title: First Transcriptomic insight into the working muscles of racing pigeons during a competition flight

status: Public on Jan 15 2023

city: Balice

first: Monika

last: Stefaniuk-Szmukier

address: ul.Krakowska 1

department: Department of Animal Molecular Biology

institute: National Research Institution of Animal Production

summary: The currently known homing pigeon is a result of a sharp one-sided selection for flight characteristics focused on speed, endurance, and spatial orientation. This has led to extremely well-adapted athletic phenotypes in racing birds. Here, we identify genes and pathways contributing to exercise adaptation in sport pigeons by applying next-generation transcriptome sequencing of m.pectoralis muscle samples, collected before and after a 300 km competition flight. The analysis of differentially expressed genes pictured the central role of pathways involved in fuel selection and muscle maintenance during flight, with a core set of genes: ARTN, NREP, CAV3, SLC25A30, SLC2A11. Variations in these genes may therefore be exploited for genetic improvement of the racing pigeon population towards specific categories of competition flights.

overall_design: The present study was performed on 12 muscle samples of m. pectoralis collected from 12 racing pigeons (Columba livia). Samples were collected from adult birds never trained for racing (K; n = 5) and birds after competing in a 300 km race (E; n = 7), who have undergone earlier flight training  All birds were bred, and raised on a private loft owner, at the same location, with the same environmental and feeding conditions. The E group was basketed the day before and transported to the place of release (300 km away from the loft).

first: Tomasz

last: Szmatoła

first: Katarzyna

last: Ropk-Molik


title: mRNA expression profiling of wild-type and ABCA1 knockout IMR90 cells during DNA damage-induced senescence

city: Seoul

first: Kyeonghwan

last: Roh

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

type: Expression profiling by high throughput sequencing

summary: We have generated ABCA1 knockout cells using CRISPR/Cas9 system and expanded single cell clones for gene expression profiling. To identify differentially expressed genes during cellular senescence in wild-type and ABCA1 knockout cells, we performed transcriptional profiling with RNA sequencing (RNA-seq) before and after senescence induction using a stress-induced senescence model (bleomycin-induced senescence).

overall_design: Wild-type and ABCA1 knockout IMR90 cells expressing hTERT were treated with bleomycin (10 ug/ml for 24 h) to induce senescence, and total RNAs from proliferating (-bleomycin) and senescent (+bleomycin, 7 days after exposure to bleomycin) IMR90 cells were isolated using the acidic phenol extraction method. One microgram of high-quality RNA samples (RIN > 7.0) was used to construct RNA-seq libraries using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina). RNA-seq was performed on an Illumina NovaSeq 6000 sequencer.

first: Yeonju

last: Kim

first: Yeji

last: Jang

first: Chanhee

last: Kang


title: Homeostatic PD-1 signalling restrains Eomes-dependent oligoclonal expansion of liver- resident CD8 T cells [scRNA-seq]

city: GOSSELIES

first: Abdulkader

last: AZOUZ

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

summary: The coinhibitory PD-1 signalling pathway plays a major role in the context of tumor-specific T cell responses. Conversely, it also contributes to the maintenance of peripheral tolerance as patients receiving anti-PD-1 treatment are prone to developing immune-related adverse events. Yet, the physiological role of the PD-1/PDL-1 axis in T cell homeostasis is still poorly understood. Herein, we show that under steady-state conditions, the absence of PD-1 signaling led to a preferential expansion of CD8+ T cells in the liver. These cells exhibited an oligoclonal TCR repertoire and a terminally differentiated exhaustion profile with high levels of the transcription factors TOX and EOMES. Using loss- or gain-of-function strategies, we could demonstrate that EOMES was required for the clonal expansion and acquisition of this differentiation program. Furthermore, single cell transcriptomics coupled to TCR repertoire analysis strongly supported the notion that these cells arise locally from liver-resident memory CD8 T cells. With these results, we uncovered an unexpected role for PD-1 signaling in liver memory T cell homeostasis.

overall_design: Using  gain-of-function strategie, we developed mice expressing Eomes in T cells to study its role in the  acquisition of a specific transcriptional program and clonal expansion of CD8+ T cells in spleen and liver.

first: Marie

last: Le Moine

last: Azouz

first: Guillem

middle: S

last: Sanchez

first: Muriel

last: Nguyen

first: Séverine

last: Thomas

first: Valdrin

last: Shala

first: Hacene

last: Dreidi

first: Sébastien

last: Denanglaire

first: Frédérick

last: Libert

first: David

last: Vermijlen

first: Fabienne

last: Andris

first: Stanislas

last: Goriely


title: The vacuolar sugar transporter EARLY RESPONSE TO DEHYDRATION 6-LIKE4 regulates fructose signaling and plant growth

city: Kaiserslautern

first: Benjamin

last: Pommerrenig

address: Paul-Ehrlich-Str. 22

department: Biology

country: Germany

institute: University of Kaiserslautern

summary: Regulation of intracellular sugar homeostasis is maintained by regulation of activities of sugar import and export proteins residing at the tonoplast. We show here that the EARLY RESPONSE TO DEHYDRATION6-LIKE4 protein, being the closest homolog to the proton/glucose symporter ERDL6, resides in the vacuolar membrane. Gene expression and subcellular fractionation studies indicated that ERDL4 was involved in fructose allocation across the tonoplast. Overexpression of ERDL4 increased total sugar levels in leaves, due to a concomitantly induced stimulation of TST2 expression, coding for the major vacuolar sugar loader. This conclusion is supported by the finding that tst1-2 knockout lines overexpressing ERDL4 lack increased cellular sugar levels. ERDL4 activity contributing to the coordination of cellular sugar homeostasis is also indicated by two further observations. Firstly, ERDL4 and TST genes exhibit an opposite regulation during a diurnal rhythm, and secondly, the ERDL4 gene is markedly expressed during cold acclimation representing a situation in which TST activity needs to be upregulated. Moreover, ERDL4-overexpressing plants show larger size of rosettes and roots, a delayed flowering time and increased total seed yield. Consistently, erdl4 knock-out plants show impaired cold acclimation and freezing tolerance along with reduced plant biomass. In summary, we show that modification of cytosolic fructose levels influences plant organ development and stress tolerance.

overall_design: Comparative gene expression analysis of Arabidopsis leaf discs incubated in differnt sugar solutions (mannitol, glucose, fructose) and analysis of WT and two ERDL4 (At1g19450)-overexpressing Arabidopsis thaliana lines

first: Khan

last: Azkia

first: Cheng

last: Jintao

first: Pommerrenig

last: Benjamin

first: Neuhaus

last: H Ekkehard


title: Chemokines expression  effect of depletion of Shp2 on Kupffer cells

city: San Diego

first: Hong

last: Gao

state: California

address: 9500 Gilman Drive

department: Medicine

country: USA

institute: University of California, San Diego

summary: To investigate the monocyte-associated chemokines and adhesion molecules of NPCs between WT and Shp2Δk mice.We established shp2f/f//Clec4f-Cre mice to deplete Shp2 of KC.

overall_design: We isolated the NPCs  from WT and KC-Shp2 knock out mice.Then we performed chemokines gene expression  analysis using data obtained from RNA-seq of NPC .

first: Li

last: Du

first: Yichun

last: Ji

first: Jiemeng

last: Zhang


title: Homeostatic PD-1 signalling restrains Eomes-dependent oligoclonal expansion of liver- resident CD8 T cells [ATAC-seq]

first: Abdulkader

last: AZOUZ

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Using  gain-of-function strategie, we developed mice expressing EOMES in T cells to evaluate the epigenetic landscapes in CD8+ T cells from the liver of EomesTg/Tg mice along with their WT (PD-1lo) counterparts.

first: Marie

last: Le Moine

last: Azouz

first: Guillem

last: Sanchez

first: Muriel

last: Nguyen

first: Séverine

last: Thomas


title: Characterization of Natural Killer Cell Sensitivity of Circulating Tumor Cells in Non-small Cell Lung Cancer using Bulk RNA-sequencing

city: Ann Arbor

first: Sunitha

last: Nagrath

state: Michigan

address: 2800 Plymouth Road

institute: University of Michigan

summary: To investigate whether circulating tumor cells exhibit NK sensitive gene expression profiles, we performed bulk RNA-sequencing on NK sensitive and NK resisitant cell lines, including two in-house derived CTC lines.

overall_design: Comparative gene expression analysis of RNA-seq data between cell lines that sensitive or resistant to NK based cytotoxicity assay.

first: Zeqi

last: Niu

first: Sarah

last: Owen


title: XCI and sex-biased expression in AT2 cells

status: Public on Jan 16 2023

city: Philadelphia

middle: C

last: Pyfrom

state: PA

address: 3800 Spruce St

institute: University of Pennsylvania

summary: Significant sex differences exist for many lung pathologies, including SARS-CoV-2 related disease (COVID-19) and pulmonary fibrosis, but the mechanistic basis for this remains unclear. Notably, Ace2, the gene encoding angiotensin-converting enzyme 2, an enzyme that plays multiple roles in SARS-CoV-2 pathogenesis, including acting as the major viral receptor, is localized on the X-chromosome. Moreover, prior work in fibroblasts suggested that Ace2 may escape X-Chromosome Inactivation (XCI), which normalizes X-lined gene expression between sexes. Alveolar type 2 cells (AT2s), which play a key role in alveolar lung regeneration, express Ace2, suggesting that aberrant XCI in AT2s could potentially impact sex-biased lung pathology. To that end, we performed RNA-seq on AT2 cells isolated from 4 male and 4 female F1 mus/cast mice. Utilizing allele-specific transcriptomics, we demonstrate that about 50% of expressed X-linked genes in mouse AT2s, including Ace2, escape XCI, the highest levels reported to date. Moreover, we observe dramatic genome-wide expression differences between male and female AT2s, likely influencing both lung physiology and pathophysiologic responses. Taken together, these studies support a renewed focus on AT2s as potential contributor to sex-biased differences in lung disease.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Alveolar Type 2 (AT2) cells from 4 male and 4 female F1 mus/cast mice.

first: Isabel

last: Sierra

first: Aaron

last: Weiner

first: Gan

last: Zhao

first: Amanda

last: Driscoll

first: Xiang

last: Yu

first: Brian

middle: D

last: Gregory

first: Andrew

middle: E

last: Vaughan

first: Montserrat

last: Anguera


title: Autophagy receptor SHISA9 orchestrates antiviral immune heterogeneity of brain glia cells and CNS inflammation

city: Rochester

first: Yanyan

last: Zheng

state: Minnesota

address: 839 16th ST SW, Apt421

institute: Mayo Clinic

summary: Brain glia cells exhibit highly heterogeneity which can modify their genetic landscape and responding sensitivity, thus achieving appropriate responses to environmental changes for maintenance of CNS homeostasis. However, technical restriction has prevented the study on the self-orchestrating activity of CNS resident immune cells. Microglia and astrocytes are predominant responding cells at early stages during CNS viral infection. Their activation not only contributes to the recruitment of peripheral immune cells that aid in viral clearance, but also increases the risk of long-term detrimental inflammatory injury associated with many neurodegenerative diseases. Optimal autophagic activity is vital to maintain brain integrity, yet the autophagy regulation of immune activity in brain glia cells remains poorly understood. Here, we identify the membrane protein SHISA9 as an autophagy cargo receptor that modulates the heterogenic immune responses during CNS infection. By 10x single-cell RNA sequencing, we identify the astrocytes with increased Shisa9 expression followed by decreased expression of inflammatory transcriptional programs. Shisa9 has temporal characteristics in modulating both antiviral and inflammatory responses in microglia and astrocytes at different stages during infection. Shisa9-/- mice are highly susceptible to herpes simplex virus encephalitis, accompanied by higher rates of pathogenic astrocytes which might contribute to neurodegeneration progression and display a more severe neuroinflammation symptoms compared to wild-type mice. Taken together, our study unravels a critical role of selective autophagy in orchestrating immune heterogeneity of different CNS resident cells through SHISA9-IKKi axis.

