title: Neoadjuvant eribulin in HER2-negative early-stage breast cancer (SOLTI-1007-NeoEribulin): a multicenter, two-cohort, non-randomized phase II trial

city: Barcelona

first: Fernando

last: Salvador Gómez

address: Balmes 89, 3º 7

institute: SOLTI

summary: Eribulin prolongs overall survival in patients with pre-treated advanced breast cancer. However, no biomarker exists to prospectively select patients who will benefit the most from this drug. SOLTI-1007-NeoEribulin is a phase II, open-label, two cohort, exploratory pharmacogenomic study in patients with clinical stage I-II HER2-negative breast cancer receiving neoadjuvant eribulin monotherapy treatment. Primary objective was to explore the association of baseline tumor gene expression with pathological complete response in the breast (pCRB) at surgery. Key secondary objectives were pCRB rates in all patients and according to HR status, gene expression changes during treatment and safety. 101 hormonal receptor-positive (HR+) and 73 triple negative breast cancer (TNBC) patients were recruited. The pCRB rates were 6.4% in all patients, 4.9% in HR+ disease and 8.2% in TNBC. The TNBC cohort was interrupted due to a progression disease rate of 30.1%. The pCRB rates differed according to intrinsic subtypes: 28.6% in HER2-E, 11.1% in Normal-like, 7.9% in Luminal B, 5.9% in Basal-like and 0% in Luminal A (HER2-E vs. others odds ratio=7.05, 95% CI 1.80-42.14; p-value = 0.032). Intrinsic subtype changes at surgery occurred in 33.3% of cases, mostly (49.0%) Luminal B converting to Luminal A or Basal-likes converting to Normal-like. Baseline tumor infiltrating lymphocytes (TILs) were significantly associated with pCR. Eribulin showed a good safety profile with a low response and pCRB rates. Patients with HER2-negative disease with a HER2-enriched profile may benefit the most from eribulin. In addition, significant biological activity of eribulin is observed in Luminal B and Basal-like subtypes.

overall_design: SOLTI-1007 NeoEribulin is an open-label, two cohort,  conducted in 3 countries at 30 trial centers, phase 2 pharmacogenomic study of single agent eribulin as neoadjuvant treatment for operable Stage I-II HER2-negative breast cancer. Cohort 1 included patients with TNBC and cohort 2 included HR-positive breast cancer. All patients received 4 cycles weeks of eribulin (1.23 mg/kg on Days 1 and 8 of every 21-day cycle). Dose reduction of eribulin to 0.97 mg/kg and 0.62 mg/kg was permitted for patients who developed grade 3 or 4 haematological or non-haematological adverse events and/or omitted of day 8 administration in previous cycle for toxicity. Treatment could be discontinued for a maximum of 14 days and could be resumed if adverse events resolved to grade 1 or below. We did safety laboratory testing (blood count and chemistry) at baseline and day 1 and 8 of every treatment cycle (3 weeks). At Cycle 2 Day1 (±5 days), a core-needle biopsy was mandatory. Surgery was performed between 2 and 5 weeks after the last dose of eribulin. Standard adjuvant chemotherapy was administered according to the physician's discretion. The last safety follow-up visit was done 30 days after surgery. Three tumor samples were obtained during the study: 1) Baseline (SCR); 2) At Cycle 2 Day 1(2W) and at surgery (SUR).

first: Tomás

last: Pascual

first: Mafalda

last: Oliveira

first: Patricia

last: Villagrasa

first: Vanesa

last: Ortega

first: Laia

last: Paré

first: Begoña

last: Bermejo

first: Serafín

last: Morales

first: Kepa

last: Amillano

first: Rafael

last: López

last: Galván

first: Jordi

last: Canes

last: Salvador

first: Paolo

last: Nuciforo

first: Isabel

middle: T

last: Rubio

first: Antonio

last: Llombart-Cussac

first: Serena

last: Di Cosimo

first: José

last: Baselga

first: Nadia

last: Harbeck

first: Aleix

last: Prat

first: Javier

last: Cortes


title: The genetic basis of structural colour variation in mimetic Heliconius butterflies [melpomene]

status: Public on Dec 10 2021

city: Sheffield

first: Nicola

middle: J

last: Nadeau

address: Western Bank

department: Ecology and Evolutionary Biology

country: United Kingdom

institute: The University of Sheffield

type: Expression profiling by high throughput sequencing

summary: We use RNAseq data to perform differential gene expression analysis to identify genes controlling structural colouration in two co-mimetic species of Heliconius butterfly - Heliconius erato and Heliconius melpomene. We use comparisons between iridescent and non-iridescent subspecies of Helcionius erato (H. e. cyrbia and H. e. demophoon, respectively) and Helcionius melpomene (H. m. cythera and H. m. rosina, respectively) at two separate developmental stages, 50% and 70% of development. In addition, in the iridescent subspecies of both H. erato and H. melpomene, we compared the iridescent wing regions (forewing and hindwing combined) to the non-iridescent androconial wing (anterior hindwing) region using differential gene expression.

sample_organism:
Heliconius melpomene rosina
Heliconius melpomene cythera

overall_design: Differential gene expression between iridescent and non-iridescent sub-species (and wing regions) of Heliconius melpomene and Heliconius erato at 50% and 70% pupal wing development.

first: Victoria

last: Lloyd


title: Identification of indoleamine 2, 3-dioxygenase 1 (IDO1) regulated genes in human glioblastoma cell line U87

city: Chicago

first: Matthew

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

country: USA

institute: Northwestern University

summary:
Transcriptome analysis of U87 cells under different treatments to identify IDO1-regulated genes
Indoleamine 2, 3-dioxygenase 1 (IDO1) is a tryptophan (Trp) catabolic enzyme that converts Trp into downstream kynurinine (Kyn). Many studies have indicated that IDO1 is a critical suppressive immune checkpoint molecule invovled in various types of cancer. Canonically, the underlying mechanism of IDO1 immunosuppressive role is related with its enzyme activity, that is the depletion of Trp and accumulation of Kyn lead to increased tumor infiltrating suppressive regulatory T cells. Recent studies, however, challenged this hypothesis and imply that tumor cell-derived IDO1 can mediate immunosuppression independent of its enzyme activity. In this study, we aim to identify genes that are regulated by IDO1 in human glioblastoma cells, a gene expression regulatory function of IDO1 that is indepent of its enzyme activity.

overall_design: U87 cells were either non-treated or treated with 20 nM human IDO1-specific siRNA for 16-18 hours, followed by human IFN-g (100 ng/ml) treatment for another 24 hours. Human IDO1 overexpressing U87 (O/E) cells were either non-treated or treated with 20 nM human IDO1-siRNA for 24 hours. At the end of experiment, total RNAs were extracted from the following 6 groups: 1) U87 NT; 2) U87 + IFNg; 3) U87 + siRNA; 4) U87 + siRNA + IFNg; 5) IDO1-O/E U87 NT; 6) IDO1-O/E U87 + siRNA and subject to microarray analysis. Each treatment group has two replicates. Experiment was repeated 3 times. Totally 36 samples were analyzed.

first: Derek

last: Wainwright

last: Genet

first: Brenda

last: Nguyen

first: Lijie

last: Zhai

first: Brian

last: Wray


title: Blood epigenome analysis before and after acupuncture treatment in an outpatient cohort of patients suffering from burnout

city: Geneva

first: Ludwig

last: Stenz

address: Rue Michel-Servet 1

department: Department of Genetic Medecine and Development

country: Switzerland

institute: University of Geneva

type: Methylation profiling by genome tiling array

summary: Genome-wide characterization of epigenetic changes in blood DNA obtained before and after acupuncture treatment in a cohort of patients suffering from Burnout. CpG methylation was measured by using the Infinium MethylationEPIC BeadChip (Illumina) across 859'500 CpGs. Burnout was clinically assessed before and after acupuncture using the Maslach Burnout Inventory (MBI).

overall_design: Longitudinal study comparing methylome variations in the same patients before and after acupuncture.

first: Marc

last: Petitpierre

first: Ariane

last: Paoloni-Giacobino


title: Analyzing the effect of Lef1 deletion in mouse intestinal adenoma cells with single-cell RNA sequencing

city: Helsinki

first: Kari

last: Alitalo

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

summary: Somatic mutations in APC or CTNNB1 genes lead to aberrant Wnt signaling and colorectal cancer (CRC) initiation and progression. Activation of Wnt pathway leads to the formation of beta-catenin-T-cell factor/Lymphoid enhancer binding factor 1 (Tcf/Lef1) complexes that activate transcription of oncogenic target genes. Lef1 is the only member of the Tcf gene family that is not expressed in the normal intestine, but is induced during intestinal tumorigenesis. Thus, we wanted to assess the role of Lef1 using genetic mouse models of intestinal adenomas and scRNA-seq technology. Tumorigenesis was initiated by inducing Apc mutation in Lgr5+ stem cells. Intestinal EpCAM+ epithelial cells of Lgr5-CreERT;Apc fl/fl (LApc) mouse and Lgr5-CreERT;Apc fl/fl; Lef1 fl/fl (LApcL) mouse were used to analyze the effects of Lef1 deletion in intestinal adenoma cells. We used WT mice as a control to distinguish adenoma cells.

overall_design: Single-cell RNA sequencing was performed on mouse intestinal EpCAM+ epithelial cells. We deleted Apc with and without Lef1 in the Lgr5+ stem cells of Lgr5-EGFP-IRES-CreERT2;Apcfl/fl;Lef1fl/fl (LApcL) or Lgr5-EGFP-IRES-CreERT2;Apcfl/fl  (LApc) mice and performed scRNA-seq at time points when they met the criteria for euthanization.  WT mouse was used as a control.

first: Sarika

last: Heino

first: Shentong

last: Fang


title: Analyzing the effect of Lef1 deletion in mouse intestinal organoids with single-cell RNA sequencing

summary: We wanted to assess the role of Lef1 in ex vivo organoids using genetic mouse models of intestinal adenomas and scRNA-seq technology. Tumorigenesis was initiated by inducing Apc mutation in Lgr5+ stem cells. Intestinal cells of Lgr5-CreERT;Apc fl/fl (LApc) mouse and Lgr5-CreERT;Apc fl/fl; Lef1 fl/fl (LApcL) mouse were used to generate adenoma organoids. Organoids were cultured without growth factors for three passages and dissociated with Tryple express. We used WT mice as a control to distinguish adenoma cells. WT organoids were cultured with growth factors.

overall_design: Single-cell RNA sequencing was performed on mouse intestinal organoids. We deleted Apc with and without Lef1 in the Lgr5+ stem cells of Lgr5-EGFP-IRES-CreERT2;Apcfl/fl;Lef1fl/fl (LApcL) or Lgr5-EGFP-IRES-CreERT2;Apcfl/fl  (LApc) mice in vivo and generated organoid cultures. WT mouse organoids were used as a control.


title: A global transgenic RNAi screen identifies transcription factors that modulate myofiber size in Drosophila.

