanced antioxidant capacity of macrophages through the glutathione metabolism pathway, while enhancing their anti-inflammatory capacity. In conclusion, CS-PA/CNP has demonstrated its superior therapeutic effect and potential clinical translational value in the treatment of periodontitis and hypertension, which also serves as a drug delivery platform to provide combinatorial therapeutic options for periodontitis with complicated pathogenesis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BMDMs co-cultured with PgLPS or CS-PA/CNP

first: Bin

last: Hu

first: Xue-Qing

last: Zhang

first: Sheng-Zhong

last: Duan


title: Splenic and adipose B cells from wild-type and Nlrp3-/- mice

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Adipose and splenic B cells are expanded with age in wild-type mice, but not Nlrp3-/- mice. This comparison is to address the transcriptional changes that are dependent upon age or Nlrp3.

overall_design: Wild-type and Nlrp3-/- mice were aged to 3- or 18-24m of age for isolation and sorting of Live Cd45+ B220+ Cd19+ CD3- CD11b- Cd93- CD21-CD23-  from visceral adipose or spleen.

first: Christina

last: Camell

first: Patrick

last: Günther

first: Vishw

last: a Dixit

last: L Schultze


title: ERMAP improves inflammatory bowel disease by regulating macrophage and T cell functions

city: Guiyang

first: lu

last: xia

address: No. 28, Guiyi street, Yunyan District, Guiyang City, Guizhou Province

institute: Guizhou medical university

summary:
Background & aims: Both macrophages and T cells play a critical role in inflammatory bowel disease (IBD) development. Since our previous studies have shown that a novel immune checkpoint molecule ERMAP affects macrophage polarization and negatively regulate T cell responses, we investigated the effects of ERMAP on IBD progression in mice.
Methods: Using an dextran sodium sulfate (DSS)-induced IBD mice model, knockdown of ERMAP in RAW264.7 macrophages, ERMAP gene knockout mice, and Global gene expression analysis by RNA-seq, We investigate the effect of ERMAP on IBD by regulation of T cells and macrophages, NOD-like receptor (NLR) protein family pathway in macrophages.
Results: We show here that administration of ERMAP protein significantly increases the proportion of anti-inflammatory M2-type macrophages and inhibits T cell activation and proliferation in IBD mice induced by DSS. Knockdown of ERMAP in RAW264.7 macrophages reduces M2-type macrophage polarization and increases T cell responses. Adoptive transfer of macrophages from ERMAP knockout mice exacerbates DSS-induced IBD. Global gene expression analysis by RNA-seq shows that ERMAP inhibits the NLR protein family pathway in macrophages.
Conclusions: Our results suggest that ERMAP protein has the potential to be used in the treatment of IBD by regulating macrophage and T cell functions.

overall_design: Comparison of differential genes in RAW264.7 after knockdown of ERMAP by RNA-seq

first: Lu

last: Xia

first: Min


title: Time series RNA-Seq of the olfactory epithelia of the mouse

first: Congrong

summary: A series of RNA-Seq experiment were conducted to study the transcriptome changes of olfactory sensory neurons during the critical period. We conducted RNA-seq of the olfactory epithelia at P0, P3, P7, P14, and P21 to identify the gene expression changes in the olfactory epithelia. We also performed RNA-Seq experiment of the olfactory epithelia from Kir2.1 transgenic mice at the same time points to understand the effect of neural activity deprivation on the transcriptome.

overall_design: For wildtype animal experiment, mouse olfactory epithelia samples from 4 replicates of P0 mice, 3 replicates of P3 mice, 3 replicates of P5 mice, 4 replicates of P7 mice, 3 replicates of P10 mice, 3 replicates of P14 mice, and 3 replicates of P21 mice. For Kir2.1 experiment, 4 replicates of P0 Kir2.1 mice, 3 replicates of P3 Kir2.1 mice, 3 replicates of P5 mice, 4 replicates of P7 Kir2.1 mice, 4 replicates of P10 Kir2.1 mice, 3 replicates of P14 Kir2.1 mice, and 3 replicates of P21 Kir2.1 mice were used.

first: Yunming

last: Wu

first: Limei

last: Ma

first: Jillian

last: Blanck

first: Allison

last: Scott

first: Shiyuan

last: Chen

first: Huzaifa

last: Hassan

first: Kate

last: Hall

last: Perera


title: Effect of depletion of histamine receptor HRH1 on gene expression of histamine treated human endothelial cells

city: Beijing

first: Jiayi

address: Taiping Road 27, Haidian district

institute: National Center of Biomedical Analysis, Beijing

summary: To investigate the function of histamine signal perceived by HRH1 in the regulation of endothelial angiogenic process, we knocked down HRH1 using shRNA from histamine treated endothelial cells.