overall_design: Mice brains were isolated from WT and Shisa9-/- mice with HSV-1 infection for 3/7 days and analyzed by scRNA-seq

first: Liqiu

last: Wang


title: Next Generation Sequencing Facilitates Transcriptomes Quantitative Analysis of HEK293T cells transfected with the plasmids respectively encoding RfxCas13d, crRNA and NeuN.

status: Public on Jan 14 2023

city: Beijing

first: Yunfei

last: Li

state: China

address: 38 Xueyuan Road, Haidian District, Beijing

department: Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China

country: China

institute: Peking University

summary: To determine what effect the collateral activity of RfxCas13d has on HEK293T cells upon targeting overexpressed NeuN. The plasmids encoding RfxCas13d, NeuN and NT/targeting crRNA into HEK293T cells. After 24 hours of transfection, cells were collected and extracted for total RNA. Then, we performed RNA-seq to compare the differentially expressed genes between cells transfected with targeting crRNAs and non-targeting crRNA.

overall_design: mRNA profiles of HEK293T cells transfected with the plasmids respectively encoding RfxCas13d, NeuN and crRNA.


title: RNA-sequencing of melanoma-derived tumor-infiltrating lymphocytes (TILs)

city: Amsterdam

first: Wouter

last: Moolenaar

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

summary: We report the differential gene expression patterns of TILs from two patients after treating the cells with lysophosphatidic acid (LPA) for 2 or 3 hours. Among the common LPA-regulated genes are transcription factors and other immediate early genes as well as T-cell regulatory cell-surface molecules

overall_design: Examination of differentially regulated genes in melanoma TILs from two patients.

first: Maaike

last: van Zon

first: Iris

last: de Rink


title: RNA-seq analysis about SARS-CoV-2 infected trophoblast cells

city: Tainjin

first: Weiyu

last: Zhang

address: No.38 Tongyan Road, Jinnan District

institute: Nankai University

summary: infection of  EPSC-TSCs, EVTs and STBs derived from human EPSCs by SARS-CoV-2  in the presence or absence of remedesivir and GC376 treatment

overall_design: Derivating of hTSCs from human EPSCs and the subtype STBs and EVTs for SARS-CoV-2 infection

first: Degong

last: Ruan


title: Homeostatic PD-1 signalling restrains Eomes-dependent oligoclonal expansion of liver- resident CD8 T cells.

first: Abdulkader

last: AZOUZ

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

overall_design: Refer to individual Series


title: RNA-seq of decitabine- and RG3039-treated WT HL-60 cells

status: Public on Jan 13 2023

city: Palo Alto

first: Abolfazl

last: Arab

state: CA

address: 3160 Porter Dr

institute: Arc Institute

summary: We performed stranded RNA-seq on HL-60 cells treated with decitabine for 6 hours, 72 hours and 120 hours in duplicate.

overall_design: We assessed differential RNA expression by treatment condition (decitabine, RG3039, both drugs and DMSO).

first: Alex

last: Ge


title: Circulating MicroRNAs Targeting LIGHT as Diagnostic Biomarkers during Asthma Attack

city: Shenzhen

first: Fei

last: Shi

address: Dongbeimen street,Shenzhen, Guangdong, China

institute: Shenzhen People’s Hospital

summary: Bronchial asthma is one of the most common respiratory diseases. Reversible airflow limitation, persistent airway inflammation and airway hyperresponsiveness, and air remodeling is its main characterization. The morbidity and mortality rates of asthma increase due to air pollution. MicroRNAs are small molecules that regulate gene expression playing a part in inflammatory diseases. The designed current study aims to compare and screen circulating microRNAs targeting LIGHT as diagnostic biomarkers during asthma attack through microRNA microarray and Real Time PCR assay. Methods: Serum from 40 patients with asthma attack and 20 normal subjects was collected to detect circulating microRNAs expression profile through miRNA microarray. It is revealed that the significant differences of microRNAs level between asthmatic patients and normal controls. Target gene predictive analysis of differentially expressing microRNAs was performed to screen the miRNAs targeting LIGHT gene basing on the TargetScan bioinformatics software. Real Time PCR was conducted to further verify the realiability of the miRNA microassay and the screened specific miRNAs targeting LIGHT. Results: Asthmatic patients had a significant upper expression of miR-512-3p, miR-513b-5p, miR-5691 and lower level of miR-107, miR-140-5p, miR-17-5p compared with healthy subjects. The level of miR-140-5p and miR-107 in plasma of asthmatic patients were tightly correlated with their eosinophilic inflammation. The plasma miR-140-5p and miR-107 were needed to perform further investigation to evaluate the role as biomarkers in diagnosis of asthma.

overall_design: The serum from Mild asthmatic patient group, moderate to severe asthmatic subject group and age- and sex-matched healthy control group (n=5 in each group) were enrolled as experimental subjects of microRNAs microarray.

first: Junjie

last: Dai

first: Yujie

last: Du


title: Next Generation Sequencing Facilitates Transcriptomes Quantitative Analysis of N2A cells transfected with the plasmids respectively encoding RfxCas13d/dRfxCas13d and crRNA.

summary: To determine what effect the collateral activity of RfxCas13d has on N2acells. The plasmids encoding RfxCas13d/dRfxCas13d and crRNA were transfected into N2a cells. After 48 hours of transfection, GFP-positive cells were collected using FCAS and extracted for total RNA. Then, we analyzed the transcriptome of each group with RNA-seq and analyzed the differential genes among the groups.

overall_design: mRNA profiles of N2A cells transfected with the plasmids respectively encoding RfxCas13d/dRfxCas13d and crRNA.


title: Effects on gene expression by Aff3-deficiency

city: Tokushima

first: Koji

last: Yasutomo

address: 3-18-15 Kuramoto-cho

department: Graduate school of Biomedical Sciences

country: Japan

institute: Tokushima University

summary: To analyze the effect of Aff3-deficeincy on gene expression in B cells, we employed cDNA microarray analysis. The data indicated that the deficiency altered the expressions of very limited number of genes.

overall_design: CD43-negative B cells were purified from Aff3+/- or Aff3-/- mouse spleen, and cultured in the presence of 10 ug/mL LPS and 10 ng/mL IL-4 for 3 days, and total RNA was extracted from these cells and used for the analysis.

first: Shin-ichi

last: TSUKUMO

last: YASUTOMO


title: Comprehensive comparison of adaptive immune response by inactivated SARS-CoV-2 vaccine between young and old

city: Guangzhou

first: Lipeng

last: Mao

state: Guangdong

address: No.601, West Huangpu Avenue

department: Department of Microbiology and Immunology

institute: Jinan University

summary:
Purpose:  Construction of a SARSCoV2 vaccine TCR specific machine learning model using single-cell TCR technology sequencing
Methods：PBMCs were isolated from peripheral venous blood of HLA-A2+ healthy donors. PBMCs were incubated with antibody cocktail and then RapidSpheres, then the magnet was applied and unbound CD8+ T cells were recovered from the supernatant. According to the above method of CD8+ T activation, CD8+ T cells specific for ancestral epitopes were obtained by stimulating with the corresponding mutant ancestral peptides. Activation-specific CD8+ T cells were labeled with tetramers-PE and CD8-APC and then sorted out by flow cytometer FACS Canto (BD). The following protocol describes surface protein staining with hashtag antibodies for protein detection outside of the single cell V(D)J signature barcoding technique for differentiating CD8+ T cells with different epitope specificities after mixing up samples. The following is the hashtag information corresponding to the ancestral epitopes of the mutant strains. B.1.1.7 corresponds to the ancestral epitope ORF1a 1707-16 , ORF1a 2225-34 , ORF1a 2230-38. B.1.617.2 corresponds to the ancestral epitope M 82-90 . B.1.617.3 corresponds to the ancestral epitope ORF1a 2240-49, ORF1a 3683-92 , and ancestral epitope S 2-11 of B.1.526.2 without labeled hashtag protein. Cell number and viability were checked after surface protein hashtag staining (cell viability > 80%). Then droplet-encapsulation single-cell sequencing experiments were performed, and 10,000 living single cells were loaded onto each of the Chromium Controller (10x Genomics). After droplet-encapsulation, single-cell cDNA synthesis, amplification and sequencing libraries were generated using Chromium Single Cell 5' Feature Barcode Library Kit (10x Genomics),Chromium
The result showed the inactivated vaccine is less protective in older adults, who take longer to develop effective antibodies, and the TCR diversity of each epitope specific repertoire decreased in the elderly. In addition, we found inactivated vaccines could stimulate the proliferation of related B cells in the body, thereby reducing the diversity of BCR in the body. Compared with the young, the elderly is less likely to produce antibody related BCR clones and the same is true for TCR diversity.
Conclusions: The result showed the inactivated vaccine is less protective in older adults, who take longer to develop effective antibodies, and the TCR diversity of each epitope specific repertoire decreased in the elderly. In addition, we found inactivated vaccines could stimulate the proliferation of related B cells in the body, thereby reducing the diversity of BCR in the body. Compared with the young, the elderly is less likely to produce antibody related BCR clones and the same is true for TCR diversity.

overall_design: single-cell RNA-seq and TCR-seq

first: Chanchan

last: Xiao


title: Uterine epithelial Gp130 orchestrates hormone response and epithelial remodeling for successful embryo attachment in mice

city: Sagamihara

first: Junya

last: Ito

state: Kanagawa

address: 1-17-71 Fuchinobe, Chuo-ku

department: School of Veterinary Medicine

institute: Azabu University

summary: To investigate the molecular mechanism underlying Gp130-mediated LIF signaling in the endometrium during embryo implantation, we generated mice with uterine epithelium-specific deletion of Gp130.  We report the sequencing of the uterine transcriptome of control and uterine epithelium-specific Gp130-deficient mice at day 4 (1600h) of pregnancy.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for murine endometrium at day 4 (1600h) of pregnancy between control and uterine epithelium-specific Gp130-deficient mice.

first: Takafumi

last: Namiki

first: Jumpei

last: Terakawa

first: Hironobu

last: Murakami


title: STAT5BN642H is a driver mutation for T-cell neoplasia (RRBS)

city: Wien

first: Ha T T

last: Pham

address: SCHWARZSPANIERSTR 17

country: Austria

institute: Ludwig Boltzmann Institute for Cancer Research

type: Methylation profiling by high throughput sequencing

summary: The most frequent mutation in STAT5B is the Asp642His (N642H) mutation that was found in >90 leukemic/lymphoma patients. The development of novel treatment against STAT5BN642H has been hindered by the unavailability of a suitable model and the lack of the direct causal effect of STAT5BN642H on T-cell neoplasia development. We herein demonstrate that mice expressing human STAT5BN642H in the hematopoietic compartment rapidly develop leukemia/lymphoma. The disease is fully transplantable and characterized by the expansion of CD8+ T-cells. hSTAT5BN642H displays persistent and enhanced tyrosine phosphorylation upon cytokine stimulation. This leads to drastic changes in the gene expression profile accompanied by specific alterations in DNA methylation patterns that result in the acceleration of cell cycle progression. hSTAT5BN642H transcriptional activities in T-cell can be inhibited by inhibition of upstream kinases or transcriptional coregulaters, including JAKs, HDACs and BET Bromodomain containing protein. In particular, treatment with ruxolitinib, a JAK kinase inhibitor dramatically reduced tyrosine phosphorylation of hSTAT5BN642H resulting in decreased organ infiltration in vivo. We conclude that hSTAT5BN642H is sufficient to cause leukemia in vivo and JAK inhibitors are potential therapy for leukemic patients with the hSTAT5BN642H.

