title: Single-Cell Transcriptomics Reveals the Differentiation and Spatial Signatures underlying Sheep Hair Follicle Heterogeneity and Wool Curvature

status: Public on Jan 12 2022

city: Yangzhou

first: Shanhe

last: Wang

address: Wenhui road

institute: Yangzhou University

summary: Here, Single-cell suspensions from the wavy wool and straight wool lambskins were prepared for unbiased single-cell RNA sequencing (scRNA-seq). Based on UAMP analysis, we identified 19 distinct populations from 15,830 single-cell transcriptomes and delineated their cellular identity from specific gene expression profiles. Furtherly, novel marker gene was applied in identifying dermal papilla cells isolated in vitro. By using pseudotime ordering analysis, we successfully constructed the epithelium cell lineage differentiation trajectory and revealed the dynamic gene expression profiles of matrix progenitors’ commitment to the hair shaft and inner root sheath (IRS) cells. Meanwhile, intercellular communication between different cell populations was inferred based on CellChat and the priori knowledge of ligand-receptor pairs, as a result strong intercellular communication and associated signaling pathways were revealed. Besides, to clarify the molecular mechanism of wool curvature, differentially expressed genes in specific cells between straight wool and curly wool were identified and analyzed. Our findings here provide unbiased and systematic view of transcriptional organization of sheep hair follicle, reveal the differentiation and spatial signatures underlying sheep hair follicle heterogeneity and wool curvature, which will provide a valuable resource for understanding the molecular pathways involved in sheep hair follicle development.

overall_design: To gain insight into the transcriptional heterogeneity of the anagen hair follicle cells and the molecular mechanisms of wool curvature, we performed scRNA-seq on Hu sheep skins from straight wool individuals and waved wool individuals. We detected 19,097 genes in skin cells for straight wool group and 19,059 genes for waving wool group. After removing low quality cells, we obtained 15830 single-cell transcriptome profiles from these two groups (7,263 for straight wool group and 8,567 single cells for waving wool group)

first: Wang

last: Shanhe

first: Sun

last: Wei


title: In vivo Genome-scale CRISPR-Cas9 knockout screening

status: Public on Jan 14 2022

city: Shanghai

first: Jingyu

last: Lang

address: 320 Yueyang Road

country: China

institute: Shanghai Institutes for Biological Sciences

summary: To identify essential gene responding to anti-PD-1 immunotherapy, we performed in vivo Genome-scale CRISPR-Cas9 knockout screening. We found that cohesin complex invovled in regulation of anti-PD-1 immunotherapy.

overall_design: We performed two rounds of in vivo screening in two cell types.

first: Yumin

last: Han


title: Targeting Histone Demethylase LSD1 for Treatment of Deficits in Autism Mouse Models

status: Public on Jan 13 2022

city: Buffalo

first: Zhen

last: Yan

state: NY

address: 955 Main St

country: USA

institute: SUNY Buffalo

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Targeting Histone Demethylase LSD1 for Treatment of Deficits in Autism Mouse Models [ChIP-seq]

summary: We performed chromatin immunoprecipitation sequencing (ChIPseq) to profile genome-wide occupancy of H3K4me2 in PFC from WT mice and Shank3 +/∆C Tau mice.

overall_design: Examination of the transcriptional changes of target genes related to the alteration of H3K4me2 from isolated nuclei of 6-week-old Shank3 +/∆C and 6-week-old control (C57BL/6 x C3H) mice from PFC tissue were compared.

first: Fengwei

last: Yang

first: Jamal

last: Williams


title: Targeting Histone Demethylase LSD1 for Treatment of Deficits in Autism Mouse Models [RNA-seq]

summary: We performed RNAseq experiments to examine genome-wide transcriptional changes in PFC of Shank3 +/∆C mice with or without GSK-LSD1 treatment.

overall_design: mRNA via RNAseq analysis of two 6- to 8-week-old Shank3 +/∆C mice with GSK-LSD1, and two 6- to 8-week-old Shank3 +/∆C mice with vehicle, and two 6- to 8-week-old control (WT; C57BL/6 x C3H) mice with vehicle from PFC tissue were compared.


title: Transcriptome sequence of oriental melon fruit at diferent stages in two cultivars

city: Shenyang

first: Hongyan

last: Qi

state: Liaoning

address: No.120 Dongling Road, Shenhe District

department: College of Horticulture

institute: Shenyang Agricultural University

summary:
Purpose: the goals of this study are to compare fruit of two clitivars oriental melon transcriptome profiling (RNA-seq) at different stages to explore carotenoid potentail carotenoid accumulation mechanism
Methods:The transcriptome sequence of two cultivars oriental melon fruits at different stages were generated by deep sequencing with three repeats using Illumina. The sequence reads that passed filters were mapped to melon genome (http://cucurbitgenomics.org/organism/18) using HISAT2 software. The differently expressed genes were identify by |log2(FoldChange)| > 0 & padj <= 0.05, and qRT–PCR validation was performed using SYBR Green assays
Result:Using an optimized data analysis workflow, we mapped about 40 million sequence reads per sample to the melon genome. The differentially expressed genes were functionally classified by GO and KEGG enrichment. We focused on carotenoid metabolism related gene and validated using qRT-PCR. The results showed RNA-seq and qRT-PCR were highly correlated.
Conclusion: Our study provided transcriptome sequence of oriental melon fruits at different stages in two cultivars. The optimized data analysis workflows reported here should provide comparative framework of expression profiles. Our transcriptome characterization contribute to analyze gene functions and metabolic process of oriental melon.

overall_design: Oriental melon fruits mRNA profiles of different stages in two cultivars.

first: Xiaoyu

last: Daun

first: Cai

last: Jiang

first: Yaping

last: Zhao

first: Ge

last: gao

first: Meng

last: Li


title: Ruxolitinib cream in the treatment of cutaneous lichen planus: A prospective, open-label study

city: Rochester

first: Chantal

last: McCabe

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

summary: Ruxolitinib is a Janus kinase 1/2 inhibitor (JAK1/2) that blocks signal transduction of interferon-gamma, a critical cytokine involved in the pathogenesis of cutaneous lichen planus (LP). In this prospective phase II study, we investigated the efficacy of topical ruxolitinib in cutaneous LP and performed transcriptomic analysis pre- and post-therapy. Twelve patients with cutaneous LP applied topical ruxolitinib twice daily for 8 weeks. Primary endpoints were change in total lesion count and modified Composite Assessment of Index Lesion Severity (mCAILS) score in index treated and untreated index control lesions at week 4. Total lesion count decreased by a median of 50 lesions (interquartile range 25, 723; p<0.001). mCAILS scores decreased by a mean difference of 7.6 (standard deviation 8.8, p=0.016) between index treated and control lesions. Type I and II interferon pathways were enriched in LP and responsive disease displayed downregulation of interferon-stimulated genes (ISGs). In this small pilot study, topical ruxolitinib was highly effective in the treatment of cutaneous LP. Transcriptomic analysis confirmed LP as an interferon-driven disease and downregulation of ISGs correlated with disease response.

overall_design: Whole transcriptomic analysis was performed on lesional and control (normal skin) tissue pre-therapy (n=19, 10 respectively) and lesional responsive and refractory post-therapy (n=13, 5 respectively).

first: Caitlin

middle: M

last: Brumfiel

first: Meera

middle: H

last: Patel

first: Kevin

middle: J

last: Severson

last: Zhang

first: Xing

first: Jaxon

middle: K

last: Quillen

first: Samantha

last: Zunich

first: Emily

middle: L

last: Branch

first: Steven

middle: A

last: Nelson

first: Mark

middle: R

last: Pittelkow

first: Aaron

last: Mangold


title: RNAseq analysis of the transcriptome of an Arabidopsis mutant, ahl13, elicitated by pstDC3000 or flg22

city: 福州市

first: baomin

last: Feng

state: 福建省

address: 福建农林大学, 上下店路15号， 诚智楼C4层

institute: 福建农林大学

summary:
Purpose: The experiment is to compare the NGS-derived seedling and leaf transcriptome profiling (RNAseq) of an Arabidopsis mutant ahl13 with that of wild type upon bacterial pathogen (pst DC3000) and flagellin elicitation.
Method： The mRNA profiles of 10-day-old wild-type (WT) and AHL13 knockout (ahl13, SALK_014014) Arabidopsis were generated by RNAseq using Illumina NovaSeq6000. The sequence reads were passed through quality filters and mapped to Arabidopsis genome by TopHat2 followed by transcript splicing and quantitation by Cufflinks. DESeq was done to analyze differential gene expressions. qRT–PCR validation was performed using SYBR Green assays
Result: We mapped about 20 million sequencing reads per sample to the Arabidopsis genome and identified approximately 28,000 transcripts in the Arabidopsis Col-0 and ahl13 mutant using TopHat2. Differentially expressed genes were identified using DESeq2 and about 166 genes show up-regulation in ahl13 upon DC3000 infection (FC>2, FDR<0.01)
Conclusions: The ahl13 mutant exhibit differential transcription profile from that of Col-0 upon DC3000 treatment but similar upon flg22 treatment.

overall_design: The mRNA profiles of wild type (WT, Col-0) and ahl13-/- Arabidopsis elicitated by a bacterial pathogen (DC3000) or flg22

first: Qianqian

last: Chen

first: Baomin


title: Type I interferon activates MHC class I-dressed CD11b+ conventional dendritic cells to promote protective anti-tumor CD8+ T cell immunity

city: Cambridge

first: Ellen

last: Duong

state: MA

address: 500 Main Street, 76-401

department: Koch Institute for Integrative Cancer Research; Biology Department

institute: Massachusetts Institute of Technology

summary: Tumor-infiltrating antigen-presenting cells, such as dendritic cells (DC), have the capacity to shape anti-tumor T cell responses. While tremendous progress has been made in unraveling the role of Batf3-driven DC1 in the anti-tumor immune response, the contributions of other tumor-infiltrating DC subsets remain poorly understood. Furthermore, tumor-infiltrating DC exist in a range of functional states with differential impacts on anti-tumor immunity. In this study, we sought to identify and characterize the functionally relevant DC states associated with a productive anti-tumor T cell response. By comparing the DC infiltrate of spontaneously regressing tumors and progressing tumors, we identified a novel activation state of CD11b+ conventional DC in tumors, which expressed an interferon-stimulated gene signature (‘ISG+ DC’). ISG+ DC were activated by type-I-interferon-induced signaling and could generate protective CD8+ T cell responses by cross-dressing with tumor-derived peptide-MHC complexes. Stimulatory ISG+ DC induced by exogenous IFNβ addition drove robust anti-tumor T cell responses in poorly immunogenic tumors even in the absence of DC1.

overall_design: Sorted live CD45+ immune cells from pooled MC57-SIY tumors (at day 7 post-tumor inoculation in Rag2-/- C57BL/6 hosts) were sequenced.

first: Tim

middle: B

last: Fessenden

first: Emi

last: Lutz

first: Teresa

last: Dinter

first: Leon

last: Yim

first: Sarah

last: Blatt

first: Arjun

last: Bhutkar

first: Karl

middle: D

last: Wittrup

first: Stefani

last: Spranger


overall_design: Sorted DC populations from pooled MC57-SIY tumors (at day 7 post-tumor inoculation in WT and Rag2-/- C57BL/6 hosts) were analyzed by bulk RNA-sequencing.


