title: identification of differentially expressed Long Non-coding RNA profiles in advanced gastric cancer

first: EOJIN

last: KIM

address: 73, Goryeodae-ro, Seongbuk-gu

department: Department of Pathology

institute: Korea University College of Medicine

summary: Long non-coding RNAs (lncRNAs) may contribute to tumorigenesis and cancer progression by regulating the gene in various cancers, including advanced gastric cancer (AGC).  To investigate differentially expressed lncRNAs in AGC, we use whole transcriptome sequencing in 3 pairs of human gastric adenocarcinoma and the corresponding normal tissues.

overall_design: We used high-throughput sequencing to detect differentially expressed lncRNAs in 3 advanced gastric cancer and 3 paired normal tissue (Control)


title: The phospholipid transporter PITPNC1 links KRAS to MYC to prevent autophagy in lung and pancreatic cancer

status: Public on Aug 10 2023

city: Pamplona

first: Silvestre

last: Vicent

state: Outside the US or Canada

address: 55 PIO XII Ave

department: Oncology

country: Spain

institute: Center for Applied Medical Research (CIMA)

type: Expression profiling by high throughput sequencing

summary: RNA profiling of mut KRAS lung cancer cells (A549) where PITPNC1 is depleted using two specific shRNAs

overall_design: Comparison of GFPsh-transduced A549 cells compared to PITPNC1sh-expressing cells. 3 replicates per condition were used


title: Chemo- versus immuno-precipitation of G-quadruplex-DNA (G4- DNA): a direct comparison of the efficiency of the antibody BG4 versus the small-molecule ligands TASQs for G4 affinity capture

city: Nanjing

first: zhenyu

last: luo

state: Jiangsu

address: Xuanwu

department: College of Agricuture

country: China

institute: Nanjing Agricultural University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The reliability of the BG4-IP-seq protocol, along with the straightforward access to rice genomic DNA, makes this system ideal for comparing the pull-down efficiency of the antibody BG4 versus the small-molecular baits BioTASQ and BioCyTASQ. These two TASQs (for template-assembled synthetic G-quartets) are biotinylated biomimetic ligands that were successfully employed for fishing G4-RNAs out from human cell lysates, in a protocol referred to as G4RP-seq, which belong to the toolbox of seq-based techniques used to interrogate G4-RNA prevalence, comprising rG4-seq, DMS-seq, Keth-seq and SHALiPE-seq. We reasoned that the ability of TASQs to isolate G4-DNA deserves both to be investigated and to be compared to that of BG4. We thus report here on these investigations.  which provides the very first comparison of the efficiency of the immuno- versus chemo-  precipitation of G4s, under strictly identical experimental conditions.

overall_design: 10 samples

first: Y

last: Feng

first: W

last: Zhang

first: Luo

last: Zhenyu


title: Fatty acids reshape the cytotoxicity and epigenetics of tumor-resident CD8+ T cells by maintaining SCML4 expression

city: Jinan

first: Maoxiao

address: Beiyuan Street 247

institute: Department of Clinical Laboratory

summary:
To study the function of SCML4 in Trm or TILs, we established a Jurkat cell line overexpressing SCML4.
We then performed gene expression profiling using data obtained by RNA-seq of Jurkat cells stably overexpressing SCML4.

overall_design: Comparative gene expression profiling of RNA-seq data from Jurkat cells stably overexpressing SCML4 versus control Jurkat cells.

first: Xiaoyan

last: Liu

first: Xiaodong

last: Hao

first: Yidan

last: Ren

first: Yuli

last: Wang

first: Lutao

last: Du

first: Chuanxin

first: Yunshan


title: TPL2 kinase activity regulates microglial inflammatory responses and promotes neurodegeneration in tauopathy mice

city: South San Francisco

first: Brad

middle: A

last: Friedman

state: CA

address: 1 DNA Way

department: Neuroinformatics

country: USA

institute: Genentech, Inc.

summary: TPL2 (MAP3K8) is a central signaling node in the inflammatory response of peripheral immune cells.  We find that TPL2 kinase activity modulates microglial cytokine release and is required for microglia-mediated neuron death in vitro.  In acute in vivo neuroinflammation settings, TPL2 kinase activity regulates cytokine levels and activation states of microglia.  In a tauopathy model of chronic neurodegeneration, loss of TPL2 kinase activity reduces neuroinflammation and rescues synapse loss, brain volume loss, and behavioral deficits.  Single-cell RNAseq analysis indicates protection in the tauopathy model was associated with reductions in activated microglia subpopulations as well as infiltrating peripheral immune cells.  Overall, using various models, we find that TPL2 kinase activity promotes multiple harmful consequences of microglial activation in the brain including cytokine release, iNOS induction, astrocyte activation, and immune cell infiltration.  Consequently, inhibiting TPL2 kinase activity could represent a potential therapeutic strategy in neurodegenerative conditions.

overall_design: ~3-month-old WT or TPL2-KD mice were injected with PBS vehicle control or LPS (10 mg/kg) (n =5 per condition). 24 hours later, mice were perfused with cold PBS and the mouse hemi brains were immediately sub-dissected and preserved in RNAlater.

first: Yuanyuan

first: Jesse

middle: E

last: Hanson


title: RNA-seq of metformin treatment in liver in WT, Raptor Ser-Ala mutant, Tsc2-null, Raptor mutant;Tsc2-null, and Ampk-null

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

summary: Despite being the frontline therapy for Type 2 diabetes, the mechanisms of action of the biguanide drug metformin are still being discovered. In particular, the detailed molecular interplays between the AMPK and the mTORC1 pathway in the hepatic benefits of metformin are still ill-defined. Metformin-dependent activation of AMPK classically inhibits mTORC1 via TSC/RHEB. But several lines of evidence suggest additional mechanisms at play in metformin inhibition of mTORC1. Here we investigated the role of direct AMPK-mediated serine phosphorylation of RAPTOR in a new RaptorAA mouse model, in which AMPK phospho-serine sites Ser722 and Ser792 of RAPTOR were mutated to alanine. Metformin treatment of intact murine liver requires AMPK regulation of both RAPTOR and TSC2 to fully inhibit mTORC1, and this regulation is critical for the transcriptional response to metformin. Transcriptionally, AMPK and mTORC1 were both important for regulation of anabolic metabolism and inflammatory programs triggered by metformin treatment. The hepatic transcriptional response in mice on high fat diet treated with metformin was largely ablated by AMPK-deficiency under the conditions examined, indicating the essential role of this kinase and its targets in metformin action in vivo.

overall_design: Mice maintained on 45% high fat diet for 12 weeks, fasted overnight, refed for 1h, and treated with 200 mpk metformin or saline for 4 hours

first: Jeanine

middle: L

last: Van Nostrand

first: Reuben

middle: J

last: Shaw

first: Kristina

last: Hellberg

first: En-Ching

last: Luo

first: Eric

first: Alina

last: Dayn

first: Jingting

last: Yu

first: Maxim

middle: N

last: Shokhirev

first: Yelena

first: Gene

middle: W

last: Yeo


first: Silvestre

last: Vicent

summary: RNA profiling of FOSL1- and KRAS-regulated transcriptomes in human lung cancer cells harboring KRAS mutation

overall_design: H358 cell line was transduced with tet-inducible lentiviral plasmids expressing a control shRNA (GFPsh) or a specific shRNA to FOSL1 or KRAS

first: Vicent

last: Silve


title: CRSP: Comparative RNA-seq pipeline for species lacking both of sequenced genomes and reference transcripts

city: Cleveland

first: Peng

last: Jiang

state: OH

address: 2121 Euclid Ave

institute: Cleveland State University

summary: RNA sequencing (RNA-seq) has been a widely used high-throughput method to characterize transcriptomic dynamics spatiotemporally. However, typical RNA-seq data analysis pipelines depend on either a sequenced genome or reference transcripts. This constriction makes the use of RNA-seq for species lacking both of sequenced genomes and reference transcripts challenging. To solve this problem, we developed CRSP, an RNA-seq pipeline integrating multiple comparative species strategy but not depending on a specific sequenced genome or reference transcripts. Benchmarking suggests the CRSP tool can achieve high accuracy to quantify gene expression levels.

overall_design: Human ES (H1) RNA-seq


title: LAMC2-regulated transcriptome

summary: RNA profiling of pancreatic cancer cells (HPAFII) where LAMC2 is depleted using a specific shRNA

overall_design: Comparison of GFPsh-transduced HPAFII cells compared to LAMC2sh-expressing cells. 3 replicates per condition were used

first: Silve


title: RNA-seq of mouse embryonic kidney stromal cells with stabilized or deficient β-catenin expression

city: Hamilton

first: Darreb

last: Bridgewater

state: Ontario

address: 1280 Main Street West

country: Canada

institute: McMaster University

summary: The goal of this study was to identify β-catenin target genes in the developing renal stroma. We conducted a gene expression analysis in E12.5 and E13.5 renal stromal cells with either stabilized (β-catSO) or deficient (β-catSD) β-catenin expression. Expression of some candidate β-catenin targets was validated at the protein level by immunohistochemistry.

overall_design: Stromal cells were isolated from E12.5 and E13.5 wild-type, β-catSO and β-catSD FoxD1Cre-eGFP mouse kidneys using fluorescence activated cell sorting (FACS). Three kidneys from each genotype were used for cell isolation. RNA profiles of the isolated cells were generated using the Illumina HiSeq system.

first: Anna

last: Li

first: Felix

last: Boivin

first: Joanna

last: Cunanan

last: Dvorkin-Gheva

first: Erin

last: Deacon

first: Darren


title: AMPK regulation of Raptor and TSC2 mediate Metformin effects on transcriptional control of anabolism and inflammation

first: April

last: Williams

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

overall_design: Refer to individual Series


title: Hepatitis B virus X protein contributes to hepatocellular carcinoma via upregulation of KIAA1429 methyltransferase and mRNA m6A hypermethylation of HSPG2/Perlecan [MeRIP-Seq]

status: Public on Aug 09 2023

city: Suzhou

first: Enakshi

last: Sivasudhan

address: 111, Ren'ai Road, Suzhou Industrial Park

institute: Xi'an Jiaotong Liverpool University

type: Methylation profiling by high throughput sequencing

summary: Chronic hepatitis B virus (HBV) remains to be the most common risk factor of hepatocellular carcinoma (HCC). While work has primarily focussed on understanding the direct and indirect mechanisms of Hepatitis B virus X protein (HBx) mediated hepatocarcinogenesis, from genetic and epigenetic perspectives, its influence on RNA modification mediated onset of liver malignancies is less well understood. This study explored the role of HBV-encoded HBx in altering the m6A methylome profile and its implications on the pathogenesis of HCC. We established HBx expressing stable HCC cell lines, Huh7-HBx and HepG2-HBx, and explored the transcriptomic and epitranscriptomic profiles by RNA-seq and MeRIP-seq, respectively. Preliminary results suggest that HBx promotes liver cell proliferation, migration, survival and overall m6A methylation in HCC cells and is involved in modulating the extracellular matrix. We show that HBx mediates liver cell transformation by upregulating KIAA1429 methyltransferase. HBx also drives the expression and hypermethylation of the extracellular matrix protein HSPG2/Perlecan and promotes tumourigenesis. Our findings indicate a potential interaction between KIAA1429 and HSPG2, thus could be novel targets in combating HBx-driven HCC and warrants further investigation.

overall_design: To decipher the underlying mechanisms by which HBx exerted tumour promoting effects in HCC, we carried out MeRIP sequencing to display the m6A epitranscriptomic changes in Huh7 cells that stably express HBx.