overall_design: DNA methylation profiling by RRBS of CD8+ T cells from  2 wild-type (WT), 2 transgenic hSTAT5B, and 2x transgenic hSTAT5N642H mutant mice, RRBS with 50 bp single-end libraries sequenced on HiSeq 3000/4000 (Illumina)

first: Ha

middle: T

first: Barbara

last: Maurer

first: Florian

last: Halbritter

first: Matthias

last: Farlik

first: Christoph

last: Bock

first: Richard

last: Moriggl


title: Ribo-seq of decitabine-treated WT HL-60 cells

first: Abolfazl

last: Arab

summary: Ribolog was used to compare translational efficiency across conditions (https://github.com/goodarzilab/Ribolog). Briefly, Ribolog applies a logistic regression to model individual Ribo-seq and RNA-seq reads in order to provide estimates of logTER (i.e., logFC in TE) and its associated p-value across the coding transcriptome.

overall_design: Ribosome profiling was performed as previously described (PMID: 28579404) on HL-60 cells treated with DMSO or decitabine.

first: Albertas

last: Navickas

first: Alex

last: Ge

first: Hani

last: Goodarzi

first: Hosseinali

last: Asgharian


title: PD-1 blockade and CDK4/6 inhibition augment nonoverlapping features of T cell activation in metastatic cancer

city: Boston

first: Stephanie

last: Dougan

state: MA

address: 1 Jimmy Fund Way

department: Cancer Immunology & Virology

institute: Dana-Farber Cancer Institute

summary: We performed single-cell RNA-sequencing and T-cell receptor clonotype tracking of breast and ovarian cancer patients treated with the CDK4/6 inhibitor ribociclib and PD-1 blockade. We identified evidence of two orthogonal treatment-associated phenomena: expansion of T cell effector populations and promotion of T cell memory formation.

overall_design: Peripheral blood mononuclear cells (PBMCs) from metastatic breast (n = 5) and ovarian (n = 1) cancer patients were isolated before and after combination treatment with the CDK4/6 inhibitor ribociclib and an anti-PD1 monoclonal antibody. Tumor-infiltrating lymphocytes were also obtained. T cells were sorted by flow cytometry from those samples and subjected to single-cell RNA-sequencing and single-cell TCR-sequencing.

first: Lestat

middle: R

last: Ali

first: Ana

last: Garrido-Castro

first: Patrick

middle: J

last: Lenehan

first: Naima

last: Bollenrucher

first: Courtney

last: Stump

first: Michael

first: Shom

last: Goel

first: Geoffrey

middle: I

last: Shapiro

first: Sara

middle: M

last: Tolaney

middle: K


title: MeRIP-seq of decitabine-treated WT HL-60 cells

summary: We performed data preprocessing, m6A peak calling, motif analysis, meta-gene plotting, and differential RNA methylation analysis using multiple tools. Scripts are publically avalible https://github.com/abearab/imRIP.

overall_design: We performed MeRIP-seq as previously described (PMID: 30212448) on HL-60 cells treated with decitabine or DMSO.


title: Comprehensive comparison of adaptive immune response by inactivated SARS-CoV-2 vaccine between young and old [RNA-seq]

first: Lipeng

last: Mao

summary:
Purpose:Comprehensively compared the adaptive immune response of SARS-CoV-2 inactivated vaccines in young and elderly.

Methods:CD8+ T, CD4+ T and B cells were purified from PBMCs with EasySep Human  positive/negative selection . PBMCs were incubated with antibody cocktail and then RapidSpheres, then the magnet was applied and unbound CD8+ T, CD4+ T and B cells were recovered from the supernatant. Briefly, the cells were stained with the corresponding CD8+ T, CD4+ T and B-cell  antibodies for 30 minutes at 4°C in the dark, and the purity of the cells was detected separately by flow cytometry, and all could reach more than 95%. Total RNA was isolated from CD8+ T, CD4+ T and B cells of 3 young and older people using TRIzol Reagent (Invitrogen)  (7-days post second vaccination dose) . RNA purity was checked by the NanoPhotomerer spectrophotometer (IMPLEN), and integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies). Then cDNA libraries were constructed using 0.1 µg RNA per sample with the NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia). After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 250 bp paired-end reads were generated.

The result showed the inactivated vaccine is less protective in older adults, who take longer to develop effective antibodies, and the TCR diversity of each epitope specific repertoire decreased in the elderly. In addition, we found inactivated vaccines could stimulate the proliferation of related B cells in the body, thereby reducing the diversity of BCR in the body. Compared with the young, the elderly is less likely to produce antibody related BCR clones and the same is true for TCR diversity.
Conclusions: The result showed the inactivated vaccine is less protective in older adults, who take longer to develop effective antibodies, and the TCR diversity of each epitope specific repertoire decreased in the elderly. In addition, we found inactivated vaccines could stimulate the proliferation of related B cells in the body, thereby reducing the diversity of BCR in the body. Compared with the young, the elderly is less likely to produce antibody related BCR clones and the same is true for TCR diversity.

overall_design: A total of 36 fastq files from the young and old, pre- and post- vaccine of CD4+ T, CD8+ T and B cells were finally got.

first: Chanchan

last: Xiao

first: Zhiyao

last: Ren

first: Bei

last: Zhang


title: Expression profiling of invasion associated molecules in head and neck cancer cells

city: Taoyuan

first: Ann-Joy

last: Cheng

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

country: Taiwan

institute: CGU

summary:
Three isogenic HNC cell sublines with highly invasive properties were established. Invasion-associated genes were identified by comparison of transcriptomic profiles between HNC parental cell lines and the invasive sublines via Affymetrix cDNA microarrays.
We used cDNA microarray to compare gene expression of invasion subline cells  and parental cells in head and neck cancer.

overall_design: Invasion subline cells and parental cells

first: Yin-Ju

last: Chen

first: Guo-Rung

last: You

first: Joseph

last: Chang

first: Chun-Yu

last: Huang


title: RNA-Sequencing of Transaldolase and Aldose Reducatase Deficiency in Mouse Liver

city: Syracuse

first: Frank

middle: A

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

summary: Oxidative stress modulates carcinogenesis in the liver; however, direct evidence for metabolic control of oxidative stress during pathogenesis, particularly, of progression from cirrhosis to hepatocellular carcinoma (HCC), has been lacking. Deficiency of transaldolase (TAL), a ratelimiting enzyme of the non-oxidative branch of the pentose phosphate pathway (PPP), elicits growth restriction, and predisposes to cirrhosis and HCC in mice and humans. Here, we show that mitochondrial oxidative stress and disease progression from cirrhosis to HCC and acetaminophen-induced liver necrosis are critically dependent on NADPH depletion by aldose reductase (AR), while this enzyme protects from carbon trapping in the PPP and stunted growth in TAL deficiency. Both TAL and AR are confined to the cytosol, however, their inactivation distorts NADPH production and mitochondrial oxidative stress into opposite directions.

overall_design: Adult mice with heterozygous deletion of transaldolase (TAL+/-) were created and fully backcrossed for >10 generations onto the C57BL/6 strain. TAL+/- and Akr1b3-deficient aldose reductase (AR) knockout (ARKO) strains were crossed to generate double-knockout (DKO) mice lacking both TAL and AR. Both TAL-deficient and DKO mice were breed as heterozygotes for the TAL locus. Wild-type (WT or TAL+/+AR+/+), TAL-deficient (TALKO or TAL-/-AR+/+), AR-deficient (ARKO or TAL+/+AR-/-), and double-knockout (DKO, or TAL-/-AR-/-) mice were matched for age and gender in each experiments. Livers were harvested from adult mice and RNA processed for RNA-Sequencing.

first: Zachary

last: Oaks

first: Andras

last: Perl


title: Epigenetic profiling reveals developmental traits of adult thymus-derived Vγ4+ γδ T cells

city: Hannover

first: Tao

last: Yang

address: Carl-Neuberg-Straße 1

institute: Hannover Medical School

summary: Recent advances in next-generation sequencing technologies elucidated gene regulatory networks and TCR signaling molecules underlying functional differentiation into γδ1 and γδ17 cells that now provide valid resources to define developing CD24+ γδ, γδ1 and γδ17 cells. The γδ1 cell subsets express key transcription factors of cytotoxicity and IFNγ-production, such as Tbx21 (encoding T-bet) and Eomes, as well as natural killer receptor (NKRs). Development of γδ17 cells is favorable in the early life period, regulated by Notch signaling and a network of transcriptional regulators including cMaf, Sox13, Blk, and Rorc that are essential for functional differentiation. However, detailed knowledge about molecular programs of Vγ4 cells, including their potential to become γδ1 or γδ17 cells during adult thymus development, is lacking. Here we employed transcriptional and epigenetic analysis of Vγ4 cells under steady-state conditions and after induction of de novo T cell development from adult thymus precursor cells.

overall_design: Sort Vγ4 γδT cells from thymus and peripheral lymph nodes, then do 5'-RNA single cell sequencing and Single cell ATAC-seq (10x genomics)

first: Sarina

last: Ravens


title: Time-series RNA-seq of decitabine-treated WT HL-60 cells

first: Abolfazl

last: Arab

overall_design: We assessed differential RNA expression and stability by treatment condition (decitabine and DMSO) and time (6, 72 and 120 hours).

first: Alex

last: Ge


title: Fox Family Protein Jumu Reads 6mA-DNA Codes and Contributes to Zygotic Gene Activation

first: Shunmin

last: He

address: 1 Beichen West Road,  Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

summary: N6-methyladenine (6mA) DNA modification in eukaryotic genomes has emerged as a potential epigenetic mark. However, little is known about how 6mA epigenetic codes are read and interpreted in higher eukaryotes. Here we investigate 6mA genome-wide distributions in multiple higher eukaryotes. Using Drosophila as a pioneer system, we show that 6mA exhibits defined patterns and preferentially marks zygotic genes in early embryos. Moreover, we identify that the Fox-family protein, Jumu, is a "6mA-DNA reader" and functions in concert with DMAD to contribute to zygotic gene activation. Further methylome analysis reveals that 6mA modification has common features in genomic DNA from mouse, rat and monkey, and that "forkhead-domain-binding motifs" are enriched in 6mA-marked DNA of these genomes, in a way similar to Drosophila. Collectively, our findings identify the 6mA DNA reader protein and suggest a conserved 6mA-based mechanism in higher eukaryotes.

sample_organism:
Drosophila melanogaster
Macaca mulatta
Mus musculus
Rattus norvegicus

overall_design:
SMRTseq data of DMAD knock down fly head
mRNA profiles of different stages (0.75h, 3h, 6h), DMAD knockdown( dsRNA(DMAD) ), Jumu knockdown( dsRNA(DMAD) ) and control ( dsRNA(GFP) ) embryos were generated by deep sequencing, using Illumina Hiseq2500.
Different stages and tissues of four species 6mA were generated by deep sequencing, using Illumina Hiseq2500.

