title: ACUTE BLEEDING AND STORED RED BLOOD CELLS TRANSFUSION ATTENUATES LIVER REGENERATION FOLLOWING PARTIAL HEPATECTOMY

first: Rinat

last: Abramovitch

address: Hadassah Ein Kerem

department: Institute for Gene Therapy

institute: Hadassah Medical Organization

summary: Our aim was to study the impact of bleeding and red blood cell (RBC) resuscitation on liver regeneration. We assessed the impact of RBC storage time on liver regeneration following 50% partial hepatectomy (PHx) in rats, and explored possible contributing molecular mechanisms using immunohistochemistry, RNA-Seq, and macrophage depletion.

overall_design: Adult male Sprague-Dawley rats were cannulated (femoral artery) for bleeding the animals (controlled haemorrhage;  3ml of blood was extracted at a rate of 1 ml/min) and for administration of blood/fluids (resuscitation). PHx- Resection of 50% of the total liver mass was performed. Liver samples were harvested from 3 rats / group on day one post PHx.

first: Nathalie

last: Abudi

first: Idit

last: Matot


title: Laminin111-based defined culture promoting self-renewing human pluripotent stem cells with properties of the early post-implantation epiblast

status: Public on Nov 13 2022

city: Jerusalem

first: Michal

last: Gropp

address: Hadassah Ein-Kerem

country: Israel

institute: Hadassah Medical Center

type: Expression profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Chronic myeloid leukaemia stem cells present an aberrant gene expression signature that is not affected by tyrosine kinase inhibitors

status: Public on Nov 14 2022

city: London

first: Eduardo

last: Gomez Castaneda

address: 30 Guilford Street

department: Institute of Child Health

country: United Kingdom

institute: UCL

summary: Tyrosine kinase inhibitors (TKI) revolutionised the treatment of CML at the beginning of the century. However, TKI do not eliminate the leukaemia stem cells, which can reinitiate the disease upon treatment withdrawal. Thus, finding new therapeutic targets in CML stem cells is key to find a curative treatment. Using microarray datasets, we defined a list of 227 genes which were differentially expressed in CML stem cells compared to healthy controls but were not affected by TKI. Two of them, CD33 and PPIF, are targeted by gemtuzumab-ozogamicin and cyclosporin A, respectively. We treated CML and control CD34+ cells with either drug with or without imatinib to investigate the therapeutic potential of the TKI independent gene expression signature. Cyclosporine A in combination with imatinib reduced the number of CML CFC compared with non-CML controls, but at concentrations not achievable in the clinical practice. Gemtuzumab-ozogamicin showed a EC50 of 146ng/mL, well below the plasma peak concentration of 630ng/mL observed in AML patients and below the EC50 of 3247ng/mL observed in non-CML cells. Interestingly, gemtuzumab-ozogamicin seems to promote cell cycle progression in CML CD34+ cells and we found it to activate the RUNX1 pathway in a RNAseq experiment. This suggests that targeting the tyrosine kinase inhibitor independent gene expression signature in CML stem cells could be exploited for the development of new therapies in CML.

overall_design: Bulk RNAseq of CML CD34+ cells. Cells were treated with 100ng/mL of gemtuzumab-ozogamicin, 3uM cyclosporine A, 2uM imatinib or a combination of 100ng/mL of gemtuzumab-ozogamicin+2uM imatinib for 72 hours.

last: Gómez-Castañeda

first: Heather

last: Jørgensen

first: Lisa

last: Hopcroft

first: Simon

last: Rogers


title: Expression data (messenger RNA) from developing Neural Tubes of mouse embryos

city: LOUISVILLE

first: Partha

last: Mukhopadhyay

state: KY

address: 501 S PRESTON ST

department: Division of Craniofacial Development & Anomalies

country: USA

institute: University of Louisville

summary: Morphogenesis of the mammalian neural tube (NT) is reliant on precise, spatio-temporal expression of numerous genes and coordinated interaction of signal transduction and gene regulatory networks, disruption of which may contribute to the etiology of neural tube defects (NTDs). MicroRNAs (miRNAs) as well as their downstream messenger RNA (mRNA) targets are key modulators of cell and tissue differentiation. To define potential roles of miRNAs and mRNAs in development of the murine neural tube (NT), total RNA preparations from gestation day (GD)-8.5, -9.0 and -9.5 (crtitcal period of NT developemnt) mouse embryos were used to hybridize both microRNA arrays and messenger RNA arrays, to identify miRNAs and mRNAs co-expressed in the same developing NT tissue samples.

overall_design:
We used total RNA preparations from gestation day (GD)-8.5, -9.0 and -9.5 mouse neural tubes to perform global miRNA- and mRNA gene expression profiling analyses of the developing murine neural tube.
We used total RNA preparations (4x biological replicates/sample) from neural tubes of gestation day (GD)-8.5, -9.0 and -9.5 mouse embryos to perform global miRNA- and mRNA gene expression profiling analyses of the developing murine neural tube. One of the objectives of this study is to identify the constitutively and differentially expressed miRNAs and mRNAs within the developing neural tube. For messenger RNA profiling we used Affymetrix GeneChip® Mouse Genome 430 version 2.0 arrays. For microRNA profiling we used Affymetrix GeneChip® microRNA version 2.0 arrays.

first: M

middle: M

last: Pisano

first: Robert

last: Greene


title: Laminin111-based defined culture promoting self-renewing human pluripotent stem cells exhibiting properties of early post-implantation epiblast cells [Bulk_RNA_Seq]

summary: In our study we sought to develop cultures highly enriched for self-renewing human pluripotent stem cells (hPSCs) with an early post-implantation phenotype, capturing the formative pluripotency phase in vitro. Our results demonstrate that hPSCs cultured on LN111 in defined conditions (LN-hPSCs) generate cultures highly enriched for genetically stable, self-renewing hPSCs exhibiting properties similar to the early-post implantation epiblast, including competence to give rise to the germ cell lineage. To analyze the global transcriptome of LN-hPSCs in comparison with conventional/primed and naive hPSCs, we performed RNA-seq of the three  hPSC lines cultured under LN, primed, and naïve conditions.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for three independent hPSC lines HES-1 (ES01), HES-2 (ES02) (Reubinoff et al., 2000), and and H7 (WA07, NIH registry # 0061) (Thomson et al., 1998) cultured under LN, primed and naïve conditions.

first: Benjamin

middle: E

last: Reubinoff


title: Characterization of splice isoform switching during human kidney development

city: Ramat Gan

first: Tomer

last: Kalisky

address: Max and Anna Webb

department: Electrical Engineering

institute: Bar Ilan University

summary: Background: Nephrons are the functional units of the kidney. During kidney development, cells from the cap mesenchyme – a transient kidney-specific progenitor state – undergo a mesenchymal to epithelial transition (MET) and subsequently differentiate into the various epithelial cell types that create the tubular structures of the nephron. Faults in this transition can lead to a pediatric malignancy of the kidney called Wilms’ tumor that mimics normal kidney development. While human kidney development has been characterized at the gene expression level, a comprehensive characterization of alternative splicing is lacking.     Methods: We performed RNA sequencing on cell populations representing early, intermediate, and late developmental stages of the human fetal kidney, as well as three blastemal-predominant Wilms’ tumor patient-derived xenografts.     Results: We identified a set of transcripts that are alternatively spliced between the different developmental stages. Moreover, we found that cells from the earliest developmental stage have a mesenchymal splice-isoform profile that is similar to that of blastemal-predominant Wilms’ tumors. RNA binding motif enrichment analysis suggests that the mRNA binding proteins ESRP1, ESRP2, RBFOX2, and QKI regulate mRNA splice isoform switching during human kidney development.     Conclusions: These findings illuminate new molecular mechanisms involved in human kidney development and pediatric kidney tumors.

overall_design: We performed RNA sequencing on three cell populations representing early, intermediate, and late developmental stages of the human fetal kidney, and on three blastemal-predominant Wilms’ tumor patient-derived xenografts.

first: Nissim

last: Ben-Haim


title: Next Generation Sequencing Facilitates Quantitative Analysis of c-myc Over-expression and Acute High-Intensity Contraction on Skeletal Muscle mRNA Transcriptomes

city: Nagoya

first: Satoru

last: Ato

state: Aichi

address: Gokiso-cho, Showa-ku

department: Department of life science and applied chemistry

country: Japan

institute: Nagoya Institute of Technology

summary: Purpose of this study was to compare the effect of c-myc over expression and acute high intensity muscle contraction on mRNA transcriptome in skeletal muscle

overall_design: Skeletal muscle mRNA-Seq of c-myc over-expression and muscle contraction in 11-week old female C57B/6 mice

first: Yuki

last: Tamura

first: Riki

last: Ogasawara


title: Differential expression and correlation analysis of mRNA and miRNA based on Brain transcriptome in the discus fish (Symphysodon aequifasciatus)

city: Hangzhou

first: li

last: lei

address: xiashas street num 6

country: China

summary: The discus fish (Symphysodon aequifasciatus) is an ornamental fish, which occupies important position on the freshwater aquarium trade. We built two cDNA libraries from an adult male brain and an adult female brain, and performed RNA-sequencing for identifying sex-biased candidate genes , a total number of 40209 non-redundant genes (unigenes) were obtained, of which 250 unigenes were significant overexpressed in the male brain, and 436 unigenes were significant overexpressed in the female. A total of 439 miRNAs were identified, of which 60 miRNAs were differentially expressed between male brain and female brain. These results can provide important evidence for better understanding the molecular mechanisms of the brain's amphoteric dimorphism in discus fish

overall_design: 2 brain samples, male and female

first: Yinan

last: Liu

first: Zaizhong

last: Chen

first: Yuanshuai

last: Fu

first: Bin

last: Wen


title: Genome wide expression change by Tet-O-YAP5SA C4-2 cells treated with/without Dox

city: Dallas

first: Xu

last: Li

state: Texas

address: 6000 Harry Hines Blvd.

department: Molecular Biology

institute: University of Texas Southwestern Medical Center at Dallas

summary: to investigate the role of activated YAP in prostate cancer progression. C4-2 cells were used as the model.