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: Myofiber atrophy occurs with aging and in many diseases but the underlying mechanisms are incompletely understood. Here, we have used >1,100 muscle-targeted RNAi interventions to comprehensively assess the function of 447 transcription factors in the developmental growth of body wall skeletal muscles in Drosophila. This screen identifies new regulators of myofiber atrophy and hypertrophy, including the transcription factor Deaf1. Deaf1 RNAi increases myofiber size whereas Deaf1 overexpression induces atrophy. Consistent with its annotation as a Gsk3 phosphorylation substrate, Deaf1 and Gsk3 induce largely overlapping transcriptional changes that are opposed by Deaf1 RNAi. The top category of Deaf1-regulated genes consists of glycolytic enzymes, which are suppressed by Deaf1 and Gsk3 but are upregulated by Deaf1 RNAi. Similar to Deaf1 and Gsk3 overexpression, RNAi for glycolytic enzymes reduces myofiber growth. Altogether, this study defines the repertoire of transcription factors that regulate developmental myofiber growth and the role of Gsk3/Deaf1/glycolysis in this process.

overall_design: RNA-sequencing data from Drosophila body wall skeletal muscles (n=3/genotype) with the following genotypes:   Mef2>whiteRNAi(BL#33623)   [control RNAi]  Mef2>Deaf1RNAi(BL#32512)   [muscle-specific Deaf1 RNAi]  Mef2>+   [control, no transgene]  Mef2>Deaf1   [muscle-specific Deaf1 overexpression]  Mef2>Gsk3CA(BL#5255).  [muscle-specific Gsk3 overexpression]

first: Flavia

middle: A

last: Graca

first: Natalie

last: Sheffield

first: Melissa

last: Puppa

first: Liam

middle: C

last: Hunt

first: Fabio

last: Demontis


title: Single-cell analysis of Villin-Cre;Apc min;Lef1 fl/fl (VApcMinL) and ApcMin intestinal adenoma cells at the age of 11 wks

summary: Comparison of Villin-Cre;Apc min;Lef1 fl/fl (VApcMinL) and ApcMin adenoma cells at the age of 11 wks. 2-3 male mice and 3-10 tumors per group were used in the experiment. Experiment was repeated twice (ApcMin2 and VApcMinL2 samples).

overall_design: We analyzed two samples, aiming with both samples to 5,000-8,000 cells. For tumor dissociation, 3-10 tumors of approximately same size and from similar locations in the intestines were removed from 11-week-old ApcMin and VApcMinL mice. Tumors were incubated with enzymes (4 mg/ml Dispase II, 1 mg/ml Collagenase I, 1 mg/ml Collagenase H and 1 U/ml DNase I) for 30 min at +32°C, followed by incubation with trypsin-EDTA for 15 min at +37°C. Cells were filtered through 40 μm mesh and subjected to scRNA-seq without FACS sorting.


title: Single cell analysis of Villin-Cre;Apc min;Lef1 fl/fl (VApcMinL) and ApcMin Epcam- cells and CD45-Epcam- stromal cells from lamina propria at the age of 11 wks.

summary: Comparison of Villin-Cre;Apc min;Lef1 fl/fl (VApcMinL) and ApcMin Epcam- cells and CD45-Epcam- stromal cells from lamina propria at the age of 11 wks. Two male mice per group was used in the experiment.

overall_design: We analyzed two samples, aiming with both samples to 8,000-10,000 cells. EDTA treatment 20min +37°C. Liberase TL treatment 60min +37°C. FACS: DAPI-Ter119-Epcam-CD45- intestinal stromal cells


title: Transcriptome sequencing analysis of naïve CD4+ T cells treated with NETs or control vehicle

city: Wuhan

first: Han

last: Wang

state: Hubei

address: 1095 Jiefang Avenue

department: Department of Gastroenterology,

country: China

institute: Tongji Hospital, Tongji Medical College,

summary:
Purpose: We found neutrophil extracellular traps (NETs) can affect the differentiation of naïve CD4+ T cells. This sequencing aims to explore the gene profile change of neutrophil extracellular traps (NETs) on naïve CD4+ T cells.
Methods: Total RNA was extracted from the T cells treated with NETs or vehicle for 72h and send to sequencing. Sequencing libraries were generated using NEBNext®UltraTMRNA Library Prep Kit for Illumina® (NEB, USA) and sequenced on an Illumina platform. Paired-end reads were then generated and evaluated for quality control. Clean raw data with high quality were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software. For quantification, FeatureCouts was used to count the read numbers mapped of each gene. Differential expression analysis between two groups (three biological replicates per condition) was performed using DESeq2 R package.
Results: Using an optimized data analysis workflow, we mapped around 40 million sequence reads per sample with total mapping rate around 96%. Total 23,249 transcripts in the NETs and Vehicle group were identified.  Approximately 7% of the transcripts (1675) showed differential expression between the  with p value <0.05.  Top differential expressed genes were then enriched based on KEGG and GO database. Altered expression genes in the most enrichment pathways were confirmed with qRT–PCR and western blot, demonstrating the high degree of sensitivity of the RNA-seq method. The top differential expressed genes provide new insigts for the mechanism of T cell differentiation affected by NETs.
Conclusions: Our study represents the first detailed analysis of naïve CD4+ T cells treated with NETs. Most differentital expressed genes were enriched in metabolic pahtways, which prompted us to further explore the related mechanism of the novel phenotype.

overall_design: Naïve CD4+ T cells mRNA profiles of NETs or vehicle treated group

first: Hai

last: Huang

first: Allan

last: Tsung


title: RNA-Seq Analysis of the Human Surfactant Air-Liquid Interface Culture Reveals Alveolar Type II Cell-like Transcriptome

city: Oxford

first: Altar

middle: Mert

last: Munis

state: Oxfordshire

address: L4 Academic, John Radcliffe Hospital

institute: University of Oxford

summary: In this study we investigate the effects of SALI culture conditions on the transcriptional profile of the constituent H441 cells. We further analyze the transcriptomics of the model in the context of surfactant metabolism and the disease phenotype through SFTPB-knockout SALI cultures. By comparing the gene expression profile of SALI cultures with that of human lung parenchyma obtained via single-cell RNA-sequencing, we found that SALI cultures are remarkably similar to human alveolar type II cells implying clinical relevance of the platform as a non-diseased lung model.

overall_design: mRNA profiles of wild-type and SFTPB KO H441 cells grown in submerged and SALI culture conditions

middle: M

first: Benjamin

last: Wright

first: Frederic

last: Jackson

first: Helen

last: Lockstone

first: Stephen

last: Hyde

first: Catherine

last: Green

first: Deborah

middle: R

last: Gill


title: RNA-sequencing to idendify differentially expressed mRNAs after knockdown of YTHDF2 in cerebellar granule cells

city: Shenzhen

first: Lixin

last: Yang

address: 1088 Xueyuan Avenue, Shenzhen

department: brain institute

institute: Southern Universith of Science and Technology

summary: To identify differentially expressed mRNAs after knockdown of YTHDF2 in granule cells, we perfomed RNA-seq. Cultured granule cells were infected with lentiviral shYthdf2 or shCtrl. Total RNA was collected and subjected to construct sequencing libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB). After sequencencing, the filtered reads were mapped to the mouse reference genome (GRCm38) using STAR v2.5 with default parameters. The resulting bam files were fed to HTSeq tool to count the number of RNA-seq reads, which was further normalized to calculate FPKM. Differential expression analysis of two groups (shYthdf2 vs shCtrl) (three biological replicates per group) was performed using the DESeq R package (version 1.18.0). Altogether 923 mRNA were differentially regulated, among which 587 mRNA were upregulated after YTHDF2 KD. This study provides a gene list which shows differentially expressed mRNAs after knockdown of YTHDF2 in granule cells.

overall_design: 3 replicates in each group

first: Jun

last: Yu

first: Sheng-Jian

last: Ji


title: Anti-YTHDF1 and anti-YTHDF2 RIP-Seq to identify the target mRNAs for YTHDF1 and YTHDF2, respectively

summary: To identify the target mRNAs of the m6A reader protein YTHDF1 and YTHDF2, we carired out anti YTHDF1 and anti YTHDF2 RNA Immunoprecipitation (RIP) followed by RNA-sequencencing. Using EZ-Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit (Millipore), RNA from P6-P8 wild type mouse cerebellum was pulled down by rabbit polyclonal anti-YTHDF1 (proteintech) or polyclonal anti-YTHDF2 (proteintech) and then sequenced on Illumina HiSeq3000 platform. The filtered reads were mapped to the mouse reference genome (GRCm38) using STAR v2.5 with default parameters. The resulting bam files were fed to HTSeq tool to count the number of RNA-seq reads, which was further normalized to calculate FPKM. To determine which gene is enriched, we computed the FPKM from RIP elute to input and any fold change greater than 2 was considered enriched. Finally, Biological replicates of anti-YTHDF1 RIP-Seq and anti-YTHDF2 RIP-Seq identified 506 and 596 mRNAs transcripts, respectively. This study provides gene lists which shows mRNA binding with YTHDF1 and YTHDF2 in mouse cerebellum.

overall_design: 2 replicates, each containing input and IP samples


title: Whole genome bisulfite sequencing of mouse DC subsets

status: Public on Dec 09 2021

city: NEW DELHI

first: Prafullakumar

last: Tailor

state: DELHI

address: Aruna Asaf Ali Road

country: India

institute: National Institute of Immunology

type: Methylation profiling by high throughput sequencing

summary: Diet plays an important role in lifestyle disorders and our study from Methionine Choline deficient diet induced non-alcoholic fatty liver disease led to specific decrease in pDC fraction from murine spleens. Delineating the role for individual components identified correlation of L-methionine supplementation with representation of pDC subtype. Considering implication of L-methionine in maintaining methylation status, we investigated the DNA methylation profiles among DC subtypes.  Whole genome bisulfite sequencing analysis identified that pDCs display distinctly methylated regions in comparison to cDC subsets whereas comparable methylation in cDC1 and cDC2 served as a control. Further analysis of the pathways associated with DMRs, we reported that inhibition of MAPK pathway guides DC development towards pDC subtype. We demonstrate that supplementation with S-adenosylmethionine but not Homocysteine reversed the defect in pDC development induced by methionine deficiency. Overall, our study identifies important role for methionine in pDC biology.

overall_design: Examination of DNA methylation profile of pDC, cDC1 and cDC2 subsets from murine spleens

first: Singh

last: Bhupendra

first: Venkataraman

last: Ramya

first: Budhwar

last: Roli

first: Tailor

last: Prafullakumar


title: Mouse and human share conserved transcriptional programs for interneuron development

city: Beijing

first: xiaoqun

last: wang

state: Beijing

address: 15 Datun Road, Chaoyang District

department: Institute of Biophysics

institute: Chinese Academy of Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Genetic variation confers susceptibility to neurodevelopmental disorders by affecting the development of specific cell types. Changes in cortical and striatal ɣ-aminobutyric acid-expressing (GABAergic) neurons are common in autism and schizophrenia. Here we used single-cell RNA sequencing to characterize the emergence of cell diversity in the human ganglionic eminences, the transitory structures of the human fetal brain where striatal and cortical GABAergic neurons are generated. We identified regional and temporal diversity among progenitor cells underlying the generation of a variety of projection neurons and interneurons. We found that these cells are specified within the human ganglionic eminences by gene regulatory networks similar to those previously identified in rodents. Our findings reveal an evolutionarly conserved regulatory logic controlling the specification, migration, and differentiation of GABAergic neurons in the human telencephalon.

overall_design: The human ganglionic eminences at GW09, GW11, GW12,  GW13, GW16 and GW18 were dissociated for single-cell RNA-seq (10x Genomics Chromium)

first: Y

last: Shi

first: X

last: Wang


title: Study on VEGF regulation mechanism of acupuncture improving endometrial receptivity in IVF-ET

city: 南京

first: qian

last: li

address: 仙林大道

institute: 南京中医药大学

summary: We find that the Endometrial Blood Vessel Generation is an important part ofthe establishment of Endometrial Receptivity. We have demonstrated inprevious experiments: Acupuncture in IVF-ET treatment can effectively improve Endometrial Receptivity and improve the pregnancy rate, therefore, we proposea VEGF signaling pathway in Acupuncture can improve Endometrial receptivity, thus improving the success rate of IVF-ET Hypothesis. Around the hypothesisintends to adopt the rat model of IVF-ET, through methods of acupuncture, acupuncture combined with blocker, research the related indexes effect performance that acupuncture on the VEGF signaling pathway in endometrial. Using experimental techniques such as Morphological observation, ELIAS, Immunohistochemistry, Real-time quantitative PCR, Methylation-sensitive high-resolution melting curve method(MS-HRM), to complete the research ofobserving the Effect of acupuncture interference IVF-ET, Blocking the impaction VEGF to the effect, the relationship VEGF or gene methylation inits receptors with effect. From the molecular level clarify the adverse effects and mechanism action that acupuncture will improve IVF-ET superovulation of endometrial receptivity, through adjust VEGF signaling pathway, to provide a scientific basis for acupuncture in IVF-ET treatment

overall_design: The samples were divided into two comparison groups: control vs. model, and control vs. treatment.