title: The site of breast cancer metastases dictates their clonal composition and reversible transcriptomic profile

city: Heidelberg

first: Delphine

last: Merino

state: Victoria

address: Level 5, ONJ Centre, 145 Studley Rd, Heidelberg

department: Translational Breast Cancer Program

country: Australia

institute: Olivia Newton-John Cancer Research Institute

summary: Intratumoral heterogeneity is a driver of breast cancer progression, but the nature of the clonal interactive network involved in this process remains unclear. Here, we optimized the use of optical barcoding to visualize and characterize 31 cancer subclones in vivo. By mapping the clonal composition of thousands of metastases in two clinically relevant sites, the lungs and liver, we found that metastases were highly polyclonal in lungs but not in the liver. Furthermore, the transcriptome of the subclones varied according to their metastatic niche. We also identified a reversible niche-driven signature that was conserved in lung and liver metastases collected during patient autopsies. Among this signature, we found that the tumor necrosis factor–α pathway was up-regulated in lung compared to liver metastases, and inhibition of this pathway affected metastasis diversity. These results highlight that the cellular and molecular heterogeneity observed in metastases is largely dictated by the tumor microenvironment.

overall_design: Bulk RNA-sequencing data of two subclones of LeGO-barcoded MDA-MB-231 cells from primary tumors and metastatic sites (lung & liver) in NOD-SCID-IL2Rγc−/− (NSG) mice

first: Jean

last: Berthelet

first: Verena

middle: C

last: Wimmer

first: Holly

last: Whitfield

first: Antonin

last: Serrano

first: Thomas

last: Boudier

first: Stefano

last: Mangiola

first: Michal

last: Merdas

first: Farrah

last: El-Saafin

first: David

last: Baloyan

first: Jordan

last: Wilcox

first: Adam

last: Parslow

first: Anthony

middle: T

last: Papenfuss

first: Belinda

last: Yeo

first: Matthias

last: Ernst

first: Bhupinder

last: Pal

first: Robin

last: Anderson

first: Melissa

last: Davis

first: Kelly

last: Rogers

first: Frederic

last: Hollande


title: Analysis of tissue-derived alveolar and monocyte-derived alveolar macrophages at day 7 and day 14 post-nippostrongylus brasiliensis infection.

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

summary: Alveolar macrophages from Cx3cR1-CreER x Rosa26-tandem dimer Tomato(TdT) control and infected mice were sort-purified on live CD45+CD64+F4/80+CD11c+SiglecF+ and then sorted based on expression of TdT, with tissue-resident cells being TdT- and monocyte-derived cells TdT+. Illumina-compatible libraries were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina (catalog no. E7645S; New England BioLabs) and sequenced using an Illumina NextSeq 550 in a single-end 75-base pair (bp) read configuration. Bulk RNA-seq analysis was performed in accordance with the nf-core RNA-seq guidelines v.1.4.2. The output reads were aligned to the GRCm38 genome using STAR, followed by gene count generation using featureCounts and StringTie. Read counts were normalized and  compared for differential gene expression using DESeq2 with significance at a false discovery rate-adjusted P<0.05. We report that at day 7 monocyte-derived alveolar macrophages  had a gene expression profile distinct from tissue-derived alveolar macrophages while by day 14 the monocyte-derived macrophages had assumed gene expression profiles more similar to tissue-derived alveolar macrophages, as determine by pairwise Euclidean distance calculation and principal components analysis.

overall_design: Examination and analysis of tissue-resident alveolar macrophages versus monocyte-derived macrophages at two different time points post-nippostrongylus brasiliensis infection.

first: John

last: Ponessa

first: Mark

last: Siracusa

first: William

last: Gause


title: Genome-wide chromatin state in non-failing and dilated cardiomyaphty human left ventricles

city: Cleveland

first: Chia-Feng

last: Liu

state: OH

address: 9500 Euclid Avenue,

department: Cardiovascular & Metabolic Sciences

institute: Cleveland Clinic Lerner Research Institute


title: WT and lincRNA-EPS knockout iBMMs that knocked down PKR or not

city: Jiangsu suzhou

first: Jingfei

last: Zhu

state: CN

address: Chongwen Road 215123

institute: ISM

summary: Test transcripts in control and siPKR WT and lincRNA-EPS knockout iBMMs

overall_design: There are four samples included with two replicates, and the WN sample is the control group


title: WT and lincRNA-EPS knockout iBMMs that infected with VSV or not

summary: Test transcripts in mock and VSV infected WT and  lincRNA-EPS knockout iBMMs

overall_design: There are four samples included with two replicates, and the WT-Mock sample is the control group


title: lncRNA-sequencing in a rat model of hypoxic pulmonary hypertension (HPH)

city: Nanjing

first: Ruifeng

last: Zhang

address: 87Dingjiaqiao Road

institute: Zhongda Hospital of Southeast University

type: Non-coding RNA profiling by high throughput sequencing

summary: lncRNA sequencing for 6 samples  of the HPH (10% fractional inspired oxygen) and the control(N, 21% fractional inspired oxygen) groups.

overall_design: Examing 2 conditions (HPH, 10% fractional inspired oxygen and N, 21% fractional inspired oxygen), each with 3 replicates


title: m7G-MeRIP-sequencing in a rat model of hypoxic pulmonary hypertension (HPH)

type: Methylation profiling by high throughput sequencing

summary: m7G-MeRIP-sequencing for 6 samples  of the HPH (10% fractional inspired oxygen) and the control(N, 21% fractional inspired oxygen) groups.

overall_design: Examing 2 conditions(HPH, 10% fractional inspired oxygen and N, 21% fractional inspired oxygen), each with 3 replicates


title: Inflammatory fibroblasts mediate resistance to neoadjuvant therapy in rectal cancer

city: Frankfurt

first: Adele M.

last: Nicolas

state: Deutschland (DEU)

address: Paul Ehrlich StraBe 42 44, Frankfurt Main, Frankfurt Main

country: Germany

institute: Georg Speyer Haus

summary: Standard cancer therapy targets tumor cells while not considering the possible collateral damage on the tumor microenvironment that could impair therapy response. Employing patient-derived tumor organoids and primary stroma cells or a novel murine rectal cancer model, we show that tumor cell-derived IL-1a polarizes cancer-associated fibroblasts (CAFs) towards a pro-inflammatory phenotype causing an elevated oxidative DNA damage mediated by reactive nitrogen species (NOS) and subsequently sensitizing iCAFs to a p53-mediated therapy-induced senescence, which triggers changes in matrisome composition culminating in chemoradiotherapy resistance and disease progression. Consequently, IL-1 inhibition, prevention of iCAF senescence or senolytic therapy sensitizes mice to irradiation. Importantly, rectal cancer patients with poor response to radiotherapy are characterized by an increased number of CAFs, a dominant inflammatory CAF gene signature as well as lower IL-1 receptor antagonist (IL-1RA) serum levels. Low baseline IL1RA gene expression predicts poor outcome while IL-1RA serum levels are associated with a single nucleotide polymorphism (SNP) in IL1RA (rs4251961 T/C). Moreover, conditioned supernatant from patient tumor organoids sensitizes fibroblasts to undergo radiation-induced senescence in an IL-1-dependent manner. Collectively, we unravel a critical role for inflammatory CAFs in cancer therapy and identify IL-1 signaling as an attractive target for stroma-repolarization and prevention of CAF senescence.

overall_design: Total RNA sequencing of 117 locally advanced rectal cancer (RCA) samples collected from baseline, pre-chemoradiotherapy (CRT) formalin-fixed paraffin-embedded (FFPE) biopsies (total of 105 pre-CRT samples) and post-CRT FFPE surgical specimens (total of 12 post-CRT samples). RCA patients were treated with neoadjuvant CRT followed by surgical resection. 26 patients post-CRT showed complete pathological response (i.e. complete tumor regression in the rectal wall and lack of residual metastatic lymph nodes: ypT0N0M0) while 79 RCA patients were without pCR (non-pCR).

first: Adele

first: Florian

last: Greten

first: Emmanouil

last: Fokas


title: Transcriptional heterogeneity among subclonal populations of MDA-MBA-468 triple-negative breast cancer cells

city: Boston

first: Joan

middle: S.

last: Brugge

address: 240 Longwood Avenue

department: Department of Cell Biology

institute: Harvard Medical School

summary: Intratumoral heterogeneity has been described for various tumor types and models of human cancer, and can have profound effects on tumor progression and drug resistance. This study describes transcriptional heterogeneity among subclonal populations (SCPs) derived from a single triple-negative breast cancer cell line.

overall_design: Bulk RNA-sequencing (RNA-seq) analysis was performed on 22 SCPs and the parental cell line grown in vitro (two samples for parental and SCP32, and 1 sample of each other SCP).

first: Hendrik

last: Kuiken

first: Laura

last: Selfors

middle: S


title: Epigenome analysis of parental and ABT-199 resistant AML cell lines

city: North Chicago

first: Shaun

last: Grosskurth

state: Illinois

address: 1 North Waukegan Road

institute: AbbVie

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of parental, ABT-199 resistant population, and ABT-199 resistant clones from 3 acute myelogenous leukemia (AML) cell lines (MOLM-13, MV-4-11, OCI-AMLO2). The Illumina Infinium MethylationEPIC Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs from AML cell line samples. Samples include 4 ABT-199 sensitive parental MOLM-13 population samples, 4 ABT-199 resistant MOLM-13 population samples, 3 ABT-199 resistant MOLM-13 S2 clone samples, 3 ABT-199 resistant MOLM-13 S5 clone samples, 4 ABT-199 resistant MOLM-13 S6 clone samples, 3 ABT-199 sensitive parental MV-4-11 population samples, 3 ABT-199 resistant MV-4-11 population samples, 3 ABT-199 sensitive parental OCI-AML2 population samples, 3 ABT-199 resistant OCI-AML2 population samples, 3 ABT-199 resistant OCI-AML2 S1 clone samples, 3 ABT-199 resistant OCI-AML2 S2 clone samples, 3 ABT-199 resistant OCI-AML2 S8 clone samples.

overall_design: Bisulphite converted DNA from the 39 samples were hybridised to theIllumina Infinium MethylationEPIC Human DNA Methylation Beadchip

first: Relja

last: Popovic

first: Bridget

last: Riley-Gillis

first: Priyanka

last: Vijay

first: Sujana

last: Ghosh

first: Charles

last: Lu

first: Joel

last: Leverson

first: Qi

first: Lina

last: Han

first: Yanan

last: Jia

first: Alessia

last: Lodi

first: Haijiao

first: Rongqing

last: Pan

first: Sergej

middle: N

last: Konoplev

first: Tianyu

last: Cai

first: Shannon

last: Sweeney

first: Saravanan

last: Ganesan

first: Jeremy

last: Ryan

first: Yulia

last: Jitkova

first: Kenneth

last: Dunner

first: Wencai

last: Ma

first: Stephen

last: Kurtz

first: Vivian

last: Ruvolo

first: Helen

first: Connie

last: Weng

first: Ce

last: Shi

first: Cassandra

last: Ramage

first: Natalia

last: Baran

first: Richard

middle: E

first: Venkata

last: Battula

first: Yingchang

last: Mi

first: Jing

last: Wang

first: Courtney

last: DiNardo

first: Michael

last: Andreeff

first: Jeffery

middle: W

last: Tyner

first: Aaron

last: Schimmer

first: Anthony

last: Letai

first: Rose

last: Padua

first: Carlos

last: Bueso-Ramos

first: Stefano

last: Tiziani

first: Marina

last: Konopleva


title: Transcriptional heterogeneity among xenograft tumors derived from subclonal populations of MDA-MBA-468 triple-negative breast cancer cells

first: Joan

last: Brugge

overall_design: Bulk RNA-sequencing (RNA-seq) analysis was performed on 4 SCPs of the MDA-MB-468 cell line.  Three tumors per SCP were analyzed.