overall_design: Comparative gene expression profiling analysis of RNA-seq data in established Tet-O-YAP5SA C4-2 cells treated with/without Dox for 24 hours

first: Shu

last: Zhuo

first: Jin

last: Jiang


title: USP7 regulates the ncPRC1 Polycomb axis to stimulate genomic H2AK119ub1 deposition uncoupled from H3K27me3 [ChIP-seq]

status: Public on Nov 12 2022

city: Belfast

first: Yaser

last: Atlasi

address: Lisburn Road

department: patrick G Johnston Centre for Cancer research

institute: Queen's University Belfast

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Ubiquitin-specific protease 7 (USP7) has been implicated in cancer progression and neurodevelopment. However, its molecular targets remain poorly characterized. We combined quantitative proteomics, transcriptomics, and epigenomics to define the core USP7 network. Our multi-omics analysis reveals USP7 as a control hub that links genome regulation, tumor suppression, and histone H2A ubiquitylation (H2AK119ub1) by noncanonical Polycomb-repressive complexes (ncPRC1s). USP7 strongly stabilizes ncPRC1.6 and, to a lesser extent, ncPRC1.1. Moreover, USP7 represses expression of AUTS2, which suppresses H2A ubiquitylation by ncPRC1.3/5. Collectively, these USP7 activities promote the genomic deposition of H2AK119ub1 by ncPRC1, especially at transcriptionally repressed loci. Notably, USP7-dependent changes in H2AK119ub1 levels are uncoupled from H3K27me3. Even complete loss of the PRC1 catalytic core and H2AK119ub1 has only a limited effect on H3K27me3. Besides defining the USP7 regulome, our results reveal that H2AK119ub1 dosage is largely disconnected from H3K27me3.

overall_design: ChIP-seq analysis of H3K27me3  in RING1A/B-DKO DLD1 cells expressing  DOX inducible RING1A   contributor: Erasmus Genomics CTU

first: A

last: Sijm

first: Y

first: J

middle: A

last: van der Knaap

middle: W

last: van der Meer

first: G

last: Chalkley

first: K

last: Bezstarosti

first: D

middle: H

last: Dekkers

first: W

last: Doff

first: Z

last: Ozgur

middle: F

last: van IJcken

last: Demmers

first: C

middle: P

last: Verrijzer


title: Gene expression profile of endothelial cells in a 3D-casted mold of a human aneurysm.

city: Suita

first: Isao

last: Ono

address: 6-1 Kishibe-Shinmachi

institute: National Cerebral, and Cardiovascular Center

summary: Because the IA lesion morphology is complex, the blood flow conditions loaded on endothelial cells in each part of the lesion in situ vary greatly.

overall_design: We created a 3D-casted mold of the human unruptured IA lesion and cultured endothelial cells on this model, which was then perfused with culture media to model physiological flow conditions. Then, gene expression profiles of endothelial cells in each part of the IA lesion were analyzed.

first: Tomohiro

last: Aoki


title: Laminin111-based defined culture promoting self-renewing human pluripotent stem cells exhibiting properties of early post-implantation epiblast cells [LN_hPSC_RRBS]

first: Michal

last: Gropp

overall_design: Comparative DNA methylation profiling analysis of reduced representation bisulfite sequencing (RRBS) data for hPSC lines HES-1 (ES01) and HES-2 (ES02) (Reubinoff et al., 2000), cultured under LN, conventional/primed and naïve conditions.

first: Ofra

last: Sabag

first: Benjamin

last: Reubinoff


title: Single cell expression data from ICM cells of mouse blastocysts

city: Boston

first: Ruslan

last: Sadreyev

state: MA

address: 185 Cambridge St

institute: Harvard Medical School/ Mass General Hospital

summary:
Transcriptional reactivation of the paternal X chromosome occurs in specific cells of the mouse blastocyst between E(mbryonic day)3.5 and E4.5 during pre- to peri-implantation development. While the trophectoderm (TE) and the primitive endoderm (PE) maintain Xist RNA expression and thereby imprinted silencing of genes on the Xp, the epiblast (EPI) cells within the inner cell mass (ICM) gradually downregulate Xist and undergo XCR. To identify differentially expressed genes with potential roles in the XCR process, we performed single-cell expression profiling of ICM cells of blastocysts prior (E3.5, EPI Xist+), during (E4.25, EPI Xist+/Xist-) and after (E4.5, EPI Xist-) XCR.
Single cell cDNAs were then assigned to cell-type of origin using qPCR for lineage-specific marker genes (epiblast: Nanog+, PE: Gata6+, TE: Cdx2+). Cells were considered of male sex if they expressed the male marker Eif2s3y or female sex in absence of Eif2s3y and presence of Xist expression in PE cells of the same embryo. Furthermore, female E4.5 epiblast cDNAs were classified according to Xist expression as before (Xist+) or after (Xist-) downregulation during XCR.

overall_design: Single cell expression data of ICM cells of E3.5, E4.25 and E4.5 blastocysts were generated using the V1V3 method described in detail in [Kurimoto, K. et al., Nucleic acids research 34, e42 (2006); Kurimoto, K., Yabuta, Y., Ohinata, Y. and Saitou, M., Nature protocols 2, 739-752 (2007)].

first: Bernhard

last: Payer


title: Explore the effect of m6A reader YTHDF1 on RNAs half-life

city: Changsha

first: Jiong

last: Li

address: No.138, Tongzipo Road

department: Department of Radiology

institute: The Third Xiangya Hospital, Central South University

summary: In order to evaluate mRNA dynamic, we performed 4SU-TT-seq to estimate RNA synthesis and degradation rates in HEK293 cell line. After 1h exposure to the nucleoside analog 4-thiouridine (4SU), 4sU is incorporated into newly transcribed RNA, and the resulting 4sU-labeled RNAs are isolated and sequenced. The sequencing results revealed that parts of mRNAs in YTHDF1 deficient cells tends to be more stable than mRNAs from wild type

overall_design: Both the nascent and total RNA are detected for half-life calculations

first: L

middle: K

last: Wei

last: Xin

last: Hong


title: Setd2 reprograns lipid metabolism for the resolution of inflammation II

city: shanghai

first: kun

last: chen

address: No.800 Xiangyin Road, Yangpu District

institute: Zhejiang University

summary: Purpose: The goal of this study is to identify differential expression profiles between WT and Setd2-KO in BMDMs induced by  LPS for a time-course stimulaiton. Methods: We profiled RNA-seq in bone marrow-derived macrophages stimulated with LPS for 0h, 12h, 24h.  Results: We find significant up and down regulated genes in Setd2-KO BMDMs under LPS stimulation.

overall_design: WT and Setd2-KO BMDMs were stimulated with LPS for 0h, 12h, 24h, and then subjected to RNA seq.

first: Xuetao

last: Cao

first: Kun

last: Chen


title: Setd2 reprograns lipid metabolism for the resolution of inflammation

summary: Purpose: The goal of this study is to identify dynamic expression profiles of epigenetic genes in BMDMs induced by  LPS for a time-course stimulaiton. Methods: We profiled RNA-seq in bone marrow-derived macrophages stimulated with LPS for 0h, 4h, 8h, 12h, 24h.  Results: Epigenetic genes showed distinct expression patterns under LPS stimulation in different times

overall_design: mBMDMs were stimulated with LPS for 0h, 4h, 8h, 12h, 24h, and then subjected to RNA seq.


title: Expression data (microRNA) from developing Neural Tubes of mouse embryos

first: Partha

last: Mukhopadhyay

first: M

last: Pisano

first: Robert

last: Greene


title: The immuno-modulation of exosomes via miRNAs in Zhikong scallop Chlamys farreri

city: Qingdao

first: Mengqiang

last: Wang

state: Shandong

address: Nanhai Road

institute: The Institute of Oceanology, Chinese Academy of Science

type: Non-coding RNA profiling by high throughput sequencing

summary: As marine invertebrates, scallops lack adaptive immunity and employ innate immunity as the front line and almost the solo defense mechanism to protect them against invaders. Accumulating research achievements demonstrated that exosomes could act as innate immune effectors that contribute to host defense mechanism. To better understand the immune functions of exosomes in Chlamys farreri, miRNA profiles of hemocytes from scallops injected with PBS, with normal exosomes and LPS stimulating exosomes, respectively, were generated by deep sequencing, in triplicate.

overall_design: Hemocytes miRNA profiles of scallops injected with PBS, with normal exosomes and LPS stimulating exosomes, respectively, were generated by deep sequencing, in triplicate, in triplicate, using Illumina Hiseq2500.


title: Single-cell RNA-sequencing of human lung monocytes and macrophages from MISTRG mice on day 21 or day 36 post-transplantation with human CD34+ hematopoietic stem and progenitor cells (HSPCs)

status: Public on Nov 11 2022

city: Stockholm

first: Tim

last: Willinger

address: Center for Infectious Medicine (CIM), Alfred Nobels allé 8, level 7

department: Department of Medicine Huddinge

country: Sweden

institute: Karolinska Institutet

summary: The ontogeny of human lung macrophages derived from blood monocytes is poorly understood. In this study, we employed single-cell RNA-sequencing to investigate the heterogeneity of HSPC-derived human lung monocytes and macrophages in the MISTRG humanized mouse model.

overall_design:
We defined the single-cell gene signatures of human CD45+CD11b+HLA-DR+ myeloid cells in the lungs of MISTRG mice 21 days or 36 days after transplantation with human CD34+ HSPCs.

**As Swedish legislation and GDPR prevent unrestricted distribution of raw sequencing data, raw sequence data cannot be provided, including through controlled access databases.***

first: Evren

last: Elza


title: CircRNAs in BALF exosomes and plasma as diagnostic biomarkers in patients with acute respiratory distress syndrome caused by severe pneumonia

first: he

last: sun

address: dongfang hospital

institute: east hospital

summary: To screen and validate abnormally expressed circRNAs in exosomes from BALF of patients with ARDS caused by severe pneumonia, and then evaluate the diagnostic values of these circRNA for ARDS

overall_design: CircRNAs expression profile was obtained by microarray analysis in BALF exosomes of discovery cohort. Competitive endogenous RNA network construction and functional enrichment analysis were performed.

first: He

last: Sun

first: Wei

last: Gao

first: Rongzhang

first: Si

first: Xia

last: Gu

first: Han

last: Xia

first: Zheng

last: Lou

first: Feilong

first: Qiang


title: ChIP-seq of PtrVCS2 fuse FLAG overexpression plants

city: Harbin

first: Xiufang

last: Dai

address: Hexing Road 26#, Xiangfang District

department: School of Forestry, State key laboratory of tree genetics and breeding

institute: Northeast Forestry University

summary: ChIP-seq was carried out with FLAG antibody using stem cambium tissues from PtrVCS2-FLAG overexpression plants

overall_design: Six samples were analyzed, including input DNA, 3 biological replicates and IP DNA, 3 biological replicates


title: Plasmodium Infection induces gene expression changes in spleen lymphocytes

city: xiamen

first: Qingxiang

address: Xiang'an south way

institute: Xiamen University

summary: Plasmodium infection induced trained immunity in mice. As splenomegaly is obvious upon Plasmodium infection, we aim to determine whether the the protective effect of plasmodium-induced trained immunity is due to the effector function induced by splenomegaly.

overall_design: Mice were infected with Plasmodium yoelii for 4 weeks and subjected to CLP-induced sepsis for twenty-four hours. Spleen were harvest and the total RNA were extracted for RNAseq analysis.