first: Guoqiang

first: Jiajia

last: Wang

first: Yajie

last: Gao

first: Zhenping

first: Xiudeng

last: Zheng

first: Weini

last: Li

first: Jiao

last: Yuan

first: Yuewan

last: Luo

first: Xiaona

first: Wenxin

first: Peng

first: Chuan

first: Yi

last: Tao

first: Qinmiao

last: Sun

first: Dahua


title: Multi-omics profiling visualizes dynamics of cardiac development and functions [ChIP-Seq]

city: Nanjing

first: Jimiao

address: 101Longmian Avenue, Jiangning District, Nanjing 211166, P.R. China

institute: Nanjing Medical University

summary:
Cardiogenesis is a tightly-regulated dynamic process through a continuum of differentiation and proliferation events. Transcriptional activation is the predominant early step for initiating cardiac formation in mammals.
We then applied ChIP-seq analysis against histone modifications H3K4me1, H3K4me3, H3K27ac and RNAPol II in E10.5 mouse hearts to evaluate the instant activity of transcription factors, which is believed to serve as a powerful tool to study regulatory processes.

overall_design: ChIP-seq for the histone modifications H3K4me1, H3K4me3, H3K27ac and RNA pol II of mice hearts from embryonic day 10.5.

first: Yayun

last: Gu

first: Yan

last: Zhou

first: Jiani

last: Xu


title: Targeting Menin disrupts the KMT2A/B and polycomb balance to paradoxically activate bivalent genes [CRISPR]

city: Melbourne

first: Mark

last: Dawson

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

summary: Precise dynamic control of activating H3K4me3 and repressive H3K27me3 histone modifications at bivalent gene promoters is essential for normal development and frequently corrupted in cancer. Using whole genome CRISPR/Cas9 screens we identify specific roles for MTF2-PRC2.1 and PCGF1-PRC1.1 polycomb complexes, and MLL1/2-COMPASS-like complex components in maintaining bivalency. Contrary to expectations, loss of Menin or inhibition of the Menin-MLL1/2 interaction, induces activation of bivalent genes via loss of polycomb-mediated repression and defines distinct roles for MLL1/2 and Menin in gene regulation. Whilst Menin and MLL1/2 contribute to maintenance H3K4me3 at active genes, a separate Menin-independent function of MLL1/2 opposes polycomb mediated repression at bivalent genes. MLL1/2 are essential for basal transcription and, although dispensable for transcription factor driven activation, facilitate transcriptional consistency during dynamic changes in gene expression. This functional partitioning of COMPASS complex components reveals therapeutic opportunities to target oncogenic and immunosuppressive functions of PRC2 through pharmacological inhibition of Menin.

overall_design: CRISPR screen for MHC low or high cells

first: Christina

last: Sparbier

first: Marian

middle: L

last: Burr


title: YM155 in combination with EZH2 inhibiton induces synthetic lethality

city: Memphis

first: JUN

last: YANG

state: TN

address: 262 Danny Thomas Place

department: Surgery

institute: St Jude Children's Research Hospital

summary:
EZH2 inhibitors have been developed to treat certain cancers. To maximize the anticancer acttivity of EZH2 inhibition, we combined an EZH2 inhibitor EPZ6438 with YM155, which leads to dramatic cell death.
We used microarrays to detail the global gene expression profiles.

overall_design: BE2C cells treated with either 5uM EPZ6438, 5nm YM155 or combination of EPZ6438 and YM155 for 8hours and 12hours. RNA were extracted by Rneasy kit from QIAGEN, which were subject to Affymetrix hybridization with GeneChip™ Human Gene 2.0 ST Array.

first: Jun

last: Yang


title: High-throughput sequencing analysis of the gene expression regulated by Rhox6 knockdown in mouse embryonic stem cells

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

institute: Anhui University

summary: Purpose:The goals of this study is to analyze the candidate genes motified by Rhox6 knockdown to promote the mouse embryonic stem cell (ESC) self-renewal through High-throughput sequencing.

overall_design: 46C mouse ESCs infected with Scramble control and Rhox6 shRNA lentiviruses and cultured in serum-containing medium for 24h were collected by using Trizol. Two repeat groups were set for each treatment group. These samples were sent to MajorBIO (Shanghai, China) company to do deep sequencing by using illumina Hiseq.

first: Shoudong

last: Ye


title: Runx1 Controls Auditory Sensory Neuron Diversity (CKO)

first: Brikha

middle: Raj

last: Shrestha

address: 243 Charles Street

department: Otolaryngology

institute: Harvard Medical School

summary: As the primary sensory neurons of the auditory system, Type I spiral ganglion neurons (SGNs) encode sound stimulus properties critical for the formation of auditory percept in higher brain areas. Their functional heterogeneity is thought to contribute to our ability to hear a wide range of sound intensities and against background noise, but how SGN diversity arises during development is poorly understood. Here we studied the role of the transcription factor Runx1 in establishing SGN heterogeneity in the mouse cochlea by single cell RNA-sequencing.

overall_design: Runx1 expression was ablated embryonically in SGNs using  mice bearing a floxed Runx1 allele, tdTomato transgene and the bhlhb5-Cre transgene. Cochlear tissues, including spiral ganglia, were harvested from mice of both sexes at P30-P33 and single cell suspensions were created using collagenase and papain for enzymatic dissociation. After fluorescence-activated cell sorting for enrichment of tdTomato+ SGNs, dual-indexed single cell transcriptomic libraries were then created using the 10X Genomics Chromium Single Cell 3' GEM Library and Gel Bead Kit v3. Libraries were sequenced using the NextSeq 500/550 High Output Kit v2.5 (75 Cycles, Illumina).


title: Targeting Menin disrupts the KMT2A/B and polycomb balance to paradoxically activate bivalent genes [CUT&TAG]

summary: Precise control of activating H3K4me3 and repressive H3K27me3 histone modifications at bivalent promoters is essential for normal development and is frequently corrupted in cancer. By coupling a cell surface readout of bivalent MHC class I gene expression with whole genome CRISPR/Cas9 screens, we identify specific roles for MTF2-PRC2.1, PCGF1-PRC1.1 and Menin- KMT2A/B complexes in maintaining bivalency. Unexpectedly, genetic loss or pharmacological inhibition of Menin phenocopies the effects of polycomb disruption, resulting in derepression of bivalent genes in both cancer cells and pluripotent stem cells. Whilst Menin and KMT2A/B contribute to H3K4me3 at active genes, a separate Menin-independent function of KMT2A/B maintains H3K4me3 and opposes polycomb-mediated repression at bivalent genes. Release of KMT2A from active genes following Menin targeting alters the balance of polycomb and KMT2A at bivalent genes, facilitating gene activation. This functional partitioning of Menin-KMT2A/B complex components reveals novel therapeutic opportunities that can be leveraged through inhibition of Menin.

overall_design:
CUT&TAG for H3K4me3, H3K27me3 and H2AK119 in K562 Cas9 expressing, MEN1 KO, EED KO and PCGF1 KO cells.
CUT&TAG for: 1) H3K4me3, H3K27me3 and H2AK119 in K562 Control sgRNA, MTF2 sgRNA and AEBP2 sgRNA cells; 2) H3K4me3 in K562 Cas9 expressing and KMT2A/B KO cells pre-treated with EZH2i +/- interferon gamma.
CUT&RUN for MLL1 in K562 Cas9 expressing and MEN1 KO cells.

first: Andrea

last: Gillespie

first: Enid

last: Lam


title: Multi-omics profiling visualizes dynamics of cardiac development and functions

last: Gao

summary: The function and phenotype transitions of heart may be specific to one or other chamber. To provide the omics data sets from chambers separately, we conducted spatial transcriptomics of E10.5 hearts to identify unique gene profiles that correspond to distinct anatomical regions in early cardiac development. We obtained curated expression data consisting of 6,798 genes across 332 individual capture spots. We then performed differential gene expression (DGE) analysis between anatomical regions and gene set enrichment analysis of each cluster’s upregulated genes to characterize identified clusters in early cardiogenesis.

overall_design: 10X Visium was used to create a transcriptomic atlas of mouse embryonic day 10.5 heart.


title: Runx1 Controls Auditory Sensory Neuron Diversity (iCKO)

overall_design: Runx1 expression was ablated postnatally in SGNs using mice bearing a floxed Runx1 allele, tdtomato transgene and the tamoxifen-inducible Runx1-CreER transgene. Mice were injected with Tamoxifen at P1, then cochlear tissues, including spiral ganglia, were harvested from mice of both sexes at P27-P29 and single cell suspensions were created using collagenase and papain for enzymatic dissociation. After fluorescence-activated cell sorting for enrichment of tdTomato+ SGNs, dual-indexed single cell transcriptomic libraries were then created using the 10X Genomics Chromium Single Cell 3' GEM Library and Gel Bead Kit v3. Libraries were sequenced using the NextSeq 500/550 High Output Kit v2.5 (75 Cycles, Illumina).


title: Targeting Menin disrupts the KMT2A/B and polycomb balance to paradoxically activate bivalent genes

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

overall_design: Refer to individual Series


title: Microarray analysis of wild-type (WT; Ler-0) and smn2-90 mutants to identify SMN2-regulated defense-related genes

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

institute: Kanazawa University

summary: Transcriptome analysis to identify genes up- and down-regulated genes in smn2-90 mutant compared with WT plants with or without flg22 elicitation.

overall_design: In total 8 samples (Two biological replicates of uninoculated WT and  smn2-90 mutant plant, flg22-treted WT and  smn2-90 mutant plant) were used

first: Kazuya

last: Ichimura

first: Momoko

last: Takagi


first: Jimiao

summary:
Cardiogenesis is a tightly-regulated dynamic process through a continuum of differentiation and proliferation events. Key factors and pathways governing this process remains incompletely understood.
Thus, we conducted bulk RNA-seq of mice hearts from embryonic day 10.5 to postnatal week 8 to investigate the gene expression changes.

overall_design: RNA-Seq analysis of mice hearts from embryonic day 10.5 to postnatal week 8

last: Gu


title: Peripheral blood immune cell profiles of corneal transplant with and without acute rejection

city: Edinburgh

first: Max

last: Bylesjo

state: Scotland

address: BioCube 1, Edinburgh BioQuarter, 13 Little France Road

country: United Kingdom

institute: Fios Genomics Ltd

summary: Acute rejection (AR) of corneal transplants (CT) has a profound effect on subsequent graft survival but detailed immunological studies in human CT recipients are lacking. In this multi-site, cross-sectional study, clinical details and blood samples were collected from adults with clinically-diagnosed AR of full thickness (FT)-CT (n=35) and posterior lamellar (PL)-CT (n=21) along with Stable CT recipients (n=177) and adults with non-transplanted corneal disease (n=40). For those with AR, additional samples were collected 3 months later. Immune cell analysis was performed by whole-genome microarrays (whole blood) and high dimensional multi-color flow cytometry (peripheral blood mononuclear cells). For both, no activation signature was identified within the B cell and T cell repertoire at the time of AR diagnosis. Nonetheless, in FT- but not PL-CT recipients, AR was associated with differences in B cell maturity and regulatory CD4+ T-cell frequency compared to stable allografts. Our results suggest that, in contrast to solid organ transplants, genetic or cellular assays of peripheral blood are unlikely to be clinically exploitable for prediction or diagnosis of AR. However, further investigation of circulating B cell and T cell subpopulations may provide insights into the regulation of anti-donor immune response in human CT recipients with differing AR risk.