first: Jingxian

last: Zhou

first: Jiongming

last: Ma

first: Siying

last: Liu

first: Zhiliang

last: Lu

first: Jia

last: Meng

first: Neil

last: Blake

first: Rong

last: Rong


title: RNA-seq of metformin treatment in primary murine hepatocytes in WT, Raptor Ser-Ala mutant, Tsc2-null, Raptor mutant;Tsc2-null, and Ampk-null cells

summary: Despite being the frontline therapy for Type 2 diabetes, the mechanisms of action of the biguanide drug metformin are still being discovered. In particular, the detailed molecular interplays between the AMPK and the mTORC1 pathway in the hepatic benefits of metformin are still ill-defined. Metformin-dependent activation of AMPK classically inhibits mTORC1 via TSC/RHEB. But several lines of evidence suggest additional mechanisms at play in metformin inhibition of mTORC1. Here we investigated the role of direct AMPK-mediated serine phosphorylation of RAPTOR in a new RaptorAA mouse model, in which AMPK phospho-serine sites Ser722 and Ser792 of RAPTOR were mutated to alanine. Metformin treatment of primary hepatocytes and intact murine liver requires AMPK regulation of both RAPTOR and TSC2 to fully inhibit mTORC1, and this regulation is critical for the transcriptional response to metformin. Transcriptionally, AMPK and mTORC1 were both important for regulation of anabolic metabolism and inflammatory programs triggered by metformin treatment.

overall_design: 5h treatment of 2mM Metformin or 0.1uM INK-128 in serum-starved primary murine hepatocytes in the absence or presence of 15 minute pre-treatment with 1nM Insulin

first: Jeanine

last: Van Nostrand

first: Reuben

last: Shaw

first: Kristina

last: Hellberg

first: En-Ching

last: Luo

first: Eric

first: Alina

last: Dayn

first: Jingting

last: Yu

first: Maxim

last: Shokhirev

first: Yelena

first: Gene

last: Yeo


title: Selenomethionine against titanium particle-induced osteolysis by regulating the ROS-dependent NLRP3 inflammasome activation via the β-catenin signaling pathway

city: Changchun

first: Tongjian

last: Zhao

address: 1266 Fujin Road

institute: School of Pharmaceutical Sciences, Jilin University

summary: Wear debris-induced osteolysis, especially titanium (Ti) particles-induced osteolysis, is the most common cause of arthroplasty failure with no effective therapy. Previous studies have suggested that inflammation and impaired osteogenesis are associated with Ti particles -induced osteolysis. Selenium (Se) is an essential trace element in the human body, which forms selenomethionine (Se-Met) in nature, and selenoproteins has strong anti-inflammatory and antioxidant stress effects. In this study, the effects of Se-Met on Ti particles-induced osteolysis were observed and the potential mechanism was explored. We found that exogenous Se-Met relieved osteolysis induced by Ti particles in two animal models and MC3T3-E1 cells. We found that the addition of Se-Met effectively inhibited Ti particle-induced inflammation by regulating ROS-dependent NLRP3 inflammasome activation. These therapeutic effects were abrogated in MC3T3-E1 cells that had received a β-catenin antagonist, suggesting that Se-Met alleviates inflammatory osteolysis via the β-catenin signaling pathway. Collectively, these findings indicated that Se-Met may serve as a potential therapeutic agent for treating Ti particle-induced osteolysis.

overall_design: MC3T3-E1 cells were obtained from the Cell Bank of the Chinese Academy of Sciences (Shanghai, China). MC3T3-E1 cells were maintained in α-MEM (Gibco, Brooklyn, NY) containing 10% FBS, 100 μg/ml streptomycin, and 100 U/ml penicillin in a 5% CO2 humidified atmosphere at 37 °C, adherent cells were cultured until the cells reached approximately 90% confluence. The osteogenic medium was α-MEM supplemented with 10% FBS, 10 mM β-glycerophosphate, 0.5 mM vitamin C, and 0.1 μM dexamethasone. The induction time of Osteogenesis was induced for 14 d. Osteolysis was induced by adding 10 μg/cm2 Ti particles. Cells were cultured in 6-well plates at a density of 1 × 105 cells/well in an incomplete medium and stimulated with 10 μg/cm2 Ti particles solution, with or without Se-Met (5 μM) for 24 h. The culture medium and cells were collected for further experiments

first: Ruixuan

first: Zhicheng

first: Yongjian

last: Yuan

first: Long

last: liu


title: Mitochondria dysregulation contributes to secondary neurodegeneration progression post-contusion injury in human 3D in vitro triculture brain tissue model.

city: Medford

first: David

last: Kaplan

state: MA

address: 4 Colby street

department: Biomedical Engineering

institute: Tufts University

summary: Traumatic Brain injury-induced disturbances in mitochondrial fission-and-fusion dynamics have been linked to the onset and propagation of neuroinflammation and neurodegeneration. However, cell-type-specific contributions and crosstalk between neurons, microglia, and astrocytes in mitochondria-driven neurodegeneration after brain injury remain undefined. We developed a human three-dimensional in vitro triculture tissue model of a contusion injury composed of neurons, microglia, and astrocytes and examined the contributions of mitochondrial dysregulation to neuroinflammation and progression of injury-induced neurodegeneration. Pharmacological studies presented here suggest that fragmented mitochondria released by microglia are a key contributor to secondary neuronal damage progression after contusion injury, a pathway that requires astrocyte-microglia crosstalk. Controlling mitochondrial dysfunction thus offers an exciting option for developing therapies for TBI patients.

overall_design:
To investigate the role of mitochondria dysfunction in brain injury-induced neurodegeneration.
We performed gene expression profiling analysis using data obtained from bulk RNA-sequencing of human 3D in vitro tricultures composed of neurons, astrocytes and microglia with or without selecting mitochondria fission inhibitor P110, 24 hours after Controlled cortical impact injury.
Human microglia cells were differentiated from 2 healthy donors - human YZ1 and ND41866*C; data presented from 2 independent experiments (microglia differentiation + tricultures seeding); the injured groups were compared to their corresponding sham groups with or without P110 treatment. Human neurons were differentiated from induced Neural Stem cells developed in Prof. David Kaplan lab; astrocytes were human primary astrocytes purchased from Sciencell Research Laboratories


title: Pregnane X receptor promotes ehtanol-induced hepatosteatosis in female mice

city: Seattle

first: Julia

middle: Yue

last: Cui

state: WA

address: 4225 Roosevelt Way NE Suite #100

department: Occupational and Health Sciences

institute: University of Washington

summary:
The pregane X receptor (PXR), a xenobiotioc-sensing nuclear receptor has been implicated in alcohol-associated liver disease (ALD). The role of PXR signaling in potentiating ethanol (EtOH)-induced hepatotoxicty in male wild-type (WT) mice was reported previously, however, how PXR signaling modulated EtOH-induced hepatotoxicty in female is still unknown.
Several mRNAs that are involved in retinol and steroid hormone biosynthesis, chemical carcinogeneiss, and arachidonic acid metabolism were increased by EtOH in a PXR-dependent manner. Overall, female PXR-null mice are resistant against chronic EtOH-induced hepatotoxicity than their WT counterparts.

overall_design: The female WT and PXR-null mice were fed a 5% EtOH-containing diets or a paired-fed control diets for 8 weeks followed by gene expression (Affymetrix microarray)

first: Sarah

last: Kim

first: Maxwell

last: Gyamfi


title: A Novel Strategy for Preparation of ADSCs-Osteogenic Microtissues Based on CEFFE and Mechanisms for Enhancing Osteogenic Activity

city: ChangSha

first: dingyu

last: Wu

address: 87 Xiangya Road

institute: Xiangya Hospital

summary: Bone tissue engineering is considered the optimal solution for the repair of large bone defects. Previous studies by our team have demonstrated the effectiveness of a "bottom-up" microtissue engineering strategy using bone marrow mesenchymal stem cells (BMSCs) to improve the utilization efficiency of seed cells. However, this strategy requires the extraction of bone marrow, which is associated with significant trauma and difficulties in obtaining the cells. Adipose-derived mesenchymal stem cells (ADSCs), obtained from aspirated adipose tissue, offer a less invasive and more accessible alternative, but their osteogenic capacity is noticeably weaker, severely limiting their application as seed cells in bone tissue engineering repair.Cell-free fat extract (CEFFE) is a cell-free liquid component extracted from adipose tissue, which exhibits beneficial properties such as promoting proliferation, antioxidation, anti-apoptosis, and angiogenesis. In this study, during the preparation of ADSC-based osteogenic microtissues, we first discovered that CEFFE significantly enhanced the osteogenic activity of ADSCs. Furthermore, we observed the formation of dense osteogenic membranes as early as day 7 of osteogenic induction. When the microtissues based on CEFFE-treated ADSCs were implanted subcutaneously in nude mice, we found a significant enhancement in their osteogenic activity. Finally, to further investigate the mechanism underlying the enhancement of ADSC osteogenic differentiation by CEFFE, we performed transcriptomic analysis of CEFFE-treated ADSCs and validated the activation of the key PI3K-Akt pathway using Western blotting.In conclusion, this study presents a novel approach for the preparation of ADSC-based osteogenic microtissues using CEFFE and provides insights into the mechanisms underlying the enhancement of osteogenic activity. These findings hold significant implications for the field of bone tissue engineering and offer potential advancements in the clinical translation of ADSC-based therapies.

overall_design: In this study, we aimed to investigate the effects of CEFFE on ADSCs and its role in enhancing osteogenic activity. Firstly, we obtained ADSCs and CEFFE and validated their characteristics. Subsequently, we examined the changes in proliferation and differentiation abilities of ADSCs when exposed to CEFFE during the osteogenic induction process. Furthermore, we utilized CEFFE to enhance the osteogenic activity of ADSCs during the preparation of osteogenic microtissues, resulting in the formation of denser osteogenic membranes as early as day 7. These osteogenic microtissues were then implanted subcutaneously in nude mice, and the specimens were evaluated through macroscopic observation, micro-CT imaging, and histological staining. Finally, transcriptomic analysis was conducted on ADSCs treated with CEFFE to investigate its effects, and the main pathways were validated using Western blotting (WB) analysis.

first: Mengqi

last: Nie

first: Xizhe

last: Li

first: Shaorong

last: Lei

first: Dingyu


title: Ribosome profiling of  metformin treatment in primary murine hepatocytes in WT, Raptor Ser-Ala mutant, Tsc2-null, Raptor mutant;Tsc2-null, and Ampk-null cells

first: April

last: Williams

summary: Despite being the frontline therapy for Type 2 diabetes, the mechanisms of action of the biguanide drug metformin are still being discovered. In particular, the detailed molecular interplays between the AMPK and the mTORC1 pathway in the hepatic benefits of metformin are still ill-defined. Metformin-dependent activation of AMPK classically inhibits mTORC1 via TSC/RHEB. But several lines of evidence suggest additional mechanisms at play in metformin inhibition of mTORC1. Here we investigated the role of direct AMPK-mediated serine phosphorylation of RAPTOR in a new RaptorAA mouse model, in which AMPK phospho-serine sites Ser722 and Ser792 of RAPTOR were mutated to alanine. Metformin treatment of primary hepatocytes and intact murine liver requires AMPK regulation of both RAPTOR and TSC2 to fully inhibit mTORC1, and this regulation is critical for the translational response to metformin.