first: Yanhui

last: Zhu

first: Shih-chin

last: Cheng


title: Transcriptome analysis of the oxygen induced retinopathy (OIR) model at 5 different timepoints

city: Biberach an der Riß

first: Kolja

last: Becker

address: Birkendorfer Str. 65

department: Global Computational Biology and Digital Sciences

country: Germany

institute: Boehringer Ingelheim Pharma GmbH & Co. KG

summary: High-throughput sequencing of murine retina of the oxygen induced retinopathy (OIR) model compared to control mice at 5 consecutive days (P12-P16)

overall_design: Acoording to the standard OIR model, mice were kept for 5 days under hyperoxic conditions and returned to normoxic conditions at P12. Starting from P12, retinae were collected from 5 consecutive days (P12, P13, P14, P15, P16).

first: Carina

last: Weigelt


title: Exploring the downstream genes of PKP2

city: Nanchang

first: Yi

last: Sang

state: Jiangxi

address: No.128,Xiangshan North Road

institute: Nanchang University

summary: Plakophilin 2 (PKP2), encodes a plakophilin protein that belongs to the member of desmosomal proteins.PkP2 regulates some cell biological functions, but its downstream genes are not clear, so we constructed a stable cell line using H460 cells and identified its downstream target genes by RNA-seq technology

overall_design:
To explore the downstream genes of PKP2,we performed RNA-seq to screen after overexpression of PKP2 in H460 cells.
We used  pSin-puro delivering PKP2 to overexpression of PKP2  in H460 cells.

first: Chun


title: The mitochondrial gene CMPK2 functions as a rheostat for macrophage homeostasis in inflammation

city: New Delhi

first: Vivek

last: Rao

address: Sukhdev Vihar

department: Immunology and Infectious Disease Biology

country: India

institute: CSIR-Institute of Genomics and Integrative Biology

summary: We report the impact of altered CMPK2 expression in THP1 macrophages. CMPK2 silencing THP1 macrophages (CM) were constructed by stably expressing siRNA against CMPK2. Scrambled siRNA expressing THP1 cells were used as control (SC). THP1 macrophages stably expressing CMPK2 fused with mCherry was used as CMPK2 overexpressing macrophages (OE). Control cells were constructed by overexpressing mCherry alone (VC). The RNA sequencing was used to identify genes that are differentially expressed in CMPK2 modified THP1 macrophages.

overall_design: Identifing the effect of CMPK2 alteration in THP1 macrophage inflammatory response

first: Prabhakar

last: Arumugam


title: DNA methylation profiling for 850k reannotation and normalization evaluation [450k]

city: Gosselies

first: Martin

last: Bizet

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

summary: Illumina Infinium DNA Methylation (5mC) profiling arrays are a popular technology to measure genome-scale distribution of 5mC at low cost and high throughput, especially in cancer and other complex diseases. Following the success of the HumanMethylation450 array (450k), Illumina released the MethylationEPIC array (850k) featuring increased coverage of enhancers in addition to regulatory regions primarily covered by the 450k (i.e. promoters, gene bodies). Despite its widespread use, the analysis of 850k data remains suboptimal as it mostly still relies on Illumina’s default annotation, which underestimates enhancers and long noncoding RNAs (lncRNAs). We thus developed an approach, based on ENCODE and LNCipedia databases, that greatly improves Illumina’s default annotation of enhancers and long noncoding transcripts. Comparisons between the re-annotated 850k and its precursor, the 450k, or RRBS, another high-throughput 5mC profiling technology, revealed that the 850k covers at least three times more enhancers and lncRNAs than the other two technologies. We further investigated the reproducibility of the three technologies and applied various normalisation methods to 850k data, showing that most of them reduce variability to a level below that of RRBS. When analyzed with our new annotation and normalization pipeline, profiling for 5mC changes in breast cancer biopsies with the 850k highlighted aberrant enhancers methylation as the predominant feature, confirming previous reports. In conclusion, our study provides an updated analysis pipeline for 850k data based on a refined probe annotation and normalization that allows for the improved analysis of methylation at enhancers and long noncoding transcripts.

overall_design: Total genomic DNA from HCT116 cells wild type, HCT116 cells double-knockout for DNMT1 and DNMT3B were analysed for 5mC changes using Infinium 450k

first: Matthieu

last: Defrance

first: Emilie

last: Calonne

first: Gianluca

last: Bontempi

first: Christos

last: Sotiriou

first: Jana

last: Jeschke


title: Integrated Expression Profiling of MicroRNAs and Messenger RNAs in the Developing Neural Tube

city: LOUISVILLE

first: Partha

last: Mukhopadhyay

address: 501 S PRESTON ST

institute: University of Louisville

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

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

platform_organism:
Mus musculus
synthetic construct

overall_design: Refer to individual Series


title: DNA methylation profiling for 850k reannotation and normalization evaluation


title: Epigenetic regulation of gene expression in mouse Hematopoietic cell after Plasmodium stimulated

last: Gao

summary: Plasmodium infection induced change in the hematopoietic stem cell (HSC) compartment. Here we addressed whether a prior Plasmodium infection would imapct the epignetic profile of HSCs by ATAC-seq.

overall_design: Isolated Cells  by Flow Cytometry, Lineage- ckit+Cd34+ came from bone marrow.  Two replicates were prepared for each sample.


title: Single-cell RNA sequencing reveals CD74high CCL5high retinal microglia initiating immune cells infiltration in autoimmune uveoretinitis

city: Chongqing

first: Zongren

last: Xu

state: Chongqing

address: 1 Youyi Road, Yuzhong District, Chongqing, China

department: ophthalmology department

institute: The First Affiliated Hospital of Chongqing Medical University

summary: In this study, we found that microglia have a considerable number of cells compared to T cells, indicating an equally critical role of microglia in the progression of autoimmune uveitis. We further identified a specific microglial subpopulation expressed with high levels of CD74 and CCL5, which may be directly related to inflammation regulation in autoimmune uveitis and named inflammation-associated microglia (IAMs). Decreasing the number of IAMs by gene regulation methods or CD74/CCL5 neutralizing antibodies effectively reduced inflammation in EAU mice and delayed disease progression. A mechanistic study indicated that the CD74/CCL5 axis was mainly responsible for the regulation of the immune response in autoimmune uveitis. The intracytoplasmic domain of CD74 (CD74–ICD) may be cleaved by the SPPL2A protease and then activate the NF-kB-dependent inflammation pathway in IAM, resulting in the production of CCL5, which recruits peripheral T cells into the retina and causes an inflammatory burst in autoimmune uveitis mice. Decreasing the level of CD74 or CCL5 could effectively reduce uveitogenic T cell infiltration and relieve the autoimmune response in EAU mouse models, indicating the potential therapeutic value of CD74 and CCL5 in autoimmune uveitis.

overall_design: We used single-cell RNA sequencing to explore the pathogenesis of EAU during the course of disease development. We continually detected the clinical manifestations and pathologic changes of uveitis after mice were immunized with IRBP for different days. The slit-lamp results showed that the inflammatory signs of EAU mice were most obvious at day 14, including conjunctival hyperemia and posterior synechiae. The clinical score results suggested that the inflammatory response may begin at day 10 after immunization, reach a peak at 14 days, and gradually recover over the course of disease. Thus, we choosed day 0, day 14, day 21 and day 28.

first: Liao

last: Xingyun

first: Xu

last: Zongren

first: Zhou

last: Hongxiu

first: Hou

last: Shengping


title: DNA methylation profiling for 850k reannotation and normalization evaluation [850k]

overall_design: Total genomic DNA from HCT116 cells wild type, HCT116 cells double-knockout for DNMT1 and DNMT3B, breast tumour and adjacent normal biopsies were analysed for 5mC changes using Infinium 850k


title: Retinoid X receptor promotes hematopoietic stem cell fitness and quiescence and preserves hematopoietic homesotasis [Single Cells]

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary: Hematopoietic stem cells (HSCs) balance self-renewal and differentiation to maintain hematopoietic fitness throughout life. In steady-state conditions, HSC exhaustion is prevented by the maintenance of most HSCs in a quiescent state, with cells entering the cell cycle only occasionally. HSC quiescence is regulated by retinoid and fatty-acid ligands of transcriptional factors of the nuclear retinoid X receptor (RXR) family. Here, we show that dual deficiency for hematopoietic RXRa and RXRb induces HSC exhaustion, myeloid cell/megakaryocyte differentiation, and myeloproliferative-like disease. RXRa and RXRb maintain HSC quiescence, survival, and chromatin compaction; moreover, transcriptome changes in RXRa;RXRb-deficient HSCs include premature acquisition of an aging-like HSC signature, MYC pathway upregulation, and RNA intron retention. Fitness loss and associated RNA transcriptome and splicing alterations in RXRa;RXRb-deficient HSCs are prevented by Myc haploinsufficiency. Our study reveals the critical importance of RXRs for the maintenance of HSC fitness and their protection from premature aging.

overall_design: snRNA-seq of mouse LSKs using 10x Genomics 3' v2.

first: Mercedes

last: Ricote

first: José

middle: a

last: Cancelas

first: M

last: Menéndez-Gutiérrez

first: Jesús

last: Porcuna

first: Haixia

last: Niu

first: Ramesh

last: Nayak


title: Retinoid X receptor promotes hematopoietic stem cell fitness and quiescence and preserves hematopoietic homesotasis [Bulk]

overall_design: Here, we performed a low input bulk RNAseq experiment. LT-HSCs and MPPs were sorted and total RNA was extracted using Arcturus PicoPure kit and RNAeasy mini kit (QIAGEN). Then, RNA samples (5ng) were used for library preparation. Libraries followed next generation paired end sequencing.


title: Extra-hematopoietic immunomodulatory role of the guanine exchange factor DOCK-2

city: Salzburg

first: Rodolphe

last: Poupardin

address: Strubergasse 22

country: Austria


title: Extra-hematopoietic immunomodulatory role of the guanine exchange factor DOCK-2 [MethylCap-Seq]

summary: The molecular basis of stromal immunomodulation is still unresolved. Here, we show a novel function for dedicator of cytokinesis 2 (DOCK2) in regulating extra-hematopoietic immune function of three independent stromal cell sources: induced pluripotent stem cells (iPSC)-derived mesodermal stromal cell (iPS-MSC), severe combined immunodeficiency (SCID) patient-derived fibroblasts and CRISPR/Cas9 knockout cells (iPS-MSCDOCK2KO). We first reprogrammed human mesenchymal stromal cells (MSC) into iPSC before differentiating the iPSCs back into MSC. Immature iPS-MSCs lacked immunosuppressive potential. Successive phenotypic maturation facilitated immunomodulatory function, while maintaining clonogenicity, comparable to parental MSCs. Sequential RNA-seq displayed time-dependent immune-related gene expression eventually resembling parental MSCs. SCID patient-derived fibroblasts harboring bi-allelic DOCK2 mutations also showed significantly reduced immunomodulatory capacity compared to non-mutated fibroblasts. CRISPR/Cas9-mediated DOCK2 knockout in healthy iPSCs resulted in significantly reduced immunomodulatory capacity, reduced F-actin stress-fibers, and a disturbed subcellular localization of CDC42 activation. We provide first evidence for extra-hematopoietic immunomodulation by the guanin exchange factor DOCK2. This suggests that persisting immune disease after successful blood stem cell transplantation in SCID patients could in part be due to loss-of-function DOCK2 mutations.