overall_design: Microarray gene expression profiling of a subset of 330 samples from 263 corneal transplant (CT) patients and 28 healthy volunteers (301 subjects total) was performed using Affymetrix Clariom S arrays. Corneal transplants were either full thickness (FT) or posterior lamellar (PL). Differential expression analysis of transcriptomic profiles from samples taken at the enrolment visit (baseline) was performed comparing FT-CT and PL-CT patients with Acute Rejection (n=34) to those with stable CTs (n=87). In addition, a paired comparison was performed between FT-CT patients with acute rejection sampled at the time of acute rejection diagnosis relative to 3 months after (13 pairs).

first: Jesper

last: Hjortdal

first: Matthew

last: Griffin

first: Marion

last: Cadoux

first: W

last: Armitage

first: Peadar

last: Mac Gabhann

first: Conor

last: Murphy

first: Uwe

last: Pleyer

first: Derek

last: Tole

first: Bertrand

last: Vabres

first: Malcolm

last: Walkinshaw

first: Pierre-Antoine

last: Gourraud

first: Matilde

last: Karakachoff

first: Sophie

last: Brouard

first: Nicolas

last: Degauque


title: Role of epigenetic therapy in the modulation of tumor growth and migration in human castration resistance prostate cancer cells with neuroendocrine differentiation

city: Bologna

first: Maria Giulia

last: Bacalini

address: Via Altura 3

department: Brain Aging Laboratory

country: Italy

institute: IRCCS Istituto delle Scienze Neurologiche di Bologna

type: Methylation profiling by genome tiling array

summary: Neuroendocrine transdifferentiation (NED) of prostate cancer cells and aberrant activation of survival pathways involved in tumorigenesis are among the events that lead to the development of resistance to anti-androgen therapy and are associated with poor prognosis in patients with castration resistance prostate cancer (CRPC).  Most of these molecular events appear to be mediated by epigenetic mechanisms, in particular DNA methylation. In this study, we evaluated the antitumor activity and epigenetic modulation of two epigenetic drugs, 5-aza-2’-deoxycytidine (AZA) and S-adenosylmethionine (SAM) in two human CRPC cell lines with NED (NED-CRPC), DU-145 and PC-3. The effects of AZA and SAM on the cell growth proliferation, cell cycle, apoptosis, migration and genome-wide DNA methylation profiling have been evaluated through MTT assay, DNA flow cytometry with propidium iodide, and Annexin V-FITC/propidium iodide staining, wound-healing assay and Infinium450k microarray, respectively. Both epigenetic drugs showed a prominent antitumor activity in NED-CRPC cell line exerted through perturbation of cell cycle progression, induction of apoptosis and migration arrest. AZA and SAM reversed NED in DU-145 and PC-3, respectively. Moreover, AZA treatment profoundly modified DNA methylation pattern, sustaining a pervasive hypomethylation of the genome, with a relevant effect on several pathways involved in regulation of cell migration, cell proliferation and apoptosis. Among these, the Wnt/beta-catenin signaling appeared to be the most directly involved. In conclusion, both AZA and SAM showed a relevant antitumor activity on NED-CRPC cell lines. This opens a new scenario in the therapy of this lethal variant of prostate cancer.

overall_design: DU-145 cells were treated with 10-4M AZA or 2.5*10-4M SAM

first: Alessandra

last: Dicitore

first: Davide

last: Gentilini

first: Maria-Giulia

first: Giovanni

last: Vitale


title: Spatial landscapes of the fed, fasted and refed livers from C57BL/6J mice - spatial transcriptomics

status: Public on Jan 12 2023

city: Jinan

first: Yuan

last: Detian

email: yuandt@sdu.edu.cn, lishiyang@sdu.edu.cn

address: Wenhuaxi Road 44

institute: Shandong University

summary: Spatial heterogeneity and plasticity of the mammalian liver is critical for systemic metabolic homeostasis in response to fluctuating nutritional status. Here, we generated a high-resolution transcriptomic landscape of the livers from mice that were either fed chow (fed), fasted for 18 h (fasted), or fasted for 18 h and then refed for 6 h (refed) using spatial transcriptomics (ST) and quantified changes in gene expression. This work provides a critical foundation for future mechanistic studies of liver metabolic heterogeneity and plasticity, and will help to understand the zonated pathology during liver disease progression.

overall_design: The livers from C57BL/6J mice that were either fed chow (fed), fasted for 16 h (fasted), or fasted for 16 h and then refed for 6 h (refed) were subject to 10x Visium spatial transcriptomics.

first: Shiguan

last: Wang

first: Bowen

last: Xu

first: Peng

last: Zhang

first: Detian

last: Yuan


title: Targeting Menin disrupts the KMT2A/B and polycomb balance to paradoxically activate bivalent genes [RNA-seq]

first: Mark

last: Dawson

overall_design: RNAseq of K562 cells with treatment with MENIN inhibitor or CRISPR KO for EED, MEN1 or PSIP1

first: Christina

last: Sparbier

first: Marian

last: Burr


title: AmpliSeq transcriptome profiling of human adipose tissue senescent progenitor cells

city: Toulouse

first: Anne

last: Bouloumie

address: 1 avenue du Pr Jean Poulhès

country: France

institute: Inserm

summary: Transcriptomic profile of human adipose tissue progenitor cells was performed as follows. For AmpliSeq transcriptome sequencing library construction,  AmpliSeq™ Library PLUS, AmpliSeq Transcriptome Human Gene Expression Panel and AmpliSeq CD indexes SetA kits were purchased from Illumina and sequencing libraries were constructed as described in AmpliSeq for Illumina Transcriptome Human Gene Expression Panel reference guide (Illumina). Equimolar concentrations of libraries were pooled at 4 nM and denatured and diluted as described in Denature and Dilute Libraries Guide (Illumina) and adjusted to final concentration of 1.4 pM. Resulting library was sequenced on NextSeq 500 using NextSeq 500/550 High Output v2 kit with 2 X 151 bp cycle. Generated raw files were converted to FASTQ files and used for data analysis. AmpliSeq transcriptome FASTQ files were analyzed on Array studio V10.0 (Omicsoft, Qiagen). Following raw read QC, first and last 10 bases were trimmed and mapped to reference genome Human.B38. The read count data was generated using GeneModel RefGene20170606. Resulting data was normalized by DESeq package, transformed to log2 value and used for ANOVA analyses.

overall_design: Transcriptomic profiling of immuno-selected progenitor cells from subcutaneous adipose tissue derived from 3 patients (3X3=9 samples) at passage 1, passage 6 and at passage 1 treated with H2O2 .

first: Valentin

last: Jargaud

first: Yaligara

last: Veeranagouda

first: Michel

last: Didier

first: Jean-Claude

last: Guillemot

last: Bouloumié

first: Nathalie

last: Boulet

last: Rémaury


title: Targeting Menin disrupts the KMT2A/B and polycomb balance to paradoxically activate bivalent genes [ChIP-seq]

overall_design:
ChIPseq for H3K4me3, SUZ12 and MENIN in MENIN KO, or MEN inhibitor treated K562 cells.
ChIPseq for MLL1 in embyonic stem cell line H9 pre-treated with DMSO, Menin inhibitor, EZH2 inhibitor or both Menin and EZH2 inhibitors
ChIP-reChIP for H3K4me3 and H3K27me3 in K562 Cas9 cells.


title: Single cell RNA-sequencing reveals cellular heterogeneity and trajectories of wheat root tip.

city: Beijing

first: Zhen

middle: Zhen

last: Du

state: Beijing

address: No. 2, Yuanmingyuan West Road, Malianwa Street, Haidian DistrictNo. 2, Yuanmingyuan West Road, Malianwa Street, Haidian District

institute: Institute of Plant Protection,Chinese Academy of Agricultural Sciences

summary: We performed scRNA-seq to Chinese Spring (CS) cultiva of wheat, and captured 13,063 wheat (CS) root cells with 2523 mean UMIs, 43 417 mean reads and 1851 median genes per cell. One cell type was formed by clustered cells showing similar gene expression profiles. The dimensionality reduction algorithms used in this study are PCA (Principal Components Analysis) and t-SNE (t-distributed Stochastic Neighbor Embedding). Results of dimensionality reduction based on PCA are visualized by t-SNE for clustering, and the clustering algorithm adopts SNN to obtain the optimal cell clusters.Finally, we obtained 16 clusters.

overall_design: We performed scRNA-seq to analyze one sample root tip cells of hexaploid bread wheat (CS, Chinese Spring cultivar), without replicates and control, reference samples.

first: Zhenzhen

first: Huanyu

last: Jia

first: Bin

first: Han

last: Wong

first: Boming

last: Wu

first: Wanquan

last: Chen

first: Li

last: Gao


title: Androgen receptor variant 7 non-canonical genome integrity functions in prostate cancer

city: PHILADELPHIA

first: Adam

last: Ertel

address: 233 S 10TH ST

department: Cancer Biology

institute: Thomas Jefferson University

summary: Androgen receptor variant 7 (AR-V7) has been proposed to have independent functional roles different from full length AR. Here we study the functional roles of AR-V7 in chemotherapy castration resiatnt prostate cancer models by ChIp-sequencing approaches.

overall_design: AR-V7 Genome binding/occupancy profiling by high throughput ChIP-sequencing in prostate cancer cells.

first: Brittiny

last: Dhital

first: Sandra

last: Santasusagna

first: Peiyao

last: Li

first: Josep

last: Domingo-Domenech

first: Veronica

last: Rodriguez-Bravo


title: Long-Term Cell Fate and Functional Maintenance of Human Hepatocyte through Stepwise Culture Configuration

city: Los Angeles

first: Meng

address: 2003 Zonal Avenue

institute: University of Southern California

summary: Humanized Liver Chimeric Mice (HLCM)-derived human hepatocytes (HLCM-HH) were maintained in the absence (non-treatment; NT) or presence of either 2% DMSO or DMSO2 (140mM)-containing medium for 7 days. HepG2 cells and Huh7 cells were cultured with 2% DMSO containing medium for 7 days. Then total cellular RNA was extracted for the subsequent poly-A based mRNA sequencing analysis.

overall_design: Freshly isolated Humanized Liver Chimeric Mice (HLCM)-derived human hepatocytes (HLCM-HH) cultured with 2% DMSO containing media for 7 days were further maintained in the absence (non-treatment; NT) or presence of either 2% DMSO or DMSO2 (140mM)-containing medium for an additional 7 days. HepG2 cells and Huh7 cells were cultured with 2% DMSO containing medium for 7 days. Then total cellular RNA was extracted for the subsequent poly-A based mRNA sequencing analysis.

first: Takeshi

last: Saito


title: Plasma Time Course Feeding Study

city: Houston

first: David

state: TX

address: One Baylor Plaza Suite 400D

department: Molecular & Human Genetics

institute: BCM

type: Non-coding RNA profiling by high throughput sequencing

summary: Determine miRNA expression patterns in plasma of healthy individuals before and after consuming plant-based meals

overall_design: Fifteen study subjects were asked to fast then eat a meal provided by the study team.  Blood samples were collected either every 30 minutes or every hour.

first: Ryan

last: Spengler

first: Maria

last: Giraldez

first: Muneesh

last: Tewari


title: Superenhancer-driven lncRNA FASRL in hepatocellular carcinoma [RNA-seq]

city: Guangzhou

last: Peng

address: No. 107 Yanjiang West Road

institute: Sun Yat-Sen Memorial Hospital

summary: Superenhancers drive abnormal gene expression in tumors and promote malignancy. However, the relationship between superenhancer-associated lncRNA and abnormal metabolism is unknown.