first: Qian

last: Li

first: Youbing

last: Xia


title: Vitamin C deficiency causes cell type-specific epigenetic reprogramming and acute tubular necrosis

first: Zihui

address: 2 Yabao Road, Chaoyang District, Beijing

institute: Capital Institute of Pediatrics

summary: The recently described roles of vitamin C as an epigenetic regulator playsa crucial role in normal physiological development and pathological conditions.However, the epigenetic regulatory role of vitamin C in renal homeostasis andpathogenesis remains largely unknown. We aim to reveal that vitamin C deficiency promoted acute tubular necrosis,and provide a potential mechanism for epigenetic therapy in preventing the progression of chronic kidney disease.

overall_design: scRNA-seq, WGBS and MeRIP-seq profiles of  wild type (WT) and  Gulo-/- mice

first: Weimin

last: Ci


title: Small RNA GcvB regulates oxidative stress response of Escherichia coli through its control of OxyR

first: Xian

last: Ju

state: Guangdong province

address: 1066 Xueyuan Avenue, Fuguang Community, Taoyuan Street, Nanshan District, Shenzhen

department: College of Life Sciences and Oceanology

institute: Shenzhen University

summary: We investigated the gene expression changed in the NCM3722 wild-type and gcvB deletion strains grown in glucose minimal medium, aiming to find novel target genes controlled by small RNA GcvB. In total, five differentially expressed genes (DEGs) were identified by Illumina sequencing using a cutoff with fold change>2 and q-value<0.01. Following physiological and molecular studies identified that the physiological roles of GcvB were beyond amino acids transportation and it regulates oxdative stress response of Escherichia coli through its control of OxyR.

overall_design: Study gene expression in E. coli NCM3722 wild-type and gcvB deletion strains grown in glucose minimal medium.

first: Conghui

last: You


title: ATAC-seq in hippocampal GABAergic cells of SMARCA3 cKO mice

city: New York

first: Tom

middle: Samuel

last: Carroll

state: New York

address: 1230 York Avenue

department: Bioinformatics

institute: The Rockefeller University

summary: Purpose: To identify chromatin accessibility changes in CCK hippocampal interneurons from SMARCA3 cKO mice Method: Genetically expressing GFP nuclei were sorted from CCK+ or GAD2+ cells from WT or SMARCA3 cKO mice, and were used for ATAC seq using Nextseq sequencer. Results: Biostatistical analysis identified 3552 genes that were altered by SMARCA3 cKO in CCK cells.

overall_design: 6 hippocampi were pooled for one ATAC sample. We used mice that were CCK cre+/GAD2 cre+ crossed with L10-EGFP+ mice and SMARCA3 fl/fl and littermates without SMARCA3 fl/fl controls.

first: Gali

last: Umschweif

first: Thomas

middle: S


title: MSL3 coordinates a transcriptional and translational meiotic program in female Drosophila

city: Albany

first: Prashanth

last: Rangan

state: NY

address: 1400 Washington

department: Biological Sciences

institute: RNA Institute

summary: Gamete formation from germline stem cells (GSCs) is essential for sexual reproduction. However, the regulation of GSC differentiation and meiotic entry are incompletely understood. Set2, which deposits H3K36me3 modifications, is required for differentiation of GSCs during Drosophila oogenesis. We discovered that the H3K36me3 reader Male-specific lethal 3 (MSL3) and the histone acetyltransferase complex Ada2a-containing (ATAC) cooperate with Set2 to regulate entry into meiosis in female Drosophila. MSL3 expression is restricted to the mitotic and early meiotic stages of the female germline, where it promotes transcription of genes encoding synaptonemal complex components and a germline enriched ribosomal protein S19 paralog, RpS19b. RpS19b upregulation is required for translation of Rbfox1, a known meiotic cell cycle entry factor. Thus, MSL3 is a master regulator of meiosis, coordinating the expression of factors required for recombination and GSC differentiation. We find that MSL3 is expressed during mouse spermatogenesis, suggesting a conserved function during meiosis.

overall_design: Ovary mRNA profiles of 1-5-day old control flies (hsbam, samples 1-2) were compared to experimental flies (MSL3 RNAi and NC2b RNAi, samples 7-10).  Ovary mRNA profiles of 1-5-day old control flies (hsbam, samples 3-4) were compared to experimental flies (Set2 RNAi, samples 5-6).Ovary mRNA profiles of 1-5-day old control flies (bam RNAi, samples 11-12) were compared to experimental flies (bam RNAi;S19b mutant, samples 13-14). Ovary profiles of total mRNA and polysome-enriched mRNA from 1-5-day old control flies (hsbam_T and hsbam_P, samples 15-18) were compared to experimental flies (S19b RNAi_T and S19b_P; samples 19-22). Ovary profiles of 1-5 day old wild type flies (Whole_Ovaries, sample 23) were used for reference of developmental staging of samples. Ovary profiles were generated by deep sequencing, in singlet (sample 23) or duplicate (samples 1-2, 3-4, 5-6, 7-8, 9-10, 11-12, 13-14, 15 and 17, 16 and 18, 19 and 21, 20 and 22) using Illumina NextSeq500.

first: Alicia

last: McCarthy

first: Kahini

last: Sarkar

first: Elliot

last: Martin

first: Maitreyi

last: Upadhyay

first: Jennifer

last: Lin

first: Seoyeon

last: Jang

first: Nathan

middle: D

last: Williams

first: Paolo

middle: E

last: Forni

first: Michael

last: Buszczak


title: Cadherin-12 regulates neurite outgrowth through PKA/Rac1/Cdc42 pathway in cortical neurons

city: Nantong

first: tuchen

last: guan

address: 19 Qixiu Road

institute: Nantong University

summary: Cadherins play an important role in tissue homeostasis, as they are responsible for cell-cell adhesion during embryogenesis, tissue morphogenesis, and differentiation. In this study, we identified Cadherin-12 (CDH12), which encodes a type II classical cadherin, as a gene to promote neurite outgrowth in a vitro model consist of neurons with differentiated intrinsic growth ability. First, the effects of CDH12 on neurons were evaluated by RNA interference, and the result indicated that the knock down of CDH12 expression restrained the axon extension of E18 neurons. The transcriptome profile of the neurons with or without siCDH12 treatment revealed a set of pathways positively correlated with the effect of CDH12 on neurite outgrowth. We further revealed that CDH12 affected Rac1/Cdc42 phosphorylation in PKA dependent manner by testing with H-89 and 8-Bromo-cAMP sodium salt. Moreover, we investigated the expression of CDH12 in brain, spinal cord, and dorsal root ganglion during development by using immunofluorescence staining. Thereafter, we explored the effects of CDH12 on neurite outgrowth in vivo. A zebrafish model of CDH12 knockdown was established by using NgAgo-gDNA system and registered the vital role of CDH12 in peripheral neurogenesis. In summary, our study is the first to report the effect of CDH12 on axonal extension in vitro and in vivo and we provided a preliminary explanation for the mechanism.

overall_design: RNA-seq of  E18 cortical neurons with or without CDH12 siRNA treatment

first: Beibei

last: Guo

first: Mengwei

last: Qi

first: Shuai

last: Huang

first: Run

last: Zhuo

first: Wenxue

last: Zhang

first: Yufang

first: Man

last: Xu

first: Mei

last: Liu

first: Tuchen

last: Guan

first: Yan


title: Long-term repair of porcine articular cartilage using cryopreservable, clinically compatible human embryonic stem cell-derived chondrocytes

city: Los Angeles

first: Denis

last: Evseenko

state: CA

address: 1450 Biggy St

department: Orthopaedic Surgery

institute: University of Southern  California

summary: Osteoarthritis (OA) impacts hundreds of millions of people worldwide, with those affected incurring significant physical and financial burdens. Injury to the articular surface is a major contributing risk factor for the development of OA. Current cartilage repair strategies are moderately effective at reducing pain but often replace damaged tissue with biomechanically inferior fibrocartilage. Here we describe the development, transcriptomic ontogenetic characterization and quality assessment at the single cell level, as well as the scaled manufacturing of an allogeneic pluripotent stem cell-derived articular chondrocyte formulation that exhibits long-term functional repair of porcine articular cartilage. These results define a new potential clinical paradigm for articular cartilage repair and mitigation of the associated risk of OA.

overall_design: Single-cell mRNA sequencing for human chondrocytes from embryonic chondroprogenitors, fetal, juvenile and adult chondrocytes along with embryonic stem cell (ESC), ESC-derived chondrocytes and human bone marrow derived mesenchymal stem cells (MSCs) cultured on membrane using 10x Genomics.

first: Ben

last: Van Handel


title: RNA-seq of BM and Day 3 wound Gr-1+ cells from non-diabetic and diabetic mice

city: Manchester

first: Kimberly

last: Mace

address: Michael Smith Building, Oxford Road

department: Division of Cell Matrix Biology & Regenerative Medicine

institute: University of Manchester

summary: Gr-1+ cells were isolated from non-diabetic (Lepr +/-) and diabetic (Lepr -/-) mouse bone marrow (BM) and dissociated wounds on day 3 following wounding. RNA was sequenced by GATC, and reads were mapped to mm9 genome. The prupose of the studey was to identify intrinsic factors (or Gr-1+ myelid cells) contributing to chronic inflammation in diabetic wounds.

overall_design: 10 non-diabetic and 10 diabetic mice were used in this study. They were divided into 2 groups each: 2x 5 non-diabetic and 2x 5 diabetic mice. On Day 3 following wounding, Gr-1+ cells were isolated from enzymatically digested wounds and bone marrow. Each group of 5 was pooled to generate 2 non-diabetic BM RNA samples (HBM), 2 diabetic BM samples (DBM), 2 non-diabetic wound samples (HW) and 2 diabetic wound samples (DW).

first: Tanja

last: Torbica


title: TCR affinity defines tumor-specific CD8 T cell differentiation and dysfunction

first: Andrea

last: Schietinger

address: 1275 York Avenue

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

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

overall_design: Refer to individual Series


title: Innate triggering and antiviral effector functions of activin A

status: Public on Dec 08 2021

first: Timothy

last: Hinks

state: United Kingdom

address: John Radcliffe Hospital, Headley Way, Oxford

department: NDM Experimental Medicine - New College

institute: University of  Oxford

summary: Transcriptomic analyses delineated strikingly congruent patterns of gene regulation in hepatocytes stimulated with recombinant activin A and IFNα in vitro.  Activin A mRNA, encoded by the INHBA gene, is induced upon activation of RIG-I, MDA5 and TLR7/8 viral nucleic acid sensors in vitro, across multiple cell lines and also in human peripheral blood mononuclear cells

overall_design: we first used microarray analysis and RNA sequencing to analyse the effects of activin A upon hepatocytes at the transcriptional level and examine its intersection with the type I IFN axis

first: N

last: Ramamurthy

first: E

last: Marchi

first: K

last: Al-Hourani

first: R

last: Eichinger

first: L

middle: N

last: Lee

first: P

last: Fabris

first: H

last: Drakesmith

last: Klenerman


title: Evaluation of off-target effects of gapmer antisense oligonucleotides using human cells

city: Kawasaki

first: Takao

last: Inoue

state: Kanagawa

address: 3-25-26, Tonomachi

department: Division of Molecular Target and Gene Therapy Products

country: Japan

institute: National Institute of Health Sciences

summary:
Antisense oligonucleotide (ASO) has the potential to induce off-target effects due to complementary binding between the ASO and unintended RNA with a sequence similar to the target RNA. In this study, we evaluated off-target effects of gapmer ASOs, which cleave the target RNA in an RNase H-dependent manner, by introducing the ASO into human cells and performing microarray analysis.
Our data indicate that gapmer ASOs induce off-target effects depending on the degree of complementarity between the ASO and off-target candidate genes. Based on our results, we also propose a scheme for assessment of off-target effects of gapmer ASOs.