overall_design: MethylCap-seq analysis of the maturation of induced pluripotent stem cells (iPSCs) derived from Mesenchymal stromal cells (bone marrow and unbilical cord derived MSCs) into MSCs compared to their parental MSCs

first: Dirk

last: Strunk


title: Different expressed microRNAs in exosome from HepG2 cells regulated by PBLD

city: guangzhou

first: LU

last: HAN

state: Guangdong province

address: No.1838, baiyun avenue north, baiyun district

department: Department of gastroenterology

institute: Nanfang Hospital，southern medical university

summary: Different expressed microRNAs in exosome from HepG2 cells by comparing the PBLD-overexpression group and the control group.

overall_design: Extracted total RNA of HepG2 cells-derived exosomes from PBLD-overexpression group and the control group were processed following the standard Agilent protocol, and each group has three biological replicated samples. Agilent human miRNA array detection and data normalization were conducted subsequently.

first: Lu

last: Han

first: Lin

last: Xin

first: Qun

last: Yan

first: Chuncai

last: Gu

first: Mengshu

last: Li

first: Lei

last: Pan

first: Yan

last: Meng

first: Side

last: Liu

first: Aimin


title: Dynamic transcriptome profiling of mouse spleen infected with extraintestinal pathogenic Escherichia coli

city: nanjing

first: ren

last: haiyan

address: No. 1 Weigang, Nanjing, China

institute: Nanjing Agricultural university

summary: Extraintestinal pathogenic Escherichia coli (ExPEC) is a common bacterial strain causing diverse diseases in humans and animals. To analyse the detailed mechanisms underlying ExPEC-mediated sepsis in humans, the transcriptome response of mice at 3h,6h, and 12h after ExPEC infection was analyzed by RNA-seq of mouse spleen samples.

overall_design:
The transcriptome response of mice to intraperitoneal injection with ExPEC was analyzed by RNA-seq of mouse spleen samples.
4 groups with 3 biological replicates, 3P1-3 for the PBS-injected group at 3 hpi (designated g1), 3X1-3 for the ExPEC-infected group at 3 hpi (designated g2), 6X1-3 for the ExPEC-infected group at 6 hpi (designated g3), and 12X1-3 for the ExPEC-infected group at 12 hpi (designed g4).

first: Haiyan

last: Ren

first: XuHua

last: Chen


title: Extra-hematopoietic immunomodulatory role of the guanine exchange factor DOCK-2 [RNA-Seq]

overall_design: RNAseq analysis of the maturation of induced pluripotent stem cells (iPSCs) derived from Mesenchymal stromal cells (bone marrow and unbilical cord derived MSCs) into MSCs compared to their parental MSCs


title: Effect of recombinant Shh on gene expression  of primary rat nucleus pulposus cells

status: Public on Nov 10 2022

first: Libangxi

address: 183 Xinqiao Main Street Shapingba, Chongqing 400037, People’s  Republic of China

institute: Department of Orthopedics Xinqiao Hospital, Army Medical University

summary: In order to study the effect of recombinant Shh (rShh) on nucleus pulposus cells, primary nucleus pulposus cells from SD rats were obtained.Then, nucleus pulposus cells were treated with rShh at 200 ng/ml(dissolved in dmso) for 48h. Similarly, we treated nucleus pulposus cells with the same concentration of DMSO as the control group, and analyzed the data of 3 biological repeats of RNA-seq in each group for gene expression profile analysis.

overall_design: Comparison of gene expression profiles of RNA-seq data from nucleus pulposus cells treated with rShh and nucleus pulposus cells in control group

first: Liabangxi

first: Chencheng

last: Feng


title: Sequence and dynamics of SARS-CoV-2 host cell interactions inferred from    transcriptome analyses

city: Heidelberg

first: Lukas

last: Adam

address: Im Neuenheimer Feld 267

department: BioQuant

institute: Heidelberg University

summary: The worldwide spread of severe acute respiratory syndrome-related coronavirus-2 (SARS-  CoV-2) caused an urgent need for an in-depth understanding of virus-host interactions. Here,  we dissected the dynamics of virus replication and the host cell transcriptional response to  SARS-CoV-2 infection at a systems level by combining time-resolved RNA sequencing with  mathematical modeling. We observed an immediate transcriptional activation of  inflammatory pathways linked to the anti-viral response followed by increased expression of  genes involved in ribosome and mitochondria function, thus hinting at rapid alterations in  protein production and cellular energy supply. At later stages, metabolic processes, in  particular those related to xenobiotic metabolism, were downregulated. To gain a deeper  understanding of the underlying transcriptional dynamics, we developed an ODE model of  SARS-CoV-2 infection and replication. Mathematical modeling of SARS-CoV-2 replication  suggested a strong inhibitory effect of SARS-CoV-2 proteins on the anti-viral response and a  large excess of virus transcripts over the translation capacity. Our study provides insights into  the sequence of SARS-CoV-2 virus-host interactions and facilitates the identification of  druggable host pathways supporting virus replication.

overall_design: RNA-sequencing of SARS-CoV-2 infected Caco-2 cells at different timepoints after viral infection (0h, 1h, 2h, 4h, 7h, 12h, 24h & 48h). Mock samples were used as control at t=4h,12h,48h. Replicates (n=3) were obtained for each time point

first: Megan

last: Stanifer

first: Fabian

last: Springer

first: Jan

last: Mathony

first: Chiara

last: Di Ponzio

first: Roland

last: Eils

first: Steeve

last: Boulant

first: Dominik

last: Niopek

first: Stefan

last: Kallenberger


title: Distinct B-Cell Specific Transcriptional Contexts of the BCL2 Oncogene Impact Pre-Malignant Development in Mouse Models [RNA-Seq]

city: Rennes

first: Delphine

last: Rossille

address: 2 avenue du Pr. Léon Bernard

country: France

institute: INSERM U1236-MOBIDIC

summary: We designed two different BCL2 deregulation models in transgenic mice, whereby the oncogene was either associated with the IgH3′RR superenhancer, as in t(14;18), or inserted into the kappa light chain locus. We compared the impact of these models on B-cell fate and lymphoid tissues. Linkage to the IgH superenhancer showed a quite specific impact on germinal center B cell populations. The Ig kappa model was much less specific and strongly boosted the plasma cell in-flow and the accumulation of long-lived plasma cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data, made from total RNA from lymphoid tissues of immunized mice

first: Cogné

last: Michel

first: Rossille

last: Delphine


title: Prostate cancer cell lines resistant to docetaxel induced by gradient concentration

city: Shanghai

first: Xinan

state: Shanghai

address: Wulumuqi road 12#

department: urology department

institute: Huashan Hospital

summary: We added docetaxel to the culture medium of prostate cancer cell lines PC3 and DU145, and gradually increased the concentration. After a long time of culture, we obtained a docetaxel resistant prostate cancer cell lines.

overall_design: Gradient concentration induction was used to culture PC3 and DU145 resistance cell lines to docetaxel. The concentrations of docetaxel started at 10nm/ml for DU145 and 0.5nm/ml for PC3. Double the concentration of docetaxel in the medium when cell division was vigorous till the IC50 of DU145 come to 1800nm/ml and 15nm/ml for PC3. Named the resistance cell lines with DU145-R and PC3-R. All cells were cultured in a humidified incubator with 5% CO2, 100 units/mL penicillin, and 100 mg/mL streptomycin.

first: Zheyu

last: Zhang


title: Transcriptomic responses to cold stress in Dendrobium huoshanense C.Z. Tang et S.J. Cheng

city: Hefei

first: Shihai

last: Xing

state: Anhui

address: No.1 Qianjiang Road, Xinzhan District

institute: Anhui University of Chinese Medicine

summary: Dendrobium huoshanense C.Z. Tang et S.J. Cheng is a perennial epiphytic herb of family Orchidaceae, which main metabolites are polysaccharides, flavonoids, etc. Low temperature is the main environmental factor that limits the growth and development of plants, and even threatens the survival of plants. However, Changes that occur at the molecular level in response to low temperatures are poorly understood in D. huoshanense. To understand the molecular mechanism of cold tolerance, we performed transcriptomic analysis on two time points of 0 d (control group) and 7 d (cold stress group). A total of 37.63 Gb transcriptomic data were generated using the MGI 2000 platform. These reads were assembled into 170,754 transcripts, and 23,724 differentially expressed genes (DEGs) were obtained. Pathway analysis indicated that “flavonoid biosynthesis”, “anthocyanin biosynthesis”, “flavone and flavonol biosynthesis”, and “plant hormone signal transduction” might play a vital role in D. huoshanense responses to cold stress. Several important pathways genes such as genes encoding polysaccharides, flavonoid, and plant hormone-signaling transduction kinase were identified under cold stress. In addition, the contents of mannose and total flavonoids increased under cold stress. Twelve DEGs in polysaccharides, flavonoid, and hormone pathways were selected from transcriptome analysis for quantitative real-time PCR (qRT-PCR) validation. Our results provide a transcriptome database and candidate genes for further study of D. huoshanense cold stress.

overall_design: Six samples, three replicates

first: Fei

last: Meng


title: Expression of TCF3 target genes defines a subclass of diffuse large B-cell lymphoma characterized by up-regulation of MYC target genes and poor clinical outcome following R-CHOP therapy

city: Kingston

first: David

last: LeBrun

state: Ontario

address: 88 Stuart street

department: Pathology and Molecular Medicine

country: Canada

institute: Queen's University

summary: Fifty-eight retrospectively-ascertained local cases of diffuse large B-cell lymphoma (DLBCL) were segregated into two large subgroups with divergent overall survival through expression profiling of 135 transcripts including 92 regulated downstream of TCF3 or recurrently mutated in DLBCL or Burkitt lymphoma

overall_design: The cohort consist of patients who presented at Kingston Health Sciences Centre (KHSC) from 2001 to 2011 and had: 1) diagnosis of de novo DLBCL; 2) available baseline and outcome clinical data; 3) treatment with R-CHOP; and, 4) sufficient formalin-fixed, paraffin-embedded (FFPE), pre-treatment biopsy material

first: K

last: Tyryshkin

first: D


title: Retinoid X receptor promotes hematopoietic stem cell fitness and quiescence and preserves hematopoietic homesotasis

first: Nathan

last: Salomonis


title: Borrelia burgdorferi gene expression from inside its tick vector during a bloodmeal

city: San Francisco

first: Seemay

last: Chou

state: CA

address: 499 Illinois St, 4th Floor

institute: Chan Zuckerberg Biohub

summary: Borrelia burgdorferi, the causative agent of Lyme disease, is transmitted to vertebrate hosts by Ixodes ticks. As it moves from tick to host, B. burgdorferi must adapt to survive in a vastly different environment. During the tick bloodmeal, which lasts several days, B. burgdorferi is primed for mammalian infection, growing increasingly virulent as it senses cues from its surroundings in the tick. This conditioning is dependent on key transcriptional regulators; however, the downstream transcriptional changes occurring inside of the tick that promote B. burgdorferi transmission and infection are poorly understood due to technical difficulties in sequencing the B. burgdorferi transcriptome from inside of ticks. We developed a protocol to enrich and sequence B. burgdorferi from inside the tick, and we measured global transcriptional changes occurring in feeding ticks. We identified 192 genes that change expression twofold over the course of the tick bloodmeal, which were predominantly located on the plasmids of the genome. The majority of the upregulated genes encode proteins found at the cell envelope or proteins of unknown function, including 45 upregulated genes encoding outer surface lipoproteins. These genes that increase during feeding are candidates for future functional studies, which can help identify new targets for methods that aim to control the spread of Lyme disease.