overall_design: In this work, we aimed to investigate the specific mechanism by which superenhancer-related lncRNAs function in lipid metabolism in hepatocellular carcinoma.


title: Superenhancer-driven lncRNA FASRL in hepatocellular carcinoma [ChIP-seq]


title: Predictors of success in establishing orthotopic patient-derived xenograft models of triple negative breast cancer

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

summary: Triple negative breast cancer (TNBC) is an aggressive subtype of breast cancer, with approximately 50% of patients having residual disease after neoadjuvant chemotherapy (NACT) and worse prognosis with higher residual cancer burden (RCB). Patient-derived xenograft (PDX) models of breast cancer are an effective discovery platform and tool for preclinical pharmacologic testing and biomarker identification. There is a need for PDX models encompassing the heterogeneity of TNBC both pre- and post- therapy and for identifying clinical and molecular features of patient’s tumors that are associated with success in establishing these models.  Using fine-needle aspirates (FNAs), we established orthotopic PDX models of TNBC from the primary breast tumors of patients prior to and following neoadjuvant systemic therapy while enrolled in the ARTEMIS trial (NCT02276443). ARTEMIS is a prospective neoadjuvant clinical trial for women with primary TNBC who are treated with four cycles of Adriamycin combined with cyclophosphamide (AC) followed by taxane +/- different experimental therapies. Serial biopsies were obtained from patients prior to treatment (pre-therapy), from poorly responsive disease after four cycles of AC (mid-NACT), and in cases of AC-resistance, after a three-month course of different experimental therapies and/or additional chemotherapy (post-NACT). Our study cohort includes a total of 269 FNA biopsies from 217 women, generating a total of 62 successful PDX models (overall success-rate = 23%). This cohort includes five serial pre- and mid-NACT PDX pairs, as well as one serial pre-, mid-, post-NACT triplet. Success of PDX engraftment was generally higher from cancers that proved to be treatment-resistant: whether poor response to AC determined by ultrasound measurements mid-NACT (p=0.063), RCB II/III status after NACT (p=0.046), or metastatic relapse within two years of surgery (p=0.008). TNBC molecular subtype determined from gene expression microarrays of pre-NACT tumor revealed no significant association with PDX engraftment rate (p=0.877). Finally, we developed a statistical model predictive of PDX engraftment using percent Ki67 positive cells in the patient’s diagnostic biopsy, positive lymph node status at diagnosis, and low volumetric reduction of the patient’s tumor following AC treatment.  This novel bank of 62 PDX models of TNBC provides a valuable resource for biomarker discovery and preclinical therapeutic trials aimed at improving neoadjuvant response rates for patients with TNBC.

overall_design: We established 207 treatment-naïve patient-derived xenograft tumors from triple negative breast cancer tumors and profiled the gene expression profiles on Affymetrix microarrays.

first: Gloria

middle: V

last: Echeverria

first: Shirong

last: Cai

first: Yizheng

last: Tu

first: Jiansu

last: Shao

first: Emily

last: Powell

first: Abena

middle: B

last: Redwood

first: Yan

last: Jiang

first: Aaron

last: McCoy

first: Amanda

last: Rinkenbaugh

first: Rosanna

last: Lau

first: Alexander

last: Trevarton

first: Chunxiao

last: Fu

first: Rebekah

last: Gould

first: Elizabeth

last: Ravenberg

first: Lei

last: Huo

first: Rosalind

last: Candelaria

first: Lumarie

last: Santiago

first: Beatriz

last: Adrada

first: Deanna

last: Lane

first: Gaiane

last: Rauch

first: Wei

last: Yang

first: Jason

last: White

first: Stacy

last: Moulder

first: W

middle: F

last: Symmans

first: Susan

middle: G

last: Hilsenbeck

first: Helen

last: Piwnica-Worms


title: Geometric engineering of organoid culture for enhanced organogenesis in a dish

city: Philadelphia

first: Dan Dongeun

last: Huh

state: Pennsylvania

address: 210 South 33rd Street 315S Skirkanich Hall

institute: University of Pennsylvania

summary: Here we introduce a facile, scalable engineering approach to enable long-term development and maturation of organoids. We have redesigned the configuration of conventional organoid culture to develop a platform that converts single injections of stem cell suspensions to radial arrays of organoids that can be maintained for extended periods without the need for passaging. Using this system, we demonstrate accelerated production of intestinal organoids with significantly enhanced structural and functional maturity, and their continuous development for over 4 weeks. Furthermore, we present a patient-derived organoid model of inflammatory bowel disease (IBD) and its interrogation using single-cell RNA sequencing to demonstrate its ability to reproduce key pathological features of IBD. Finally, we describe the extension of our approach to engineer vascularized, perfusable human enteroids, which can be used to model innate immune responses in IBD. This work provides an immediately deployable platform technology towards engineering more realistic organ-like structures in a dish.

overall_design: Intestinal epithelial cells isolated from enteroids of the control and IBD patients were analyzed using scRNAseq.

first: Dan

first: Sunghee

last: Park


title: Transcriptome profiles of Snap29 knockout and wild-type mouse embryonic stem cells by RNA-seq analysis

city: NanJing

first: Yumei

last: Jia

address: Xiaolingwei Street, Xuanwu District, Nanjing

institute: NanJing Agricultral University

summary: Embryonic stem cells have the characteristics of self-renewal and pluripotent differentiation, and have broad application prospects in clinical practice. With the deepening of the research process, ESCs are expected to become the source of donor cells for regenerative medicine and cellular agriculture. Autophagy is a highly conserved catabolic process mediated by lysosomes in eukaryotic cells to meet cellular demands for metabolites and energy. Autophagy is a key process in maintaining cellular homeostasis by removing misfolded or aggregation-prone proteins and damaged organelles. Previous studies have reported that ATG3, ULK1, and other key factors in the formation stage of autophagosomes play a crucial role in maintaining the pluripotency of mouse embryonic stem cells. However, there are few reports on the regulation and molecular mechanism of SNARE proteins that mediate autophagosome-lysosome fusion, including Vamp8, Stx17, and Snap29, on the pluripotency of mESCs. The role of the SNARE protein Snap29 in regulating the self-renewal and pluripotent differentiation ability of mESC remains elusive. To better understand transcriptional landscape and signal transductions, we performed RNA-seq analysis of Snap29 knockout (KO) and wild-type (WT) mESCs at undifferentiated state and mESCs-derived-cells of differentiation .

overall_design: We sought to construct a mESCs cell line depleting of the autophagy-specific SNARE gene Snap29 by CRISPR/Cas9 technology. The molecular mechanism was explored through transcriptome analysis to better reveal the conditions of pluripotency maintenance. mESCs with biological triplicates were collected for RNA extraction and RNA-seq analysis simultaneously. We collected Snap29 knockout, wild-type mESCs at undifferentiated state (D0) and differentiated cells at day14 (D14) for RNA-seq analysis.

first: Renpeng

last: Guo


title: Galectin-7 reprograms skin carcinogenesis by fostering innate immune evasive programs

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

summary: Disruption of skin homeostasis by environmental insults activates pathologic circuitries leading to inflammation and carcinogenesis. Galectin-7 (Gal-7), a lectin preferentially expressed in keratinocytes, has been implicated in wound healing and defective skin repair. Here we report using genetically-engineered mouse models and human samples, essential roles for Gal-7 during skin carcinogenesis via coordinated intracellular and extracellular mechanisms. Heightened Gal-7 expression delineated malignant lesions in non-melanoma skin cancer (NMSC) patients and shaped the course of skin carcinogenesis in mice. Intracellularly, increased Gal-7 conferred genomic instability to skin lesions and favored transcription of inflammation-related genes reprogramming the immune landscape toward a myeloid immunoregulatory profile. Extracellularly, Gal-7 accelerated skin carcinogenesis through glycan-dependent induction of monocytic myeloid-derived suppressor cells with enhanced immune regulatory activity. Our findings identify a lectin-driven molecular circuitry that promotes skin carcinogenesis by coupling genomic instability, transcriptional regulation and myeloid immunosuppressive programs, suggesting a potential therapeutic target for the treatment of NMSC.

overall_design: Trasncriptomic analysis of skin papillomas derived from the two-stage carcinogenesis model (DMBA/TPA) in wild-type (WT), Lgals7-/- (KO) and Tg46 transgenic mice constitutively expressing Gal-7 under the Keratin-14 promoter.

first: Juan

middle: P

last: Cerliani

first: Gabriel

last: Rabinovich


title: Superenhancer-driven lncRNA FASRL in hepatocellular carcinoma

first: Li

last: Peng

overall_design: Refer to individual Series


title: Profiling placental DNA methylation associated with maternal SSRI treatment during pregnancy

city: Boston

first: Maitreyi

last: Mazumdar

address: Department of Neurology

institute: Boston Children's Hospital & Harvard Medical School

summary:
Background:
Selective serotonin reuptake inhibitors (SSRIs), used to treat prenatal maternal depression, have been associated with neurobehavioral disturbances in exposed neonates, though the underlying molecular mechanisms remain poorly understood. In utero exposure to SSRIs may have an effect on DNA methylation (DNAme) in the human placenta, which is an epigenetic mark that is established during development and is associated with gene expression.
Methods:
Chorionic villus samples from 64 human placentas were profiled with the Illumina MethylationEPIC BeadChip and clinical assessments of maternal mood were collected at multiple time points during pregnancy. Case distribution was 20 SSRI-exposed cases and 44 SSRI non-exposed cases.  Maternal depression using a mean maternal Hamilton Depression score >8 to indicate symptomatic depressed mood (“maternally-depressed”) further classified cases into SSRI-exposed, maternally-depressed (n=14); SSRI-exposed, not maternally-depressed (n=6); SSRI non-exposed, maternally-depressed (n=20); and SSRI non-exposed, not maternally-depressed (n=24). To provide a replication cohort, Illumina 450K DNAme profiles were obtained from 34 additional cases from an independent cohort (n=17 SSRI-exposed, n=17 SSRI non-exposed).
Results:
No CpGs were differentially methylated at FDR < 0.05 comparing SSRI-exposed to non-exposed placentas, while adjusting for mean maternal Hamilton Depression score, nor comparing SSRI-exposed maternally-depressed to SSRI-non-exposed maternally-depressed cases. At a relaxed threshold of FDR < 0.25, five CpGs were differentially methylated (|Δβ| > 0.03) by SSRI exposure status. Four of these CpGs were covered by the 450K array and were examined in the replication cohort, but none replicated. Amongst SSRI non-exposed cases, No CpGs were differentially methylated (FDR < 0.25) comparing maternally depressed to not depressed cases. In sex-stratified analyses for SSRI-exposed versus non-exposed cases (females n=31; males n=33), three additional CpGs in females, but none in males, were differentially methylated at the relaxed FDR < 0.25 cut-off.
Conclusions:
We did not observe large-scale alterations of DNAme in placentas exposed to maternal SSRI treatment compared to placentas with no SSRI exposure. We also found no evidence for altered DNAme in maternal depression-exposed versus depression non-exposed placentas. This novel work in a prospectively-recruited cohort with clinician-ascertained SSRI exposure and mood assessments would benefit from future replication.