overall_design: The  Huh-7 cells were seeded in 12-well plates (n = 4/group) and transfected with the LNA-gapmer ASOs using Lipofectamine® 2000 according to the manufacturer’s protocol.Cells treated with transfection reagent in the absence of ASO were used as a control. After a further 24 h,  total RNA was isolated.

first: Tokuyuki

last: Yoshida


title: Evaluation of the consequences of ALYREF silencing on gene expression patterns in colorectal cancer cells

city: Graz

first: Christiane

last: Klec

state: Styria

address: Stiftingtalstraße 24

department: Oncology

country: Austria

institute: Medical University of Graz

summary: In order to uncover the underlying mechanisms behind the observed oncogenic phenotype of ALYREF in colorectal cancer in vitro and in vivo, we applied a whole transcriptome analysis to find deregulated genes upon ALYREF silencing.

overall_design: HCT116 colorectal cancer cells were transfected with 20 nM ALYREF siRNA or negative control siRNA for 48 hours and RNA was isolated and sent to analysis. Three independent experiments have been performed.

first: Martin

last: Pichler


title: Nascent polypeptide within the exit tunnel stabilizes the ribosome to counteract risky translation

city: Nagatsuta-cho,Midori-ku, Yokohama-shi

first: Yuhei

last: Chadani

department: Institute of Innovative Research

institute: Tokyo Institute of Technology

summary: Continuous translation elongation, irrespective of amino acid sequences, is a prerequisite for living organisms to produce their proteomes. However, the risk of elongation abortion is concealed within nascent polypeptide products. For example, negatively charged sequences with occasional intermittent prolines, termed intrinsic ribosome destabilization (IRD) sequences, destabilizes the translating ribosomal complex. Thus, some nascent chain sequences lead to premature translation cessation. Here, we show that most potential IRD sequences in the middle of open reading frames remain cryptic by two mechanisms: the nascent polypeptide itself that spans the exit tunnel and its bulky amino acid residues that occupy the tunnel entrance region. Thus, nascent polypeptide products have a built-in ability to ensure elongation continuity by serving as a bridge and thus by protecting the large and small ribosomal subunits from dissociation.

overall_design: Ribosome profiling

first: Nobuyuki

last: Sugata

first: Tatsuya

last: Niwa

first: Yosuke

last: Ito

first: Shintaro

last: Iwasaki

first: Hideki

last: Taguchi


title: Cx3Cr1-Cre induction leads to microglial activation and IFN-1 signaling caused by DNA-damage in early postnatal brain

city: Bangalore

first: Hiyaa

middle: Singhee

last: Ghosh

state: Karnataka

address: GKVK Campus, Bellary Road

institute: National Center for Biological Sciences

summary: Cx3cr1CreER driven Cre-recombinase (Cre) is a widely used genetic tool for enabling gene manipulation in microglia and macrophages. However, an in-depth analysis for the possible detrimental effects of Cre-activity in microglia, surprisingly remains missing. Here we demonstrate an age-dependent sensitivity of microglia to Cx3cr1-Cre-toxicity, wherein Cre-induction specifically in early postnatal microglia is detrimental for microglial development, proliferation and function. Tamoxifen (TAM) induced Cre-activity leads to microglial activation, type1-interferon (IFN-1) signaling and increased phagocytosis, causing aberrant synaptic pruning during early postnatal period and anxiety behavior in later age. The detrimental effects of Cre-induction are caused due to DNA-damage induced toxicity in microglia, and is limited to the early postnatal period, showing no detrimental effects in adult microglia. Thus, our study reveals the age-dependent vulnerability of microglia to Cre-activity, thereby highlighting age-dependencies of Cre-action, which could be especially applicable in the broader context of environment-responsive cell-types.

overall_design: Analysis of FACS-sorted microglia from Tamoxifen vs Vehicle treated neonatal brains of Cx3cr1-CreER positive mice

first: Vinaya

last: Sahasrabuddhe


title: Concurrent Mapping of Multiple Epigenetic Marks and Co-enrichment Using ACT2-seq

city: Bethesda

first: Keji

last: Zhao

state: MD

address: Building 10 Room 7B06A

department: National Heart, Lung, and Blood Institute

institute: national Institute of Health

summary: Genome-wide profiling of epigenetic marks is a core technology in molecular genetics. Co-occupancy of different epigenetic marks or protein factors on chromatin is often inferred from their existence at the same genomic locations. However, this strategy does not provide direct evidence whether the epigenetic marks or protein factors occupy the same chromatin loci in the same cell due to the existence of cellular heterogeneity.  To address this issue, we report a technique termed ACT2-seq that is capable of concurrently profiling multiple epigenetic marks in a single biological sample. While profiling simultaneously different epigenetic marks or protein factors genome-wide, ACT2 is capable of directly detecting co-occupancy of two different marks or factors on chromatin. This strategy provides direct evidence of co-localization without requiring complex single-molecule, single-cell, or magnetic bead-based approaches. We conclude that ACT2 presents an attractive option for epigenomic profiling due to its ease of use, potential for reducing sample and sequencing costs, and ability to profile co-occupancy of different epigenetic marks and protein factors on chromatin

overall_design: A method for profiling co-occupancy of different epigenetic marks or protein factors on chromatin

first: Benjamin

last: Carter

first: Wai

middle: L

last: Ku


title: TIFAB Accelerates MLL-AF9-Induced Acute Myeloid Leukemia Through Upregulation of HOXA9

city: Cleveland

first: Chen

state: OH

address: 2130 Cornell Rd

department: Pathology

institute: Case Western Reserve University

summary: Comparison of transcriptome between vector-transduced (control) and TIFAB-transduced murine MLL-AF9 leukemia stem cells

overall_design: Leukemia stem cells (defined as lin−c-kit+Sca1−CD16+CD34+) were sorted by FACS from mice receiving MLL-AF9-transduced Kit+Sca1+Lin- bone marrow cells (isolated from NIKERT2 mice) and retrovirally transduced with empty vector (Con) or TIFAB (TIFAB). The transduced cells were sorted and injected into sublethally (6.5Gy) irradiated recipient mice, then leukemia stem cells from full-blown leukemic mice were isolated and used for RNA sequencing analysis.


title: Nucleus Type-Specific DNA Methylomics Reveals Epigenetic “Memory” of Prior Adaptation in Skeletal Muscle

city: Lexington

first: Yuan

last: Wen

state: Kentucky

address: 760 Press Ave

institute: University of Kentucky

summary: Using a mouse model of conditional and inducible in vivo fluorescent myonuclear labeling (HSA-GFP), sorting purification of nuclei, low-input reduced representation bisulfite sequencing (RRBS), and a translatable and reversible model of exercise (progressive weighted wheel running, PoWeR), we provide the first nucleus type-specific epigenetic information on skeletal muscle adaptation and detraining along with whole muscle transcriptomics.

overall_design: Human skeletal actin promoter reverse tetracycline transactivator tetracycline response element driven histone 2B green fluorescent protein mice (termed HSA-GFP) were generated to label resident myonuclei at the onset of experimentation. A 4-month-old cohort of these mice were subjected to PoWeR for 8 weeks (6 months old when euthanized, 6M PoW, or “trained”), and another cohort was trained then detrained for 12 weeks to reverse training adaptations (9 months old when euthanized, 9M PoW+DT, or “detrained”); age-matched untrained mice served as controls (6M UT and 9M UT).

first: Murach

last: Kevin


title: Nucleus Type-Specific DNA Methylomics Reveals Epigenetic "Memory" of Prior Adaptation in Skeletal Muscle

summary: Using a mouse model of conditional and inducible in vivo fluorescent myonuclear labeling (HSA-GFP), sorting purification of nuclei, low-input reduced representation bisulfite sequencing (RRBS), and a translatable and reversible model of exercise (progressive weighted wheel running, PoWeR), we provide the first nucleus type-specific epigenetic information on skeletal muscle adaptation and detraining.

overall_design: Human skeletal actin promoter reverse tetracycline transactivator tetracycline response element driven histone 2B green fluorescent protein mice (termed HSA-GFP) were generated to label resident myonuclei at the onset of experimentation. A 4-month-old cohort of these mice were subjected to PoWeR for 8 weeks (6 months old when euthanized, 6M PoW, or "trained"), and another cohort was trained then detrained for 12 weeks to reverse training adaptations (9 months old when euthanized, 9M PoW+DT, or "detrained"); age-matched untrained mice served as controls (6M UT and 9M UT).

first: Kevin

last: Murach


title: Growth Inhibition and Induction of Innate Immune Signaling of Chondrosarcomas with Epigenetic Inhibitors

first: Chao

last: Lu

address: 1130 Saint Nicholas Ave

department: Genetics & Development

institute: Columbia University Medical Center

summary: In this study, our results demonstrated preclinical activity of combined DNMT and HDAC inhibition against chondrosarcomas and suggest that targeted epigenetic therapies could effectively augment the immune-reactivity of chondrosarcomas and may sensitize these immune-cold tumors to immune checkpoint blockade.

overall_design: 2 RNA-seq samples

first: Xiao

last: Chen

first: Tahir

last: Sheikh


title: Targeted nanopore DNA sequencing of mouse naive CD4 T cells activated under Treg polarizing conditions

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

summary: Suppressive regulatory T cell (Treg) differentiation is controlled by diverse immunometabolic signaling pathways and intracellular metabolites. Here we show that cell-permeable α-ketoglutarate (αKG) alters the DNA methylation profile of naive CD4 T cells activated under Treg polarizing conditions, markedly attenuating FoxP3+ Treg differentiation and increasing inflammatory cytokines.

overall_design: 5-methylcytosine (5mC) was studied in two independent experiments with 3 conditions each: thymic Tregs (tTregs), and in vitro CD4 T cells differentiated under Treg polarizing conditions (Tregs) with or without treatment with dimethyl ketoglutarate (DMK). Samples within each experiment were barcoded and multiplexed before Cas9 enrichment and nanopore sequencing.

first: Chloe

last: Goldsmith

first: Nami

last: Taylor

first: Valerie

last: Dardalhon


title: A bioactive extract rich in triterpenic acid and polyphenols from Olea europaea promotes systemic immunity and protects Atlantic salmon smolts against furunculosis

city: Santiago

first: Felipe

middle: E.

last: Reyes-López

state: Santiago

address: Av. Libertador Bernado O'Higgins 3363

country: Chile

institute: Universidad de Santiago de Chile

summary: Deciphering the dietary immunomodulatory effects of a feed additive rich in triterpenic compounds and polyphenols (AQUOLIVE®, NATAC Biotech SL, Spain) on the systemic immune response and disease resistance of Atlantic salmon (Salmo salar L.) smolts.

overall_design: Transcriptomic analysis was conducted in order to determine the differences on gene expression level between these two dietary strategies at head kidney specific level. The experimental design included two conditions: (1) fish fed basal diet with no phytogenic feed additives (AQUOLIVE®) (control); (2) fish fed 0.15% inclusion of AQUOLIVE® (10% olive bioactive compounds, 8.0% triterpenic acid and 2% polyphenols) from olive fruit extract. After 133 days of feeding trial, total RNA were extracted invidually from Atlantic salmon (S. salar) head kidney fed basal diet or an experimental diet containing 0.15% inclusion. Total RNA samples were grouped into 3 pools (n= 6 fish for each condition). The transcriptomic analysis was done following a reference design using the control diet group as reference.