overall_design: 2h treatment of 2mM Metformin or 0.1uM INK-128 in serum-starved primary murine hepatocytes in the absence or presence of 15 minute pre-treatment with 1nM Insulin

first: Jeanine

last: Van Nostrand

first: Reuben

last: Shaw

first: Kristina

last: Hellberg

first: En-Ching

first: Eric

first: Alina

first: Jingting

first: Maxim


title: Hepatitis B virus X protein contributes to hepatocellular carcinoma via upregulation of KIAA1429 methyltransferase and mRNA m6A hypermethylation of HSPG2/Perlecan [RNA-Seq]

first: Enakshi

last: Sivasudhan

overall_design: To decipher the underlying mechanisms by which HBx exerted tumour promoting effects in HCC, we carried out RNA sequencing to display the transcriptional changes in Huh7 and HepG2 that stably express HBx. We used two biological replicates per sample and compared between untreated (without Dox treatment) and treated (with Dox treatment).

first: Jingxian

last: Zhou

first: Jiongming

last: Ma

first: Siying

last: Liu

first: Zhiliang

last: Lu

first: Jia

last: Meng

first: Neil

last: Blake

first: Rong

last: Rong


title: Impact of Endogenous Pneumococcal Hydrogen Peroxide on the activity and release of Pneumolysin

city: Giessen

first: Mobarak

last: Abu Mraheil

state: Hessen

address: Schubertstrasse 81

department: Institute for Medical Microbiology

country: Germany

institute: Justus-Liebig University Giessen

summary: Streptococcus pneumoniae is the leading cause of community-acquired pneumonia. The release of the pore-forming cholesterol-dependent cytolysin (CDC) pneumolysin (PLY) and hydrogen peroxide (H2O2), a physiological metabolite, is an important virulence determinant of pneumococci.

overall_design: To investigate the impact of endogenous pneumococcal hydrogen peroxide on the activity and release of pneumolysin we grew the bacterial strains, generated PLYC428S and isolated PLY, determined hemolitic activity, detected and quantified PLY, performed adhesion assay, as well as RNA sequencing.


title: Leukemic progenitor compartment serves as a prognostic measure  of cancer stemness in acute myeloid leukemic patients

first: Mickie

last: Bhatia

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

summary: Single cell RNA sequencing of patient derived AML samples or xenografted human AML cells

overall_design: Droplet-based single cell RNA sequencing of patient derived AML samples or xenografted human AML cells

first: Allison

last: Boyd

first: Cameron

middle: G

last: Hollands

first: Mick


title: Circ_0000235 Targets MCT4 to Promote Glycolysis and Progression of Bladder Cancer by Sponging miR-330-5p

city: Guangzhou

first: Ning

last: Jiang

state: Guangdong

address: Industrial middle 253, Haizhu district

institute: Southern Medical University

summary: Warburg effect plays a crucial role in bladder cancer (Bca) development. However, the mechanism by which glycolysis is involved in Bca remains poorly understood. CircRNAs commonly play a regulatory role in tumor progression. Our study discovered and identified a novel circRNA, hsa_circ_0000235 (circ235), and investigated its role in the glycolytic process, which further results in the progression of Bca. We applied qRT-PCR to assess its clinicopathological relevance and evaluated its proliferation, migration, and glycolytic capacity. We investigated its mechanism using RNA immunoprecipitation, dual-luciferase reporters, and fluorescence in situ hybridization. The findings demonstrated that circ235 was dramatically increased in Bca tissues and was related to a worse prognosis. In vitro studies revealed that circ235 accelerated the rate of extracellular acidification and promoted glucose uptake and lactate manufacture in Bca cells. Additionally, it strengthened the capacity of Bca cells to proliferate and migrate. Experiments on animals revealed that downregulating circ235 dramatically reduced carcinogenesis and tumor growth.  Cir235 activates monocarboxylate transporter 4 (MCT4) by sponging miR-330-5p, which promotes glycolysis and tumor growth. In conclusion, these findings imply that circ235 may be a viable molecular marker and therapeutic site for Bca.

overall_design: To investigate the downstream signaling pathways regulated by circ_0000235 in bladder cancer, we treated T24 cell line with siRNAs targeting two different targets and established two biological replicate samples.


title: A single-cell atlas of gene expression and chromatin accessibility changes associated with cocaine addiction in the rat amygdala (snATAC-Seq Multiome)

city: La Jolla

first: Jessica

middle: Lu

address: 9500 Gilman Drive

institute: University of California San Diego

summary: The amygdala plays a key role in the negative emotional states associated with the relapse to drug seeking behavior. Neuroanatomical and functional observations have uncovered the role of discrete amygdala subregions in different aspects of these negative affective states. However, the underlying transcriptional regulatory programs driving the function of distinct amygdala cell types remains unknown. We generated an atlas of single nucleus gene expression and chromatin accessibility in the amygdala of rats with low and high cocaine addiction-like behaviors after prolonged abstinence from extended access to cocaine intravenous self-administration. We identified thousands of cell type-specific differentially expressed genes, suggesting that negative affective states are associated with cell type-specific mechanisms which are enriched for molecular pathways, including energy metabolism and GABAergic synapses in excitatory and somatostatin neurons. We demonstrate that higher addiction severity is linked to excessive GABAergic inhibition and, using pharmacological inhibition, we find that addiction-like phenotypes are regulated by the metabolite methylglyoxal which is an agonist at GABA-A receptors. By analyzing differences in chromatin accessibility, we predict upstream transcriptional regulators associated with addiction-like behavior and find discordant regulation of key transcription factors among distinct cell populations. Overall, we provide a comprehensive characterization of cell type-specific transcriptional changes in the amygdala during protracted abstinence and use these insights to identify a novel target for pharmacological intervention.

overall_design: snRNA-seq and snATAC-seq data generated using 10X Genomics Chromium Single Cell Multiome ATAC + Gene Expression

first: Giordano

middle: D

last: Guglielmo

first: Aaron

last: Ho

first: Marsida

last: Kallupi

first: Narayn

last: Pokhrel

first: Hai-Ri

last: Li

first: Apurva

middle: S

last: Chitre

first: Daniel

last: Munro

first: Pejman

last: Mohammadi

first: Lieselot

last: Carrette

first: Olivier

last: George

first: Abraham

last: Palmer

first: Graham

middle: P

last: McVicker

first: Francesca

last: Telese


title: A single-cell atlas of gene expression and chromatin accessibility changes associated with cocaine addiction in the rat amygdala (snRNA-Seq Multiome)

last: Zhou


title: Transcription factor expression repertoire basis for epigenetic and transcriptional subtypes of colorectal cancers

city: Baltimore

first: Yuba

middle: R

last: Bhandari

state: MD

address: 1650 Orleans Street

institute: The Johns Hopkins University School of Medicine

type: Methylation profiling by genome tiling array


title: Knock in p38g and knock out p38d effect on gene expression in TLR4 signalling in bone marrow derived macrophages using LPS.

city: Madrid

first: Ana

last: Cuenda

state: Madrid

address: C. Darwin, 3

department: DEPARTMENT OF IMMUNOLOGY AND ONCOLOGY

institute: National Biotechnology Centre (CNB-CSIC)

summary: Evidence implicating p38γ and p38δ (p38γ/p38δ) in inflammation are mainly based on experiments using p38γ/p38δ deficient (p38γ/δ-/-) mice, which show low levels of TPL2, the kinase upstream of MKK1-ERK1/2 in myeloid cells. This could obscure p38γ/p38δ roles, since TPL2 is essential for regulating inflammation. Here we generated a p38γD171A/D171A/p38δ-/- (p38γ/δKIKO) mouse, expressing kinase-inactive p38γ and lacking p38δ. This mouse exhibited normal TPL2 levels, making it an excellent tool to elucidate specific p38γ/p38δ functions. p38γ/δKIKO mice showed a reduced inflammatory response and less susceptibility to LPS-induced septic shock and Candida albicans infection than wild-type mice. Gene expression analyses in LPS-activated WT and p38γ/δKIKO macrophages revealed that p38γ/p38δ regulated numerous genes implicated in innate immune response.

overall_design: WT and p38γ/δKIKO bone marrow derived macrophages were stimulated with 100 ng/ml LPS for 0, 30 and 60 min, and gene expression was analysed by RNA-sequencing (RNA-Seq) to identify target genes specifically affected by the lack of p38γ kinase activity and p38δ expression.

first: Alejandra

last: Escós

first: Ester

last: Díaz-Mora

first: Michael

last: Pattison

first: Pilar

last: Fajardo

first: Diego

last: González-Romero

last: Risco

first: José

last: Martín-Gómez

first: Éric

last: Bonneil

first: Nahum

last: Sonenberg

first: Seyed

middle: M

last: Jafarnejad

first: Juan

last: Sanz-Ezquerro

first: Steven

middle: C

last: Ley


title: Affymetrix array expression data from colon polyps

summary:
The tubular adenoma sample cohort (accrued by Janssen Pharmaceuticals) consisted of 127 high-risk baseline adenoma samples acquired retrospectively by Avaden Biosciences. High risk patients are defined here as presenting a tubular adenoma ? 10mm, 3 or more adenomas, adenomas with villous histology or adenomas showing high-grade dysplasia based on Lieberman et al.
Patients with familial adenomatous polyposis (FAP) and Lynch syndrome were excluded. All patients received at least one baseline colonoscopy for which clinical and pathological records were available. Adenoma tissue was available as archival, formalin-fixed, paraffin-embedded (FFPE) blocks.

overall_design: Expression dataset (N=61 samples) for the colon polyps was derived using Affymetrix Array platform (HT HG-U133 Plus PM) and was processed using affy package with Robust Multichip Average (RMA) normalization.

first: Vinod

last: Krishna

first: Rachael

last: Powers

first: Sehej

last: Parmar

first: Sara-Jayne

last: Thursby

first: Ekta

last: Gupta

first: Ozlem

last: Kulak

first: Prashanth

last: Gokare

first: Joke

last: Reumers

first: Liesbeth

last: Van Wesenbeeck

first: Kurtis

last: Bachman

first: Stephan

middle: B

last: Baylin

first: Hariharan

last: Easwaran


title: Effect of persistent ER stress on gene expression of pancreatic ductal adenocarcinoma cell AsPC1

city: Wuhan

first: Jingfeng

last: Li

address: Xiao hong shan zhong qu

department: Wuhan Institute of Virology

institute: University of Chinese Academy of Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: To investigate the changes of gene expression in pancreatic ductal adenocarcinoma cells under persistent endoplasmic reticulum stress, we treated AsPC-1 cells with 30 nM thapsigargin (Tg) for more than 14 days (designated as AsPC-1-Tg). To investigate whether the effects of persistent ER stress on gene expression is permanent or reversible, we cultured AsPC-1-Tg cells in a medium without Tg (designated as AsPC-1-Tg-Re) for 4 days. In this study, we then performed gene expression profiling analysis using data obtained from high-throughput RNA-seq (include mRNA, lncRNA, circRNA and miRNA) of AsPC-1 (WT), AsPC-1-Tg (TG) and AsPC-1-Tg-Re (RE) cells. Three biological replicates of each sample were used for RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for AsPC-1 (WT), AsPC-1-Tg (TG) and AsPC-1-Tg-Re (RE) cells.

first: Chaoyang


title: Gene expression profile at single cell level of mouse primary airway cells from DNAAF5 mutants

city: St Louis

first: Amjad

last: Horani

address: 660S Euclid Ave

institute: Washington University

summary: DNAAF5 is an cilia assembly factor. We used single cell RNA sequencing (scRNA-seq) to analyze the changes in cells types and gene expression profile of mutant cells compared to WT littermates

overall_design: Tracheal cells were isolated and differentiated using Air-liquid phase conditions, and analyzed using scRNAseq.