overall_design: We profiled gene expression from Borrelia burgdorferi enriched from ticks feeding on mice across four days of a bloodmeal (1 day, 2 days, 3 days, and 4 days after attachment).

first: Anne

middle: L

last: Sapiro

first: Beth

last: Hayes


title: Expression data from subcutaneous PDAC xenograft tumor tissue of lactation mice and ctrl mice.

first: YingNa

last: Liao

address: No. 25, Lane 2200, Xietu Road, Shanghai

institute: Shanghai Cancer institute

summary:
Progestin secretion increases remarkably during pregnancy and lactation.
To explore how prolactin affect tumor growth, we used microarray to detailed the different expressed genes between lactation mice and ctrl mice.

overall_design: For obtaining subcutaneous xenograft tumor, a total of 2 × 106 KPC1199 cells were injected subcutaneously in the right back of the mouse once it was pregnant or started breastfeeding. All mice including control mice were sacrificed after injection for 20 days at the same age.

first: PeiQi

last: Huang


title: NR2F2 is a key downstream effector of NF1 loss in estorgen receptor positive breast cancer (ATAC-seq)

city: Leuven

first: Peihua

last: Zhao

address: Herestraat 49

institute: KU Leuven

summary:
NF1 loss-of-function mutations are enriched in hormone receptor positive (HR+) metastatic breast cancer (MBC) and mediate endocrine therapy resistance. To identify therapeutic vulnerabilities in this context, we performed CRISPR/Cas9 screens in wildtype and NF1 knockout isogenic HR+ models and identified NR2F2, an orphan nuclear receptor, to be essential specifically in NF1 loss cells. The NR2F2 dependence was induced as a consequence of NR2F2 upregulation via the activation of the MAPK pathway in these cells. Enforced overexpression of NR2F2 was sufficient to confer endocrine therapy resistance in the absence of NF1 loss, while of NR2F2 knockout or knockdown could enhance the efficacy of endocrine therapies in NF1 WT and NF1 loss models. Mechanistically, our comprehensive multi-omics approaches revealed that NR2F2 modulates chromatin accessibility and regulates ER-dependent transcription through its interaction with ER, transcriptional coregulators and chromatin remodelers at chromatin. Specifically, increased NR2F2 in NF1 loss cells dramatically enhanced the association with transcriptional corepressors, which resulted in attenuation of chromatin accessibility and ER occupancy, and impaired ER transcriptional program. Our findings identify the nuclear receptor NR2F2 as a downstream effector of NF1 loss, and it is essential and potentially druggable mediator of endocrine therapy resistance.
We performed chromatin accessibility profiling analysis using data obtained from ATAC-seq of MCF7 sgNT, sgNF1, sgNR2F2 and double knockout (DKO) cells.

overall_design: Comparative chromatin accessibility analysis across these cell models.

first: Yanyan

last: Cai

first: Sarat

last: Chandarlapaty


title: The RNA polymerase II subunit B gene(POLR2B) functions as a growth regulator in human glioblastoma

city: Suzhou

first: Zimu

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

summary: Glioblastoma multiform (GBM) is the most common and aggressive brain tumor with dismissal prognosis. POLR2B encodes the second largest subunit of the RNA polymerase II, but its genomic status and function in GBM remains unclear. To explore POLR2B-dependent gene regulation, RNA-seq analysis was performed. Compared with the control group, POLR2B knockdown DBTRG-05MG cells showed differently expressed genes.

overall_design: mRNA profiles of DBTRG-05MG cells transfected with scramble shRNA (sh-Scb) or sh-POLR2B  were generated by RNA sequencing, in double, using Illumina NovaSeq6000.

first: Xiaolu

last: Li

first: Jian

last: Pan


title: Single-cell RNA sequencing reveals cellular and molecular reprograming landscape of brain tumors

first: Wei

last: Jin

address: 668 Hongqu road

department: Shanghai cancer center

institute: Fudan University

summary: Brain malignancies encompass gliomas and brain metastases originating from extracranial tumors. To reveal the specific characteristics of gliomas and lung-to-brain metastases (LC), we applied single-cell RNA sequencing to profile immune and nonimmune cells in glioma and LC samples. Our analysis revealed that immune cells are present in heterogeneous subpopulations and that LC reprograms cells, including microglia, macrophages, neutrophils, endothelial cells, and T cells, with unique cell proportions and gene signatures. Particularly, we identified that a subset of macrophages was associated with poor prognosis. In addition, ROS-producing neutrophils was found to play an important role in angiogenesis. Furthermore, endothelial cells participated in active communication with fibroblasts. Metastatic epithelial cells exhibited heterogeneity in DNA copy number variation and we identified one subpopulation with stem cell-like phenotype. Further understanding of the heterogenicity of the tumor microenvironment and tumor cells will be crucial for successful immunotherapy development for lung cancer.

overall_design: Single-cell RNA sequencing analysiss of 4 gliomas and 10 lung-to-brain metastases by BD Rhapsody system.

first: He-Fen

last: Sun

first: Liang-Dong

first: Lao

middle: I

last: Weng

first: Xuan

first: Bao-Jin

last: Xu

first: Yi-Qun

last: Cao


title: LYL1 facilitates AETFC assembly and gene activation by recruiting CARM1 in t(8;21) AML [CHIP-seq]

city: Beijing

first: Qian

last: Chen

address: Qinghuayuan Stress

institute: Tsinghua University

summary:
Transcription factors (TFs) play critical roles in hematopoiesis, and their aberrant expression can lead to various types of leukemia. The t(8;21) leukemogenic fusion protein AML1-ETO (AE) is the most common fusion protein in acute myeloid leukemia and can enhance hematopoietic stem cell renewal while blocking differentiation. A key question in understanding AE-mediated leukemia is what determines the choice of AE to activate self-renewal genes or repress differentiation genes. Toward the resolution of this problem, we earlier showed that AE resides in the stable AETFC complex and that its components co-localize on up- or down-regulated target genes and are essential for leukemogenesis.
In the current study, using biochemical and genomic approaches, we show that AE-containing complexes are heterogeneous, and that assembly of the larger AETFC (containing AE, HEB, E2A, LYL1, LMO2 and LDB2) requires LYL1. Furthermore, we provide strong evidence that the LYL1-containing AETFC preferentially binds to active enhancers and promotes AE-dependent gene activation. Moreover, we show that coactivator CARM1 interacts with AETFC and facilitates gene activation by AETFC. Collectively, this study describes a novel role of oncoprotein LYL1 in AETFC assembly and gene activation by recruiting CARM1 to chromatin for AML cell survival.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for CARM1 as well as the histone modifications H3K27ac and H3K4me1 in Kasumi-1 cells.

first: Murat

last: Cevher

first: Qi

last: Jiang

first: Xiaojian

first: Robert

middle: G

last: Roeder

first: Mo


title: Multi-omics and imaging mass cytometry characterization of human kidneys to identify pathways and phenotypes associated with kidney damage

city: Gothenburg

first: Rasmus

last: Ågren

address: Pepparredsleden 1

institute: AstraZeneca

summary: Despite  the  recent  advances  in our understanding of the role of lipids, metabolites and related enzymes in mediating kidney injury, there is limited integrated multi-omics data identifying potential metabolic pathways driving human kidney damage (KD). The limited availability of kidney biopsies from living donors with kidney disease has remained a major constraint. Here, we validated the use of deceased transplant donor kidneys as a good model to study kidney disease in humans and characterized these kidneys using imaging and multi-omics approaches. We demonstrated that changes in kidney injury and inflammatory markers following KD were consistent with the changes in pre-donation renal function in donors. Neighborhood and correlation analyses of imaging mass cytometry data showed that a subset of renal cells (e.g., fibroblasts) are associated with the expression profile of renal immune cells, potentially linking these cells to kidney inflammation. Integrated transcriptomic and metabolomic analysis of human kidneys showed that renal arachidonic acid metabolism and seven other metabolic pathways were upregulated following KD. To validate the therapeutic potential of targeting the arachidonic acid pathway, we demonstrated increased levels of cytosolic phospholipase A2 (cPLA2) protein and related lipid mediators (e.g., prostaglandin E2) in the injured kidneys. The inhibition of cPLA2 reduced injury and inflammation in human renal proximal tubular epithelial cells (RPTEC) in vitro. This study identifies cell types and metabolic pathways that may be critical for controlling inflammation associated with KD in humans.

overall_design: Frozen kidney cortex samples were put in RNA later stabilization solution (Thermo Fisher Scientific, UK) and stored at -80°C until use. Samples were moved into Agencourt RNAdvance Tissue kit (Beckman Coulter) lysis buffer and homogenized at 1000 rpm for 2min with 5mm Stainless Steel Bead (Qiagen) using 1600 MiniG Tissue Homogenizer (SPEX SamplePrep). Next, total RNA was extracted using Agencourt RNAdvance Tissue kit including DNase treatment for 15 min at 37 ̊C (Ambion DNaseI, ThermoFisher) on an automated Biomek i7 Hybrid system (Beckman Coulter). RNA quantification and quality control was performed on 48 capillary Fragment Analyzer 5300 system (Agilent). All samples showed fragment distribution values (% DV200) above 74 and were subjected to a total RNA-seq library preparation using KAPA RNA HyperPrep Kit with RiboErase (Roche) with 450ng of input RNA, 5min fragmentation at 95  ̊C, and 9 PCR cycles performed on a Tecan Fluent 1080 system (Tecan). Resulting  libraries were quantified on 48 capillary Fragment Analyzer 5300 system showing 295bp average peak size, and pooled equimolarly to a final concentration of 1.9nM. 51bp paired-end sequencing was performed on a v1.5 S1 NovaSeq 6000 kit (Illumina) including 1% of 1.9nM PhiX v3 control (Illumina).

first: Asowata

last: Evans

first: Romoli

last: Simone

first: Tan

last: Jennifer

first: Jachimowicz

last: Daniel

first: Agren

last: Rasmus

first: Woollard

last: Kevin


title: ASFV I73R acts on HEK-293T

city: Wuhan

first: Zhou

last: Shen

state: Hubei

address: 1 Shi-zi-shan Street

institute: Huazhong agriculture university

summary: Idenrify the function of pI73R

overall_design: 3 groups in triplicates


title: LYL1 facilitates AETFC assembly and gene activation by recruiting CARM1 in t(8;21) AML.