first: Ricardo

last: Salomón

first: Eva

last: Vallejos-Vidal

first: Enric

last: Gisbert


title: Profiling DNA G-quadruplex structures at single-cell level

first: Angela

last: Simeone

address: 200 Hathersage Rd

institute: Genomic Services QIAGEN

summary: Single-cell sequencing data uncovers cellular heterogeneity and enables studies of underlying molecular variations within cell population. Here, we adapted CUT&Tag to profile DNA secondary structure G-quadruplexes at single-cell resolution for the first time and single-cell G-quadruplex maps readily distinguished cell types in a mixed population and revealed variable frequency of G-quadruplexes observed in a given sample.

overall_design: Genome-wide distribution of DNA G-quadruplex structures were profiled with bulk or single nuclei G4 CUT&Tag protocol using BG4 antibody in three cell lines (K-562, U2OS, MCF-7). Technical and biological replicates have been performed to assess reproducibility and sensitivity.

first: Winnie

middle: W

last: Hui

first: Katherine

middle: G

last: Zyner

first: David

last: Tannahill

first: Shankar

last: Balasubramanian


title: Neurexin-3 defines synapse- and sex-dependent diversity of GABAergic inhibition in ventral subiculum

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

institute: University of Zurich

summary: Ventral subiculum (vSUB) is integral to the regulation of stress and reward, however the intrinsic connectivity and synaptic properties of the inhibitory microcircuit are poorly understood. Neurexin-3 (Nrxn3) is highly expressed in hippocampal inhibitory neurons, but its function at inhibitory synapses has remained elusive. Using slice electrophysiology, imaging, and single-cell RNA sequencing, we identify multiple roles for Nrxn3 at GABAergic parvalbumin (PV) interneuron synapses made onto vSUB regular spiking (RS) and burst spiking (BS) principal neurons. Surprisingly, we found that intrinsic connectivity of vSUB and synaptic function of Nrxn3 in vSUB are sexually dimorphic. We reveal that vSUB PVs make preferential contact with RS neurons in males, but BS neurons in females. Furthermore, we determined that despite comparable Nrxn3 isoform expression in male and female PV neurons, Nrxn3 maintains synapse density at PV-RS synapses in males, but suppresses presynaptic release at the same synapses in females.

overall_design: 29 samples from 4 male individuals, 29 samples from 3 female individuals

first: Emma

last: Boxer

first: Charlotte

last: Seng

last: Lukacsovich

first: JungMin

last: Kim

first: Samantha

last: Schwartz

first: Matthew

middle: J

last: Kennedy

first: Jason

last: Aoto


title: Effect of PIP4Ks on gene expression and alternative splicing levels in U2OS cells

city: Chandigarh

first: Amit

last: Kumar

state: Chandigarh

address: Sector-39 A

institute: CSIR-IMTECH

summary: Here we report the function of PIP4K isoforms in differential gene expression in physiological and UV conditions. Our data indicate that PIP4K2A knockdown adversely affects UV-induced gene expression and alternative splicing which is rescued by simultanous knockdown of PIP4K2B.

overall_design: RNA-seq of U2OS cells containing wildtype ctrl; PIP4K2A knockdown ctrl; PIP4K2B knockdown ctrl; PIP4K2A/2B knockdown ctrl; wildtype UV; PIP4K2A knockdown UV; PIP4K2B knockdown UV; PIP4K2A/2B knockdown UV

first: Poorwa

last: Awasthi

first: Paramjeet

last: Singh

first: Vipin

middle: K

last: Yadav

first: Mohamood

last: Adhil

first: Nitisha

last: Mehrotra

first: Kajal

last: Karsaulia

first: Juan

last: Muñoz

first: Sheelendra

middle: P

first: SriGanesh

last: Jammula

first: Gururaj

last: Kidiyoor

first: Manuel

last: Munoz


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and atrn-/- brain Transcriptomes

city: Nanjing

last: Li

state: Jiangsu

address: No.12, Xuefu Road

institute: Qingshun Zhao

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare the brain of atrn wildtype and homozygous adult zebrafish transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods: Total RNA was isolated from single brain of the wildtype and atrn-/- zebrafish using TRIzol reagent (Invitrogen) respectively by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: Bioinformatics analysis of the transcriptome sequencing found that the steroid synthesis pathway was enriched in results of the mutant brain. By analyzing the data of male and female zebrafish with atrn mutations, it was found that the expression levels of related genes in the steroid synthesis pathway were up-regulated, mainly including the gene encoding the key enzyme for cholesterol synthesis, cyp51 and the gene encoding the key enzyme for testosterone synthesis, hsd17b7.

overall_design: Adult zebrafish brains of atrn+/+, atrn+/- and atrn-/- (4 month-post-fertilization)

first: Qingshun

last: Zhao


title: Epigenetic priming to enhance CAR-T cell cytotoxicity in bladder cancer

city: Duesseldorf

first: Michèle

last: Hoffmann

state: NRW

address: Moorenstr. 5

department: Urology

country: Germany

institute: Heinrich Heine University, Medical Faculty

summary: We sought for new treatment strategies to improve response of urothelial carcinoma (UC) patients towards immune therapy. Epigenetic inhibitors may modulate expression of immune response regulators and alter the immune phenotype of UC cells. Thus, we determined whether longterm pretreatment of UC cell lines with the DNMT inhibitor decitabine (DEC) at low dosemight enhance killing by CAR-T cells. We engineered target-specific CAR-T cells recognizing EGFR and CD44v6 on UCC. To define underlying  mechanisms we performed RNA Seq analysis for two UC cell lines treated accordingly.

overall_design: UC cell lines BFTC-905 and UM-UC-3 were treated with 100 nM Decitabine and harvested after 3 days and 7 days. According DMSO controls were collected. RNA was submitted to RNA Seq Aanalysis to identify differentially expressed genes.

first: Camilla

last: Grunewald

first: Corinna

last: Haist

first: Carolin

last: König

first: Patrick

last: Petzsch

first: Elfriede

last: Nößner

first: Constanze

last: Wiek

first: Kathrin

last: Scheckenbach

first: Karl

last: Köhrer

first: Günter

last: Niegisch

first: Helmut

last: Hanenberg

first: Arthur

last: Bister


title: Transcriptome analysis of human periodontal ligament cells under tensile loading

city: Hong Kong

first: Yifan

last: Lin

address: No.34 Hospital Road

country: Hong Kong

institute: The University of Hong Kong

type: Non-coding RNA profiling by high throughput sequencing

summary: This study explored the expression profiles of messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs) in human periodontal ligament (PDL) cells subjected to tensile loading.

overall_design: PDL cells were isolated from the teeth of five healthy individuals, cultured and exposed to tensile loading. RNA sequencing was performed to explore the mRNA and lncRNA expression profiles of PDL cells with or without tensile loading.

first: Lijian

last: Jin

first: Yanqi

last: Yang


title: Clinical optimization and molecular characterization of an engineered Type-1 regulatory T cell therapy

city: Palo Alto

first: Jeffrey

middle: Mao-Hwa

last: Liu

address: 1642 College Avenue

department: Pediatrics

institute: Stanford University

summary:
purpose: To investigate transcriptional changes in engineered Tr1 Cells
Methods: RNA sequencing of polyA enriched donor matched CD4 T cells lentiviral transduced with human IL-10 (CD4IL-10) or control GFP (CD4GFP)
Results: 142 total DEGs were identified as differentially expressed between CD4IL-10 and CD4GFP. GEO analysis found highest enrichment in genes related to cytokine signaling and cytotoxicity.
Conclusion: Engineered Tr1 cells upregulate primarily cytotoxicity related effector molecules related to the myeloid cell killing phenotype observed in Tr1 cells

overall_design: 4 donor matched pairs of of CD4GFP and CD4IL-10 were incubated for 2h in complete X-VIVO15 and then lysed for RNA sequencing

first: Molly

last: Uyeda

first: Brandon

last: Cieniewicz

first: Alma-Martina

last: Cepika

first: Maria-Grazia

last: Roncarolo


title: Changes of hepatic gene expression in C57BL/6N male mice fed high-fat high-calorie fructose (HFHC) diet for 8 weeks

city: Los Angeles

first: Sanda

last: Win

address: 2011 Zonal Ave

department: Medicine

institute: Univeristy of Southern California

summary: In murine NAFL/NASH models, high-fat high-calorie fructose (HFHC) diet fed for 16 weeks induces hepatic steatosis, inflammatory cells infilatration and early stage fibrosis. In addition, HFHC diet 16 weeks but not 8 weeks is accompanied with weight gain and insulin resistance. The aim of this study is to determine the gene expression changes in mouse liver by HFHC diet for 8weeks.

overall_design: C57BL/6N male littermates (at age 8 week) were fed ad libitum with Chow or HFHC diet (high-fat high-calorie fructose food plus high fructose drink) for 8 weeks. Liver was collected and freezed in RNAlater RNA stabilizing buffer.

first: Tin

middle: A

last: Than

first: Neil

last: Kaplowitz


title: Myocardial Rev-erb regulates metabolic diurnal rhythm in heart failure

city: Houston

first: Chih-Liang

last: Tien

state: TX

address: 1 Baylor Plaza , room 441E

institute: BCM

summary:
Rev-erbα/β are druggable components of the molecular circadian clock. Rev-erb agonists can mitigate pressure overload-induced cardiac hypertrophy and myocardial infarction in mice, while Rev-erb antagonist increases myocardial ischemia-reperfusion tolerance ex vivo at the sleep-to-wake transitionHow cardiac Rev-erb regulates heart function has not been studied in vivo.
ChIP-seq of Rev-erbα in the heart confirmed the robust diurnal rhythmicity of Rev-erbα genome binding with about 5 times more binding at ZT9 than at ZT21.

overall_design: Examination of Rev-erb binding

first: Shiyang

last: Song

first: Wenbo

last: Li

first: Yingyun

last: Gong

first: Ningxia

last: Zhu

first: Basil

last: Paul

first: Qiying

last: Fan

first: Hui

first: Weijia

last: Luo

first: Yanfeng

last: Xue

first: Rui

last: Cao

first: Wenjun

last: Zhou

first: Ortiz

last: Renee

first: Brittan

last: Stork

first: Vatsala

last: Mundra

first: Nagireddy

last: Putluri

first: Kazuhiro

last: Oka

first: Robert

middle: B

last: York

first: Chu

last: Maoping

first: Jiang

last: Chang

first: Liang

last: Xie

first: Lilei

last: Zhang

first: Zheng

last: Sun


title: A panel of DNA methylation markers for the classification of consensus molecular subtypes 2 and 3 in patients with colorectal cancer

city: Rotterdam

first: Marcel

last: Smid

address: Dr. Molewaterplein 50

department: Medical Oncology

country: Netherlands

institute: Erasmus MC

summary:
INTRODUCTION. Consensus molecular subtypes (CMSs) can guide precision treatment of colorectal cancer (CRC). Currently available dedicated assays can identify CMS1 and CMS4 cases very well while a dedicated test to distinguish CMS2 and 3 is lacking. This study aimed to identify a panel of methylation markers to distinguish between CMS2 and 3 in patients with CRC.
METHODS. Fresh-frozen tumor tissue of 239 patients with stage I-III CRC who underwent surgery between 2007 and 2014 was included. CMS classification was performed on RNA-seq data using the single-sample prediction parameter from the “CMSclassifier” package. Methylation profiles were gathered/obtained using the Infinium HumanMethylation450 BeadChip for 146 samples (124 CMS2 and 22 CMS3) . We performed adaptive group-regularised logistic ridge regression with post-hoc group-weighted elastic net marker selection to build prediction models for classification of CMS2 and CMS3 based on 15, 10 or 5 methylation markers. Data from the Cancer Genome Atlas project was used for independent validation of our obtained models.
RESULTS. Overall methylation profiles differed between CMS2 and CMS3 tumors. Group-regularisation of the methylation probes was done based on their location either relative to a CpG island or relative to a gene present in the CMS classifier. This resulted in two different prediction models and subsequently different marker panels. For both panels, even when using only 5 markers, the sensitivity, specificity, and accuracy were >90%. Independent validation of the fixed models in TCGA data showed comparable performances.
CONCLUSION. Our highly sensitive and specific methylation marker panel can be used to distinguish CMS2 and 3. This enables future development of a qPCR DNA methylation assay in patients with CRC to provide a specific and non-invasive classification tool.