overall_design:
We then performed gene expression profiling analysis using data obtained from RNA-seq of histamine treated endothelial cells (ECs) expressing shNT(Non-traget) or shHRH1.
Comparative gene expression profiling analysis of RNA-seq data for histamine treated endothelial cells expressing shNT(Non-traget) or shHRH1.


title: circular RNA Kat6b-e2 expression safeguards self-renewal and lineage differentiation of mouse embryonic stem cells

city: Tianjin

first: Niannian

last: Li

state: Tianjin

address: No. 94 Weijin Road, Nankai District, Tianjin

department: college of Life Sciences

institute: Nankai University

summary:
Circular RNA has been reported to be dynamically expressed during embryonic development and regulates human embryonic stem cells (hESCs), but the identification and regulation of functional circular RNA in mouse embryonic stem cells (mESC) remains unclear.
Here we found over 1,000 circular RNAs in different mESC states. One of these, circular RNA Kat6b-exon2 (circKat6b-e2), was significantly overexpressed in mESCs. Furthermore, short-hair RNA (shRNA) mediated knockdown of circKat6b-e2 expression significantly inhibited mESC self-renewal and EB differentiation. The transcriptome also revealed that circKat6b-e2 is required to ensure the differentiation of the mESC lineage. Finally, we also found that more Alu elements surrounding circKat6b-e2 were necessary factors for its expression.
Conclusions: our study shows that Alu element-dependent expression of circKat6b-e2 mediates mESC self-renewal and lineage differentiation.

overall_design: Three biological replicates were analyzed for each experimental condition. WT and knockdown cells were RNA-seq in ESCs or EBs-day 6.

last: wange

first: Su

last: guangsong

first: Wang

last: Wenbin


title: Histone modification ChIP-seq profile of Glioblastoma stem cells (GSCs) and Non-stem tumor cells (NSTCs)

summary: GSCs carry various epigenetic alterations at specific genomic sites functionally implicated in self-maintenance and tumor progression. We used chromatin immunoprecipitation followed by sequencing (ChIP–seq) to investigate the histone modifications of GSCs and NSTCs.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications H3K4me1, H3K4me3, H3K27ac and H3K27me3 in GSCs and NSTCs.


title: The contribution of cell hashing for single-cell analysis of acute leukemia.

city: MARSEILLE

first: MADACI

last: LAMIA

address: Parc Scientifique de Luminy case 928 163, avenue de Luminy

institute: INSERM/TAGC

summary: Although classical single cell RNA analysis is a very powerful tool, it nevertheless has several drawbacks. To overcome these two disadvantages, the cell hashing technique seems interesting. In this work, we propose to test the feasibility and the reliability of the single cell hashing technique on primary AML cells. For this purpose, we compared the transcriptomic profile of AML cells analyzed by the classical single-cell RNA sequencing approach versus the cell hashing technique.

overall_design: PBMCs were isolated from peripheral blood after centrifugation to separate them from plasma and other peripheral blood components using ficoll-Hystopaque density gradient centrifugation, in order to sequence them with single cell RNA-seq approaches

first: Lamia

last: Madaci

first: Charlyne

last: Gard

first: Sébastien

last: Nin

first: Geoffroy

last: Venton

first: Pascal

last: Rihet

first: Denis

last: Puthier

first: Béatrice

last: Loriod

first: Régis

last: Costello


title: ATAC-seq profiles of glioblastoma stem cells (GSCs), Non-stem tumor cells (NSTCs) and neural progenitor cell (NPC).

last: Chen

summary: Both chromatin accessibility and histone modifications are known to influence transcriptional regulation. We investigated the differences of chromatin accessibility among GSCs, NSTCs and NPC using ATAC-seq (assay for transposase-accessible chromatin with high throughput sequencing).

overall_design: ATAC-seq (assay for transposase-accessible chromatin with high throughput sequencing) for chromatin accessibility in GSCs (line 387, 4121 and 456), NSTCs (line 387, 4121 and 456) and NPC.


title: BLCAP knockdown HEK293 cells: shLuc vs. shBLCAP

first: Ying-Tzu

last: Huang

address: No.1 Jen Ai road section 1

department: College of Medicine

institute: National Taiwan University

summary: Transcriptional profiling of BLCAP transient knockdown HEK293 cells camparing control shLuc cells with shBLCAP cells. Goal was to determine the effects of BLCAP gene depletion on global gene expression.

overall_design: Two-condition experiment, shLuc vs. shBLCAP cells.