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

overall_design: Refer to individual Series


title: The transcription factor IRF2 drives interferon-mediated CD8+ T cell exhaustion to restrict anti-tumor immunity

city: Toronto

first: David

last: Brooks

address: 610, University Ave

institute: Princess Margaret Cancer Centre

summary: Type I Interferons (IFN-I) stimulate pro-inflammatory programs critical for immune activation, but also induce immune-suppressive feedback circuits that contribute to the failure of cancer control. Yet, how IFN-Is differentially induce these opposing programs remains enigmatic. We establish that the transcription factor Interferon Regulatory Factor 2 (IRF2) is a central feedback molecule attenuating IFN signaling and driving CD8 T cell exhaustion in the tumor microenvironment. IRF2 inhibits CD8 T cell effector function in response to sustained interferon signaling by programming T cell exhaustion. Lineage-specific deletion of IRF2 limits CD8 T cells exhaustion to maintain effector functions, thereby enabling long-term tumor control, and increased responsiveness to immune-checkpoint and adoptive cell therapies. Long-term tumor control by IRF2-deficient CD8 T cells is dependent on continuous integration of both IFN-I and IFN? signals, which in the absence of IRF2, potentiate sustained effector function instead of exhaustion. Thus, IRF2 redirects IFN signalling to drive T cell exhaustion and prevent tumor control.

overall_design: For AB-Seq experiment, MC38 Tumor-infitrating CD8 T cells from WT (Tumor WT), Irf2-/- (Tumor IRF2KO) mice. For scATAC-Seq experiment, MC38 Tumor-infitrating CD8 T cells from WT (Tumor WT), Irf2-/- (Tumor Irf2-/-) mice, as well as MC38 Tumor-infitrating CD8 T cells from mice that only lack IRF2 expression in the CD8 T cells (termed Tumor CD8-IRF2cKO mice) together with their controls Tumor CD8-IRF2cWT). For CUT&Tag - Naive isolated CD8+ T cells were isolated and invitro activated using anti-CD3 and Anti-CD28 and subjecte to either anti-IRF2 or IgG antibodies.

first: Sabelo

last: Lukhele

first: Diala

last: Abd Rabbo

first: Mengdi

last: Guo

first: Jian

first: Heidi

middle: J

last: Elsaesser

first: Madeleine

last: Carew

first: Ramy

last: Gadalla

first: Rene

last: Quevedo

first: Laura

last: Snell

first: Teresa

last: Ciudad

first: Bryan

last: Snow

first: Annick

last: You-Ten

first: Jillian

last: Haight

first: Andrew

last: Wakeham

first: Pamela

middle: S

last: Ohashi

first: Tak

last: Mak

first: Weiguo

last: Cui

first: Tracy

last: McGaha


title: LYL1 facilitates AETFC assembly and gene activation by recruiting CARM1 in t(8;21) AML [RNA-seq]

first: Qian

last: Chen

overall_design: RNA-seq when AE or LYL1 is knocked-down in Kasumi-1 cells.

first: Murat

last: Cevher

first: Qi

last: Jiang

first: Xiaojian

last: Sun

first: Robert

last: Roeder

first: Mo


title: NR2F2 is a key downstream effector of NF1 loss in estorgen receptor positive breast cancer (ChIP-seq)

first: Peihua

last: Zhao

summary:
NF1 loss-of-function mutations are enriched in hormone receptor positive (HR+) metastatic breast cancer (MBC) and mediate endocrine therapy resistance. To identify therapeutic vulnerabilities in this context, we performed CRISPR/Cas9 screens in wildtype and NF1 knockout isogenic HR+ models and identified NR2F2, an orphan nuclear receptor, to be essential specifically in NF1 loss cells. The NR2F2 dependence was induced as a consequence of NR2F2 upregulation via the activation of the MAPK pathway in these cells. Enforced overexpression of NR2F2 was sufficient to confer endocrine therapy resistance in the absence of NF1 loss, while of NR2F2 knockout or knockdown could enhance the efficacy of endocrine therapies in NF1 WT and NF1 loss models. Mechanistically, our comprehensive multi-omics approaches revealed that NR2F2 modulates chromatin accessibility and regulates ER-dependent transcription through its interaction with ER, transcriptional coregulators and chromatin remodelers at chromatin. Specifically, increased NR2F2 in NF1 loss cells dramatically enhanced the association with transcriptional corepressors, which resulted in attenuation of chromatin accessibility and ER occupancy, and impaired ER transcriptional program. Our findings identify the nuclear receptor NR2F2 as a downstream effector of NF1 loss, and it is essential and potentially druggable mediator of endocrine therapy resistance.
We performed ER chromatin binding profiling analysis using data obtained from ChIP-seq of MCF7 sgNT, sgNF1, sgNR2F2 and double knockout (DKO) cells under the conditions of full media, estrogen starvation and estrogen stimulation. We also performed NR2F chromatin binding profiling analysis using data obtained from ChIP-seq of MCF7 sgNT and sgNF1 cells under full media culture condition

overall_design: Comparative ER or NR2F2 chromatin binding analysis in these cell models.

first: Yanyan

last: Cai

first: Sarat

last: Chandarlapaty


title: HEDGEHOG/GLI Modulates The PRR11-SKA2 Bidirectional Transcription Unit in Lung Squamous Cell Carcinomas

city: Chongqing

first: sun

middle: yi

last: yun

address: 1YiXue Yuan,Yuzhong District

institute: Chongqing Medical University

summary: We previously demonstrated that proline-rich protein 11 (PRR11) and spindle and kinetochore associated 2 (SKA2) constituted a head-to-head gene pair driven by a prototypical bidirectional promoter, and this gene pair synergistically promoted the development of non-small-cell lung cancer. However, the signaling pathways leading to the ectopic expression of this gene pair remain obscure. In the present study, we first analyzed the lung squamous cell carcinoma (LSCC) relevant RNA sequencing data from the TCGA database by the correlation analysis of gene expression and gene set enrichment analysis (GSEA), revealing that the PRR11-SKA2 correlated gene list highly resembled the Hedgehog (Hh) pathway activation-related gene set. Subsequently, GLI1/2 inhibitor GANT-61 or GLI1/2-siRNA inhibited Hh pathway of LSCC cells, concomitantly decreasing the expression levels of PRR11 and SKA2. Furthermore, the mRNA expression profile of LSCC cells treated with GANT-61 was detected by RNA sequencing, displaying 397 differentially expressed genes (203 upregulated genes and 194 downregulated genes). Out of them, one gene set, including BIRC5, NCAPG, CCNB2 and BUB1, involved in cell division and interacted with both PRR11 and SKA2. These genes were verified as the downregulated genes via RT-PCR and their high expression significantly correlated with shorter overall survival of LSCC patients. Taken together, our results indicated that GLI1/2 mediated the expression of the PRR11-SKA2-centric gene set which served as unfavorable prognostic indicators for LSCC patients, potentializing new combinatorial diagnostic and therapeutic strategies in LSCC.

overall_design: We first analyzed the lung squamous cell carcinoma (LSCC) relevant RNA sequencing data from the TCGA database by the correlation analysis of gene expression and gene set enrichment analysis (GSEA), revealing that the PRR11-SKA2 correlated gene list highly resembled the Hedgehog (Hh) pathway activation-related gene set. Subsequently, GLI1/2 inhibitor GANT-61 or GLI1/2-siRNA inhibited Hh pathway of LSCC cells, concomitantly decreasing the expression levels of PRR11 and SKA2. Furthermore, the mRNA expression profile of LSCC cells treated with GANT-61 was detected by RNA sequencing, displaying 397 differentially expressed genes (203 upregulated genes and 194 downregulated genes). Out of them, one gene set, including BIRC5, NCAPG, CCNB2 and BUB1, involved in cell division and interacted with both PRR11 and SKA2. These genes were verified as the downregulated genes via RT-PCR and their high expression significantly correlated with shorter overall survival of LSCC patients.

first: Yiyun

first: Ying

last: Zhang


title: Microarray profiling analysis of microRNAs expression in diabetes samples

city: SHENYANG

first: KAI

last: TAO

state: State

address: Reconstructive and Plastic Surgery, The General Hospital of Northern Theater Command, No. 83, Wenhua Road, Shenhe District

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

summary: At present, there is no effective treatment for diabetic wounds, and the cost of treatment is high. MicroRNAs (miRNAs) plays an important role in the process of diabetic wound healing. By regulating the expression of target genes, it regulates growth factors, cytokines and signal pathways, thereby affecting various stages of ulcer healing such as hemostasis, anti-inflammatory, proliferation and remodeling. In this study, differential expression of miRNAs in diabetic wound was screened. MiR-206 was selected as the research object to detect the effect of miR-206 on the proliferation of fibroblasts and vascular endothelial cell by regulating HIF-1?. Finally, in vivo studies showed that miR-206 antagomir could promote the expression of HIF-1?, CD34 and VEGF, and further promote wound healing in diabetic rats.

overall_design: Three normal skin samples and three diabetes samples were collected in the present study.

first: Wei

last: Yang


title: Effects of the treatment with IFNβ and GM-CSF-secreting CT2A cells to wildtype CT2A tumor microenvironment post resection

status: Public on Nov 09 2022

city: Boston

first: Kok Siong

state: Massachusetts

address: 60 Fenwood Road

department: Neurosurgery

institute: Brigham and Women's Hospital

summary: To elucidate the underlying immune responses elicited by IFNβ and GM-CSF-secreting CT2A cells to brain tumor microenvironment post resection compared to placebo group and non-IFNβ and GM-CSF-secreting CT2A cell group

overall_design: Comparative gene expression profiling analysis of RNA-seq data for tumor tissues harvested from mouse brains post-resection and treatment with either sECM only, GFP-TCs (control cells), and ThTCs (IFNβ and GM-CSF-secreting cells).

first: Kok-Siong


title: Alkaline phosphatase-controllable and red light-activated RNA modification

first: fang

last: jing

state: Jiangsu province

address: Renai street

institute: Suzhou university

summary: To exploit the therapeutic mechanism of our proposed alkaline phosphatase-controllable and red light-activated RNA modification approach at the genetic level, we established an RNA-modified group (f-RCP+660 nm) and non-RNA-modified group (RCP+660 nm) in HepG2 cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HepG2 cells treated with f-RCP+660 nm and RCP+660 nm as control.