overall_design: Patients were selected from the MATCH-study, a prospective multicenter cohort study from 2007 onwards including adult patients undergoing curative surgery in one of seven hospitals in the Rotterdam region, the Netherlands (institutional review board number MEC-2007-088). All patients gave written informed consent for the storage and use of tissue samples for research purposes, and the collection of clinical data. The study has been conducted in accordance with the guidelines of the Declaration of Helsinki. DNA isolated from fresh-frozen tumor tissue of 146 patients included in the MATCH-study was used for methlyation profiling in this study.

first: I

last: van den Berg

first: M

first: R

middle: R

last: Coebergh van den Braak

last: van de Wiel

first: C

middle: H

last: van Deurzen

first: V

last: de Weerd

first: J

last: Martens

last: IJzermans

first: S

middle: M

last: Wilting


title: Genome-wide analysis of blood gene expression profile at diagnosis and post treatment in latent TB and active TB subjects

city: La Jolla

first: Bjoern

last: Peters

state: California

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

summary:
Changes in the blood transcriptome upon treatment were studied in a cohort of 42 latent tuberculosis (TB) subjects and 8 active TB subiects. Samples were collected at diagnosis (prior the start of treatment) and post treatment and gene expression studied with Illumina microarrays.
We hypothesize that individuals with latent TB at risk of developing active disease are immunologically closer to those with active TB and will thus display a blood transcriptomic signature similar to active TB subjects upon treatment. This signature should significantly differ from the one mounted by latent TB individuals at low risk of progression. Thus, monitoring blood transcriptomic changes following anti-TB therapy might inform on which latent TB subjects should be prioritized for receiving therapeutic intervention in order to prevent further transmission.

overall_design: Genome-wide microarray analysis of total RNA extracted from blood collected prior and post treament in latent TB and active TB subjects.

first: Matt

last: O'Shea

first: Julie

last: Burel


title: Pancreatic islet, pancreas and gallbladder from human and mouse

city: Campbelltown

first: Mugdha

middle: V.

last: Joglekar

state: NSW

address: Cnr Goldsmith and David Pilgrim Ave

department: School of Medicine

country: Australia

institute: Western Sydney University

summary: Collection of pancreatic islet, pancreas and gallbladder from human and mouse whole transcriptome data.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Comparing the transcriptome profile of pancreatic islet, pancreas to gallbladder (in human and mouse).  This series includes re-analyzed samples from GSE152111.

first: Wilson

last: Wong

middle: V

first: Sarang

last: Satoor

first: Ryan

last: Farr

first: David

last: Martin

first: Anandwardhan

last: Hardikar


title: Study on gene expression profiles of peripheral blood mononuclear cells from patients with atopic dermatitis stimulated by Malassezia globosa

city: Xindu district, Chengdu city

first: Mao

last: Lu

state: Sichuan

address: Baoguang Road middle segment

department: Department of Dermatovenereology,

institute: The First Affiliated Hospital, Chengdu Medical College, Chengdu, China

summary:
Malassezia is considered to be involved in the pathogenesis of atopic dermatitis (AD). However, the specific role of Malassezia in the pathogenesis of AD is still unclear, as the current studies mainly focus on the mechanism of immune responses induced by it. The studies on specific molecular mechanisms are insufficient, which is unfavorable to in-depth understand the influence of Malassezia on host immune cells.
We used microarrays to detect the influence of M. globosa on the gene expression of peripheral blood mononuclear cells (PBMCs) from AD patients.

overall_design: PBMCs were extracted from 3 cases of patients with severe AD and 3 cases of healthy control subjects by density gradient centrifugation. PBMCs were stimulated with M. globosa, establishing their own negative controls. The Affymetrix Human Prime View array was used to analyze the changes in gene expression.

first: Yuping

last: Ran


title: mRNA seq of total and polysome associated mRNAs in three different conditions

city: Bern

first: Norbert

last: Polacek

address: Freiestrasse 3

department: Chemistry and Biochemistry

institute: University of Bern

summary: We report on how the presence or absence of a 18 nt long ribosome-bound RNA affects the translation in S. cerevisiae. We observe that translation of all mRNAs is downregulated when the RNA is present.

overall_design: Analysis of total and ribosome-associated mRNA in trm10∆ cells electroporated with no RNA, rancRNA_18 or rancRNA_18-M2.

first: Lukas

last: Schneider

first: Julia

last: Reuther

first: Ioan

last: Iacovache

first: Andreas

last: Pircher

first: Walid

last: Gharib

first: Benoît

last: Zuber


title: Human islet sample RNA-seq

summary: This collection represents whole transcriptome data on human islets.. From this collection of human islets RNA-seq data we aim to identify the difference between gender, age, body mass index (BMI) at a transcriptomic level.

overall_design: Human islet preparations RNA-seq data

first: Yi

last: Chew

first: Wayne

last: Hawthorne


title: Target BUB1 kinase as a therapeutic strategy for inhibiting STAT3 signal pathway in Bladder cancer

city: Tianjin

first: Miaomiao

last: Wang

address: No. 23 Pingjiang Road, Hexi District, Tianjin

department: Urology Institute of Tianjin

institute: Second Hospital Affiliated to Tianjin Medical University

summary: The incidence for bladder urothelial carcinoma (UC), a common malignancy of the urinary tract, is about three times higher in men than in women. High expression of the mitotic kinase BUB1 is associated with a subset of human cancers, but how BUB1 drive Bladder tumorigenesis mechanism was unknown. Using a microarray approach, we identified BUB1 higher expression in BC. Moreover we found BUB1, a member of the kinase family as a STAT3 interactor and phosphorylated STAT3 at Ser727 in cell of bladder cancer. In vitro binding and kinase assays showed that BUB1 directly band STAT3 and phosphorylated STAT3. Furthermore, the BUB1/STAT3 complex promoted STAT3 target gene transcription. Depletion of BUB1 and expression of BUB1 kinase mutants abrogated target gene transcription, highlighting the essential function of the kinase activity in STAT3 target gene activation. Pharmacological inhibitors of BUB1 (2OH-BNPP1) was able to inhibit the growth of Bladder cancer cell xenograft. This kinase may present an attractive candidate for drug targeting in Bladder cancer.

overall_design: ShRNA was utilized to stably knock down BUB1 expression in 5637 cell line, while BUB1 WTRNA was transfected into 5637 cell line to establish stably overexpression cell model in 5637 cell line, then investigate the function of BUB1 gene in 5637 bladder cancer cell line.

first: J

last: Ning


title: Small RNA sequencing of mouse bone marrow derived extracellular vesicles [EV.sRNA]

city: Boston

first: Youmna

last: Kfoury

state: MA

address: 185 Cambridge street

department: Harvard stem cell institute

institute: Harvard University

summary: Mouse BM extracellular vesicles were isolated from Ocn-GFP Topaz mice using the Exoeasy and miRneasy (Qiagen). Small RNA libraries were constructed using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England biolabs). Libraries were sequenced using Hiseq2500 instrument

overall_design: Small RNA libraries were constructed from total RNA extracted from mouse bone marrow derived extracellular vesicles

middle: T

last: Scadden


title: Gene expression by RNA sequenicng of extracellular vesicle labeled Granulocyte macrophage progenitors (GMPs) [mRNA]

summary: RNA sequenicg was performed on mouse bone marrow GMPs (Lin-, cKit+, Sca1-, CD34+, CD16/32 hi) labeled by osteoblastic cell derived extracellular vesicles as indicated by GFP labeling. Cells were isolated by FACS sorting from the bone marrow of Ocn-GFPTopaz mice and total RNA was extracted using the miRNeasy micro kit from (Qiagen)

overall_design: The objective of this experiment is to compare the gene expression of mouse bone marrow GMPs that are labeled by osteoblastic cell derived extracellular vesicles to those that are not labeled


title: Small RNA sequencing of bone marrow extracellular vesicle labeled Granulocyte macrophage progenitors (GMPs) [GMP.sRNA]

summary: Small RNA sequenicg was performed on mouse bone marrow GMPs (Lin-, cKit+, Sca1-, CD34+, CD16/32 hi) labeled by osteoblastic cell derived extracellular vesicles as indicated by GFP labeling. Cells were isolated by FACS sorting from the bone marrow of Ocn-GFPTopaz mice and total RNA was extracted using the miRNeasy micro kit from (Qiagen)

overall_design: The objective of this experiment is to compare the small RNA content of mouse bone marrow GMPs that are labeled by osteoblastic cell derived extracellular vesicles to those that are not labeled


title: Epigenetic analysis of CD8 T cells in absence of IL-10R signaling in murine tumor

city: Heidelberg

first: Martina

last: Seiffert

address: Im Neuenheimer Feld 280

department: Department of Molecular Genetics

institute: German Cancer Research Center

summary: ATAC-seq analysis of CD8 T cell subsets. The goal of this study was to understand the chromatin states associated to the effect of IL-10 in preventing activation-induced exhaustion of CD8+ T cells in the context of mouse tumor. The chromatin accessibility changes induced upon α-IL-10R antibody treatment in tumor-bearing mice were studied using ATACseq.

overall_design: C57BL/6 mice were transplanted with splenocytes from leukemic TCL1 mice, and after three weeks randomized to treatment with αIL-10R blocking antibody (n=3) or the corresponding isotype control (n=3). CD8+ T cells were obtained from spleen, cell subsets (naive, memory, effector PD1int and PD1hi) were sorted by flow cytometry and ATAC-seq was performed. Additional naive CD8+ T-cell samples (n=3) were sorted from non-tumor bearing WT mice.

first: Bola

last: Hanna

first: Laura

last: Llaó Cid

first: Murat

last: Iskar

first: Lara

last: Klett

first: Marc

last: Zapatka


title: Gene expression profiling of CD8+ T-cell subsets from TCL1-AT mice

summary: Analysis of the effect of CLL development on differentation and gene expression of CD8 T-cells

overall_design: C57BL/6 mice were transplanted with murine CLL cells from Eµ-TCL1 mice. Different CD8 T-cell subsets were FACS-sorted and total RNA was isolated after 6 weeks of transplantation

last: Llaó-Cid


title: Gene expression profiling of PD-1hi effector CD8+ T-cell after IL-10R blockade

summary: Analysis of the effect IL-10R blockade on PD-1hi effector CD8+ T-cells isolated from the TCL1-AT model of CLL

overall_design: C57BL/6 mice were transplanted with murine CLL cells from Eµ-TCL1 mice. After 3 weeks, mice were treated with IL-10R blocking antibody or isotype control for two weeks.


title: Interleukin-10 receptor signaling promotes the maintenance of a PD-1int TCF-1+ CD8+ T cell population that sustains anti-tumor immunity

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

overall_design: Refer to individual Series


title: Comparison between CBP80-associated and eIF4E-associated mRNAs in actively translating poylsomes

city: Seoul

first: Yoon Ki

last: Kim

address: Anam-ro 145, Seongbuk-gu

country: South Korea

institute: Korea University

summary: Two-color microarray experiment compariing the profiles of CBP80-associated mRNAs and eIF4E-associated mRNAs in actively translating polysomes.