first: Hendrik

last: Kuiken

first: Laura

last: Selfors


title: Cis-regulatory changes in locomotor genes are associated with the evolution of burrowing behavior

city: San Francisco

first: Ryan

last: York

state: CA

address: 1328 6th Avenue

institute: Stanford University

summary: How evolution modifies complex, innate behaviors is largely unknown. Divergence in many morphological traits has been linked, at least in part, to cis-regulatory changes in gene expression, a pattern also observed for some behaviors in recently diverged populations. Given this, we compared the gene expression in the brains of two interfertile sister species of Peromyscus mice, including allele-specific expression (ASE) of their F1 hybrids, that show large and heritable differences in burrowing behavior. Because cis-regulation may contribute to constitutive as well as activity-dependent gene expression, we also captured a molecular signature of burrowing circuit divergence by quantifying gene expression in mice shortly after burrowing. We found that several thousand genes were differentially expressed between the two sister species regardless of behavioral context, with several thousand more showing behavior-dependent differences. Allele-specific expression in F1 hybrids showed a similar pattern, suggesting that much of the differential expression is driven by cis-regulatory divergence. Genes related to locomotor coordination showed the strongest signals of lineage-specific selection on burrowing-induced cis-regulatory changes. By comparing these candidate genes to independent quantitative trait locus (QTL) mapping data, we found that the closest QTL markers to these candidate genes are associated with variation in burrow shape, demonstrating an enrichment for candidate locomotor genes near segregating causal loci. Together, our results provide insight into how cis-regulated gene expression can depend on behavioral context as well as how this dynamic regulatory divergence between species can be integrated with forward genetics to enrich our understanding of the genetic basis of behavioral evolution.

sample_organism: Peromyscus maniculatus x Peromyscus polionotus

overall_design: Whole-brain mRNA profiles of burrowing P. polionotus, P. maniculatus, and their F1 hybrids

first: R

first: C

last: Hu


title: Transcriptomic consequence of Fyn knock-out in glioblastoma, and regional heterogeneity of glioblastoma upon single-cell RNA sequencing

city: Daejeon

first: Haemin

last: Chon

address: Daehak-ro 291

department: Graduate school of medical science and engineering

country: South Korea

institute: KAIST

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

overall_design: Refer to individual Series


title: Adgrg1 is a New Transcriptional Target of Hand1 During Trophoblast Giant Cell Differentiation

city: Xiamen

first: Jinhua

last: Lu

address: No. 4221, Xiangan Road, Xiangan District, Xiamen city

institute: Xiamen University

summary: The placenta, forming the maternal–fetal interface, is essential for the survival and development of the fetus. It has been shown that the basic helix-loop-helix (bHLH) transcription factor Hand1 plays an important role in trophoblast giant cells (TGCs) differentiation during placental development in mice. However, the underlying molecular mechanism remains elusive. We hereby report that Adgrg1 (GPR56), a G protein coupled receptor, was a new transcriptional target of Hand1. Hand1 activated the expression of Adgrg1 by binding to its promoter region during TGCs differentiation. Double in situ hybridization revealed co-expression of Hand1 and Adgrg1 in TGCs, and Adgrg1 was located to Prl2c2+ TGCs in the junctional zone of the placenta. Knockdown of Adgrg1 not only led to increased expression of Prl2c2, but also the improvement of cell migration during TGC differentiation. Moreover, the ligands of Adgrg1, Tgm2 and Col3a1, were expressed in Prl2c2+ TGCs located in the placental junctional zone and maternal spiral arteries, respectively, further providing preconditions for the function of Adgrg1 in TGCs. Collectively, these results demonstrate that Adgrg1 is a new transcriptional target of Hand1, affecting Prl2c2 expression and cell migration during TGCs differentiation. Tgm2 and Col3a1 may be involved in TGC differentiation regulated by Adgrg1 in the manners of autocrine or paracrine. As a transmembrane receptor, Adgrg1 perhaps could act as a potential therapeutic target for placental-associated diseases caused by abnormal trophoblast migration, providing new insights for the preventions and therapies of placenta-related diseases.

overall_design: RNA from trophoblast cells with or without 0.6 ug/ml dox under the differentiation condition for 2 days were prepared using Illumina RNA-Seq Preparation Kit and subjected sequencing with a BGISEQ-500 sequencer (China, BGI). RNA-seq raw data were initially filtered to obtain clean data after quality control. Clean data were aligned to the mouse genome (mm10) by HISAT2. Raw counts for each gene were calculated by EdgeR.


title: Therapeutic Exosomal Vaccine for Enhanced Cancer Immunotherapy by Mediating Tumor Microenvironment

city: Baoding

first: liu

last: huifang

address: NO.180 Wusi East Road

institute: Hebei University

summary: Tumor immunotherapy has been convincingly demonstrated as a feasible approach for treating cancers. Although promising, however, the immunosuppressive tumor microenvironment (TME) has been recognized as a major obstacle in tumor immunotherapy. It is highly desirable to release an immunosuppressive “brake” for improving cancer immunotherapy. Among tumor-infiltrated immune cells, tumor-associated macrophages (TAMs) play an important role in the growth, invasion and metastasis of tumors. The polarization of TAMs (M2) into the M1 type can alleviate the immunosuppression of the TME and enhance the effect of immunotherapy. Inspired by this, we constructed a therapeutic exosomal vaccine from antigen-stimulated M1-type macrophages (M1OVA-Exos). M1OVA-Exos are capable of polarizing TAMs into M1 type through downregulation of the Wnt signaling pathway. Mediating the TME further activates the immune response and inhibits tumor growth and metastasis via the exosomal vaccine. Our study provides a new strategy for the polarization of TAMs, which augments cancer vaccine therapy efficacy.

overall_design: To explore the mechanism by which M1-Exos polarizes macrophages of the M1 phenotype, the micRNA of M0-Exos and M1-Exos were extracted, and this micRNA was sequenced. The target genes of different strands of micRNA were found, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was performed on them to explore the relevant signaling pathways.

first: Fangfang

last: Lv


title: Prolonged estrogen deprivation triggers a broad immunosuppressive phenotype in breast cancer cells

city: Stockholm

first: Anastasios

middle: Erik

last: Damdimopoulos

state: Huddinge

address: Hälsovägen 7c

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

summary: Our study reveals that while antiestrogen therapies effectively limit tumor growth in ER-positive breast cancers, they also trigger a transcriptional program that favors immune evasion.

overall_design: Study of differential gene expression among wt and CSK k.o. MCF-7 breast cancer cells cultured in DMEM or Fulvestrant

first: Daniela

last: Hühn

first: Pablo

last: Marti-Rodrigo

first: Silvana

last: Mouron

first: Catherine

last: Hansel

first: Kirsten

last: Tschapalda

first: Bartlomiej

last: Porebski

first: Maria

last: Häggblad

first: Louise

last: Lidemalm

first: Miguel

last: Quintela-Fandino

first: Jordi

last: Carreras-Puigvert

first: Oscar

last: Fernandez-Capetillo


title: Integrative Transcriptomic and Proteomic Analysis Reveals Mechanisms of Silica-induced Pulmonary Fibrosis in Rats

city: Jinan

first: Cunxiang

last: Bo

state: Shandong

address: Jingshi road  NO 18877

institute: Shandong Academy of Occupational Health and Occupational Medicine

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

summary: To explore proteomic and transcriptomic changes in rat model of silicosis, transcriptomic analysis by microarray and tandem mass tags (TMT)-based proteomic analysis were performed to reveal the expression of mRNAs and proteins in lung tissues. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were applied to analyze the alterated genes and proteins. The integrated analysis was performed between transcriptome and proteome. Furthermore, the data were further verified by RT-qPCR and parallel reaction monitoring (PRM). In total, 244 differentially expressed proteins (DEPs) showed the same trend as that of the corresponding differentially expressed genes (DEGs) (named DEPs/DEGs). GM2a, CHI3L1, LCN2 and GNAI1, which were validated consistently by RT-qPCR and PRM, are involved in the extracellular matrix (ECM) and inflammation contributed to fibrosis in silicosis.

overall_design: Twenty male Wistar rats were randomly divided into two groups with 10 rats each. Rats in the model group were intratracheally instilled with 50 mg/mL silicon dioxide (1mL per rat) and rats in the control group were treated with 1.0 mL saline (1mL per rat). Twenty-eight days later, transcriptomic analysis by microarray and tandem mass tags (TMT)-based proteomic analysis were performed to reveal the expression of mRNAs and proteins in lung tissues.

first: Juan

last: Zhang

first: Linlin

last: Sai

first: Zhongjun

last: Du

first: Gongchang

last: Yu

first: Chao

last: Li

first: Ming

first: Cheng

last: Peng

first: Qiang

last: Jia

first: Hua

last: Shao


title: Oncogenic role of SOX9-DHCR24-cholesterol biosynthesis axis in IGH-BCL2 positive diffuse large B-cell lymphomas [RNA-seq]

city: Shanghai

first: JIAO

last: MA

address: No. 280 South Chongqing Road, west wing building #7 R408

department: Biochemistry and Molecular Cell Biology

institute: Shanghai Jiaotong University School of Medicine

summary: Although oncogenicity of the stem cell regulator SOX9 has been implicated in many solid tumors, its role in lymphomagenesis remains largely unknown. In this study, we showed that SOX9 is overexpressed preferentially in a subset of diffuse large B-cell  lymphomas (DLBCL) harboring IGH-BCL2 translocations. SOX9 positivity in DLBCL correlates with advanced stage of disease. Silencing of SOX9 decreased cell proliferation, induced G1/S arrest and increased apoptosis of DLBCL cells, both in vitro and in vivo. Whole transcriptome analysis and CHIP-seq assays identified DHCR24, a terminal enzyme in cholesterol biosynthesis, as a direct target of SOX9, which promotes cholesterol synthesis by increasing DHCR24 expression. Enforced expression of DHCR24 was capable of rescuing the phenotypes associated with SOX9 knockdown in DLBCL cells. In DLBCL cell line xenograft models, SOX9 knockdown resulted in lower DHCR24 level, reduced cholesterol content and decreased tumor load. Pharmacological inhibition of cholesterol synthesis also inhibited DLBCL xenograft tumorigenesis, the reduction of which is more pronounced in DLBCL cell line with higher SOX9 expression, suggesting that it may be addicted to cholesterol. In summary, our study demonstrates that SOX9 can drive lymphomagenesis through DHCR24 and the cholesterol biosynthesis pathway. This SOX9-DHCR24-cholesterol 3 biosynthesis axis may serve as a novel treatment target for DLBCL.

overall_design: mRNA profiles of SOX9 shRNA #1 vs. shCtrl & mRNA profiles of SOX9 shRNA #2 vs. shCtrl

first: Yajie

last: Shen


title: Analysis of mRNA expression in invasive malignant pleomorphic adenoma

city: Beijing

first: Zhenyuan

last: Han

address: No.22, Zhongguancun South Avenue Haidian District

institute: Peking University School of Stomatology

summary: Invasive malignant pleomorphic adenoma (IMPA) results from the malignant transformation of pleomorphic adenoma (PA). The former is a high-grade malignant tumor, whereas the latter is a benign opposite. Study on the molecular mechanism in the progression of PA to IMPA will be of benefit to elucidate the reasons for different biological behaviors among these salivary gland tumors with the same origin. But there is no valuable and non-invasive biomarker to screen IMPA currently. Studies showed many salivary molecules can detect several systemic diseases. We aimed to investigate whether salivary mRNAs (mRNA) can act as a biomarker to detect IMPA.