first: Haibin

last: Shi

first: Jing

last: Fang

first: Yali

last: Feng

first: Yuqi

last: zhang


title: Targeting UHRF1-SAP30-MXD4 axis for leukemia initiating cell eradication in myeloid leukemia

first: Jiaying

address: 320 Yue Yang Road

department: CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health

institute: Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences

summary: Aberrant self-renewal of leukemia initiation cells (LICs) drives aggressive acute myeloid leukemia (AML). Here, we report that UHRF1, an epigenetic regulator that recruits DNMT1 to methylate DNA, is highly expressed in AML and predicts poor prognosis. UHRF1 is required for myeloid leukemogenesis by maintaining self-renewal of LICs. Mechanistically, UHRF1 directly interacts with Sin3A associated protein 30 (SAP30) through two amino acids, G572 and F573 in its SRA domain, to repress gene expression. Depletion of UHRF1 or SAP30 derepresses an important target gene, MXD4, which encodes a MYC antagonist, and leads to suppression of leukemogenesis. Knockdown of MXD4 can rescue the leukemogenesis by activating the MYC pathway. Lastly, we identified a UHRF1 inhibitor, UF146, and demonstrated its significant therapeutic efficacy in the myeloid leukemia PDX model. Taken together, these studies reveal the mechanisms for altered epigenetic programs in AML and provide a promising targeted therapeutic strategy against AML.

overall_design: UHRF1 CUT-TAG was performed with UHRF1 antibody in Kasumi-1 and THP-1 cells (AML cells). We used UHRF1 shRNA to induce UHRF1 knockdown in Kasumi-1 and THP-1 cells. Kasumi-1 and THP-1 cells were transduced with UHRF1 shRNA and then AML cells were selected by puromycine for 48h,finally these AML cells were subjected to RNA-seq analysis. Kasumi-1 and THP-1 cells were treated with UHRF1 inhibitor UF146 for 24h and these cells were subjected to RNA-seq analysis.

first: Chenglong

last: Hu

first: Bingyi

last: Chen

first: Zijuan

last: Li

first: Xiao-Jian

first: Lan

last: Wang


title: Cold-treated and Fasting-treated white-browning effect in inWAT

city: Taichung

first: Shih-Chieh

last: Hung

address: No.6, Hsueh-Shih Road., North Dist.

department: Drug Development Center, Institute of New Drug Development

country: Taiwan

institute: China Medical University

summary: To investigate the white-browning effect in inguinal WAT tissue by cold-treated and fasting-treated

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control inWAT, cold-treated inWAT, and fasting-treated inWAT.

first: Yu-Ting

last: Yen

first: May

last: Chien


title: Borrelia burgdorferi gene expression in culture before and after antibody enrichment

first: Seemay

last: Chou

overall_design: We developed a protocol to enrich B. burgdorferi from feeding ticks, and we first tested it on in vitro cultured B. burgdorferi to determine if it altered downstream gene expression measurements.

first: Anne

last: Sapiro

first: Beth

last: Hayes


title: GLI1+ cells are a source of repair-supportive mesenchymal cells (RSMCs) during airway epithelial regeneration

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: Repair-supportive mesenchymal cells (RSMCs) have been recently reported in the context of naphthalene (NA)-induced airway injury and regeneration. These cells transiently express smooth muscle actin (Acta2) and are enriched with platelet-derived growth factor receptor alpha (Pdgfra) and fibroblast growth factor 10 (Fgf10) expression. Genetic deletion of Ctnnb1 (gene coding for beta catenin) or Fgf10 in these cells using the Acta2-Cre-ERT2 driver line after injury (defined as NA-Tam condition; Tam refers to tamoxifen) led to impaired repair of the airway epithelium. In this study, we demonstrate that RSMCs are mostly captured using the Acta2-Cre-ERT2 driver when labeling occurs after (NA-Tam condition) rather than before injury (Tam-NA condition), and that their expansion occurs mostly between days 3 and 7 following NA treatment. Previous studies have shown that lineage-traced peribronchial GLI1+ cells are transiently amplified after NA injury. Here, we report that Gli1 expression is enriched in RSMCs. Using lineage tracing with Gli1Cre-ERT2 mice combined with genetic inactivation of Fgf10, we show that GLI1+ cells with Fgf10 deletion fail to amplify around the injured airways, thus resulting in impaired airway epithelial repair. Interestingly, Fgf10 expression is not upregulated in GLI1+ cells following NA treatment, suggesting that epithelial repair is mostly due to the increased number of Fgf10-expressing GLI1+ cells. Co-culture of SCGB1A1+ cells with GLI1+ cells isolated from non-injured or injured lungs showed that GLI1+ cells from these two conditions are similarly capable of supporting bronchiolar organoid (or bronchiolosphere) formation. Single-cell RNA sequencing on sorted lineage-labeled cells showed that the RSMC signature resembles that of alveolar fibroblasts. Altogether, our study provides strong evidence for the involvement of mesenchymal progenitors in airway epithelial regeneration and highlights the critical role played by Fgf10-expressing GLI1+ cells in this context.

overall_design: Single-cell RNA-seq of sorted tdTom+ cells isolated from Gli1Cre-ERT2; tdTomatoflox lungs was carried out using the 10x Genomics Single Cell 3′ v3.1 RNA-seq kit. Gene expression libraries were prepared according to the manufacturer’s protocol. MULTI-seq barcode libraries were retrieved from the samples, and libraries were prepared independently.

first: Xuran

last: Chu

first: Ana

last: Vazquez-Armendariz

first: Janine

last: Koepke

last: Guenther


title: C11orf52 as a new regulator of nanomechanical properties and cell migration in prostate cancer cells

city: Fuzhou

first: Yu

middle: hua

address: 1 Keji Road, Shangjie Town, Minhou County, Fujian Province, China

institute: Fujian Normal University

summary: In this study, puncture biopsies samples of patients with benign prostatic hyperplasia (BPH), medium-risk and high-risk prostate cancer were collected for RNA-seq analysis. GO analysis showed that DEGs in the medium and high risk groups were significantly enriched in processes such as extracellular region and cell motility and migration. In addition, the BPH and medium-risk groups were significantly enriched in processes such as extracellular region, developmental process and ion transport. The BPH and high-risk groups were significantly enriched in processes such as extracellular region, cell motility, migration and immune system process. In this study, differentially expressed genes associated with risk classes were identified.

overall_design: Differentially expressed genes between benign prostatic hyperplasia, medium-risk, and high-risk prostatic carcinoma tissues

first: Yuhua

first: Hongqin

last: Yang

first: Xiaoqiong

last: Tang

first: Jinshu

last: Zeng


title: Longitudinal map of transcriptome changes in the Lyme pathogen Borrelia burgdorferi during tick-borne transmission

address: 499 Illinois St, 4th Floor


title: Mettl14-mediated m6A modification enhances the function of Foxp3+ regulatory T cells and promotes allograft acceptance

city: Chengdu

first: Yanzhuo

last: Liu

address: Address of University of Electronic Science and Technology of China (Shahe)

institute: UESTC

summary: The transcripts levels of 434 genes were upregulated and those of 277 genes were downregulated in Treg cells from Foxp3-Mettl14f/+ cKO mice compared to those genes in Treg cells from the littermate controls.

overall_design: Treg cells were isolated from Foxp3-Mettl14f/+ cKO mice and littermate controls on day 7 post-transplantation. Total RNA was extracted with TRIzol and mRNA was then separated by using a Dynabeads mRNA Purification Kit (Invitrogen). Standard Illumina sequencing was applied for sequencing. Raw RNA-sequencing reads were aligned to the mouse genome (mm10) with TopHat. Genes were considered significantly differentially expressed if the fold change was greater than 1.5-fold and less than 0.1. A GO enrichment analysis and KEGG pathways enrichment analysis were performed using online bioinformatics tools.

first: Gaoping

last: Zhao

first: Lu


title: An SWAP1-SFPS-RRC1 splicing factor complex modulates pre-mRNA splicing to promote photomorphogenesis in Arabidopsis

city: Austin

first: Enamul

last: Huq

state: TX

address: 100 East 24th St., NHB 2.616, Stop A5000 Department of Molecular Biosciences University of Texas at Austin

department: Molecular Biosciences

institute: University of Texas at Austin

summary: To investigate the molecular and physiological functions of SWAP1 in light signaling. We show that SWAP1 modulates global gene expression and alternative splicing both under dark and red light treated conditions

overall_design: 4-day-old dark grown seedlings were either exposed to the continuous red light for 3 hrs or kept in the dark. Total RNA (rRNA depleted) was extracted and used for the RNAseq library preparation. Libraries were sequence using Illumina NovaSeq 6000. Reads were aligned using STAR and then analysed using HTseq, DESeq2 and ASpli 2.0. RT-qPCR validation was performed using SYBR green assays

first: Anireddy

last: Reddy

first: Praveen

last: Kathare

first: Ruijiao

last: Xin


title: Arg2-derived peptide vaccine-induced changes in gene expression in Pan02 tumors

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Investigate changes in the gene expression in the tumor upon vaccination with an Arg2-derived peptide in a murine tumor model (Pan02)

overall_design: Pan02 tumor-bearing mice received a control vaccine or an Arg2-derived peptide vaccine on day 11 and 17. Tumors were harvested (n=4-6 per group) on day 31, RNA was extracted, and bulk RNAseq was performed.

first: Stine

last: Weis-Banke

first: Mads

last: Hald Andersen


title: Single Cell Profiling of CD45+ Spinal Cord Cells Reveals Microglial and B Cell Heterogeneity and Crosstalk Following Spinal Cord Injury

city: Rensselaer

first: Thomas

middle: R

last: Kiehl

state: NY

address: One Discovery Drive

institute: Neural Stem Cell Institute

overall_design: CD45+ cells

first: Elizabeth

last: S Fisher

first: Matthew

last: Amarante

first: Natasha

last: Lowry

first: Steven

last: Lotz

first: Farhad

last: Farjood

first: Sally

last: Temple

first: Caitlin

last: Hill


title: Cancer-associated fibroblasts promote the stemness and progression of renal cell carcinoma via exosomal miR-181d-5p

city: Nanjing

first: Hongqian

last: Guo

address: 321 Zhongshan Road

department: Department of Urology

institute: Drum Tower Hospital, Medical School of Nanjing University

summary: The mechanisms underlying the effects of cancer-associated fibroblasts (CAFs) on cancer stemness and tumor progression in renal cell carcinoma (RCC) have not been elucidated yet. In the present study, we found that the enrichment of CAFs was positively associated with tumor progression and cancer stemness in RCC. Further investigation revealed that CAFs could enhance cancer stemness through delivering exosomes to RCC cells, and miR-181d-5p was identified as the critical exosomal miRNA in CAF secreted exosomes by small RNA sequencing and subsequent screening assays. Mechanistically, exosomal miR-181d-5p transferred from CAFs to RCC cells directly suppressed the expression of ring finger protein 43 (RNF43) and activated Wnt/β-catenin signaling pathway, thus promoted cancer stemness and tumor progression. Overexpression of RNF43 strongly suppressed stemness properties and the effects could be reverted by miR-181d-5p. Overall, our findings revealed a crucial mechanism by which CAFs secreted exosomal miRNAs to enhance cancer stemness and thus promote RCC progression, suggesting a new avenue based on CAF secreted miRNAs for more effective targeted therapies.