overall_design: Relative enrichement of each mRNAs in CBP80 IP and eIF4E IP were analyzed and normalized. Relative ratio (CBP80 association/eIF4E association) was calculated.

first: Incheol

last: Ryu

first: Junho

last: Choe

first: Yoon


title: RNAseq analysis for lung resident cells from protease allergen and FK506 treated mice

status: Public on Dec 07 2021

city: Yokohama

first: Kosuke

last: Miyauchi

state: Kanagawa

address: 1-7-22 Suehiro-sho

institute: RIKEN Center for Integrative Medical Sciences

summary: There is evidence for the beneficial effect of FK506, an effective immunosuppressive agent, for the treatment of asthma; however, the mechanisms underlying these effects are unclear. Using a mouse model of airway inflammation induced by Papain, a protease allergen, and RNAseq analysis of lung innate cells, we found that FK506 inhibited the activation of ILC2s, which initiate airway inflammation, as well as the induction of TH2 cells, which cause chronic inflammation. Our findings further support the clinical value of FK506 for the treatment of allergen-induced airway inflammation and clarify its targets and mechanisms of action.

overall_design: Lung ILC2 cells, epithlial cells (type 1: AEC1 and type 2: AEC2), and basophils of mice were sorted and analyzed the transcriptome using Illumina HiSeq1500.

first: Masato

last: Kubo


title: Extracellular vesicle labeled Granulocyte macrophage progenitors


title: Genome-wide bisulfite sequencing (Xmal-RRBS) of 50 breast cancer samples for jointly using with NGS and chromosomal microarray data

city: Moscow

first: Alexey

middle: Igorevich

last: Kalinkin

state: Russia

address: Moskvorechie st., 1

department: Epigenetics

country: Russia

institute: RCMG

summary: To study the fundamental basics of patterning abnormal methylation we conducted a complex of genome-wide studies, including Xmal-RRBS on 50 breast cancer samples

overall_design:
Reduced representation bisulfite sequencing by XmaI-RRBS (Tanas et al., 2017)

Please note that the numerical values from 0 to 4 (in the characteristics columns) represents category according to TNM staging system of Malignant Tumors. T category describes the primary tumor site and size, N category describes the regional lymph node involvement and M category describes the presence or otherwise of distant metastatic spread.

middle: I

first: Alexander

middle: S

last: Tanas

first: Vladimir

last: Strelnikov


title: Genome-scale DNA methylation analysis identifies repeat element alterations that modulate the genomic stability of melanocytic nevi

city: Lebanon

first: Meghan

middle: E.

last: Muse

state: NH

address: One Medical Center Drive, DHMC

department: Epidemiology

institute: Geisel School of Medicine at Dartmouth

summary: Acquired melanocytic nevi grow and persist in a stable form into adulthood. Using genome-wide methylation profiling, we evaluated 32 histopathologically confirmed, and dermoscopically characterized nevi, with matched adjacent skin, to identify key epigenetic regulatory mechanisms involved in nevogenesis. Benign (n=13; 69% globular and 31% non-specific dermoscopic pattern) and dysplastic (n=19; 95% reticular/nonspecific dermoscopic pattern) nevi were dissimilar with only two shared differentially methylated (DM) loci. Relative to adjacent skin, benign nevi demonstrated an increase in both genome-scale methylation and methylation of Alu/LINE-1 retrotransposable elements, a marker of genomic stability, as well as global methylation. In contrast, dysplastic nevi showed evidence for genomic instability via hypomethylation of Alu/LINE-1. The difference in methylation between benign and dysplastic nevi was statistically significant for Alu (P = 0.00019) and LINE-1 (P = 0.000035) retrotransposable elements. Using dermoscopic classifications, reticular/nonspecific nevi had 59,572 CpG DM loci (Q < 0.05), whereas globular nevi had non-significant DM loci. The relative activity of reticular/non-specific nevi was evidenced by 50,720 hypomethylated loci being enriched for accessible chromatin, and 8,852 hypermethylated loci strongly enriched, for example, marks of active gene promoters, which suggests that gain of DNA methylation observed in these nevus types plays a role in gene regulation.

overall_design: Bisulphite converted DNA from paired nevus and adjacent normal skin tissue were hybridised to the Illumina HumanMethylationEPIC beadchip.

middle: E

first: Drew

last: Bergman

first: Lucas

last: Salas

first: Lisa

middle: N

last: Tom

first: Jean-Marie

last: Tan

first: Antonia

last: Laino

first: Richard

last: Sturm

first: Helmut

last: Schaider

first: H

last: Soyer

first: Brock

middle: C

last: Christensen

first: Mitchell

last: Stark


title: RNA Sequencing of WT and TET TKO cells at different developmental stages

city: Beijing

first: Heng

last: Pan

address: 49 North Garden Rd., Haidian District

institute: Peking University Third Hospital

summary: Changes in DNA methylation are associated with normal cardiogenesis, while altered methylation patterns can occur in congenital heart disease. Ten-eleven translocation (TET) enzymes oxidize 5-methylcytosine (5mC) and promote locus-specific DNA demethylation. Here we characterize stage-specific methylation dynamics and the function of TETs during directed differentiation of human embryonic stem cells (hESCs) to cardiomyocyte (CM) fate. No defect is observed using isogenic TET2, TET3 or TET2/3 double knockout lines, while TET1 knockout lines display a significant decrease in capacity to generate CTNT+ CMs. Moreover, hESCs in which all three TET genes are inactivated (TET TKO hESCs) fail entirely to generate CMs. TET-deficient cells display altered mesoderm patterning and defective cardiac progenitor specification. Genome-wide methylation analysis shows that TETs are required first to maintain hypomethylation of early regulatory genes, and subsequently for demethylation of cardiac structural genes. Mechanistically, TET knockout causes promoter hypermethylation of genes encoding WNT inhibitors, leading to hyperactivated WNT signaling and defects in cardiac mesoderm patterning. TET activity is also needed to maintain hypomethylated status and expression of NKX2-5 for subsequent cardiac progenitor specification. Finally, loss of TETs causes a set of cardiac structural genes to fail to be demethylated at the cardiac progenitor stage. Our data demonstrate key roles for TET proteins to control methylation dynamics at sequential steps during human cardiac development.

overall_design: RNA-Sequencing was perfromed at WT and TET TKO cells (n=2) at cardiac mesoderm (CME) stage on day 3, and cardiac progenitor (CP) stage on day 6

first: Yahui

last: Lan


title: Pantothenate metabolism fuels T cell antitumor immunity

city: Toronto

first: Pamela

last: Ohashi

state: Ontario

address: 610 University Ave

country: Canada

institute: Princess Margaret Cancer Centre

summary: Metabolic programming is a central regulator of T cell activation, differentiation and effector function. These metabolic processes are intricately linked to the anti-tumor properties of T cells and manipulation of T cell metabolism has shown promise in enhancing immunotherapy. To gain further insight into the metabolic pathways associated with increased anti-tumor T cell function, we utilized a metabolomics approach to interrogate the metabolic profile of three different CD8+ T cell subsets each with varying degrees of anti-tumor activity in murine models. These subsets include IFN-γ+ Tc1, IL-17+ Tc17 and IL-22+ Tc22 CD8+ effector subsets, of which Tc22 cells display the most robust anti-tumor activity. Here, we show that Tc22s were distinct in their up-regulation of the pantothenate/coenzyme A (CoA) pathway and requirement for oxidative phosphorylation (OXPHOS) for differentiation. Further investigation revealed that the exogenous administration of CoA metabolically reprogrammed T cells to increase OXPHOS and adopt the CD8+ Tc22 phenotype independent of polarizing conditions via the transcription factors HIF-1α and the aryl hydrocarbon receptor (AhR). CoA-treated CD8+ T cells demonstrated enhanced anti-tumor function and persistence following adoptive transfer in murine tumor models. Treatment of mice with the CoA precursor pantothenate also enhanced the efficacy of anti-PD-L1 antibody therapy in preclinical models. These findings were extended to human melanoma patients, as we correlated increased pre-treatment plasma pantothenate levels with response to anti-PD1 antibody therapy. Collectively, our data demonstrate that pantothenate and its metabolite CoA drive T cell polarization, bioenergetics and anti-tumor immunity.

overall_design: Tc0 cells, Tc22 cells and Tc0 cells treated with CoA, compared in triplicate. All cell populations were extracted from each mouse (matched per sample).

first: Michael

last: St-Paul

first: Sam

last: Saibil

first: Azin

last: Sayad

first: Pam


title: TGF-β-induced miR143/145 influences differentiation, insulin signaling and exercise response in human skeletal muscle [small RNA-seq]

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary: Physical training improves insulin sensitivity and can prevent type 2 diabetes. However, approximately 20% of individuals lack a beneficial outcome in glycemic control. TGF-β, identified as a possible upstream regulator involved in this low response is also a potent regulator of microRNAs (miRs). Aim of this study was to elucidate the potential impact of TGF-β-driven miRNAs on individual exercise response. Non-targeted long and sncRNA sequencing analyses of TGF-β1-treated human skeletal muscle cells corroborated the effects of TGF-β1 on muscle cell differentiation and the induction of extracellular matrix components, and identified several TGF-β1-regulated miRs. qPCR validated a potent upregulation of miR143/145 and miR181a2 by TGF-β1 in both human myoblasts and differentiating myotubes. Human skeletal muscle biopsy donors participating in a supervised 8-week endurance training intervention (n=40) were categorized as responder based on fold change ISIMats (≥ +1.1) or low responder. In skeletal muscle of low responders, TGF-β signaling and miR143/145 levels were stronger induced by training than in responders. Target-mining revealed HDACs, MYHs and insulin signaling components INSR and IRS1 as potential miR143/145 targets. All these targets were down-regulated in TGF-β1-treated myotubes. Transfection of miR mimics in differentiated myotubes validated MYH1, MYH4, and IRS1 as miR143/145 targets. Elevated TGF-β signaling and miR143/145 induction in skeletal muscle of low responders might obstruct improvements in insulin sensitivity by training in two ways: By negatively impacting cell fusion and myofiber functionality via miR143 suppressing its novel targets MYH1/4; by directly impairing insulin signaling via reduction of INSR by TGF-β and fine-tuned IRS1 suppression by miR143.

overall_design: Human skeletal muscle cells treated with TGF-β1, TGF-β1 + SB431542, or control cells. Data was analysed by small RNAseq.

first: Simon

last: Dreher

first: Selina

last: Höckele

first: Peter

last: Huypens

first: Martin

last: Irmler

first: Christoph

last: Hoffmann

first: Tim

last: Jeske

first: Maximilian

last: Hastreiter

first: Anja

last: Moller

first: Andreas

middle: L

last: Birkenfeld

first: Hans

middle: U

last: Häring

last: Peter

last: Hrabě de Angelis

first: Cora

last: Weigert


title: TGF-β-induced miR143/145 influences differentiation, insulin signaling and exercise response in human skeletal muscle [RNA-seq]

overall_design: Human skeletal muscle cells treated with TGF-β1, TGF-β1 + SB431542, or control cells. Data was analysed by RNAseq.


title: ERRBS of WT and TET TKO cells from stem cell (SC) to cardiomyocyte (CM)

first: Heng

last: Pan

overall_design: ERRBS was performed at four time points: stem cell stage (SC) at day 0, cardiac mesoderm (CME) at day 3, cardiac progenitor (CP) stage at day 8 and beating cardiomyocyte (CM)  at day 14 in WT and TET TKO cells. For TKO cells can not generate beating CMs,  eRRBS was not performed with day 14 TKO cells).