overall_design: Patients samples of invasive malignant pleomorphic adenoma (IMPA, n=5) and corresponding normal tissues (control; n=5) were retrieved during surgery and placed in RNA Later stabilization fluid and then kept at minus 80 until required.

first: Z

middle: Y

last: Tian


title: Interrupting the nitrosative stress fuels tumor-specific cytotoxic T lymphocytes in pancreatic cancer

city: Verona

first: Stefano

last: Ugel

address: Piazzale L.A. Scuro, 10

department: Medicine

country: Italy

institute: University and Hospital Trust of Verona

summary: Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest tumors owing to its robust desmoplasia, low immunogenicity, and recruitment of cancer-conditioned, immunoregulatory myeloid cells. These features strongly limit the success of immunotherapy as a single agent, thereby suggesting the need for the development of a multitargeted approach. The goal is to foster T lymphocyte infiltration within the tumor landscape and neutralize cancer-triggered immune suppression, to enhance the therapeutic effectiveness of immune-based treatments, such as anticancer adoptive cell therapy (ACT).We examined the contribution of immunosuppressive myeloid cells expressing arginase 1 and nitric oxide synthase 2 in building up a reactive nitrogen species (RNS)-dependent chemical barrier and shaping the PDAC immune landscape. We examined the impact of pharmacological RNS interference on overcoming the recruitment and immunosuppressive activity of tumor-expanded myeloid cells, which render pancreatic cancers resistant to immunotherapy.PDAC progression is marked by a stepwise infiltration of myeloid cells, which enforces a highly immunosuppressive microenvironment through the uncontrolled metabolism of L-arginine by arginase 1 and inducible nitric oxide synthase activity, resulting in the production of large amounts of reactive oxygen and nitrogen species. The extensive accumulation of myeloid suppressing cells and nitrated tyrosines (nitrotyrosine, N-Ty) establishes an RNS-dependent chemical barrier that impairs tumor infiltration by T lymphocytes and restricts the efficacy of adoptive immunotherapy. A pharmacological treatment with AT38 ([3-(aminocarbonyl)furoxan-4-yl]methyl salicylate) reprograms the tumor microenvironment from protumoral to antitumoral, which supports T lymphocyte entrance within the tumor core and aids the efficacy of ACT with telomerase-specific cytotoxic T lymphocytes. Tumor microenvironment reprogramming by ablating aberrant RNS production bypasses the current limits of immunotherapy in PDAC by overcoming immune resistance.

overall_design: Characterization of immune cells infiltrating PDAC in C57Bl/6 mice treated or not with AT38 using Chromium 10x single-cell RNA-seq (scRNA-seq) data.

first: Francesco

last: De Sanctis

first: Alessia

last: Lamolinara

first: Federico

last: Boschi

first: Chiara

last: Musiu

first: Simone

last: Caligola

first: Rosalinda

last: Trovato

first: Alessandra

last: Fiore

first: Cristina

last: Frusteri

last: Anselmi

first: Ornella

last: Poffe

first: Tiziana

last: Cestari

first: Stefania

last: Canè

first: Silvia

last: Sartoris

first: Rosalba

last: Giugno

first: Giulia

last: Del Rosario

first: Barbara

last: Zappacosta

last: Del Pizzo

first: Matteo

last: Fassan

first: Erica

last: Dugnani

first: Lorenzo

last: Piemonti

first: Salvatore

last: Paiella

first: Roberto

last: Salvia

first: Rita

last: Lawlor

first: Vincenzo

last: Corbo

first: Park

last: Youngkyu

first: David

last: Tuveson

first: Claudio

last: Bassi

first: Aldo

last: Scarpa

first: Manuela

last: Iezzi

last: Bronte


title: High-throughput sequencing of prostate cancer and paracancerous tissue

city: Wuhan

first: Gang

last: Luo

state: Hubei

address: 26 Shengli Street

institute: Huazhong University of Science and Technology

summary: Prostate cancer is one of the most common tumors of the male genitourinary system. Emerging research have confirmed that circRNAs play an important role in the occurrence and development of tumors. However, the correlation of circular RNA with PCa remains unclear. Here, the circRNA expression profiles in PCa and paracancerous tissues were established by high-throughput sequencing.

overall_design: Three pairs of prostate cancer tissues and adjacent normal tissues were collected, and the expressions of mRNA, circRNA and lncRNA in the tissues were detected by high-throughput sequencing


title: Transcriptomic expression profiling of mouse PBMCs treated with a Plasmdium berghei protein, PbTIP

city: New Delhi

first: Agam

middle: Prasad

last: Singh

state: Delhi

address: Aruna Asaf Ali Marg

department: IDL

country: India

institute: NII

summary: Plasmodium immune evasion strategies hugely contribute to the success of parasite in its host and of various immune evasion strategies, parasite often expresses molecular mimics of host molecules to manipulate the host responses. In this study, we report a Plasmodium hypothetical protein which is homologous to its human T cell immunomodulatory protein and possess the potential to suppress the immune responses. This Plasmodium berghei protein, PbTIP, is expressed as a surface protein of merozoites and reduce inflammatory response of macrophages while up-regulating the anti-inflammatory cytokines such as TGF-β and IL-10 in-vitro. The immunosuppressive effect of PbTIP was studies systemically by treating mouse with recombinant PbTIP (10mg/kg) for four consecutive days followed by mouse PBMCs isolation and transcriptome profiling. GST protein treated mouse PBMCs were taken as control here.

overall_design: We performed Next Generation sequencing to compare transcriptome profiles of mouse PBMCs treated with PbTIP as compared to the control.

first: Inderjeet

last: Kalia

middle: P


title: New genetic biomarkers to differentiate pathogenic and clinically relevant Bacillus cereus strains

city: Jouy-en-Josas

first: Cyprien

last: Guérin

address: INRAE - Domaine de Vilvert

country: France

institute: INRAE

summary: Bacillus cereus is the second leading cause of collective food poisoning in France. B. cereus is also associated with severe clinical infections leading to patient death in 10% of the cases. The emergence of B. cereus as a foodborne and opportunistic pathogen has intensified the need to distinguish strains of public health concern. In this work, by performing a screen on a large collection of B. cereus strains of varying pathogenic potential, we identified genetic determinants capable of discriminating B. cereus strains inducing negative clinical outcomes. The combination of 4 biomarkers is sufficient to accurately discern clinical strains from harmless strains. Three of the biomarkers are located on the chromosome, with a fourth one identifying a plasmid carried by most pathogenic strains. A 50 kbp region of this plasmid promotes the virulence potential of these strains and could thus be defined as a new pathogenicity island of B. cereus. These new findings help in the understanding of B. cereus pathogenic potential and complexity and may provide tools for a better assessment of the risks associated with B. cereus contamination to improve patient health and food safety.

overall_design: The transcriptome study by RNAseq was carried out on 15 strains representative of the three collections in triplicates

first: Benjamin

last: Glasset

first: Rozenn

last: Dervyn

first: Pierre

last: Nicolas

first: Nalini

last: Ramarao


title: Promoter-wide profiling of DNA methylation in prefrontal cortex of Camk2-mutPolg mouse.

city: Wako

first: Junko

last: Ueda

state: Saitama

address: 2-1 Hirosawa

department: Center for Brain Science

country: Japan

institute: RIKEN

summary: Camk2-mutPolg mouse carries the transgene of mutated polymerase gamma under Camk2 promoter. By the mutation, polymerase gamma lost its proof-reading activity, and thus tg mouse accumulates deletions and mutations in mitochondrial DNA in neurons. This mouse showed behavioral alterations similar to mood disorders. To examine the epigenetic status in the brain cells, we have performed promoter-wide DNA methylation analysis in neurons and nonneurons of the tg mouse.

overall_design: In total 26 samples; 2 reference files, 6 files from neuronal nuclei of prefrontal cortices of TG mouse, 6 files from nonneuronal nuclei of prefrontal cortices of TGmouse, 6 files from  neuronal nuclei of prefrontal cortices of control, 6 files from nonneuronal nuclei of prefrontal cortices of control.


title: Transcriptional heterogeneity among MDA-MBA-468 triple-negative breast cancer cells

first: Joan

last: Brugge

overall_design: Single-cell RNA sequencing (scRNA-seq) analysis was performed on parental MDA-MBA-468 cells.

first: Hendrik

middle: J

last: Kuiken

first: Laura

middle: M

last: Selfors


title: Integrated molecular characterization of patient-derived models reveals therapeutic strategies for treating CIC-DUX4 sarcoma.

city: Bologna

first: Emanuela

last: Palmerini

address: via G.C.Pupilli, 1

institute: IRCCS Istituto Ortopedico Rizzoli

summary: Capicua–double homeobox 4 (CIC-DUX4) rearranged sarcomas (CDSs) are extremely rare, highly aggressive primary sarcomas that represent a major therapeutic challenge. To identify selective therapeutic targets of CDS, we performed RNA sequencing of primary tumor samples from patients, patient-derived xenografts (PDXs) and PDX-derived cell lines and we highlighted an HMGA2/IGF2BPs/IGF2/IGF1R/AKT-mTOR axis that characterizes CDS. This highly active axis confers to CDSs sensitivity to both trabectedin, which prevents HMGA proteins from binding to IGF2BP2/3 promoters, and PI3K/mTOR inhibitor NVP-BEZ235 (dactolisib). Combined treatments with trabectedin and NVP-BEZ235 completely abolish the activation of the IGF2/IGF1R/AKT/mTOR axis and the in vivo growth of CDS tumors. The development of representative PDXs and PDX-derived cell lines models has helped to identify the unique sensitivities of CDS towards AKT/mTOR inhibitors and trabectedin, revealing a mechanism-based therapeutic strategy to fight this lethal cancer.

overall_design: This study aims to identify a specific transcriptional signature that characterizes CDS in order to highlight selective therapeutic targets. For this goal we performed RNA-seq on four CDS and four EWS tumor samples along with PDXs, and corresponding cell lines. GSEA and leading edge analysis revealed a selective gene expression signature and molecular dependence of CDS on an oncogenic axis, whose functional relevance was assessed in PDXs and corresponding cell lines. These models presented a high correlation score with their original tumors based on gene expression profile, and maintain the phenotypic characteristics assessed by  morphological and immunohistochemistry analysis. We tested the feasibility of CDS-derived PDXs and CDS PDX-derived cell lines to determine disease-specific pharmacological vulnerabilities and their usefulness to prioritize actionable drug targets in a timely manner. In particular, we tested their in vitro and in vivo chemosensitivity to two chemicals compounds, trabectedin and/or NVP-BEZ235 (alone or in combination), which target genes of the oncogenic axis that characterizes CDS, to offer a rationale for disease-driven treatments.

first: Marianna

last: Carrabotta

first: Maria

middle: A

last: Laginestra

first: Giorgio

last: Durante

first: Caterina

last: Mancarella

first: Lorena

last: landuzzi

first: Alessandro

last: Parra

first: Francesca

last: Ruzzi

first: Lisa

last: Toracchio

first: Alessandra

last: De Feo

first: Veronica

last: Giusti

first: Michela

last: Pasello

first: Alberto

last: Righi

first: Pier

middle: L

last: Lollini

last: palmerini

first: Davide

last: Donati

last: Manara

first: Katia

last: Scotlandi


title: Transcriptional heterogeneity of MDA-MBA-468 triple-negative breast cancer cells

first: Joan

last: Brugge


title: RNA-seq of AMPKa1-deficient bone-marrow-derived macrophages

city: Ulm

last: Caratti

address: Helmholzstraße 8/1

institute: University of Ulm

summary: To identify cross-talk between the cytoplasmic kinase AMPK and the nuclear receptor, glucocorticoid receptor, during inflammatory responses, bone-marrow-derived macrophages lacking the catalytic domain of AMPK, AMPKa1, were exposed to vehicle, dexamethasone, a synthetic glucocorticoid, lipopolysaccharide, crushed muscle extract (damage-associated molecular patterns) or a combination of the inflammatory stimulus and dexamethasone.