last: Brody


title: Genetic and molecular regulation of increased photosynthetic cell number contributes to leaf size heterosis in Arabidopsis

city: Beijing

first: Wenwen

last: Liu

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

summary: Heterosis is an important genetic phenomenon that has been observed and widely utilized in agriculture. However, the genetic and molecular bases of heterosis are unclear. Through transcriptome-wide association studies (TWAS) and expression quantitative trait locus (eQTL) analysis to integrate genome, transcriptome, and phenotype of a half-sibling Arabidopsis hybrid population, we report that the genetic and molecular bases of variations in leaf growth heterosis can be explained by the varied expression levels of growth-regulating genes resulting from distinct sets of heterozygous eQTLs carried by the half-sibling hybrids. In F1 relative to parent, the degree of up-regulated gene expression in the cell cycle pathway in the shoot apex and the photosynthesis pathway in the true leaf positively correlates with true leaf area heterosis level, and this is affected by the accumulation of superior heterozygous eQTLs. This was further corroborated by the major contribution of increased photosynthetic cell number to leaf area heterosis in the population.

overall_design: mRNA profiles of seedling shoot apex at 6 days after sowing (DAS) and the first true leaf at 15 DAS in a half-sibling Arabidopsis hybrid population containing 96 hybrids and their parents

first: Guangming

last: He

first: Wang

middle: X

last: Deng


title: Synj 1 modulates functional recovery after motor-incomplete spinal cord injury in male mice carriers of human ApoE4.

city: New York

first: Jens

last: Hansen

state: NY

address: 1425 Madison Ave

department: Department of Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Apolipoprotein E epsilon 4 (ApoE4) is the second most common variant of ApoE, being present in ~14% of population. Clinical reports identify ApoE4 as a genetic risk factor for poor outcomes after traumatic SCI and the spinal cord disease (SCD) cervical myelopathy. To date, there are no interventions to mitigate the potent effects of ApoE4 to reduce recovery of function after SCI/D. Studies in human and mouse brain link ApoE4 to elevated levels of synaptojanin 1 (synj1), a lipid phosphatase that dephosphorylates phosphoinositol 4,5-bisphosphate (PIP2) to inositol 4-monophosphate (PIP1). Synj1 regulates rearrangements of the cytoskeleton and the endocytosis and trafficking of synaptic vesicles. We report here that, as compared to ApoE3 mice, levels of synj1 mRNA and protein were elevated in spinal cords from healthy ApoE4 mice associated with lower PIP2 levels. Using a moderate severity model of contusion SCI in mice, we found that genetic reduction of syn1 improved locomotor function recovery at 14 days after SCI in ApoE4 mice without altering spared white matter. Genetic reduction of synj1 did not alter locomotor recover of ApoE3 mice after SCI. Bulk RNA-sequencing revealed that at 14 days after SCI in ApoE4 mice, genetic reduction of synj1 upregulated genes involved in glutaminergic synaptic transmission just above and below the lesion. Overall, our findings provide evidence for a link between synj1 to poor outcomes after SCI in ApoE4 mice through mechanisms that remain speculative but may include greater function of excitatory glutaminergic synapses.

overall_design: At 4 months of age, male mice expressing human ApoE3 or ApoE4 variants, that either had one inactive synj1 allele (synj1+/-) or two normal synj1 alleles (synj1+/+), were subjected to a motor-incomplete spinal cord contusion or a laminectomy (sham) at level of thoracic vertebrae T9. At 14 days post-surgery, spinal cord tissues from three animals per group were collected immediately rostral or caudal from the lesion epicenter, and were used for total RNA extraction and later bulk RNA seq studies.

first: Carlos

middle: A

last: Toro

first: Mustafa

last: Siddiq

first: Kaitlin

last: Johnson

first: Jiqing

last: Cao

first: Adriana

last: Pero

first: Ravi

last: Iyengar

first: Dongming

last: Cai

first: Christopher

last: Cardozo


title: Transcriptomics and proteomics analyses reveal the anti-cancer properties of extract from Hypnea musciformis macroalgea in liver and intestinal cancer cells

city: Larissa

first: Antonis

last: Giakountis

address: Biopolis-Mezourlo

department: Biochemistry and Biotechnology

country: Greece

institute: University of Thessaly

summary:
To investigate the molecular effect of Hypnea musciformis macroalgea extract on HepG2 and Ls174 cancer cell lines we  isolated total RNA from cultured cells with and without the extract after 24 hr incubation
We then performed gene expression profiling analysis performed in biological triplicates using data obtained from 3’ RNA-seq of 2 different cells with and without the extract at the IC50 concentration

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HepG2 and Ls174 cells with and without the microalgea extract

first: Dimitrios

last: Stagkos


title: Illumina 450k methylation data from colon polyps

first: Yuba

last: Bhandari

overall_design: Illumina Infinium 450K beadchip dataset from 61 colon polyp samples

first: Vinod

last: Krishna

first: Rachael

last: Powers

first: Sehej

last: Parmar

first: Sara-Jayne

last: Thursby

first: Ekta

last: Gupta

first: Ozlem

last: Kulak

first: Prashanth

last: Gokare

first: Joke

last: Reumers

first: Liesbeth

last: Van Wesenbeeck

first: Kurtis

middle: E

last: Bachman

first: Stephan

last: Baylin

first: Hariharan

last: Easwaran


title: Mouse kidney tissue: UUO-METTL3fl/fl, cre T vs. UUO-METTL3fl/fl, wt

city: Hefei

first: Wei-Jian

last: Ni

state: Anhui

address: No. 17 Lujiang Road

department: Anhui Provincial Hospital, The First Affiliated Hospital of USTC

institute: University of Science and Technology of China

summary: The mRNA transcriptome and m6A methylation microarray profiling of mouse kidney tissues. Kidney tissues from the sham-operated group and unilateral ureteral ligation/obstruction (UUO) kidney tissues were compared. The latter were mainly fibrotic kidney tissues. The goal was to identify the effect of the renal fibrosis on gene expression and corresponding m6A modifications during kidney fibrosis.

overall_design: Single-condition experiment, UUO-METTL3fl/fl, cre T vs. UUO-METTL3fl/fl, wt kidney tissue. Biological replicates. 1 UUO-METTL3fl/fl, cre T, 1 UUO-METTL3fl/fl, wt kidney tissue replicates.

first: Xiao-Ming

last: Meng


title: Illumina 850k methylation data from colon polyps

overall_design: Illumina Infinium EPIC (850K) beadchip dataset from 66 colon polyp samples


title: Mouse kidney tissue: Control vs. UUO

overall_design: Single-condition experiment, control vs. UUO kidney tissue. Biological replicates. 3 control replicates, 3 UUO kidney tissue replicates.


title: ZEB1 is regulated by K811 acetylation to promote stability, NuRD complex interactions, EMT, and NSCLC metastasis

city: Houston

first: Carl

last: Gay

state: TX

address: 1515 Holcombe Blvd

department: Thoracic-Head & Neck Med Onc

institute: The University of Texas MD Anderson Cancer Center

summary:
To understand the role of Zeb1 acetylation in regulating its function a Zeb1 acetyl-mimetic and acetyl-deficient mutant expressing NSCLC cell line was generated.
We then performed gene expression profiling analysis using data obtained from RNA-seq of GFP-vector, Zeb1 wild-type, Zeb1 deficient, and Zeb1 mimetic.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 393P cells with GFP-vector (negative control), Zeb1-WT (wild-type), Zeb1_deficent, Zeb1_mimetic, three different samples submitted, 2 replicates per sample per cell line.

first: Mabel

last: Perez-Oquendo

first: B

middle: L

last: Rodriguez

first: Don

last: Gibbons


title: mRNA expression data from macrophages in malignant pleural effusion of wild type and IL-10 deficency mice

first: Xin-Yu

last: Shi

address: 8 Gongti Nanlu

department: Department of Respiratory and Critical Care Medicin

institute: Beijing Chao-Yang Hospital

summary: Malignant pleural effusion (MPE) is a common medical problem caused by multiple malignancies especially lung cancers and always along with a poor therapeutic outcome.Interlukin-10 (IL-10) promotes the formation and development of malignant pleural effusion (MPE). In the current study, our results showed that IL-10 deficiency decreased the percentage of macrophages in mice MPE and regulated M1/M2 polarization in vivo and vitro. The migration capacity of tumor cells was suppressed, and apoptosis was promoted when co-cultured with MPE macrophages in the absence of IL-10.

overall_design: MPE macrophages from WT and IL-10−/− mice were collected for RNA extraction.The mRNA profiles were sequenced using an Illumina HiSeq sequencer with pair end 150 bp reading length (Illumina, San Diego, CA).

first: Xue-Bin

last: Pei

first: Feng-Shuang

last: Yi


title: Single-cell transcriptomic analysis uncovers intratumoral heterogeneity and drug-tolerant persister in ALK-rearranged lung adenocarcinoma

city: Hong Kong

first: Hoi-Hin

last: Kwok

address: Sassoon Road

institute: The University of Hong Kong

summary: Acquired drug resistance is the major therapeutic obstacle to maintenance treatment of advanced-stage non-small cell lung cancer. Lung adenocarcinoma (ADC) harboring driver mutations also showed poor response to immune checkpoint inhibitors (ICIs). Underlying mechanisms of how drug insensitivity evolves remain unclear. Here we explored the intratumoral heterogeneity of tyrosine kinase inhibitor (TKI)-resistant anaplastic lymphoma kinase (ALK)-rearranged lung ADC organoids using single-cell RNA-sequencing (scRNA-seq) transcriptomic analysis. IL-17 signaling pathway was found highly induced in a subpopulation of pre-existing ALK-TKI-resistant cells. These drug-tolerant persister (DTP) cells, also found to have high surface intracellular adhesion molecule 1 (ICAM-1) expression level, were more resistant towards ALK-TKI and expressed a higher level of cancer-stem cell transcriptional factors. Moreover, tumor cells with high ICAM-1 expression were found spatially correlated with RORɣt+ Th17 infiltration in ALK-rearranged NSCLC resected tumor tissues. In conclusion, our data revealed marked intratumoral heterogeneity in ALK-rearranged tumor, and pre-existing DTP cells may contribute to the development of drug insensitivity in ALK-rearranged lung ADC.

overall_design: Single-cell transcriptomic analysis. To investigate the intratumoral heterogeneity in ALK-rearranged lung ADC, we have generated ALK-rearranged LCOs from lung ADC patients (TS485T-O was derived from resected primary tumor, and FA34-O were derived from malignant pleural effusion, -O = organoids). Continuous exposure to escalating concentration of ALK-TKIs led to the emergence of acquired resistance. Single-cell RNA sequencing (scRNA-seq) analysis on TKI-sensitive and -resistant tumor organoids TS485T-O and FA34-O was performed (-C = crizotinib resistant; -A = alectinib resistant).

first: Huiyu

last: Li

first: Jiashuang

last: Yang

first: Junyang

last: Deng

first: Nerissa

last: Lee

first: Timmy

last: Au

first: Alva

middle: K

last: Sit

first: Michael

last: Hsin

first: Stephanie

last: Ma

first: Lydia

last: Cheung

first: Luc

last: Girard

first: Junya

last: Fujimoto

first: Ignacio

middle: I

last: Wistuba

first: Boning

last: Gao

first: John

last: Minna

first: David

last: Lam


title: Exposure to Benzyl butyl phthalate deteriorates oocyte quality by inducing oxidative stress-related apoptosis and DNA damage in mice

city: Nanjing

first: Yilong

last: Miao

address: Weigang No.1

institute: Nanjing Agricultural University

summary: Benzyl butyl phthalate (BBP) is a chemical softener and plasticizer commonly used in toys, food packaging, wallpaper, detergents, and shampoos. The estrogenic actions of BBP have detrimental effects on humans and animals. This study investigated the specific influence of BBP on mouse oocyte maturation using in vitro and in vivo models. The results indicated that BBP exposure disrupted spindle organization, chromosomal arrangement, and the distribution of cortical actin, and led to the failure of oocyte meiotic maturation and early embryo development. Singe-cell transcriptome analysis found that BBP exposure altered the expression levels of 588 genes, most associated with mitochondria-related oxidative stress. Further analysis demonstrated that the detrimental effects of BBP involved the disruption of mitochondrial function and oxidative stress-induced early apoptosis. Nicotinamide mononucleotide supplementation reduced the adverse effects of BBP. Collectively, these findings revealed a mechanism of BBP-induced toxicity on female reproduction, and showed that nicotinamide mononucleotide provides an effective treatment for BBP actions.