first: Lan

last: Yahui

first: Pan

last: Heng


title: Inhibition of Soluble Epoxide Hydrolase is Protective Against the Multiomic Effects of a High Glycemic Diet on Brain Microvascular Inflammation and Cognitive Dysfunction

city: Davis

first: Saivageethi

last: Nuthikattu

state: CA

address: 550 Hutchison Dr

department: Internal Medicine, Cardiovascular division

institute: University of California Davis

summary:
Diet is a modifiable risk factor for cardiovascular disease (CVD) and dementia, yet relatively little is known about the effect of a high glycemic diet (HGD) on the brain microvasculature.  The objective of our study was to determine the molecular effects of a HGD on hippocampal microvessels and cognitive function, and to determine if a soluble epoxide hydrolase (sEH) inhibitor (sEHI), known to be vasculoprotective and anti-inflammatory, modulates these effects.
Global hippocampal microvascular gene expression was fundamentally different for mice fed the HGD vs the LGD.  The HGD response was characterized by differential expression of 608 genes involved in cell signaling, neurodegeneration, metabolism, and cell adhesion/inflammation/oxidation effects reversible by t-AUCB and hence sEH inhibitor correlated with protection against Alzheimer’s dementia.

overall_design: Wild type male mice were fed a low glycemic diet (LGD, 12% sucrose/weight) or a HGD (34% sucrose/weight) with/without the sEHI, trans-4-[4-(3-adamantan-1-yl-ureido)-cyclohexyloxy]-benzoic acid (t-AUCB), for 12 wks. Brain hippocampal microvascular gene expression was assessed by microarray and data analyzed using a multiomic approach for differential expression of protein and non-protein coding genes, gene networks, functional pathways, and transcription factors.

first: Dragan

last: Milenkovic

first: Jennifer

last: Norman

first: John

last: Rutledge

first: Amparo

last: Villablanca


title: TET1-V5 ChIP-seq

overall_design: V5 CHIP-seq was perfromed at D7 cardiac progenitor (CP) cells in the background of TET1-V5 endogenously tagged H1 stem cell line


title: The cardiac glycoside deslanoside imposes an anticancer effect on prostate cancer involving multiple signaling pathways

city: Shenzhen

first: Jin-Tang

middle: and

last: Dong

state: Guangdong

address: 1088 Xueyuan Blvd., Research Building 2B

institute: Southern University of Science and Technology

summary: Prostate cancer (PCa) is a leading cause of cancer-related deaths among men worldwide, and advanced prostate cancers are mostly incurable. It is urgently needed to find new therapeutic options. Deslanoside is a cardiac glycoside, the efficacy of which on cancers has never been reported. In this study, we investigated the effects of deslanoside on advanced PCa for the first time. RNA-sequencing results identified 141 differentially expressed mRNAs in deslanoside-treated PCa cells compared to untreated cells, which were significantly enriched in the cancer-associated pathways, including necroptosis, MAPK signaling pathway, NOD-like receptor signaling pathway, focal adhesion, small lung cancer, GnRH signaling pathway, IL-17 signaling pathway, TNF signaling pathway and apoptosis. Kaplan-Meier plotter analysis identified the effects of 11 deslanoside-influenced genes on recurrence-free survival and 4 genes on overall survival. Taken together, these results repurpose that a novel utilization of deslanoside in prostate cancer, which exerts profound inhibitory effects on advanced PCa progression.

overall_design: Prostate cancer mRNA profiles of DMSO-treated and Deslanoside-treated cells

first: Qingqing

last: Huang

first: Mingcheng

last: Liu

first: A

last: Jun

first: Xiawei

last: Li


title: TGF-β Induction of miR-143/145 Is Associated to Exercise Response by Influencing Differentiation and Insulin Signaling Molecules in Human Skeletal Muscle

first: Johannes

last: Beckers


title: MiRNA regulation of T cell exhaustion in cutaneous T cell lymphoma [CTCL_miRNA]

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: Cutaneous T cell lymphoma (CTCL) is characterized by the proliferation of CD4+ T cells in a background of chronic inflammation, where malignant CTCL cells escape immune surveillance and are not eliminated. To study how miRNAs (miRs) regulate T cell exhaustion in this disease, we performed miRseq analysis, qRT-PCR, and in situ hybridization on 45 primary CTCL samples, 3 healthy skin samples, and CTCL cell lines, identifying miR-155-5p, -130b-3p and -21-3p. Moreover, miR-155-5p, -130b-3p, and -21-3p positively correlated with immune checkpoint gene expression in lesional skin samples and were enriched in the IL6/JAK/STAT signaling pathway by gene set enrichment analysis.

overall_design: miRNAs related to CTCL tumors

first: Zhen

last: Han

first: Christiane

last: Querfeld


title: Genome-wide screens identify calcium signalling as a key regulator of IgE+ plasma cell differentiation and survival

city: London

first: Pavel

last: Tolar

state: London

address: 1 Midland Rd

country: United Kingdom

institute: Francis Crick Institute

summary: In this experiment the transcriptional profiles of B cell subsets from in vitro B cell cultures were compared using RNA-seq.

overall_design: Transcriptional profiles were generated from three independent biological replicates in four flow sorted immune cell subsets, and one bulk sample from earlier in the culture (day 6). Gene expression profiles were compared between all samples.

first: Rebecca

last: Newman

first: Harshil

last: Patel


title: Hfq RIL-seq in Salmonella

city: Würzburg

first: Jörg

last: Vogel

address: Josef-Schneider-Straße 2

department: Institute for Molecular Infection Biology

institute: Würzburg University

summary: We have used the RIL-seq technique to map the global RNA-RNA interactome on the sRNA chaperone Hfq in Salmonella enterica.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: RIL-seq (Melamed et al. 2016) with Hfq in Salmonella

first: Gianluca

last: Matera

first: Milan

last: Gerovac


title: RNA Sequencing reveals induction of specific renal inflammatory pathways in a rat model of malignant hypertension

first: Philipp

last: Kirchner

address: Murtenstrasse 31

department: Pathology

summary: In malignant hypertension, far more severe kidney injury occurs than in the “benign” form of the disease. The role of high blood pressure and the renin-angiotensin-aldosterone system are well recognized, but the development of malignant nephrosclerosis remains incompletely understood.  Using the rat model of two-kidney, one-clip renovascular hypertension in which some but not all animals develop malignant nephrosclerosis, we performed an unbiased analysis of genes by RNA-sequencing to identify transcriptional changes in the kidney specific for malignant nephrosclerosis. Differential gene expression was assessed in three groups: malignant hypertension (MH), non-malignant hypertension (NMH) and normotensive, sham operated controls (sham). To distinguish MH from NMH, we considered two factors: weight loss and typical renovascular lesions. Mean blood pressure measured intraarterially was elevated to a similar degree in MH (220.0±6.5 mmHg) and NMH (192.0±6.4 mmHg) compared to controls (119.5±1.7 mmHg, p<0.05). 886 genes were exclusively regulated in MH only. Principal component analysis revealed a separated clustering of the three groups. The data pointed to an upregulation of many inflammatory mechanisms in MH including pathways, which did previously attract relatively little attention in the setting of hypertensive nephrosclerosis: Transcripts from all three complement activation pathways were upregulated in MH compared to NMH but not in NMH compared with controls; immunohistochemistry confirmed complement deposition in MH exclusively. The expression of chemokines attracting neutrophil granulocytes (CXCL6) as well as actual granulocyte infiltration were increased only in MH rats. The data suggest that these pathways may contribute to the most severe forms of hypertensive nephrosclerosis.

overall_design: Analysis of gene expression in the kidney in a animal model of renovascular hypertension elucidating the pathogenic background of malignant hypertension using RNA-Seq

first: Karl

middle: F

last: Hilgers

first: Carlos

last: Menendez-Castro

first: Arif

middle: B

last: Ekici


title: Global interpretation of novel alternative splicing events in human congenital pulmonary airway malformations

city: Xi'an

first: jiwen

last: cheng

state: Shaanxi

address: Xiwu Road

institute: Xi'an Jiaotong University

summary: To explore the long non-coding RNA (lncRNA) expression pattern of congenital lung malformations on a genome-wide scale and investigate their potential biological function in four types of congenital lung malformations.

overall_design: CPAM-Ⅰ (N=3), CPAM (N=3), ILS (N=3) and ILS-CPAM (N=3);Normal lung control samples (N=3)

first: W

last: Yang

first: J

last: Cheng

first: Y

last: Gao

first: P


title: Functional Organization of the Maternal and Paternal Human 4D Nucleome

city: Ann Arbor

first: Indika

last: Rajapakse

state: Michigan

address: 500 S State St

country: USA

institute: University of Michigan

summary: Allele-specific analysis of RNA-seq, Bru-seq, and Hi-C data from human diploid B-lymphocytes.

overall_design: Cell cycle sorted RNA-seq with 3 replicates, Bru-seq with 3 replicates, and Hi-C

first: Stephen

last: Lindsly

first: Wenlong

last: Jia

first: Haiming

last: Chen

first: Sijia

last: Liu

first: Scott

last: Ronquist

first: Can

first: Xingzhao

last: Wen

first: Gabrielle

middle: A

last: Dotson

first: Charles

last: Ryan

first: Gilbert

last: Omenn

first: Shuai

last: Cheng Li

first: Max

last: Wicha

first: Alnawaz

last: Rehemtulla

first: Lindsey

last: Muir


title: Identification of a natural beige adipose depot in mice

city: Singapore

first: Lei

last: Sun

address: 8 College Road

country: Singapore

institute: Duke-NUS

summary: Profiling the transcriptome of four adipose tissues in mice

overall_design: C57BL66/J male mice were induced obesity by high fat diet and collected adipose tissues

first: Yen

last: Lim


title: RNA-Seq analysis of 9G8-RNAi fat bodies in Drosophila

status: Public on Dec 06 2021

city: Reading

first: Justin

last: DiAngelo

state: PA

address: P.O. Box 7009, Tulpehocken Rd.

institute: Penn State Berks

summary: Previous studies from our lab have characterized a group of splicing factors called SR proteins that function to identify intron/exon borders in regulating metabolic homeostasis in the Drosophila fat body.  Decreasing the function of one SR protein, 9G8, causes an increase in triglyceride storage; however, the full complement of 9G8 target genes that regulate metabolism is unknown.  To address this question, we performed RNA sequencing on Drosophila fat bodies with 9G8 levels reduced by RNAi.

overall_design: Drosophila fat body mRNA proflies of yolk-Gal4>9G8-RNAi fat bodies compared to yolk-Gal4/+ control fat bodies (4 samples of each genotype).

middle: R


title: m6A-Seq in METTL14 R298P mutation knock-in cell clones

city: Suita

first: Atsushi

last: Kumanogoh

state: Osaka

address: 2-2 Yamadaoka

institute: Osaka University

summary: N6-methyladenosine (m6A) is the major type of RNA modiﬁcation that regulates RNA stability and gene expression, characterized by a conserved motif including 5′-(m6A)C-3′. However, the functional significance of the specific motif for m6A modification is unclear. Here, we focused on a single amino acid substitution in the m6A “writer” complex, METTL14 R298P, and created mutation knock-in cells. m6A individual-nucleotide-resolution cross-linking and immunoprecipitation and methylated RNA immunoprecipitation with next-generation sequencing (MeRIP-Seq) revealed that METTL14R298P/R298P but not METTL14WT/R298P cells had an aberrant sequence motif, 5′-(m6A)[C/T]-3′. This study reveals a mechanism underlying sequence-specific m6A modification.

overall_design: METTL14 R298P mutation knock-in cell clones were established from HEC108 cell line. m6A-seq analysis was performed on poly(A)-purified mRNA.

first: Kotaro

last: Miyake

first: Yuki

last: Kato

first: Yukio

last: Kawahara