overall_design: RNA-seq of BMDMs exposed to vehicle (DMSO), dexamethasone (100nM), lipopolysaccharide (100ng/ml), DAMPs (1ug/ml) or a combination of lipopolysaccharide and dex, or DAMPs and dex for 24 hours before RNA isolation.


title: Protocol  matters – reproducibility and rigor of DNA methylation data sets

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

department: Biomedical Sciences

institute: University of North Dakota


title: microRNA expression profile of pediatric adrenocortical tumors

city: Ribeirão Preto

first: Carlos

middle: Alberto

last: Scrideli

state: São Paulo

address: Avenida Bandeirantes 3900

department: Pediatrics

country: Brazil

institute: Ribeirao Preto Medicine School - University of Sao Paulo

summary: Here, we used a microarray technique to provide miRNA expression data of a set of 37 adrenocortical tumors (ACT) and 9 non-neoplastic adrenal controls from Brazilian patients assisted in two treatment centers in the state of São Paulo (HC-FMRP-USP and Centro Infantil Boldrini of Campinas).

overall_design: We identified miRNA signatures associated with pediatric adrenocortical tumors and patients' outcome.

first: Luciana

last: Veronez

first: Paola

middle: F

last: Fedatto

first: Carolina

last: Alves

first: Regia

last: Lira

first: Mirella

last: Baroni

first: Keteryne

middle: R

last: Silva

first: Paula

last: Santos

first: David

last: Antonio

first: Rosane

last: Queiroz

first: Sonir

last: Antonini

first: Silvio

last: Tucci

first: Luciano

last: Neder

first: José

last: Yunes

first: Silvia

last: Brandalise

first: Rodrigo

last: Panepucci

first: Luiz

middle: G

last: Tone


title: Protocol  matters – reproducibility and rigor of DNA methylation data sets [BiSulfite-seq]

first: Junguk

last: Hur

summary: While epigenetics continues to be a burgeoning research area in neuroscience, unaddressed issues related to data reproducibility across laboratories remain. Indeed, separating meaningful experimental changes from background variability is a challenge in epigenomic studies. Genome-wide DNA methylation analysis of hippocampal tissues from wild-type rats across three independent laboratories revealed that seemingly minor protocol differences resulted in significant epigenome profile changes, even in the absence of experimental intervention. Difficult-to-match factors such as animal vendors   and a subset of husbandry and tissue extraction procedures produced quantifiable variations between wild-type animals across the three laboratories. To enhance scientific rigor, we conclude that strict adherence to protocols is necessary for the execution and interpretation of epigenetic studies and that protocol-sensitive epigenetic changes, amongst naive animals, may confound experimental results.

overall_design: SAS Sprague Dawley (SD) rats were purchased from the nearest vendors (Charles River and Envigo) from our three project sites, including Legacy Research (Site #1), Trinity College (Site #2), and the University of Alabama at Birmingham (Site #3). We identified factors that are typically easy to match, factors that may not always be considered, and factors that are challenging to match. A total of 27 factors were collected in four major areas including “before-each-laboratory”, “at-each-laboratory”, “up-to-sacrifice”, and “dissection”. Rats were 8.0 to 8.3 weeks of age at the time of arrival from the vendors. Entire hippocampi (from both hemispheres) were harvested from rats (n=5~6) 18 to 27 days after arrival. Whole hippocampi from each animal were surgically dissected and flash-frozen in liquid N2 and stored at -80°C before being shipped to the University of North Dakota (UND), where samples were collected, de-identified, and stored at -80°C for deep sequencing analysis. Once collected, all samples were processed using Qiagen’s AllPrep DNA/RNA Mini Kit to individually extract RNA and DNA from each flash-frozen sample. All RNA and DNA samples were stored at -80°C before being sent frozen in dry ice to the University of Michigan Genomics and Epigenomics Core for RNA-Seq and reduced representation bisulfite sequencing (RRBS). Differentially expressed genes (DEGs) and differentially methylated CpG sites/Genes (DMCs/DMGs) were identified between each pair of project sites and examined for enriched biological functions and pathways.

first: Detlev

last: Boison

first: Farah

middle: D

last: Lubin

first: Jonathan

last: Geiger

first: Susan

last: Masino

first: Kai

last: Guo


title: Transcriptome architecture and regulation at environmental transitions of the fish pathogen Flavobacterium psychrophilum: Global RNA-Seq

first: Cyprien

last: Guérin

summary: In a context of fast development of aquaculture, infections by Flavobacterium psychrophilum, a member of the family Flavobacteriaceae, are a major sanitary concern for the salmonid farming industry worldwide. Several phenotypic traits related to pathogenesis have been documented for this bacterium, but molecular factors involved remain poorly characterized. Here, we conducted a global study of adaptation to outside- and within-host environments using a combination of in vitro transcriptomic and computational approaches. The repertoire of transcription start sites and transcriptional units was established using 5’-end and global RNA-Seq. Responses to environmental conditions were explored by expression profiling across conditions, including host-related stresses, exposure to fish mucus and plasma, growth on blood, osmotic changes or freshwater. Analysis of these data allowed to identify many new regulatory elements including alternative sigma-factors promoters, 5’ cis-encoded and trans-acting RNAs. It also revealed interconnected regulations linked to specific environmental conditions for a wide range of biological processes: proteolytic activity, iron acquisition, fatty acids metabolism, respiration under low-oxygen concentration, protein secretion and folding, efflux pumps as well as adhesion and spreading. Results reported here constitute an important resource for guiding basic and applied research on this important pathogen, and a dedicated website is provided to facilitate their exploration.

overall_design: The sample corresponds to the sequencing of the total RNA from a pool of 18 total RNA samples extracted in different biological conditions

first: Tatiana

last: Rochat

first: Erwin

last: van Dijk


title: Transcriptome architecture and regulation at environmental transitions of the fish pathogen Flavobacterium psychrophilum: 5’-end RNA-Seq

overall_design: The sample corresponds to the sequencing of the 5’-end of RNA from a pool of 18 total RNA samples extracted in different biological conditions


title: Protocol  matters – reproducibility and rigor of DNA methylation data sets [RNA-seq]


title: The variation of  bivalent histone modifications and 3D chromosome structure during germline stem cell differentiation

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

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

overall_design: Refer to individual Series


title: Whole-transcriptome sequencing of the chicken embryonic fibroblast, EGK.X blastoderm, and primordial germ cells

city: Seoul

first: JAE

middle: YONG

last: HAN

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

institute: Seoul National University

summary: Eyal-Giladi and Kochav stage X (EGK.X) blastoderm mostly consists undifferentiated progenitor (pluripotent) cells that have the potency to differentiate into all cell types. Analyzing the transcriptional programs of blastoderm is critical to understand the molecular mechanisms that underlie the developmental fate of early embryos, and practical application of blastoderm-derived pluripotent cells, including ESC. Primordial germ cells (PGC) are also undifferentiated progenitor cells that later differentiate into male and female germ cells. Analyzing the transcriptional programs of PGC is critical to understand the molecular mechanisms that underlie the developmental fate of early germ cells, and practical application of PGC in generating transgenic chickens. Therefore, we performed whole-transcriptome sequencing (WTS) in the chicken EGK.X blastoderm and PGCs together with the chicken embryonic fibroblasts (CEF, as a reference sample). CEF are differentiated and an abundant somatic cells. The generated WTS data of CEF, EGK.X blastoderm and PGC are rich resources to utilize for various focused research. As a first focused research, we utilized the generated WTS data for analyzing the expression profiling of DNA repair and apoptosis pathway genes in EGK.X blastoderm and PGC compared with CEF. DNA is the fundamental unit of inheritance and is susceptible to damage by various exogenous and endogenous sources. When the DNA is damaged, the cell sense the nature of damage through multiple surveillance mechanisms and select an appropriate DNA repair pathway to repair the damage and avoid passing the damage to a progeny of cells. When the cell fails to repair DNA damage, cell cycle progression is halted and apoptosis is initiated. Despite several genes are involved in five major DNA repair pathways and two major apoptosis pathways, a comprehensive understanding on the expression of those genes are not well-understood in chicken tissues. Through WTS analysis in CEF, stage X blastoderm and PGC, we identified that most of the DNA repair pathway genes were expressed more high in blastoderm and high in PGC than CEF. At the other hand, most of the apoptosis pathway genes were expressed low in blastoderm and PGC than CEF.

overall_design: Examination of gene expression profiling in EGK.X blastoderm and PGC (target samples) compared with CEF (reference sample) through whole-transcriptome sequencing analysis. Each sample from the White Leghorn chickens were analyzed in triplicate.

first: Deivendran

last: Rengaraj

first: Sohyoung

last: Won

first: Jae-Yong

last: Han


title: The variation of 3D Chromosome Structure were tested during germline stem cell differentiation [HiC]

summary: During in vitro spermatogenesis and transdifferentiation of female germline stem cells into haploid spermatid-like cells , the variation of chromatin organization by using in situ Hi-C were tested

overall_design: Examination of chromatin organization in 4 stages (stra8-ssc:SS;stra8-FGSC:SF;prm1-SSC:PS;prm1-FGSC:PF.) during in vitro spermatogenesis and transdifferentiation of female germline stem cells into haploid spermatid-like cells

first: Xiaopeng

last: Hu


title: Transcriptome architecture and regulation at environmental transitions of the fish pathogen Flavobacterium psychrophilum

overall_design: Transcriptional landscape exploration of F. psychrophilum OSU THCO2-90 through 64 hybridizations samples


title: The variation of  bivalent histone modifications were tested during germline stem cell differentiation [ChIP-seq]

summary: during in vitro spermatogenesis and transdifferentiation of female germline stem cells into haploid spermatid-like cells , the variation of  bivalent histone modifications were tested

overall_design: Examination of bivalent histone modifications in 4 stages (stra8-ssc:SS;stra8-FGSC:SF;prm1-SSC:PS;prm1-FGSC:PF.) during in vitro spermatogenesis and transdifferentiation of female germline stem cells into haploid spermatid-like cells


title: RNA-binding profiles of CKAP4  in human myocardial tissues

city: wuhan

first: dong

last: chen

address: GaoXin 2nd Road

institute: ablife

summary: CKAP4 as one of cardiac activated-myofibroblast protein markers may be involved in cardiac fibrosis. We assumed that CKAP4 hold a role in the regulation of cardiac fibrotic remodeling as an RNA-binding protein. Using improved RNA immunoprecipitation and sequencing (iRIP-seq), we sought to analyze the RNAs bound by CKAP4 in normal atrial muscle (IP1 group) and remodeling fibrotic atrial muscle (IP2 group) from patients with cardiac valvular disease.Binding peak-related gene cluster enrichment analysis showed these genes were mainly involved in biological processes such as signal transduction, protein phosphorylation, axonal guidance, and cell connection. Through gene annotation and correlation analysis of binding-peaks reads, we found that at least four lncRNAs including LINC00504, FLJ22447, RP11-326N17.2 and HELLPAR were CKAP4 potential binding lncRNAs in myocardial tissues.We reveal certain RNA-binding features of CKAP4 suggesting a relevant role as an unconventional RNA-binding protein in cardiac remodeling process.