overall_design: Transcriptomic analysis of matured oocytes was carried out using a protocol for single cell RNA-Seq. The constructed library was sequenced with Illumina platform.

first: Yi

last: Jiang

first: Di

last: Wang

first: Rong

last: Cheng

first: Yanan

last: Pu

first: Yangyang

last: Jiao

first: Chen

last: Zhang

first: Chunyu

first: Yan

last: Chen


title: Prolyl endopeptidase-mediated transcriptional regulation in quiescent and activated bone marrow-derived macrophages (Bulk RNA-seq)

city: Shanghai

first: Yuanwen

address: No.221 Yan’an West Road

department: Department of Gastroenterology

institute: Huadong Hospital Affiliated to Fudan University

summary: Liver fibrosis, a pathogical change commonly existing in various chronic liver diseases, can ultimately develop into life-threatening liver cirrhosis, but effective antifibrotic therapy is absent due to limited understanding of fibrogenic process.  The characteristic fibrotic scar in fibrosis is stiff and disorganized extracellular matrix (ECM) yielded by ECM remodeling, a pathogenic process with vigorous participation of aberrantly activated macrophages. Prolyl endopeptidase (PREP) is a dipeptidyl peptidase that possess both proteolytic and non-proteolytic functions. Using Prep knockout mouse, we found aggravated liver fibrosis in a NASH-related fibrosis murine model, as well as significantly altered transcriptome by in vitro M1/M2 polarization in primary macrophages after PREP ablation. Most importantly, a PREP-mediated direct transcriptional regulation to active cis-regulatory genomic regions was identified for the first time as a novel non-proteolytic function of PREP, based on significant nuclear localization of PREP and CUT&Tag-seq results. Among the PREP-downstream genes, Ctsb and Ctsd, genes encoding ECM remodeling-related profibrogenic cathepsin B and D respectively, were excessively expressed in PREP-ablated macrophages in vitro and in vivo. Our results indicates that PREP is a newly found transcriptional regulator in macrophage, and is a promising therapeutic target for fibrosis-related aberrant macrophage activation.

overall_design: Bone marrow cells isolated from femora of Prep-/- and Prep+/- littermates were cultivated under 50 ng/ml M-CSF for 7 days to obtain fully differentiated bone marrow-derived macrophages (BMDMs). Then BMDMs were left unstimulated (M0), or stimulated with 50ng/ml LPS (M1), or stimulated with 20 ng/ml recombinant murine Interleukin-4  and 20 ng/ml recombinant murine Interleukin-13 (M2) for 24 hours. Total mRNA of BMDMs was extracted and subjected to RNA-seq.

first: Shuangzhe

last: Lin


title: Prolyl endopeptidase-mediated transcriptional regulation in quiescent and activated bone marrow-derived macrophages (CUT&Tag)

overall_design: Bone marrow cells isolated from femora of Prep+/- mice were cultivated under 50 ng/ml M-CSF for 7 days to obtain fully differentiated bone marrow-derived macrophages (BMDMs). Then BMDMs were left unstimulated (M0), or stimulated with 50ng/ml LPS (M1), or stimulated with 20 ng/ml recombinant murine Interleukin-4  and 20 ng/ml recombinant murine Interleukin-13 (M2) for 24 hours. Genomic DNA of BMDMs was extracted and subjected to CUT&Tag.


title: A single-cell atlas of gene expression and chromatin accessibility changes associated with cocaine addiction in the rat amygdala [snRNA-seq]

first: Jessica

last: Zhou

overall_design: Single nuclei (sn)RNA-seq data generated with Illumina high-throughput sequencing

first: Giordano

last: Guglielmo

first: Aaron

middle: J

last: Ho

first: Marsida

last: Kallupi

first: Hai-Ri

last: Li

first: Lieselot

last: Carrette

first: Olivier

last: George

first: Abraham

last: Palmer

first: Graham

last: McVicker

first: Francesca

last: Telese


title: Female Naïve human pluripotent stem cells carry X chromosomes with Xa-like and Xi-like folding conformations

city: New Haven

first: In-Hyun

last: Park

state: CT

address: 10 AMISTAD ST # 201B

department: Genetics

institute: Yale University

summary: In naïve human pluripotent stem cells (hPSCs) that represent the pre-implantation embryonic states, epigenetic regulators for cell identity remain poorly defined.  One of the major remaining questions in naïve stem cell biology is how female cells mediate and regulate X chromosome inactivation (XCI). Recent studies incorporating single-cell RNA sequencing (scRNA-seq) have demonstrated that transcript-based technologies are insufficient to unequivocally resolve XCI regulation in a human system. Instead, 3D genomics shows immense promise for studying XCI by interrogating changes to the X chromosomes’ 3D states. Here, we sought to characterize the 3D state of the X chromosome in naïve and primed hPSCs. Using chromatin tracing, we analyzed the folding conformations of whole X chromosomes with megabase genomic resolution in multiple naïve and primed hPSC lines. Our data found that X chromosomes in female naive hPSCs exhibit a range of spatial folding conformations similar to the active X chromosome (Xa) and the inactive X chromosome (Xi) in somatic cells; these data suggest that naïve hPSCs have initiated XCI. As XCI process ultimately generates detectable differences in volume between the Xa and the Xi, we measured the radius of gyration of individual X chromosome copies across various hPSC cell lines and culture conditions. In naïve hPSCs, our results show that the X chromosomes with Xi-like conformations are not more compact than those with Xa-like conformation. This finding is directly counter to the Xi compaction typically observed in post-XCI female somatic cells. These contradictory 3D signatures of XCI suggest that female naïve hPSCs have initiated the XCI process, but are poised before XCI-driven silencing in a metastable state. As observed in H7 naïve hPSCs, this metastable state can be abolished through classically noted means, such as the loss of Xp chromatin, leading to the deleted p X chromosome (dXp). The Xp loss observed here seems to drive XIST expression and accumulation around the dXp chromosome. Overall, our findings provide insight into the previously undefined X chromosome status in naïve hPSCs in single chromosome resolution, and are critical in understanding the unique epigenetic regulation in early embryonic cells.

overall_design: Hi-C for human naive and primed hESCs

first: Benjamin

last: Patterson

first: Yoshiaki

last: Tanaka


title: Genome-wide CRISPR interference screen identifies long non-coding RNA DARS1-AS1 as a novel regulator of glioblastoma tumorigenesis.

first: Yiwen

address: 1400 Pressler Street,  Unit 1410

department: Bioinformatics & Comp Biology

institute: UT MD Anderson Cancer Center

summary: There are over 15,000 long (>200 nucleotides) noncoding RNA (lncRNAs) genes in the human genome, but only few of them has been functionally characterized. Emerging evidence has shown that long non-coding RNAs (lncRNAs) modulate diverse biological processes and mediate tumor-promoting/suppressing effects and serve as independent diagnostic/prognostic biomarkers in cancer. However, the role and function mechanism of the lncRNA/RBP-mediated regulatory circuits in determining the functional characteristics of GSCs underlying GBM pathogenesis remains poorly understood. To fill this gap, we combined CRISPR (clustered regularly interspaced short palindromic repeat) interference (CRISPRi), with large-scale computational analysis of The Cancer Genome Atlas (TCGA) to systematically identify the functional lncRNAs with clinically relevant expression in GBM.

overall_design: To identify the GBM dependency on lncRNAs with clinically relevant expression, the CRISPR interference (CRISPRi) screens on lncRNAs that showed differential expression between GBM tumors and low-grade glioma (LGG) tumors or normal brain tissues were performed in two GBM cell lines U251 and U87. RNA-seq experiments in the absence/presence of siRNA-mediated DARS1-AS1/YBX1 knockdown U251 cells were performed to explore the up/down-regulated genes by DARS1-AS1/YBX1. eCLIP-seq experiments were conducted in U251 cells to identify YBX1 directly binding mRNA.

first: Caishang

last: Zheng

first: Yanjun

last: Wei


title: Gene expression in shoot and root tissues (wild-type, ospipt6-KO)

city: Bunkyo-ku

first: Yasuhito

last: Sakuraba

state: Tokyo

address: Yayoi 1-1-1

department: Agro-Biotechnology Research Center

country: Japan

institute: The University of Tokyo

summary: To examine differential effect of the mutation of rice OsPIPT6 on the gene exoression in shoot and root tissues, we performed microarray analysis using shoot and root tissues of wild-type and ospipt6-KO mutant.

overall_design: Shoot and root tissues from 28 day-old wild-type and ospipt6-KO seedlings grown under phosphate-sufficient conditions

first: Shuichi

last: Yanagisawa


title: Analysis of total RNA and ribosome-associated RNA in HTT KO MEF versus control.

city: La Tronche

first: Julia

last: Schaeffer

address: Chemin Fortuné Ferrini

country: France

institute: Grenoble Institut Neurosciences

summary:
Purpose: We previously highlighted that the wild-type protein Huntingtin (HTT) interacts with the ribosome in mouse embryonic fibroblasts (MEF). We previously showed that HTT does not control control new protein synthesis at a global level. Hence, we sought to determine whether HTT regulates translation of specific mRNA subsets. To this end, we performed a translatome analysis in HTT-deleted versus control samples.
Methods: From HTT-deleted and control MEF, we isolated total cellular RNA via Trizol/chloroform extraction. From matching samples, we performed ribosome purification and isolated ribosome-associated RNA via Trizol/chloroform extraction of ribosome pellets. From n=3 independent pairs of replicates for total RNA and n=3 independent pairs of replicates for ribosome-associated RNA, libraries were prepared and sequenced (Genewiz) (total 12 samples). Read alignment and counting were performed using STAR and HTSeqCount softwares. We performed differential expression analysis comparing HTT-deleted samples to control samples for total RNA on one hand, and HTT-deleted samples to control samples for ribosome-associated RNA on the other hand. We did so using EdgeR with RUVseq normalization based on residuals (k=2).
Results: For each RNA hit, we analysed differential association to the ribosome normalized to differential expression, by comparing HTT-deleted and control samples. From this analysis, we identified 115 genes displaying differential ribosome association upon HTT deletion, but for which total RNA expression level was unchanged (cut-offs: false discovery rate (FDR) p- value < 0.05, |log2 fold-change| > 1). Among the pool of translationally-only regulated hits, we found genes with decreased association with the ribosome in absence of HTT (Rxfp1, Kng1, Cxcl9, Trpm6, Wnt2b); and with increased association with the ribosome in absence of HTT (Trpm2, Tox2, Ip6k3, Csf3r, Tlr1).
Conclusions: Our results highlight differential ribosome association at a single transcript level upon HTT deletion. Altogether, these data support the hypothesis that HTT regulates the translation of a specific subset of mRNA.