overall_design: Participants were recruited as part of a prospective, longitudinal cohort approved by the University of British Columbia/ Children’s and Women’s Health Centre of British Columbia research ethics board: H12-00733 (27), and written informed consent was obtained from all mothers; all procedures complied with the ethical standards on human experimentation and with the Helsinki Declaration of 1975, as revised in 2008. This specific study was additionally approved under certificate H16-02280.  64 pregnant individuals with and without prenatal diagnoses of depression, and with/without SSRI treatment plans were recruited at the British Columbia Women’s Hospital (BCWH) in the 20th week of gestation. Depression was defined as clinician-assessed depression. SSRI-exposure was defined as treatment with one of fluoxetine, paroxetine, sertraline, citalopram, escitalopram, or venlafaxine for at least 75 days including the 3rd trimester.

first: Amy

last: Inkster

first: Chaini

last: Konwar

first: Maria

middle: S

last: Peñaherrera

first: Ursula

last: Brain

first: Almas

last: Khan

first: E

last: Price

first: Johanna

last: Schuetz

first: Élodie

last: Portales-Casamar

first: Amber

last: Burt

first: Carmen

last: Marsit

first: Cathy

last: Vaillancourt

first: Tim

last: Oberlander

first: Wendy

last: Robinson


title: Characterization of methylation profiles in spontaneous preterm birth placental villous tissue

city: Gainesville

first: Heather

last: Brockway

state: FL

department: Physiology and Functional Genomics

institute: University of Florida

summary: Genome wide DNA methylation profiling of normal and pathological placental villous tissue samples. The Illumina EPIC Human DNA methylation Beadchip was used to obtain DNA methylation profiles.

overall_design: Bisulphite converted DNA from 27 samples were hybridised to the Illumina EPIC Human Methylation Beadchip

first: Helen

last: Jones


title: MUC1-C IS A MASTER REGULATOR OF SMALL CELL LUNG CANCER PROGRESSION [RNA-seq]

city: Bostone

first: Atsushi

last: Fushimi

address: 450 Brookline Ave.

institute: Dana-Farber Cancer Institute

summary: Small cell lung cancer (SCLC) is a recalcitrant malignancy associated with dysregulation of MYC signaling and the CDK-RB-E2F axis. We report that expression of the oncogenic MUC1-C protein in SCLC cells integrates activation of MYC and the E2F pathway. MUC1-C drives MYC and E2F target genes and regulates the G2/M checkpoint, mitotic spindle pathway and replication stress response (RSR). We further show that MUC1-C MYC signaling (i) induces NOTCH2, a marker of pulmonary neuroendocrine (NE) stem cells that are the proposed cell of SCLC origin, (ii) drives NE differentiation, as evidenced by expression of ASCL1 and POU3F2/BRN2, and (iii) promotes self-renewal capacity and tumorigenicity of SCLC cells. Analyses of datasets from SCLC tumors confirmed that MUC1 significantly associates with the MYC pathway. These findings uncover a master role for MUC1-C in promoting progression of the SCLC stem cell state and support MUC1-C as a potential target for SCLC treatment.

overall_design: RNA-seq in SCLC cell lines


title: RNA Sequencing and Bioinformatics Analysis of CircRNAs in Asphyxial Newborns with Acute Kidney Injury

status: Public on Jan 11 2023

first: Shuang

last: Li

address: Biomedical engineering

department: Biomedical engineering

institute: Beihang university

summary: Objective: As one kind of novel non-coding RNA with high stability and conservatism, circular RNAs (circRNAs) are involved in different biological processes. Although growing evidence has supported the important role of circRNAs in renal diseases, the specific mechanism still remains unknown in neonatal acute kidney injury (AKI). Methods: High throughput sequencing analysis was applied to investigate the expression patterns of circRNAs in the comparison between hypoxia induced AKI neonates and controls. Then, bioinformatics analysis was conducted to predict the function of differentially expressed circRNAs and construct the network of circRNA-miRNA interaction. Results: (1) We identified 296 differentially expressed circRNAs (circRNAs with Fold change > 2 and P value < 0.05). Of them, 184 circRNAs were markedly up-regulated and 112 were significantly down-regulated in the AKI group. (2) Bioinformatics analysis indicated that the parental genes of the differentially expressed circRNAs were predominantly implicated in the cell and cell part, cellular process and cancer pathways. Conclusion: This study could contribute to future research of circRNAs in the pathogenesis of neonatal AKI and facilitate the identification of novel therapeutic targets of circRNAs.

overall_design: All AKI samples were obtained from patients in NICU of the First Affiliated Hospital of Nanjing Medical University from October 2020 to November 2021. Blood samples of controls were drawn from mild to moderate indirect hyperbilirubinemia at Obstetrics at the third day after birth. Firstly, to perform the circRNA profile, 2mL peripheral venous blood were drawn from five asphyxia induced AKI infants and five controls. The time point of blood drawing is when the AKI diagnosis was established. Subsequently, peripheral blood samples were collected from 20 asphyxial AKI newborns and 16 controls. Samples were mixed with TRIzol and then frozen in liquid nitrogen until they were tested for circRNA sequencing or quantification.

first: Jingjing

last: Pan

first: Yang

last: Yang

first: Xiaoqing

last: Chen

first: Xiaoguang

last: Zhou


title: The expression profiles of exosomal miRNAs associated with response to anti-PD-1/PD-L1 monotherapy in advanced NSCLC patients.

city: Kamakura

first: Satoshi

last: Kondo

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: Exosomal miRNAs involved in response to anti-PD-1/PD-L1 monotherapy in advanced NSCLC patients were successfully identified through the microoarray analysis.

overall_design: In this study, exosomes isolated from the serum of 23 NSCLC patients before receiving anti-PD-1/PD-L1 monotherapy were used to acquire expression profiles of exosomal miRNAs associated with response to anti-PD-1/PD-L1 monotherapy.

first: Kakeru

last: Hisakane

first: Masahiro

last: Seike


title: MUC1-C IS A MASTER REGULATOR OF SMALL CELL LUNG CANCER PROGRESSION


title: RNA-seq in wild-type, METTL16-knockout, and METTL16 rescue NOMO-1 cells

city: Monrovia

first: Jianjun

department: Systems Biology

institute: Beckman Research Institute of City of Hope

summary: METTL16 belongs to methyltransferase like (METTL) family and could install m6A marks on its substrates. Here, we uncover a tumor-promoting role of METTL16 in AML and LSC self-renewal. To explore the mechanism underlying the oncogenic function of METTL16 in AML, we performed m6A-seq and RNA-seq. Via integrated analysis of m6A-seq data and RNA-seq data, we identified two bona fide targets of METTL16, BCAT1 and BCAT2. METTL16 functions as an m6A methyltransferase to regulate expression of BCAT1 and BCAT2, which contribute to reprogramming BCAA metabolism.

overall_design: NOMO-1 cells overexpressing empty vector (EV) or METTL16 as indicated were followed with endogenous METTL16 knockout by viral transduction. EV is used as control for overexpression (OE). sgNS is used as control for sgRNAs. The positive-infected cells were selected with 2ug/ml puromycin for 1-2 weeks. The cells were collected and total RNA were isolated from the whole cells via Qiazol. Ribosome RNA was depleted from total RNA using Ribo-Zero plus rRNA depletion kit.

first: Li

last: Han

first: Lei

last: Dong

first: Xiaolan

last: Deng


title: Determine the methyltransferase activities of METTL16 via MeRIP-seq (m6A-seq)

summary: METTL16 belongs to methyltransferase like (METTL) family and could install m6A marks on its substrates. Here, we uncover a tumor-promoting role of METTL16 in AML and LSC self-renewal. To explore the mechanism underlying the oncogenic function of METTL16 in AML, we performed m6A-seq and RNA-seq. Via integrated analysis of m6A-seq data and RNA-seq data, we identified two bona fide targets of METTL16, BCAT1 and BCAT2. METTL16 functions as an m6A methyltransferase to regulate expression of BCAT1 and BCAT2, which contribute to reprogramming of BCAA metabolism.

overall_design: The NOMO-1 cells were infected with sgMETTL16-1, sgMETTL16-2,and sgNS lentivirus to induce knockout of METTL16. The positive-infected cells were selected with 2ug/ml puromycin for 1-2 weeks. The cells were collected and total RNA were isolated from the whole cells via Qiazol. The poly(A) RNAs were further enriched from the total RNA and then subjected to m6A IP.


title: SN-38, an active metabolite of irinotecan, enhances anti-PD1 treatment efficacy in head and neck squamous cell carcinoma

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

institute: National Taiwan University Hospital

summary: Anti-programmed cell death 1 (PD-1) therapy shows definite but modest activity in patients with advanced/metastatic HNSCC.  Preliminary evidence suggests that SN-38, an activated form of irinotecan that activates the transcription factor FoxO3a, may suppress the expression of PD-L1 in breast and ovarian tumor models.   Here, we explore the efficacy of SN-38 in combination with anti-PD1 for HNSCC treatment. In vitro, SN-38 enhances FoxO3a expression and reduces the expression of PD-L1 dose-dependently in HNSCC cells.  Low dose SN-38 increases interferon- excretion by natural killer (NK) cells and promotes NK cell-mediated cytotoxicity of tumor cells.  In vivo studies reveal that, at non-cytotoxic drug concentrations, SN-38 significantly enhances anti-PD-1 activity in suppressing murine tumor growth.  An increased infiltration of CD8+ T cells and NK cells was found in the post-treatment tumors.  RNA-seq analysis confirms that SN-38 promotes the enrichment of immune cells and biological function genes related to the immune response became abundant in SN-38 and anti-PD1 treated tumors.  Thus, SN-38 is a potentially beneficial adjunct to checkpoint inhibitor therapy in HNSCC.  Further studies to explore its mechanism of action and possible application are mandatory.

overall_design: Gene expression profiling for

first: Y

last: Lee

middle: H

first: C

middle: T

last: Tan


title: Alterations of immune cells heterogeneities in the aged zebrafish brain at single-cell resolution II

city: Chongqing

first: jiangyong

last: he

address: Tiansheng Li Street of Beibei District

institute: southwest university

summary: Immune cells, the most core part of the immune system of the whole body, could rapidly response to the change of environment. Its roles in tissue homeostasis and disease were fairly clear except brain, an immune privilege site. Previous studies had revealed the contribution of microglia, a tissue-resident macrophage, for brain development and neuronal disease. But it was currently unknown whether the other subtypes of immune cells and which of the microglia populations program their function during different stages of development. Here, we analyzed the genes expression pattern of 26,456 immune cells from the whole zebrafish brain during adult and aged stage. Our analysis uncovered the present of lymphocyte in zebrafish brain, and gradually accumulated with aging. In addition, the number of microglia were reduced bute the diversity were increased in aged brain. Collectively, our data provide insights into zebrafish brain immune cells populations that explain the distinct composition of immune cells in adult and aged brain, which might contribute to understanding the roles of immune cells in aging-associated-disease.

overall_design: 4 scRNA-seq data of brain immune cells in adult and aged zebrafish

first: Jiangyong

last: He

first: Fangying

last: Zhao

first: Bingyue

first: Nianfei

last: Cui

first: Zhifan


title: Genomic Glucocorticoid Action in Embryonic Mouse Neural Stem Cells

city: Pittsburgh

first: Donald

middle: B.

last: DeFranco

address: 7041 Biomedical Sciences Tower 3

department: Department of Pharmacology and Chemical Biology

institute: University of Pittsburgh

summary:
The goal of this study was to measure genome-wide expression in primary mouse neural stem/progenitor cell (NSPC) cultures to determine if SOX2 ablation alters the transcriptomic response which occurs following glucocorticoid receptor activation by the synthetic glucocorticoid, Dexamethasone.
Neurosphere cultures of SOX2 knock out (KO) NSPCs and control non-deleted wild-type (WT) NSPCs (C57BL/6) derived from the fetal telencephalon were established at postnatal day zero (P0).