overall_design: iRIP-seqencing in normal atrial muscle (IP1 group) and remodeling fibrotic atrial muscle (IP2 group) from patients with cardiac valvular disease.

first: Hong

last: Zhu

first: Zhongshang

last: Xie


title: Genome wide assessment of RNA Pol II and Myc ChIP profiles in response to drug treatments in MYC-driven medulloblastoma

city: Aurora

first: Etienne

last: Danis

state: CO

institute: University of Colorado, Denver - Anschutz Medical Campus

summary: The goal of this study was to identify the potential change in promoter peak profiles for RNA Pol II and Myc in the presence and absence of the inhibitor THZ1 in MYC-driven medulloblastoma.

overall_design: RNA Pol II and Myc ChIPs were conducted in the D458 cell line in the presence or absence of THZ1 or DMSO as control. An antibody targeting total histone H3 was used as a immunoprecipitation control.

first: Bethany

last: Veo

first: Rajeev

last: Vibhakar


title: The FOXA1 transcriptional network coordinates key functions of primary human airway epithelial cells. [ChIP-Seq]

city: Cleveland

first: Ann

last: Harris

state: Ohio

address: 2109 Adelbert Rd Building

department: Genetics and Genome Sciences

institute: Case Western Reserve University

summary: The differentiated functions of the human airway epithelium are coordinated by a complex network of transcription factors. These include the pioneer factors Forkhead box A1 and A2 (FOXA1 and FOXA2), which are well-studied in several tissues, but their role in airway epithelial cells is poorly characterized. Here we define the cistrome of FOXA1 and FOXA2 in primary human bronchial epithelial (HBE) cells by ChIP-seq. Next, siRNA- mediated depletion of each factor is used to investigate their transcriptome by RNA-seq. We found that, as predicted from their DNA-binding motifs, genome-wide occupancy of the two factors showed substantial overlap, however their global impact on gene expression differed. FOXA1 is an abundant transcript in HBE cells, while FOXA2 is expressed at low levels and these factors likely both exhibit auto-regulation and cross-regulation. FOXA1 regulated genes involved in cell adhesion and the maintenance of the epithelial cell identity, particularly through repression of genes associated with epithelial to mesenchymal transition (EMT). FOXA1 also directly targets other transcription factors with a known role in the airway epithelium such as SAM-pointed domain-containing Ets-like factor (SPDEF). The intersection of the cistrome and transcriptome for FOXA1 revealed enrichment of genes involved in epithelial development and tissue morphogenesis. Moreover, depletion of FOXA1 was shown to reduce the transepithelial resistance of HBE cells confirming the role of this factor in maintaining epithelial barrier integrity.

overall_design: Examination of the cistrome of FOXA1 and FOXA2

first: Alekh

last: Paranjapye

first: Jey

last: Sabith Ebron

first: Michael

last: Mutolo

first: Shih-Hsing

last: Leir


title: The FOXA1 transcriptional network coordinates key functions of primary human airway epithelial cells.


title: Genome-wide maps of DNA methylation state in 2-week rat IUGR islets

city: Philadelphia

first: Paul

middle: Zhiping

last: Wang

state: pa

address: 3440 Market St

institute: Bioinformatics Core, IBI, UPen

summary: Intrauterine growth restriction (IUGR) increases the risk of developing type 2 diabetes in adulthood. A rat model of IUGR induced by bilateral uterine artery ligation at day 18 of gestation, which reduces the blood supply and critical substrates to the fetus, was used to assess the alterations of genome-wide DNA methylation in IUGR islets. At 2 weeks of age, pancreatic islets were isolated and genomic DNA were extracted for TruSeq-HELP tagging assay. Cytosine methylation was compared in the study.

overall_design: Examination of DNA methylation in 2 experimental conditions (IUGR and Control).

first: Yu

middle: C

last: Lien

first: Rebecca

last: Simmons

first: Xueqing

last: Lu


title: mRNA seq of WT and tp53 e7/e7 mutant in zebrafish intestine with or without gut microbiota.

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

institute: Korea Research Institute of Bioscience and Biotechnology

summary: In order to explore host factor provided by tp53 e7/e7 mutants that supports the colonization of specific microbiota, comparative transcriptomic analyses of intestines of WT vs. tp53 mutants or CV vs. GF conditions at 7 dpf were performed.

overall_design: intestinal mRNA profiles of wild type (WT) and tp53 e7/e7 mutant zabrafish at 7 days post fertilization. Zebrafish larvae intestine at 7dpf were dissected and pooled 25 larvae intestine per group using fine pins and forceps manually.

first: Jae-Geun

last: Lee

first: Jeong-Soo

first: Jong-Hwan

first: Seon-Young


title: Differential gene expression in epithelial and mesenchymal populations of HMLER cells

city: Worcester

first: Jennifer

last: Benanti

state: MA

address: 364 Plantation St. LRB525

department: Molecular, Cell & Cancer Biology

institute: UMass Medical School

summary: HMLER cells (Ras-transformed version of HMLE cells) were FACS sorted as two subpopulation using CD24 and ITGB4 antibodies. Cells which are negative for CD24 and ITGB4 were mesenchymal in morphology, while cells which are psotive for CD24 and ITGB4 were epithelial. We performed RNA sequencing and expression of several epithelial and mesenchymal phenotype associated proteins were consistent with their mrphology. In addition to the EMT related genes, these two population expressed some unique set of genes.

first: HIRA

last: GOEL

first: ARTHUR

last: MERCURIO


title: The time-dependent global micro-transcriptome of Japanese flounder in response to Vibrio anguillarum infection

city: Qingdao

first: Xianhui

last: Ning

address: 7 Nanhai Road

institute: Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences

summary: Japanese flounder (Paralichthys olivaceus) is an economic important aquaculture fish that was susceptible to Vibrio anguillarum. To fully deciphered the molecular mechanisms underlying flounder host defense against V. anguillarum infection, we perform the micro-transcriptome analysis of founder spleen with and without V. anguillarum infection at 3 time points.

overall_design: The micro-transcriptome was determined for Japanese flounder spleen from V. anguillarum-infected groups (group V) and uninfected groups (group C) at the time points of 6, 12 and 24 h. For each group per time point, three individual fish were used as biological triplicates.

first: Li

last: Sun


title: The FOXA1 transcriptional network coordinates key functions of primary human airway epithelial cells. [RNA-seq]

first: Ann

overall_design: Examination of the transcriptome following siRNA-mediated depletion of FOXA1, FOXA2 or both

first: Alekh

first: Jey


title: Gene expression signatures after immunisation with an HIV-1 recombinant Vesicular Stomatitis Virus (VSV) vaccine following three priming doses of  IL-12 pDNA enhanced HIV-1 multi-antigen pDNA vaccine (BIOVACSAFE protocol HVTN087)

city: London

first: David

last: Lewis

address: Du Cane Road

department: ICRF

country: United Kingdom

institute: Imperial College London

summary: The time course of whole blood gene expression was measured after the fourth immunisation at month 6 in participants who had been randomised into vaccine or placebo group 1 of the clinical protocol HVTN087 - A phase 1 trial to evaluate the safety, tolerability, and immunogenicity of an IL-12 pDNA enhanced HIV-1 multi-antigen pDNA vaccine delivered intramuscularly with electroporation, with an HIV-1 rVSV vaccine boost, in healthy HIV-uninfected adult participants (NCT01578889).

overall_design: A pre-immunisation baseline sample was drawn prior to the fourth immunisation at month 6 (designated day 0) and further samples collected on days 1, 3, 7 and 14 after the immunisation. All samples were collected into PaxGene tubes. On day 0 participants received either: an intramuscular rVSVHIVGAG vaccine; intramuscular saline placebo; or in two cases no injection (treatment = VSVHIVGAG / PLACEBO / NONE respectively). Participants had previously received either three intramuscular placebo injections, or three intramuscular priming doses of  IL-12 pDNA enhanced HIV-1 multi-antigen pDNA vaccine by electroporation at months 0, 1 and 3. Participants in group = 1 received all three DNA primes plus the booster VSVHIVGAG vaccine (vaccinations received = DDDV); whereas those in groups 1A, 1B, 1D and 1E had experienced some protocol deviations in that they missed one or more DNA primes or the VSV vaccination, indicated by - in vaccinations received characteristic (vaccinations received = DDD- / DD-V / D-DV / D--- respectively).

first: January

last: Weiner

first: Jeroen

last: Maertzdorf


title: Expression data from the regeneration of the liver

city: Dalian

first: shi

middle: yong

last: quan

state: Liaoning

address: No.9, west section, lvshunkou district, dalian

institute: DALIAN MEDICAL UNIVERSITY

summary:
In the partial liver resection and regeneration model, the early regeneration of the liver has strict gene regulation, and the regulation of liver genes is different in different resection proportions, which is a strictly controlled genetic procedure. Different genes are activated in liver resection of different proportions.For example, genes such as apoptotic autophagy inflammation were significantly expressed in 85% of liver resection cases.
We used microarrays to describe in detail the global program of gene expression in regenerative livers and identify different classes of up-regulated or down-regulated genes in the process.

overall_design: We selected early regenerated livers for RNA extraction and hybridization on Affymetrix microarray.In order to improve the time resolution of the expression spectrum, we selected 3 same time points of the two excision models, namely 6h, 12h and 24h; three parallel samples were taken at each time point for analysis.

first: Qin-Long

last: Liu

first: Yong-Quan

last: Shi

first: Wei


title: Oncogenic role of SOX9-DHCR24-cholesterol biosynthesis axis in IGH-BCL2 positive diffuse large B-cell lymphomas

city: Shanghai

first: JIAO

last: MA

address: No. 280 South Chongqing Road, west wing building #7 R408

institute: Shanghai Jiaotong University School of Medicine

summary: Although oncogenicity of the stem cell regulator SOX9 has been implicated in many solid tumors, its role in lymphomagenesis remains largely unknown. In this study, we showed that SOX9 is overexpressed preferentially in a subset of diffuse large B-cell lymphomas (DLBCL) harboring IGH-BCL2 translocations. SOX9 positivity in DLBCL correlates with advanced stage of disease. Silencing of SOX9 decreased cell proliferation, induced G1/S arrest and increased apoptosis of DLBCL cells, both in vitro and in vivo. Whole transcriptome analysis and CHIP-seq assays identified DHCR24, a terminal enzyme in cholesterol biosynthesis, as a direct target of SOX9, which promotes cholesterol synthesis by increasing DHCR24 expression. Enforced expression of DHCR24 was capable of rescuing the phenotypes associated with SOX9 knockdown in DLBCL cells. In DLBCL cell line xenograft models, SOX9 knockdown resulted in lower DHCR24 level, reduced cholesterol content and decreased tumor load. Pharmacological inhibition of cholesterol synthesis also inhibited DLBCL xenograft tumorigenesis, the reduction of which is more pronounced in DLBCL cell line with higher SOX9 expression, suggesting that it may be addicted to cholesterol. In summary, our study demonstrates that SOX9 can drive lymphomagenesis through DHCR24 and the cholesterol biosynthesis pathway. This SOX9-DHCR24-cholesterol 3 biosynthesis axis may serve as a novel treatment target for DLBCL.