overall_design: RNA-sequencing of total cellular RNA and of ribosome-associated RNA in HTT-deleted MEF versus control

first: J

first: H

last: Nawabi

first: S

last: Belin


title: A single-cell atlas of gene expression and chromatin accessibility changes associated with cocaine addiction in the rat amygdala [snATAC-seq]

first: Jessica

last: Zhou

address: 9500 Gilman Drive

institute: University of California San Diego

summary: The amygdala plays a key role in the negative emotional states associated with the relapse to drug seeking behavior. Neuroanatomical and functional observations have uncovered the role of discrete amygdala subregions in different aspects of these negative affective states. However, the underlying transcriptional regulatory programs driving the function of distinct amygdala cell types remains unknown. We generated an atlas of single nucleus gene expression and chromatin accessibility in the amygdala of rats with low and high cocaine addiction-like behaviors after prolonged abstinence from extended access to cocaine intravenous self-administration. We identified thousands of cell type-specific differentially expressed genes, suggesting that negative affective states are associated with cell type-specific mechanisms which are enriched for molecular pathways, including energy metabolism and GABAergic synapses in excitatory and somatostatin neurons. We demonstrate that higher addiction severity is linked to excessive GABAergic inhibition and, using pharmacological inhibition, we find that addiction-like phenotypes are regulated by the metabolite methylglyoxal which is an agonist at GABA-A receptors. By analyzing differences in chromatin accessibility, we predict upstream transcriptional regulators associated with addiction-like behavior and find discordant regulation of key transcription factors among distinct cell populations. Overall, we provide a comprehensive characterization of cell type-specific transcriptional changes in the amygdala during protracted abstinence and use these insights to identify a novel target for pharmacological intervention.

overall_design: Single nuclei (sn)ATAC-seq data generated with Illumina high-throughput sequencing

first: Giordano

last: Guglielmo

first: Aaron

last: Ho

first: Marsida

last: Kallupi

first: Hai-Ri

first: Lieselot


title: Identification of responsible genes of HCC after sustained virological response to hepatitis C virus

city: Kanazawa

first: Masao

last: Honda

address: Takara-Machi 13-1

department: Gastroenterology

institute: Kanazawa University

summary: Risk of hepatocellular carcinoma (HCC) remains after sustained virological response (SVR) in patients with chronic hepatitis C (CHC). Epigenetic abnormalities might be key regulators in the development of HCC. This study aimed to identify the genes involved in hepatocarcinogenesis after SVR. DNA methylation in liver tissues was compared between 21 CHC patients without HCC and 28 CHC patients with HCC, all of whom had achieved SVR. Through additional comparisons with 23 CHC patients before treatment and 10 normal livers, we found that the several genes were methylated and  demethylated by HCV infection and the development of HCC after achieving SVR.

overall_design: DNA methylation in liver tissues was compared between 21 CHC patients without HCC and 28 CHC patients with HCC, all of whom had achieved SVR. We performed additional comparisons with 23 CHC patients before treatment and 10 normal livers.

first: Masashi

last: Nishikawa

first: Hikari

last: Okada


title: Prolyl endopeptidase-mediated transcriptional regulation in quiescent and activated bone marrow-derived macrophages

first: Yuanwen

last: Chen

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

overall_design: Refer to individual Series


title: Human blastocysts uptake extracellular vesicles secreted by endometrial cells containing miRNAs related to implantation.

city: Valencia

first: Hortensia

last: Ferrero

state: Valencia

address: Avenida Fernando Abril Martorell 106, Torre A

department: Reproductive Medicine

institute: Instituto de Investigación Sanitaria La Fe / Fundación IVI

summary: Objective: To study the uptake by human embryos of extracellular vesicles secreted by the maternal endometrium, and to investigate their miRNA cargo, in order to describe their role in implantation and early embryo development. Design: Prospective descriptive study.  Subjects: Healthy women oocyte donors with confirmed fertility and day 5 human blastocysts. Intervention: Endometrial biopsies were collected from healthy oocyte donors undergoing transvaginal ultrasound-guided cyst aspiration for oocyte retrieval. Main Outcome Measures: Extracellular vesicle were isolated from culture media of primary human endometrial epithelial cells by ultracentrifugation. Concentration and size were analyzed by nanoparticle tracking analysis, their morphology visualized by transmission electron microscopy and extracellular vesicle protein markers expression was determined by western blotting. Vesicles were fluorescently labelled with Bodipy-TR ceramide, and their uptake by human blastocysts was analyzed using confocal microscopy. Analysis of the miRNA cargo of extracellular vesicles was performed using miRNAseq, target genes of the most expressed miRNAs were annotated and functional enrichment analysis was performed. Results: Extracellular vesicle characterization revealed a size within 100-300 nm, and expression of extracellular vesicle protein markers HSP70, TSG101, CD9 and CD81. Fluorescent microscopy showed an efficient extracellular vesicle internalization by human blastocysts within 1-2h, being the fluorescent signal stronger in the hatched area of the embryo. miRNAseq described 149 annotated miRNAs and top 37 most expressed miRNAs targeted 6,592 genes. Functional enrichment analysis of these targeted genes indicated that they participate in several processes related to embryo development, oxygen metabolism, cell cycle, cell differentiation, apoptosis, metabolism, cellular organization or gene expression. Among miRNAs contained in these EVs, hsa-miR-92a-3p, hsa-let-7b-5p, hsa-miR-30a-5p, hsa-miR-24-3p, hsa-miR-21-5p and hsa-let-7a-5p were highly implicated in all these biological processes. Conclusion: Data suggest that extracellular vesicles secreted by human endometrial epithelial cells are internalized by human blastocysts, and transport miRNAs to modulate biological processes related to implantation events and early embryo development. Knowledge of the communication system between human endometrium and embryo via miRNA cargo of these vesicles could describe new biomarkers of implantation success and embryo competence.

overall_design: Descriptive analysis of miRNA content of extracellular vesicles secreted by primary human endometrial epithelial cells (n = 3 pools of cells). Samples were collected 36 hours after the LH surge on the day of oocyte retrieval from healthy women, oocyte donors (18–35 years old with a body mass index of <30 kg/m2)

first: Marina

last: Segura-Benítez

first: Alba

last: Bas-Rivas

first: Elena

last: Juárez-Barber

first: María

last: Carbajo-García

first: Amparo

last: Faus

last: De Los Santos

first: Antonio

last: Pellicer


title: Cocaine addiction-like behaviors are associated with long-term changes in gene regulation, energy metabolism, and GABAergic inhibition within the amygdala

city: La Jolla

first: Jessica


title: Analysis of differentiation therapeutic approaches on murine breast cancer organoids

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

institute: CNIO

summary: In this experiment, we have tested the effect of microRNA-203 as a potential differentiation inducer in breast cancer organoids, derived from the PyMT mouse model. MMTV-PyVT transgenic mice express the Polyoma Virus middle T antigen under the direction of the mouse mammary tumor virus promoter/enhancer. Hemizygous MMTV-PyMT females develop palpable mammary tumors which metastasize to the lung. These mice have high penetrance of early onset of mammary cancer compared to other mammary tumor models. PyMT mice were crossed with miR-203 knock-in mice, where miR-203 expression is induced upon DOX treatment. Thus, organoids derived from the mammary gland tumors of such mouse model where evaluated in vitro. miR-203 expression was therefore induced by Doxycycline in vitro,  and compared to other well-defined differentiation media for breast cancer tissue, such as the mammary epithelial cell culture media and kit (CC-2551B; Lonza).

overall_design: The general idea was to analyze the transcriptomic proximity between miR-203 transiently-overexpressing organoids and those treated with well-defined differentiation media for breast cancer cells. In these RNA sequencing, the transcriptomic profiles of different clones were tested. Three independent pools of organoids from three different experiments were represented for each sample. Different tumors from the PyMT-miR203 mouse model were tested, named as 474, 476, 496, 366, indicated in the samples description. The treatments tested in vitro for the organoids culture were the following: control; MEGM media (as described above, CC-2551B, Lonza); DOX (to induce miR-203 transient expression in the cells); combinations of the previous treatments. All the treatments were maintained in culture for one week, followed by treatment withdrawal. Organoids were processed for RNA extraction after 3 weeks in culture.

last: Salazar

last: Graña-Castro

first: Marcos

last: Malumbres


title: Nanostring gene expression profiling of TurboCAR T cells

city: South San Francisco

first: Regina

middle: Junhui

last: Lin

state: CA

address: 210 E Grand Ave

institute: Allogene Therapeutics, Inc.

summary:
IL2 and IL15 both utilize IL2Rβ and the common gamma chain (γc) and trigger near-indistinguishable downstream signaling pathways. Yet, IL2 and IL15 differentially regulate T cell metabolism and consequently dictate distinct functional outcomes, with IL2 promoting glycolysis and exhaustion, and IL15 favoring oxidative phosphorylation and long-term persistence. Since TurboCAR.15 variants contain signaling domains derived from IL2Rβ, we sought to determine whether they more closely recapitulated IL2 or IL15 signaling.
To this end, gene expression profiles of TurboCAR.15 variants versus BCMA TurboCARs that had been conditioned and cultured in IL2 or IL15 were compared.

overall_design: Unmodified CAR T cells that had been conditioned and cultured with no cytokines, IL2, or IL15, as well as two TurboCAR.15 variants from 2 donors were analyzed.


title: Gene expression profile at single cell level of NKX6.1- and -NEUROG3 expressing cells and their progeny derived from human induced pluripotent stem cells

city: Illkirch

first: Sara

last: Jiménez

address: 1 rue Laurent Fries

institute: IGBMC

summary: We examined by single cell RNA sequencing the heterogeneity and progeny of NKX6.1 and/or NEUROG3 expressing cells produced in vitro by the differentiation of hiPSC cells

overall_design: We generated an hiPSC line where NEUROG3 is fused to a cleavable mCherry reporter and NKX6-1 to a cleavable GFP reporter (NKX6.1-GFP/NEUROG3-HA-mCherry). We differentiated the NKX6.1-GFP/NEUROG3-HA-mCherry hiPS cells towards the islet lineage until the pancreatic endocrine progenitor stage at day 13, FACS sorted the differentiated cells and sequenced the different fluorescent populations using the single-cell RNA sequencing method SortSeq.

first: Valérie

last: Schreiber

first: Reuben

last: Mercier

first: Gérard

last: Gradwohl

first: Nacho

last: Molina


title: NPM1 mutation reprograms leukemic transcription network via reshaping TAD topology

city: Hangzhou

first: Huacheng

last: Luo

state: Zhejiang

address: No. 150, Fucheng Road, Qiantang District

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

summary: C-terminal mutation of Nucleophosmin 1 (NPM1C+) was thought to be a primary driving event that reprograms leukemic-associated transcription program to transform hematopoietic stem and progenitor cells (HS/PCs). However, molecular mechanism underlying NPM1C+-driven leukemogenesis remain elusive. Here, we reported that NPM1C+ reprograms MIZ-1/MYC regulatory axis by altering NPM1-associated CTCF-driven topologically associated domains (TADs) that switched the balance of MIZ1 interaction with co-repressors MYC/G9A and coactivator p300 to control cell cycle progress and myeloid lineage-specific PU.1/CEBPa transcription networks. These alterations impaired hematopoietic cell cycle progression and myeloid differentiation. Knock-in of NPM1C+ in bone marrow HSPCs alters cell cycle regulators and myeloid master transcription factor (TF) TAD topology, chromatin accessibility, and gene regulation leading blockage of myeloid differentiation. Retention of NPM1 or reactivation of PU.1 or CEBPa within nucleus activates differentiation program by reorganizing TADs critical for myeloid TFs and cell cycle regulator, leading to blockage of NPM1C+-driven leukemogenesis. Thus, our data revealed that NPM1C+ reshapes CTCF-defined TAD topology to reprogram signature leukemic transcription program require for cell cycle progression and leukemic progression. Restoration of myeloid transcription program in nucleus reversed NPM1C+-driven transcription signature and promotes myeloid differentiation leading to mitigation of AML.