overall_design: After the third passage, biologically distinct replicates of both sexes were treated in-vitro with 100nM Dexamethasone (Dex) for 4 hours and processed for microarray gene expression analysis (n=6 WT; n=7 SOX2 KO).

first: Kimberly

middle: J

last: Berry

first: T

last: Lei

first: Miriam

last: Pagin

first: Silvia

last: Nicolis

first: Paula

last: Monaghan-Nichols


title: Brain tissue imprinting as a new strategy for in vivo longitudinal investigation of neuropsychiatric diseases

city: Carouge GE

first: ridouane

last: achargui

address: Rue de la Fontenette, 18BIS

country: Switzerland

institute: UNIGE

summary: We report the application of Bulk mRNA sequencing technology in mice for high-throughput profiling of brain tissue imprints of the orbitofrontal cortex (OFC) before addiction protocol and dissected OFC and medial prefrontal cortex after the application of an addiction protocol in the same mice. By obtaining about 21 reads per sample aftet next-generation sequencing (NGS), the goals of this study is to demonstrate compatibility of the brain tissue impriting method in mice with sequencing analysis and use the data obtained to compare differentially expressed genes before and after the developement of addiction and identify potential genes that could explain individual vulnerability to addiction.

overall_design: Examination of Bulk mRNA from addicted (perseverer) vs non-addicted (renouncer) before and after completing an addiction protocol (oDASS)

first: Ridouane

last: Achargui

first: Christian

last: luscher

first: Agnes

last: Hiver

first: Leon

last: Fodoulian


title: Characterization of the mechansims involved in resistance to EGFR inhibitors

city: Barcelona

first: Purificación

last: Muñoz

address: Av Gran Vía de L'Hospitalet 199-203

country: Spain

institute: IDIBELL

summary: We generated patient cSCC-derived xenografts (cSCC-PDXs) that recapitulate the histopathologic and molecular features of parental patient samples. Response to gefitinib treatment was tested in four independent models. cSCC34-PDXs showed intrinsic resistance to gefitinib, whereas three models (cSCC10-PDXs, cSCC16-PDXs and cSCC24-PDXs) initially showed a strong response to gefitinib, but acquired resistance after long-term treatment. RNA sequencing analysis were performed in matched untreated and gefitinib-resistant cSCC-PDXs to determine mechanisms behind gefitinib resistance.

overall_design: RNA sequencing of control (treated with vehicle solution) cSCC-PDXs vs gefitinib-resistant cSCC-PDXs from four different patients

first: Adrià

last: Peguera

first: Luís

last: Palomero


title: Microarray analysis of the expression levels of 84 informative genetic markers change in A375 and F01 cells cultured for 96h vs 24h.

city: Paris

first: annie

last: dutriaux

address: 15 rue Hélène Brion

department: Institut Jacques Monod

institute: Universite Paris Cite

summary: PCR array data for expresion of Cancer Stem Cell genes in A375M and FO1 cells after 24h and 96h growth

overall_design: Expression profiling by RT-PCR

first: A

last: Dutriaux

first: D

last: Flagiello


title: Differential ChIP-Seq of RNAPol2 and H3K4me3 during a parabolic flight

city: Zurich

first: Cora

middle: S.

last: Thiel

address: Winterthurerstrasse 190

department: Institute of Anatomy

institute: University of Zurich

summary: Primary human macrophages in in vitro conditions have been exposed to hypergravity and microgravity during the 28th DLR parabolic flight campaign

overall_design: Primary human macrophages from 3 donor samples per antibody, in biological triplicates, under the conditions 1g ground control (1g_GC), 1g inflight (1g_IF), 1.8g hypergravity (BL_hypg), and microgravity (ug). Antibodies against RNAPol2 and H3K4me3

last: Vahlensieck

first: Oliver

last: Ullrich


title: Gene expression of PD-L1 high and low pancreatic beta cells, after 20h of incubation wiht 50pg.mL of IFNγ.

first: Masaya

last: OSHIMA

address: 123 boulevard de Port Royal

institute: INSERM U1016

summary: Characterization of FACS-sorted PD-L1 high and low mouse pancreatic beta cells after 20h of incubation with low dose of IFNγ.

overall_design: Mouse pancreatic islets were isolated and treated for 20h with 50pg.mL of IFNγ. They were then dissociated into single-cell. Beta cells were selected on FACS by surface markers, and were sorted according to their expression level of PD-L1.

first: Marine

last: De Burghgrave

first: Chloé

last: Lourenço

first: Alexis

last: Fouque

first: Raphaël

last: Scharfmann


title: Alpha, beta and delta cells reponse to IFNγ

summary: Characterization of mouse pancreatic alpha, beta and delta cells responses to IFNγ

overall_design: Mouse pancreatic islets were isolated and treated for 20h with 5ng.mL of IFNγ . They were then dissociated into single-cell. Alpha beta and delta cells were purified by FACS sorting.

first: Claire

last: Berthault

first: Marc

last: Diedisheim


title: Transcriptomic analysis reveals retinal neuromodulation by sitagliptin in an experimental model of diabetic retinopathy

first: Patricia

last: Bogdanov

state: Barcelona, Spain

address: Passeig de la Vall d'Hebron 119-129  Collserola Building. Lab 144

department: Diabetes Research and Metabolism Unit

institute: Vall d'Hebron Research Institute

summary:
The aim of the study was to explore the effect of topically administered sitagliptin, an inhibitor of the enzyme dipeptidyl peptidase-4, on the retinal expression patterns of an experimental model of DR.
Background: Synaptic dysfunction and neuronal damage have been extensively associated with diabetic retinopathy (DR). Our group evidenced that chronic hyperglycemia reduces the retinal expression of presynaptic proteins, which are crucial for a proper synaptic function. The aim of the study was to explore the effect of topically administered sitagliptin, an inhibitor of the en-zyme dipeptidyl peptidase-4, on the retinal expression patterns of an experimental model of DR. Methods: Transcriptome analysis was performed comparing the retinas of 10 diabetic (db/db) mice randomly treated with sitagliptin eye drops (10 mg/mL) twice daily, and the reti-nas of 10 additional db/db mice that received vehicle eye drops. 10 non diabetic mice (db/+) were used as control group. Gene Ontology (GO) and Reactome databases were used to assess the Gene Set Enrichment Analysis (GSEA) in order to explore the most enriched biological pathways among groups. The most differentiated genes of these pathways were validated through quantitative RT-PCR. Results: Transcriptome analysis revealed that sitagliptin eye drops have a significant effect on retinal expression patterns and that neurotransmission was the most enriched biological process. Our study evidenced enriched pathways that contain genes involved in membrane trafficking, transmission across chemical synapses, vesi-cle-mediated transport, neurotransmitter receptors and postsynaptic signal transmission with negative regulation of signaling as a consequence of neuroprotector treatment with sitagliptin. This improves the modulation of macromolecule biosynthetic process with positive regulation of cell communication which provides beneficial effects for neuronal metabolism.  Conclu-sions: This study suggests that topical administration of sitagliptin ameliorates the abnormali-ties on presynaptic and postsynaptic signal transmission during experimental DR, and that this improvement is one of the main mechanisms behind the previously demonstrated beneficial effects.

overall_design: Transcriptome analysis was performed comparing the retinas of 10 diabetic (db/db) (BKS.Cg-Dock7m +/+ Leprdb/J) mice randomly treated with sitagliptin eye drops (10 mg/mL) twice daily, and the retinas of 10 additional db/db mice that received vehicle eye drops. 10 non diabetic mice (db/+) (BKS.Cg-Dock7m + Leprdb/+) were used as control group. The mice were obtained from Charles River Laboratories Inc (Calco Italy for the study). The study is based on 30 samples (the 10 highest quality RNA samples of each group) hybridized in Clariom S Mouse Arrays (ThermoFisher Scientific, Waltham, MA, USA). Bioinformatics analysis has been carried out in the Statistics and Bioinformatics Unit (UEB) at VHIR.

first: Hugo

last: Ramos

first: Anna

last: Deàs-Just

first: Rafael

last: Simó

first: Cristina

last: Hernández


title: Nicotinamide Mononucleotide administration prevents doxorubicin-induced cardiotoxicity and loss in physical activity in mice.

city: Nyon

first: Nicolas

last: Hulo

address: Avenue Reverdil 4

institute: Nuvamid SA

summary: In this study we investigated whether nicotinamide mononucleotide (NMN) could protect against Doxorubicin-induced cardiotoxicity and physical dysfunction in vivo. To assess the short- and long-term toxicity, two Doxo regimens were tested, acute and chronic. In the acute study, C57BL6/J (B6) mice were injected intraperitoneally (i.p.) once with Doxo (20 mg/kg) and NMN (180 mg/kg/day, i.p.) was administered daily for five days before and after the Doxo injection. In the chronic study, B6 mice received a cumulative dose of 20 mg/kg Doxo administered in fractionated doses for five days. NMN (500 mg/kg/day) was supplied in the mice’s drinking water beginning five days before the first injection of Doxo and continuing for 60 days after.

overall_design: Heart mRNA profiles of non treated mice were compared  with Doxo treated and doxo treated + β-NMN (acute or chronic dose).


title: Expression data from recoverin positive and negative A549 cell lines

city: Sapporo

first: Fumihito

last: Hikage

state: Hokkaido

address: S1 W16, Chuo-ku

institute: Sapporo Medical University School of Medicine

summary: We compared the transcriptional signatures of recoverin (Rec) negative lung adenocarcinoma A549 cells which had been transfected with a plasmid containing human recoverin cDNA (A549 Rec) or an empty plasmid as a mock control (A549 MOCK).

overall_design: Both cell lines were cultured in HG-DMEM culture medium supplemented with 8 mg/L d-biotin, 4 mg/L calcium pantothenate, 100 U/mL penicillin, 100 μg/mL streptomycin (b.p. HG-DMEM), 10 % CS and methylcellulose (Methocel A4M) at 37°C and 5% CO2 for 6 days.

first: Yoshihiko

last: Hirohashi

first: Tatsuya

last: Sato

first: Masato

last: Furuhashi

first: Toshihiko

last: Torigoe

first: Hiroshi

last: Ohguro


title: single-nucleus RNA-sequencing (snRNA-seq) of ex-vivo-perfused pig kidney cortex tissue

city: Hamburg

first: YU

last: ZHAO

address: Martinistr. 52

institute: Hamburg Center for Translational Immunology

summary: The pig kidney cortex tissue was collected before and after ex vivo perfusion

overall_design: Comparative gene expression profiling analysis of snRNA-seq data for perfused vs unperfused pig kidney cortex tissue

first: Tianran

last: Zhang

first: Yu

last: Zhao

first: Shuya

last: Liu


title: Effect of aging on gene expression in round spermatids from Brown Norway rats

city: Montreal

first: Bernard

last: Robaire

state: QC

address: 3655 Promenade Sir William Osler

department: Pharmacology and Therapeutics

country: Canada

institute: McGill University

summary:
To investigate the gene expression changes observed with aging in round spermatids from Brown Norway rats.
We then performed gene expression analysis using data obtained from RNA-seq of round spermatids at two time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of round spermatids from 4-6 month old (young) and 18-20 month old (aged) Brown Norway rats (N=5)

first: Heather

middle: E

last: Fice

first: B