overall_design: To identify which genes binds directly to SOX9 and the genes with SOX9-bound transcription sites

first: Jiao

last: Ma

first: Yajie

last: Shen

first: Wenhan

last: Wang

first: WeQing

last: Wei


title: The siRNA seed region is divided into two functionally different domains in RNA interference in response to 2´-OMe modifications

status: Public on Jan 11 2022

city: Tokyo

first: Yoshiaki

last: Kobayashi

address: 2-11-16 Yayoi, Bunkyo-ku

institute: The University of Tokyo

summary: To investigate effects of siRNA with 2'-O-methyl (2'-Ome) modifications on genome-wide off-targetat, we analyzed gene expression profile of HeLa cells transfected by their siRNAs.

overall_design: Total RNAs were extracted from HeLa cells transfected by unmodified or 2'-O-methyl (2'-Ome) modified siRNA and performed microarray analysis.

first: Kumiko

last: Ui-Tei


title: Peroxisome function relies on organelle-associated mRNA translation

city: Cambridge

first: Jonathan

middle: S

last: Weissman

address: 455 Main St

department: HHMI, Biology

institute: Whitehead Institute for Biomedical Research, MIT

summary: Crucial metabolic functions of peroxisomes rely on a variety of peroxisomal membrane proteins (PMPs). While mRNA transcripts of PMPs were shown to be colocalized with peroxisomes, the process by which PMPs efficiently couple translation with targeting to the peroxisomal membrane remained elusive. Here, we combine quantitative electron microscopy with proximity-specific ribosome profiling and reveal that translation of specific PMPs occurs on the surface of peroxisomes in the yeast Saccharomyces cerevisiae. This places peroxisomes alongside chloroplasts, mitochondria, and the endoplasmic reticulum as organelles that use localized translation for ensuring correct insertion of hydrophobic proteins into their membranes. Moreover, the correct targeting of these transcripts to peroxisomes is crucial for peroxisomal and cellular function, emphasizing the importance of localized translation for cellular physiology.

overall_design: Ribosome profiling of whole cell or streptavidin-purified ribosomes biotinylated by peroxisome-localized biotin ligase in yeast.

first: Noa

last: Dahan

first: Yury

last: Bykov

first: Elizabeth

last: Boydston

first: Amir

last: Fadel

first: Zohar

last: Gazi

first: Hodaya

last: Hocberg-Laufer

first: James

last: Martenson

first: Vlad

last: Denic

first: Yaron

last: Shav-Tal

first: Naama

last: Aviram

first: Einat

last: Zalckvar

first: Maya

last: Schuldiner


title: Ly6C monocyte subsets transcriptome analysis from control and ApoE-/- mice

first: Hong

last: Wang

state: PA

address: 3500 N Broad St. MERB1060

department: CMDR

institute: Temple University Lewis Katz School of Medicine

summary: Inflammatory monocyte (MC) subset differentiation is a major feature in tissue inflammatory and atherosclerosis. The underlying molecular mechanism remains unclear. This study aims to explore molecule targets and signaling which determinate immunological features in MC subsets. ApoE-/- mice were fed a normal chow diet and switched to a high-fat (HF) diet at age 8 weeks and maintained on a HF diet for 12-14 weeks. The control C57BL/6 mice were fed a normal chow diet throughout. Blood Ly6Chigh and Ly6Clow MC subsets from control and ApoE-/- mice were isolated by flow cytometry sorting and subjected for bulk high-throughput RNA-sequencing.

overall_design: Examination of 2 different monocyte in control (CT) and ApoE-/- mice

first: Pingping

last: Yang

first: Qinghua

last: Wu

first: Lizhe

last: Sun

first: Pu

last: Fang

first: Lu

last: Liu

first: Xiaofeng


title: MEG8 regulates Tissue Factor Pathway Inhibitor 2 (TFPI2) expression in the endothelium

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: A large portion of the genome is transcribed into non-coding RNA, which does not encode protein. Many long non-coding RNAs (lncRNAs) have been shown to be involved in important regulatory processes such as genomic imprinting and chromatin modification. The 14q32 locus contains many non-coding RNAs such as Maternally Expressed Gene 8 (MEG8). We observed an induction of this gene in ischemic heart disease. We investigated the role of MEG8 specifically in endothelial function as well as the underlying mechanism. We hypothesized that MEG8 plays an important role in cardiovascular disease via epigenetic regulation of gene expression. Experiments were performed in human umbilical vein endothelial cells (HUVECs). In vitro silencing of MEG8 resulted in impaired angiogenic sprouting. More specifically, total sprout length was reduced as was proliferation, while migration was unaffected. We performed RNA sequencing to assess changes in gene expression after loss of MEG8. The most profoundly regulated gene, Tissue Factor Pathway Inhibitor 2 (TFPI2), was 5-fold increased following MEG8 silencing. TFPI2 has previously been described as an inhibitor of angiogenesis. Mechanistically, MEG8 silencing resulted in a reduction of the inhibitory histone modification H3K27me3 at the TFPI2 promoter. Interestingly, additional silencing of TFPI2 partially restored angiogenic sprouting capacity but did not affect proliferation of MEG8 silenced cells. In conclusion, silencing of MEG8 impairs endothelial function, suggesting a potential beneficial role in maintaining cell viability. Our study highlights the MEG8/TFPI2 axis as potential therapeutic approach to improve angiogenesis following ischemia.

overall_design: Examination of differentially expressed genes after knockdown of lncRNA MEG8 in HUVECs

first: Veerle

last: Kremer

first: Diewertje

middle: I

last: Bink

first: Laura

last: Stanicek

first: Eva

last: van Ingen

first: Sarah

last: Hilderink

first: Anne

middle: Y

last: Nossent

first: Reinier

last: Boon


title: A phase 2, open label single arm study for evaluating safety & efficacy of apremilast in the treatment of cutaneous disease in patients with recalcitrant dermatomyositis.

city: New Orleans

first: Nakhle

last: Saba

state: LA

address: 1415 Tulane Ave, Room 118

department: Internal Medicine/Hematology

institute: Tulane University

summary:
Purpose: Studying the efficacy and safety of apremilast as an add-on therapy in patients with recalcitrant cutaneous dermatomyositis. Studying the mechanism of action of apremilast in dermatomyositis by performing RNA sequencing and immunohistochemistry on skin biopsies before and after treatment.
Methods: We enrolled 8 patients with recalcitrant dermatomyositis. Apremilast 30 mg orally twice daily was added to a stable treatment regimen of steroids and/or steroids sparing agents and patients were followed for 7 months. A CDASI, muscle score, dermatology life quality index (DLQI), and depression assessments were performed at baseline and regularly till month 7. Skin biopsies were performed at baseline and 3-months post-apremilast to study gene expression alterations.
Results: Our ORR assessed at 3 months post apremilast was 87.5%. The response was maintained at 6 months with continued decrease in CDASI and improvement in DLQI. The mean decrease in CDASI was 12.9 points (p<0.05). Apremilast was well tolerated and without any grade 3 or higher adverse events using CTCAE version 5. RNA sequencing was performed on skin biopsies from 7 patients before and 3 months after apremilast. Out of 39,076 expressed genes, there were 195 whose expression changed ≥2-fold at P<0.01 (123 down- and 72 up-regulated), several genes are known JAK-STAT targets. Using GSEA analysis, we identified 13 pathways significantly downregulated by apremilast, notably STAT1, STAT3, IL-2, IL-6, IL-12, IL-23, INFγ, and TNFα pathways. Immunohistochemical staining confirmed JAK/STAT signaling inhibition at the protein level.
Conclusions: Apremilast is a safe and efficacious add-on treatment in recalcitrant dermatomyositis with an overall response rate of 87.5%, and functions through downregulation of JAK/STAT signaling in dermatomyositis.

overall_design: Phase 2 open label single arm clinical trial, RNA gene sequencing and immunohistochemical analysis of skin biopsies before and after treatment.

first: Carole

last: Bitar

first: Katherine

last: Brag

first: Brittany

last: Stumpf

first: Paul

last: Harms

first: Erin

last: Boh

first: Jade

last: Meyers

first: Melody

last: Baddoo

first: Delong


title: Amino acid primed mTOR activity is essential for heart regeneration [bulk RNA-seq]

city: Seattle

first: Hannele

last: Ruohola-Baker

state: WA

address: 850 Republican Street

institute: Institute for Stem Cell and Regenerative Medicine

summary: Heart disease is the leading cause of death as there is no current method to repair damaged myocardium due to the limited proliferative capacity of adult cardiomyocytes. Curiously, mouse neonates and zebrafish, larvae or adult, are able to regenerate their hearts via cardiomyocyte de-differentiation and proliferation. However, a molecular mechanism of why these cardiomyocytes can re-enter cell cycle is poorly understood. Here, we identify a unique metabolic state that primes adult zebrafish and neonatal mouse ventricular cardiomyocytes to proliferate. Zebrafish and neonatal mouse hearts display elevated glutamine levels, predisposing them to amino acid-driven activation of TOR. We show that this TOR activation is required for zebrafish cardiomyocyte regeneration in vivo. After injury we observe pS6 in both the epicardium and ventricular cardiomyocytes suggesting these are amino acid primed cells necessary for regeneration. Through single cell and system-wide RNA-sequencing, LQC proteomics and microscopy we identify dramatic metabolic and mitochondrial changes during the first week of regeneration. These data suggest that regeneration of zebrafish myocardium is driven by metabolic remodeling and reveals a unique metabolic regulator, TOR-primed state, in which zebrafish and mammalian cardiomyocytes are regeneration competent.

overall_design: We performed bulk RNA-seq of zebrafish heart at embryonic/fetal day 3, adult control, and 3, and 7 days post injury.

first: Yuliang

last: Wang


title: An evolutionarily ancient Fatty Acid Desaturase is required for the synthesis of hexadecatrienoic acid, which is the main source of the bioactive jasmonate in Marchantia polymorpha

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

country: Spain

institute: Centro Nacinal de Biotecnologia-CSIC

summary: Jasmonates are fatty acid derived hormones that regulate multiple aspects of plant development, growth and stress responses. Bioactive jasmonates differ between vascular plants and bryophytes (using jasmonoyl-L-isoleucine; JA-Ile and dinor-12-oxo-10,15(Z)-phytodienoic acid; dn-OPDA, respectively), but bind an evolutionarily conserved COI1 receptor. Whilst the biosynthetic pathways of JA-Ile in the model vascular plant Arabidopsis thaliana have been elucidated, the details of dn-OPDA biosynthesis in bryophytes are still unclear. Here, we identify an ortholog of Arabidopsis Fatty Acid Desaturase 5 (AtFAD5) in the model liverwort Marchantia polymorpha and show that FAD5 function is ancient and conserved between species separated by more than 450 million years of independent evolution. Similar to AtFAD5, MpFAD5 is required for the synthesis of 7Z-hexadecenoic acid. Consequently, in Mpfad5 mutants the hexadecanoic pathway is blocked, the dn-OPDA levels almost completely depleted and normal chloroplast development is impaired. Our results demonstrate that the main source of dn-OPDA in Marchantia is the hexadecanoic pathway and the contribution of the octadecanoid pathway, i.e. from OPDA, is minimal. Remarkably, despite extremely low levels of the bioactive hormone (dn-OPDA), MpCOI1-mediated responses to wounding and insect feeding can still be activated in Mpfad5 mutants, suggesting that dn-OPDA is not the only bioactive jasmonate and COI1 ligand in Marchantia.