sample_organism:
Homo sapiens
Mus

platform_organism:
Homo sapiens
Mus

overall_design: We have finished the RNA-seq, ATAC-seq, HiC-seq for WT, XPOi treated and NPM1 wildtype overexpressed OCI-AML3 leukemia cells. LK cells (Lin- Kit+) was sorted by FACS from the bone marrow of  WT and NPM1C+ KI transgenic mice for RNA-seq, ATAC-seq and HiC-seq assay

first: Suming

last: Huang


title: An ecosystem mimicking brain development promotes metastatic growth of SCLC in the brain

city: Stanford

first: Fangfei

last: Qu

state: CA California

address: SIM1 G2065, 265 Campus Drive

institute: Stanford University

summary: Small cell lung cancer (SCLC) is a fatal form of cancer that frequently metastasizes to the brain. Here we investigated the mechanisms allowing SCLC cells to grow in the unique brain microenvironment. We found that neuronal programs upregulated in SCLC cells during tumor progression and upon growth in the brain are critical for SCLC growth in the brain. Mechanistically, the presence of SCLC cells in the brain re-activates astrocytes, which in turn promote the survival of SCLC cells by secreting neuronal pro-survival factors such as SERPINE1. We also identified Reelin, a molecule produced by developing neurons to recruit astrocytes, as a molecule secreted by SCLC cells to recruit astrocytes to the tumor site and promote SCLC growth in the brain. Thus, SCLC cells co-opt mechanisms normally at play between astrocytes and neurons to promote SCLC growth in the brain. Targeting such developmental neuronal programs may help treat brain metastases.

overall_design: 6 samples were analyzed: brain stromal cells isolated from different regions of SCLC brain allografts (2 replicates) and sham injection control (2 replicates)

first: Julien

last: Sage


title: Warming During Embryogenesis Induces a Lasting Transcriptomic Signiture in Fishes

city: Abu Dhabi

first: Daniel

middle: Michael

last: Ripley

address: NYUAD

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: RNA-seq of ventricles from 6 Scyliorhinus canicula juveniles (~5 months old) that underwent embryogenesis at 15C or 20C and were held at 15C post-hatching.

overall_design: S.canicula embryos raised at 15C and 20C. Hatchling moved to a common garden environment (15C) for ~5 months. Ventricles excised and RNA-seq performed.

first: Terence

last: Garner

first: Samantha

last: Hook

first: Ana

last: Verissimo

first: Bianka

last: Grunow

first: Timo

last: Moritz

first: Peter

last: Clayton

first: Holly

last: Shiels

first: Adam

last: Stevens


title: Prmt5 deficiency inhibits CD4+T cells migration through Klf2-S1pr1 and ameliorates EAE disease (scRNA-seq)

first: zheyi

last: chen

address: 1665 Kong Jiang Road

institute: Shanghai Jiao Tong University School of Medicine

summary: Protein arginine methyltransferase 5 (Prmt5) is the major type II methyltransferase catalyzing symmetric dimethylation, regulates cell development, homeostatic and disease processes. Prmt5 inhibition or deletion in CD4+T cells has been reported to protection against experimental autoimmune encephalomyelitis (EAE), the perfect mouse model for multiple sclerosis (MS); however, the detail mechanisms have not yet been elucidated. Here, using the mRNA  sequencing, single cell RNA sequencing and ATAC sequencing, we uncovered the unreported role of Prmt5 on T cells migration ability under the EAE condition. We found that mice condition knockout of Prmt5 in T cells were resistance with EAE, infiltrating inflammatory CD4+ T cells in center nervous system (CNS) were greatly reduced. However, T cells in spleen showed much more proliferation and activation properties in Prmt5cko mice, the number of pathogenic CD4+T cells in spleen were not reduced. We further revealed that Rora+CD4+T cells were elevated in Prmt5cko mice, but expressed lower level of S1pr1, resulting in a lack of CD4+ T cells egress from spleen and migrate to CNS, leading to pathogenic CD4+T cells were blocked in spleen. Moreover, single cell ATAC sequencing revealed that Klf2 were enriched in S1pr1 promoter and reduced in Prmt5cko mice. Correctively, our study delineated the undiscovered role of Prmt5 on T cell biology, Prmt5 may through Klf2-S1pr1 pathway and regulate T cells migration; modulating Prmt5 levels may be useful for controlling CD4+T cell migration in CD4+T cell mediated diseases including MS.

overall_design: Prmt5 CKO and control mice (3 mice per group) were induced EAE by MOG35–55/CFA immunization, on the day the score peaked, purified CD8+ and CD4+ T cells isolated from spleen were performed bulk RNA sequencing and all cells isolated from spleen were performed single cell RNA sequencing and single cell ATAC sequcing.

first: Yingxia

last: Zheng

first: Zheyi

last: Chen


title: Prmt5 deficiency inhibits CD4+T cells migration through Klf2-S1pr1 and ameliorates EAE disease


title: Prmt5 deficiency inhibits CD4+T cells migration through Klf2-S1pr1 and ameliorates EAE disease (RNA-seq)


title: Transcriptomic analysis of Alfalfa response to low selenium concentration

city: zhengzhou

first: jinke

last: hu

state: henan

address: Zhengzhou City, Henan Province

institute: zhengzhou

summary: We studied the application of transcriptome technology in alfalfa selenium (Se) treatment. Alfalfa had different states after different concentrations of Se treatment. It shows that lower concentration promoted growth and higher concentration produced toxicity. The positive regulatory effects of moderate Se (100 mg / kg) on alfalfa was determined through preliminary experiments, and the gene expression of Alfalfa under this treatment was further analyzed by transcriptome.

overall_design: The two treatments were control and 100 mg/kg selenium, with three repetitions at each treatments.

first: Qingdong

last: Wang

first: Huafeng

last: Hu

first: Jinke


title: Senescence-associated transcriptional reprogramming in leukemia cells is reversible and allows cells to persist after drug treatment

city: Toronto

first: Sam

last: Benchimol

state: ON

address: 4700 Keele St.

institute: York University

summary:
The purpose of this study was to determine whether leukemia cells can escape from drug-induced senescence; determine the phenotype of the senescent, and escaped cells, and whether senescent leukemia cells can be specifically eliminated prior to their escape.
Methods: DA3/EPOR cells were treated with 200ng/ml doxorubicin for 24 hr. Cells were confirmed to enter and exit senescence based on, proliferating and SA-gal staining. mRNA transcriptional profiles of naïve proliferating, senescent, and escaped DA3/EPOR murine leukemia cells  were generated by deep sequencing, in biological triplicate, using Illumina NovaSeq 6000 at a depth of 25 million pair-ended reads that were 100 bp in length. The sequence reads that passed quality filters, the first 13 nucleotides were removed from each read. Alignment to the MM10 indexed genome was done using HiSAT2. Read counts were genereated using HTSEQ, which were then used for differential expression. Differential expression was performed on Rstudio using EdgeR. qRT–PCR was performed for validation.
Results: We report that DA3/EPOR leukemia cells enter and escape a doxorubicin (Dox)-induced senescence, dependent on erythropoietin (EPO). EPO is necessary for DA3/EPOR cells to survive the senescent state. Senescent DA3/EPOR cells undergo a transcriptional reprogramming, which is largely reversible upon escape. Escaped DA3/EPOR cells mirror naïve, never senescent DA3/EPOR cell, and respond similarly to Dox. Senescent DA3/EPOR cells mimic a diapause-like state, and undergo metabolic changes. Senescent DA3/EPOR cells and some drug-induced senescent human acute myeloid leukemia (AML) cells can be eliminated with chloroquine, a lysosome inhibitor. Lastly, we show with The Cancer Genome Atlas publicly available data that the senescent signature is associated with decreased survival in AML and multiple other cancers.
Conclusion: Leukemia cells persist through drug treatment by entering a reversible senescent state that mimics diapause. Senescent leukemia cells depend on lysosome activity to persist, and treatment with chloroquine, a lysosome inhibitor, can eliminate senescent leukemia cells.

overall_design: Examining proliferating, doxorubicin-induced senescnt DA3/EPOR cells and DA3/EPOR cells that escape doxorubicin-induced senescence.

first: David

last: Miller

first: Kyra

last: Kerkhofs

first: Sahib

last: Madahar

first: Mark

last: Bayfield

first: Samuel


title: Prmt5 deficiency inhibits CD4+T cells migration through Klf2-S1pr1 and ameliorates EAE disease (scATAC-seq)


title: Neuronal mimicry mechanisms promote the growth of small-cell lung cancer in the brain [human astrocytes RNA-seq]

first: Fangfei

last: Qu

overall_design: 9 samples were analyzed: human astrocytes cultured alone (3) or co-cultured with human SCLC cell line NCI-H69 (3) or NCI-H82 (3)

first: Juliens

last: Sage


title: Neuronal mimicry mechanisms promote the growth of small-cell lung cancer in the brain [TA and CA RNA-seq]

overall_design: 6 samples were analyzed: astrocytes isolated from SCLC brain allografts (3 replicates) and sham injection control (3 replicates)


title: Transcriptome reveals the regulation on arginine metabolism in M.smegmatis.

first: Shuangquan

last: Yan

address: 800 Dongchuan RD. Minhang District

institute: Shanghai Jiao Tong University

summary: Analysis of changes in gene expression in MSMEG_1415 knockout strains  with or without arginine treatment.

overall_design: RNA-seq of knockout strains and parental strain (H37Rv) for comparison, grown in-vitro (7H9 medium).

first: Jianping

last: Xie


title: Gene expression profiling from human prostate cancer PC3 or DU145 cells with control or ESS2 knockdown.

city: Minato

first: Sayuri

last: Takahashi

address: 4-6-1, Shiroganedai

department: The Institute of Medical Science

summary: PC3 and DU145 cells stably transduced with control or ESS2 shRNA were established. Total RNA was isolated from 5x 10^6 cells of each

overall_design: To test the effect of depleting ESS2 on the gene expression of cancer cells, human prostate cancer cell line PC3 and DU145 were transduced with lentivirus for shRNA targeting ESS2 or non-targeting control shRNA.


title: Effect of Sirt6 depletion on gene expression of primary human chondrocytes

status: Public on Aug 08 2023

city: Philadelphia

first: John

middle: Andrew

last: Collins

state: PA

address: 1015 Walnut Street, Curtis Building, Suite 505

institute: Thomas Jefferson University

summary: To define the effect of SIRT6-mediated transcriptional regulation, RNA-sequencing was conducted on primary human chondrocytes depleted of SIRT6 and compared to cells nucleofected with a scrambled siRNA control (72 hours).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for chondrocytes nucleofected with siRNA to Sirt6 and controls

first: Mandy

last: Peffers


title: MYSM1 acts as a novel co-activator of ERα via histone and non-histone deubiquitination to confer antiestrogen resistance in breast cancer

city: shenyang

first: Ruina

last: Luan

state: Liaoning

address: shenbei district

institute: china medical university

summary: Endocrine resistance is a crucial challenge in estrogen receptor alpha (ERa)-positive breast cancer (BCa). Aberrant alteration in modulation of E2/ERa signaling pathway has emerged as the putative contributor for endocrine resistance in BCa. Herein, we demonstrate that MYSM1 as a deubiquitinase participates in modulating ERa action via histone and non-histone deubiquitination. MYSM1 is involved in maintenance of ERa stability via ERa deubiquitination. Silencing MYSM1 induces enhancement of histone H2A ubiquitination as well as reduction of histone H3K4me3, H3K9ac and H3K27ac levels at cis regulatory elements on promoter of ERa-regulated genes. ChIP-seq analysis indicate that the half-EREs are the significant enrichment sites for MYSM1 on ERa-regulated genes. MYSM1 depletion attenuates cell growth in BCa-derived cell lines and xenograft models. Knockdown of MYSM1 increases the sensitivity of antiestrogen agents in BCa cells. A virtual screen shows that the small molecule Imatinib could potentially interact with catalytic MPN domain of MYSM1 to inhibit BCa cell growth via MYSM1-ERa axis. MYSM1 is highly expressed in clinical BCa samples, especially in aromatase inhibitor (AI) non-responsive tissues. These findings clarify the molecular mechanism of MYSM1 as an epigenetic modifier in regulation of ERa action and provide a potential therapeutic target for endocrine resistance in BCa.

overall_design: MCF7 cells were treated with estrogen(E2)  and equal EtOH for 1 hour

first: Mingcong

last: He

first: Ge

last: Sun

first: Yu

last: Bai


title: Neuronal mimicry mechanisms promote the growth of small-cell lung cancer in the brain

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Expression profiles and bioinformatic analysis of circRNAs in cardiac fibrosis of db/db mice

city: Shijiazhuang

first: Lingling

last: Yuan

state: Hebei

address: No.215, Heping Road(West)

institute: The Second Hospital of Hebei Medical University

summary: To identify the differential expression of circRNAs in  cardiac fibrosis of db/db mice, db/db mice cardiac apex tissues were detected through microarray analysis at the age of 21 weeks. Compared with normal control mice, 77 circRNAs were up-regulated and 135 circRNAs were down-regulated in the chromosomes of db/db mice (fold changes ≥1.5, p-values ≤ 0.05). Moreover, Real-time qPCR was performed to validate the expression of circRNAs. In db/db mice, the top four up-regulated circRNAs, mmu_circRNA_28667, mmu_circRNA_32303, mmu_circRNA_20674, mmu_circRNA_25425 were verified. In db/db mice, the top four down-regulated circRNAs which were indexed by circBase database were verified. They were mmu_circRNA_014302, mmu_circRNA_001535, mmu_circRNA_005522 and mmu_circRNA_013422.

overall_design: Cardiac tissue samples were collected from db/db (n = 3) and C57BL/6 (n = 3) mice at age of 21 weeks. Three independent experiments were performed  at the age of 21 weeks  using different donors for each experiment.

first: Ling

first: Ting

last: Wang

first: Jin

last: Duan

first: Jing

last: Zhou

last: Li

first: Gui

middle: Z

first: Hong


title: The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase-like HHCC zinc finger

city: Flora Hill

first: M Cristina

last: Keightley

state: VIC

address: Edwards Rd

department: Rural Clinical Sciences

country: Australia

institute: La Trobe University

summary: From a forward genetic screen in zebrafish, we identified the transcription factor, ZBTB11, as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1, GFI1 and CEBPa. To better understand target genes regulated by Zbtb11, RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish.

overall_design: At 48 hours post fertilisation, single-cell suspensions were prepared from either pooled WT embryos or from pooled phenotype-sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.

first: M

first: Graham

last: Lieschke


title: Identification of host endotypes using peripheral blood transcriptomics in a prospective cohort of patients with endocarditis [pre]

city: Oviedo

first: Guillermo

last: Albaiceta

address: Avenida de Roma s/n

institute: Instituto de Investigación Sanitaria del Principado de Asturias

summary: Infective endocarditis is a severe disease caused by the infection of heart valves and endocardium by pathogenic germ.  Antimicrobial therapy and surgery remain the basis of treatment, and up to 50% of the patients require surgical replacement of the affected valves to control the infectious source. The objective of this work is to identify the existence of endotypes in a prospective cohort of patients with infective endocarditis. We performed a bulk RNA-seq form peripheral blood to cluster patients according to their transcriptomic profiles at diagnosis and during their follow-up. Clinical data, outcomes and response to surgery were assessed in a cluster-specific manner, in order to identify differences in the pathogenesis that could help to find personalized treatments and improve the outcome.

overall_design: We grouped patients with endocarditis using the transcriptome obtained during their admission and applying clustering methods and subsequent analysis of differential expression between both clusters. Thirteen of these patients (this series) underwent cardiac surgery, who underwent differential expression analysis using the temporality between before and after surgery for each of the clusters.

first: Laura

last: Amado-Rodríguez

first: Cecilia

last: López-Martínez

first: Israel

middle: D

last: Duarte-Herrera


title: Identification of host endotypes using peripheral blood transcriptomics in a prospective cohort of patients with endocarditis

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


title: Analysis of R5-/+ and Mc5rfl/fl R5-/+ lung ILC2 transcriptomes in papain induced acute lung inflammation

city: Shanghai

first: yuying

last: huang

address: 320 Yue-Yang Road

institute: Center for Excellence in Molecular Cell Science, CAS

summary: melanocortin 5 receptor (Mc5r) have various effects in immune responses. However, the involvement of Mc5r in ILC2 functions remains unclear. We identified the genes regulated by Mc5r in lung ILC2s during papain induced acute lung inflammation.

overall_design: Lung ILC2 mRNA profiles of papain stimulated R5-/+ and Mc5rfl/fl R5-/+  mice (n=2 each)

first: Yuying

last: Huang


title: Profiling Neuronal Methylome and Hydroxymethylome of Opioid Use Disorder in the Human Orbitofrontal Cortex

city: Orange

first: Janitza

last: Montalvo-Ortiz

address: 200 Edison Road

department: Psychiatry

institute: Yale School of Medicine; West Haven VA Medical Center, VA Connecticut Health Care

summary: Opioid use disorder (OUD) is influenced by genetic and environmental factors. While recent research suggests epigenetic disturbances in OUD, this is mostly limited to DNA methylation (5mC). DNA hydroxymethylation (5hmC) has been widely understudied. We conducted a multi-omics profiling of OUD in a male cohort, integrating neuronal-specific 5mC and 5hmC as well as gene expression profiles from human postmortem orbitofrontal cortex (OUD=12; non-OUD=26). Single locus methylomic analysis and co-methylation analysis showed a higher number of OUD-associated genes and gene networks for 5hmC compared to 5mC; these were enriched for GPCR, Wnt, neurogenesis, and opioid signaling. 5hmC marks also showed a higher correlation with gene expression patterns and enriched for GWAS of psychiatric traits. Drug interaction analysis revealed interactions with opioid-related drugs, some used as OUD treatments. Our multi-omics findings suggest an important role of 5hmC and reveal loci epigenetically dysregulated in OFC neurons of individuals with OUD.

overall_design:
Postmortem orbitofrontal cortex tissue were obtained from the National Post-Traumatic Stress Disorder (PTSD) Brain Bank (NPBB), a brain tissue repository at the U.S. Department of Veterans Affairs (VA). 38 samples were selected, in which 12 individuals were diagnosed with opioid use disorder (OUD+) and 26 without opioid use disorder (OUD-).
Traumatic Stress Brain Research Group
----------------------
Authors state:
The original data is a RRoxBS. However, I only have the beta values table generated using the read counts for each site. I don't have the raw data to submit.

first: Gregory

last: Rompala

first: Sheila

middle: T

last: Nagamatsu

first: José

last: Martínez-Magaña

first: Diana

last: Nuñez-Ríos

first: Jiawei

first: Matthew

last: Girgenti

first: John

middle: H

last: Krystal

first: Joel

last: Gelernter

first: Yasmin

last: Hurd


title: Downregulation of VPS13C promotes cisplatin resistance in cervical cancer by upregulating GSTP1

city: Wuhan

first: xiangyu

last: Tan

state: Hubei

address: 1095 Jiefang Avenue

department: Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College

institute: Huazhong University of Science and Technology

summary: Cisplatin resistance remains a major obstacle limiting the effectiveness of chemotherapy in cervical cancer. However, the underlying mechanism of cisplatin resistance is still unclear.

overall_design: Cervical cancer control cells and VPS13C-deficient cells were treated with cisplatin for RNA sequencing analysis

first: Xiangyu

first: Xun

last: Tian


title: Gene expression profile of ILC2 from naïve wild type mice

summary: Under unstimulated conditions, there is a low abundance of lung ILC2 cells, which adds to the complexity of analyzing the RNA transcriptome. We examined the expression profile of ILC2 cells of untreated naïve mice.

overall_design: We isolated ILC2 cells from the lungs of untreated wild-type mice and analyzed their transcriptomes.


title: Identification of host endotypes using peripheral blood transcriptomics in a prospective cohort of patients with endocarditis [pre-post_qx]

first: Guillermo

middle: M

last: Albaiceta

overall_design: We grouped patients with endocarditis using the transcriptome obtained during their admission and applying clustering methods and subsequent analysis of differential expression between both clusters. Thirteen of these patients underwent cardiac surgery, who underwent differential expression analysis using the temporality between before and after surgery for each of the clusters.

first: Laura

first: Cecilia


title: Effect of tumor growth in bone on DRG gene expression

city: Suita

first: Kenji

last: Hata

state: Osaka

address: 1-8 Yamadaoka

department: Biochemistry

institute: Osaka University graduate school of dentistry

summary: Recent studies have shown that the sensitized and excited nerves innervating the tumor establish intimate communications with cancer cells by releasing various tumor-stimulating factors for tumor progression. To understand the mechanism by which interactions of cancer cells and SNs regulate tumor growth in bone, we aimed to identify molecules released from DRGs in communication with cancer cells.

overall_design: Rat pulmonary carcinoma cells (IP-B12) which show osteolytic tumor growth in bone marrow were inoculated into the bone marrow cavity of the right tibiae in rat under general anesthesia. DRGs were collected from rat followed by the isolation of RNA. DRGs of left tibia were used as control.

first: Tatsuo

last: Okui


title: Highly reproducible and cost-effective one-pot organoid differentiation using a novel platform based on PF-127 triggered spheroid assembly

city: Beijing

first: Yangming

last: Wang

address: No.5 Yiheyuan Road, Haidian District

department: Institute of Molecular Medicine, College of Future Technology

institute: Peking University

summary: Using a novel platform based on the findings that Pluronic F-127 (PF-127) could trigger highly uniform spheroid assembly, we develop a one-pot organoid differentiation strategy. Using our strategy, we successfully generate cortical, nephron, hepatic, and lung organoids with improved reproducibility compared to previous methods while reducing the original costs by 80-95%. In addition, we adapt our platform to microfluidic chips allowing automated culture. We showcase that our platform can be applied to tissue-specific screening, such as drug toxicity and transfection reagents testing. And, we generate NEAT1 knockout tissue-specific organoids and show NEAT1 modulates multiple signaling pathways fine-tuning the differentiation of nephron and hepatic organoids and suppresses immune responses in cortical organoids. In summary, our strategy provides a powerful platform for advancing organoid research and studying human development and diseases.

overall_design: We use bulk RNA-seq analyses to suggest functions of PF-127 to hESCs, and prove that our methods are robust for generating multiple types of organoids from all three germ layers. Additionally, we use the lncRNA NEAT1 knockout organoids to perform RNA-seq to study tissue-specific gene regulation functions of NEAT1.

first: Xiao-Shan

last: Zhang

first: Gang

last: Xie

first: Shuangjin

last: Ding

first: Yi-Xia

last: Wu


title: Downregulation of VPS13C promotes cisplatin resistance in cervical cancer by upregulating GSTP1 [SiHa]