overall_design: Transcriptomic analysis of Mpfad5 mutants 4 replicates  Mpfad5 (Experiment)  vs Tak-1 (Control)

first: Gonzalo

last: Soriano

first: Sophie

last: Kneeshaw

first: Guillermo

last: Gimenez-Alemán

first: Angel

last: Zamarreño

first: José

last: Franco‑Zorrilla

first: M

last: Rey-Stolle Valcarce

first: Coral

last: Barbas

last: García-Mina

first: Roberto

last: Solano


title: Amino acid primed mTOR activity is essential for heart regeneration

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

overall_design: Refer to individual Series


title: Cell cycle defects underlie childhood-onset cardiomyopathy associated with Noonan syndrome

city: Munich

first: Gianluca

last: Santamaria

state: Germany

address: Ismaninger Strasse 22

department: Department of Medicine I

institute: Klinikum rechts der Isar – Technical University Munich

summary: Childhood-onset myocardial hypertrophy and cardiomyopathic changes are associated with significant morbidity and mortality early in life, particularly in patients with Noonan syndrome, a multisystemic genetic disorder caused by autosomal dominant mutations in genes of the Ras-MAPK pathway. Although the cardiomyopathy associated with Noonan syndrome (NS-CM) shares certain cardiac features with the hypertrophic cardiomyopathy caused by mutations in sarcomeric proteins (HCM), such as pathological myocardial remodeling, ventricular dysfunction and increased risk for malignant arrhythmias, the clinical course of NS-CM significantly differs from HCM. This suggests a distinct pathophysiology that remains to be elucidated. Here, by analysis of sarcomeric myosin conformational states, histopathology and gene expression in left ventricular myocardial tissue from NS-CM, HCM and normal hearts complemented with disease modeling in cardiomyocytes differentiated from patient-derived PTPN11N308S/+ induced pluripotent stem cells, we demonstrate distinct disease phenotypes between NS-CM and HCM and uncover cell cycle defects as a potential driver of NS-CM.

first: Santamaria

last: Gianluca


title: RNASeq analysis of human Cal33 xenografts in nu/nu mice upon radiotherapy +/- metformin treatment

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

summary:
Purpose: We aim to identify transciptional changes of Cal33 xenografts upon radiotherapy +/- metformin treatment in vivo
Method: Cal33 cells were heterotopically transplanted onto NMRI nude mice and subjected to fractionated irradiation with 5x 2 Gy ± 5x 250 µg/g metformin treatment starting on d4 after inoculation. After 5 days of therapy, tumors were explanted, total RNA was extracted, and subjected to RNAseq analysis.

overall_design: RNAseq analysis of human Cal33 xenografts in nu/nu mice on d5 upon radiotherapy (5x 2 Gy) +/- metformin treatment (5x 250µ/g bodyweight)

first: Ulrike

last: Schoetz

first: Diana

last: Klein

first: Kirsten

last: Lauber


title: Difference gene analysis in K562 cells

city: beijing

first: mayun

last: mayun

state: beijing

address: NO.1 West Beichen Road, Chaoyang District

institute: institute of microbiology

summary: Purpose:RNA sequencing (RNA-Seq) was performed to analyze the differential expression of genes in control and lncRNA-up91 knockdown K562 cells

overall_design: Control (sh-luc) and lncRNA-up91 knockdown (sh-up91) K562 cell line for RNA-Seq

first: Yun

last: Ma

first: Ji-Long

last: Chen


title: Amino acid primed mTOR activity is essential for heart regeneration [scRNA-seq]

first: Hannele

last: Ruohola-Baker

summary: Heart disease is the leading cause of death as there is no current method to repair damaged myocardium due to the limited proliferative capacity of adult cardiomyocytes.  Curiously, mouse neonates and zebrafish, larvae or adult, are able to regenerate their hearts via cardiomyocyte de-differentiation and proliferation.  However, a molecular mechanism of why these cardiomyocytes can re-enter cell cycle is poorly understood.  Here, we identify a unique metabolic state that primes adult zebrafish and neonatal mouse ventricular cardiomyocytes to proliferate.  Zebrafish and neonatal mouse hearts display elevated glutamine levels, predisposing them to amino acid-driven activation of TOR. We show that this TOR activation is required for zebrafish cardiomyocyte regeneration in vivo. After injury we observe pS6 in both the epicardium and ventricular cardiomyocytes suggesting these are amino acid primed cells necessary for regeneration. Through single cell and system-wide RNA-sequencing, LQC proteomics and microscopy we identify dramatic metabolic and mitochondrial changes during the first week of regeneration. These data suggest that regeneration of zebrafish myocardium is driven by metabolic remodeling and reveals a unique metabolic regulator, TOR-primed state, in which zebrafish and mammalian cardiomyocytes are regeneration competent.

overall_design: We performed single cell RNA-seq of zebrafish heart pre-injury, and 3, 7 days post injury

first: Yuliang

last: Wang


title: Danger signal initiates differentiation of monocytes into osteopontin‑producing macrophages III

city: Leipzig

first: Manuela

last: Rossol

address: Liebigstr. 19

institute: University of Leipzig

summary:
Purpose: We report the application of single-cell RNA sequencing for profiling the genexpression of different monocyte types in order to characterize monocytes that differentiate into macrophages under danger signal in comparison to conventional GM-CSF and M-CSF macrophages
Methods: Monocytes freshly isolated from PBMCs were differentiated into GM-CSF, M-CSF, and danger-signal induced macrophages. Two million cells of each macrophage population were tagged accordingly with TotalSeq™‑B Hashtags. Single cell RNA sequencing was performed on all macrophage populations in order to characterize cells from each population. ScRNAseq analysis was performed with the R package Seurat on 16470 barcodes after filtering.
Results: Cluster analysis reveals distinct separation of all three macrophage populations.
Conclusion: The clear difference in overall gene expression profile suggests that macrophages exposed to danger signal differentiate into a novel macrophage type in contrast to conventional GM-CSF and M-CSF monocytes.

overall_design: mRNA profiling of differentiated macrophages

first: Tobias

last: Hagemann


title: Danger signal initiates differentiation of monocytes into osteopontin‑producing macrophages II

summary: Analysis of gene expression of monocytes differentiating into different macrophages and dendritic cells.  All cells were activated with lipopolysaccharide after differentiation.

overall_design: Total RNA isolated from macrophages or dendritic cells (n = 4 donors).

first: Anne

last: Hoffmann


title: Danger signal initiates differentiation of monocytes into osteopontin‑producing macrophages

summary: Analysis of gene expression of monocytes differentiating into macrophages in the presence of a danger signal. Kinetic analysis (1 day, 2 days, 4 days, 7 days) and analysis of lipopolysaccharide stimulated 7 day macrophages in comparison to unstimulated 7 day macrophages.

overall_design: Total RNA isolated from fresh monocytes or macrophages cultured for different time points (n = 4 donors).


title: Cholecystokinin 1 Receptor (Cck1R) Activation Restores Normal mTORC1 signaling and is Protective to Purkinje cells of SCA Mice

city: Minneapolis

first: Christine

middle: M.

last: Henzler

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota, Twin Cities (Minneapolis, MN, US)

summary: Spinocerebellar Ataxias (SCAs) are a group of genetic diseases characterized by progressive ataxia and neurodegeneration, often in cerebellar Purkinje neurons. A SCA1 mouse model, Pcp2-ATXN1[30Q]D776, has severe ataxia in absence of progressive Purkinje neuron degeneration and death. Previous RNA-seq analyses identified cerebellar up-regulation of the peptide hormone Cholecystokinin (Cck) in Pcp2-ATXN1[30Q]D776 mice. Importantly, absence of Cck1 receptor (Cck1R) in Pcp2-ATXN1[30Q]D776 mice confers a progressive disease with Purkinje neuron death. A Cck1R agonist, A71623 administered to Pcp2-ATXN1[30Q]D776;Cck-/- and Pcp2-AXTN1[82Q] mice dampened Purkinje neuron pathology and associated deficits in motor performance. In addition, A71623 administration improved motor performance of Pcp2-ATXN2[127Q] SCA2 mice. Moreover, the Cck1R   agonist A71623 corrected mTORC1 signaling and improved expression of calbindin in cerebella of AXTN1[82Q] and ATXN2[127Q] mice. These results indicate that manipulation of the Cck-Cck1R pathway is a potential therapeutic target for treatment of diseases involving Purkinje neuron degeneration.

overall_design: Cerebellar mRNA profiles of 5-week, 12-week and 28-week old Cck-/- and ATXN1[30Q]D776/Cck-/- mice

first: Emily

last: Wozniak

first: Zhao

first: Melissa

last: Ingram

first: Harry

middle: T

last: Orr


title: Gene expression of two Ewing sarcoma cell lines (SK-N-MC, TC-71), transfected with inducible re-expression of TCF7L1 or Empty control

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

institute: German Cancer Research Center (DKFZ)

summary: This dataset comprises trnscriptome data of two Ewing sarcoma cell lines (SK-N-MC and TC-71) after re-expression of the gene TCF7L1

overall_design: 4 samples were normalized (log2) with Affymetrix Expression Console Software (v1.4) using SST-RMA algorithm. Gene expression data were annotated at gene level with the Affymetrix library for Clariom D arrays (human).

first: Florencia

last: Cidre-Aranaz

first: Martin

last: Orth

last: Grünewald


title: Genome Wide CUT&Tag in Day 7 and Day 10 human terminally maturing erythroblasts

city: Rochester

first: Zachary

last: Murphy

state: NY

address: 601 Elmwood Ave box 703

institute: University of Rochester

summary: Occupancy of Ser5-Pol2 and Ser2-Pol2

overall_design: Genome wide polymerase occupancy was generated by CUT&Tag

last: Smith


title: Expression profiling of Ythdc2 ht and Ythdc2 iKO pachytene spermatocytes in mouse.

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

summary: We report the differentially expressed genes caused by inducible deletion of YTHDC2 in pachytene spermatocytes. A large number of differentially epxressed genes were identified.

overall_design: RNA-Seq was used to evaluate the gene expression differences caused by conditional deletion of Ythdc2 in mouse pachytene spermatocytes. Three biological replicas of Ythdc2fl/- and Ythdc2fl/- Ddx4-CreERT2 (iKO) spermatocytes were used for RNA-seq.

first: Rong

last: Liu

first: David

last: Homolka

first: Seth

last: Kasowitz

first: Jordan

last: Shaked

first: N

middle: A

last: Leu

first: Gordon

last: Ruthel

first: P

middle: J


title: Natural variation in the transcriptional response of Drosophila melanogaster to oxidative stress

city: Planegg-Martinsried

first: Sonja

last: Grath

state: Bavaria

address: Grosshaderner Str. 2

department: Department Biology II

institute: Ludwig-Maximilians University Munich

summary: Broadly distributed species must cope with diverse and changing environmental conditions, including various forms of stress. Cosmopolitan populations of Drosophila melanogaster are more tolerant to oxidative stress than those from the species’ ancestral range in sub-Saharan Africa, and the degree of tolerance is associated with an insertion/deletion polymorphism in the 3’ untranslated region of the Metallothionein A (MtnA) gene that varies clinally in frequency. We examined oxidative stress tolerance and the transcriptional response to oxidative stress in cosmopolitan and sub-Saharan African populations of D. melanogaster, including paired samples with allelic differences at the MtnA locus. We found that the effect of the MtnA polymorphism on oxidative stress tolerance was dependent on the genomic background, with the deletion allele increasing tolerance only in a northern, temperate population. Genes that were differentially expressed under oxidative stress included MtnA and other metallothioneins, as well as those involved in glutathione metabolism and other genes known to be part of the oxidative stress response or the general stress response.

overall_design: RNA sequencing was performed on pools of whole heads of 5-7 day old male flies, either treated with menadione sodium bisulfite (MSB) or not.

first: Timothy

last: Ramnarine

first: John

last: Parsch