overall_design: Exosomes were isolated from three paired primary NFs and CAFs, respectively. Total RNA of exosomes was extracted . After checking the quantity and integrity, 1.5 µg of total RNA for each sample was used to generate the small RNA library, and then the libraries were sequenced on an Illumina Hiseq 2500 platform and further subjected to the following analyses.

first: Meng

last: Ding

first: Xiao

middle: Z

first: Xiaoqing

last: Chen

first: Wenli

last: Diao

first: Yansheng

last: Kan

first: Wenmin

last: Cao

first: Wei

first: Bo

last: Jiang

first: Haixiang

last: Qin

first: Jie

last: Gao

first: Junlong

last: Zhuang

first: Qing

last: Zhang


title: African Ancestry Associated Gene Expression Profiles in Triple Negative Breast Cancer Underlie Altered Tumor Biology and Clinical Outcome in Women of African Descent

city: New York

first: Melissa

middle: Boneta

last: Davis

state: New York

department: Surgery

institute: Weill Cornell Medicine

summary: Women of sub-Saharan African descent have disproportionately higher incidence of Triple Negative Breast Cancer (TNBC), and TNBC-specific mortality. Population comparative studies show racial differences in TNBC biology, including higher prevalence of basal-like and Quadruple-Negative subtypes in African Americans (AA). However, previous investigations relied on self-reported race (SRR) of primarily United States (US) populations. Due to heterogenous genetic admixture, and biological consequences of social determinants, the true association of African ancestry with TNBC biology is unclear. To address this, we conducted RNAseq on an international cohort of AAs, west and east Africans with TNBC. Using comprehensive genetic ancestry estimation in this African-enriched cohort, we found expression of 613 genes associated with African ancestry and 2000+ associated with regional African ancestry. A subset of African-associated genes also showed differences in normal breast tissue. Pathway enrichment and deconvolution of tumor cellular composition revealed tumor-associated immunological profiles are distinct in patients of African descent.

overall_design: Determination of African-ancestry associated gene signatures in Triple Negative Breast Cancer using a RNAseq cohort of women of African descent, including Ghanaian, Ethiopian and African American women

first: Rachel

middle: N

last: Martini

middle: B


title: Transcriptomic profile analysis of the left atrium in spontaneously hypertensive rats at the early stage

first: du

last: jianlin

address: 74 Linjiang Road

department: Cardiology

institute: The Second Affiliated Hospital of Chongqing Medical University

summary: Before morphological changes at the early stage of hypertension, how overloaded hypertension influences the transcriptomic profile of the left atrium remains unclear, therefore, RNA-sequencing was performed to define the RNA expressing profiles of left atrium in spontaneously hypertensive rats (SHR) and normotensive Wistar-Kyoto rats (WKY) as a control group. At the same time, we compared the RNA expressing profiles changes in ARB-treated (valsartan, 30mg/kg/d) and ARNI-treated (sacubitril/valsartan, 60mg/kg/d) SHR to reveal the distinct effects on the left atrium. A total of 1558 differentially expressed genes were found in the left atrium between WKY rats and SHRs. Bioinformatics analysis revealed that these mRNAs could regulate the upstream pathways in atrial remodeling through atrial fibrosis, inflammation, electrical remodeling, and cardiac metabolism. The regulated transcripts of left atrial tissue in both the ARB-treated and ARNI-treated groups were related to metabolism. Compared with ARB, transcripts in ARNI-treated rats were mapped to the cGMP-PKG signaling pathway.

overall_design: SHRs were randomly divided into 3 groups: model group (n=3), rats were administered with saline (7.5mL/kg/d) for 4 weeks; ARB-treated group (n=3), rats were treated with valsartan (30mg/kg/d) for 4 weeks; ARNI-treated group (n=3), rats were fed with sacubitril/valsartan (60mg/kg/d) for 4 weeks. And WKY rats as the control group (n=3), administered with saline (7.5mL/kg/d) for 4 weeks. Gene expressing profiles in the 4 groups were generated by RNA-sequencing.

first: Jianlin

last: Du

first: Qinghua

last: Fang

first: Jiangjun

last: Wei

first: Xianglin

last: Long


title: Identification and functional analysis of m6A in the mammary gland tissues of dairy goats at the early and peak lactation stages

city: 泰安

first: 君

middle: 舒

last: 王

state: 山东省

address: 泰前街道

department: 动物科技学院

institute: 山东农业大学

summary:
In this study, m6A-modified Methylated RNA immunoprecipitation sequencing (MeRIP-seq) and transcriptome sequencing (RNA-seq) were used to identify the key genes with m6A modification during mammary gland development and lactation in dairy goats.
The results showed that m6A methylation occurred at 3,927 loci, which were significantly enriched in the 3' untranslated coding region(3’UTR) and the termination codon region. In the early stage (E) and peak stage (P) of lactation, m6A methylation occurred extensively in mammary tissues, and a total of 725 differentially expressed m6A-modified genes were obtained, all negatively correlated with mRNA expression. In addition, gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that different methylated genes were mainly involved in the growth and apoptosis of mammary epithelial cells through signaling pathways related to mammary gland development and lactation, such as the mitogen-activated protein kinase (MAPK) and phospholipase D pathways.

overall_design: The aim of this study was to explore differentially expressed m6A-methylated genes in the mammary gland tissues of Laoshan dairy goats during the early and peak lactation stages through Methylated RNA immunoprecipitation sequencing (MeRIP-Seq) and to analyze the mechanism of regulation of the development and lactation of mammary gland tissue in the early and peak lactation stages in dairy goats.

first: zhibin

last: ji

first: qing

last: li


title: unCTC: Unbiased characterisation of single circulating tumor cell transcriptomes II

city: New Delhi

first: Sarita

last: Poonia

state: Delhi

address: IIITD

department: Computational Biology

institute: IIITD

summary: The identification and characterisation of Circulating Tumour Cells (CTCs) is important to get insights into the biology of metastatic cancers, monitoring disease progression, and potential use in liquid biopsy-based personalised cancer treatment. The major limitation of CTC isolation is due to their heterogeneous nature, altered phenotype from primary tumour and availability in limited numbers. In the past years, several techniques have been developed to detect CTCs from peripheral blood, based on canonical markers. These methods are, however, prone to miss a larger set of CTCs due to variable or no expression of these markers. Furthermore, CTC enrichment processes are not free from White Blood Cell (WBC) contamination. Single cell RNA sequencing (scRNA-Seq) of CTCs provides a wealth of information about their tumors of origin as well as their fate. The first and most important roadblock encountered in CTC scRNA-Seq data analysis is confirmation of CTC capture. We present unCTC, an R software for unsupervised and semi-supervised characterisation of CTC transcriptomes, in contrast with WBCs. unCTC features various standard and novel computational/statistical modules for clustering, Copy Number Variation (CNV) inference, and marker based verification of the malignant phenotypes. Notably, we propose Deep Dictionary Learning using K-means clustering cost (DDLK) that robustly clusters scRNA-Seq profiles of CTCs and WBC contaminates to characterise heterogeneity among the concerned cell population. Interestingly, DDLK performs better as gene expression data is transformed into pathway enrichment profiles. To demonstrate the utility of unCTC, we produce scRNA-Seq profiles of breast CTCs enriched by the integrated ClearCell® FX/PolarisTM workflow that works on the principles of size selection and negative enrichment for CD45, a pan leukocyte marker.

overall_design: 96 CD45+ live cells were captured using Fluidgm C1 single cell system and processed for whole transcriptome library preparation.

first: Debarka

last: Sengupta

first: Naveen

last: Ramalingam


title: The identification of TCF1+ progenitor exhausted T-cells in THRLBCL may predict a better response to PD-1/PD-L1 blockade

city: MILAN

first: Maria Rosaria

last: Sapienza

state: Italy

address: Via Ripamonti, 435

department: Division of Haematopathology

country: Italy

institute: IEO, European Institute of Oncology IRCCS

summary: T-cell/histiocyte rich large B-cell lymphoma (THRLBCL) is a rare and aggressive variant of diffuse large B cell lymphoma (DLBCL) that usually affects young to middle-aged patients, with disseminated disease at presentation. The tumor microenvironment (TME) plays a key role in THRLBCL, due to its peculiar cellular composition (less than 10% neoplastic B-cells interspersed in a cytotoxic T-cell/histiocyte rich background). A significant percentage of THRLBCL is refractory to RCHOP-based regimens and to CAR-T therapy; thus, the development of a specific therapeutic approach for these patients still represents an unmet clinical need. To better understand the interaction of immune cells in THRLBCL TME and identify more promising therapeutic strategies, we compared the immune gene expression profiles of 12 THRLBCL and 10 DLBCL samples, using the Nanostring PanCancer Immune Profiling panel. Gene co-expression network analysis identified the predominant role of the PD-1/PD-L1 axis in the modulation of the immune response. Furthermore, the PD-1/PD-L1 activation was flanked by the overexpression of as many as 48 genes related to the functional exhaustion of T-cells. Globally, THRLBCL TME was highly interferon-inflamed and severely exhausted. The immune gene profiling findings strongly candidate THRLBCL for anti-PD-1 therapy, but also allowed us to take a step forward in understanding THRLBCL TME. Of therapeutic relevance, we identified a subset of TCF1+ progenitor exhausted T-cells enriched in THRLBCL patients. This subset of TCF1+ exhausted T-cells correlates with good clinical response to immune checkpoint therapy and may improve prediction of anti-PD-1 response in THRLBCL patients.

overall_design: In the study presented here, formalin-fixed, paraffin-embedded (FFPE) archival specimens of THRLBCL (n = 12) and DLBCL (n = 10) were selected for gene expression profiling (GEP) analysis.

first: Maria

first: Valentina

last: Tabanelli

first: Saveria

last: Mazzara

first: Stefano

middle: A

last: Pileri


title: Identification of transcription factors dictating blood cell development using a bidirectional transcription network-based computational framework [RNAseq_THP1_GSK-LSD1]

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

summary: Genome-wide transcription factor binding profiles provide valuable insights into hematopoietic development and malignancies. Today, advanced computational methods exploit cis-regulatory information to predict complex gene regulatory networks controlled by transcription factors. However, these prediction methods still require large amounts of reference data or experimental expertise. Here, we present a low-requirement network-based computational framework that exploits bidirectional transcription marked regulatory elements to identify important transcription factors driving hematopoietic decision making. Using CAGE-seq we predicted TF binding and confirmed experimentally validated TF important in cell conversion strategies by exploiting bidirectional regions. Next, we applied our framework to predict driving transcription factors in induced normal erythropoiesis and early myelopoiesis, as well as in acute myeloid leukemia associated MLL-AF9-driven immortalisation. Our approach allowed the identification of experimentally validated as well as thus far unexplored transcription factors in these processes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wildtype THP1 cells and GSK-LSD1 induced THP1 cells.

first: B

middle: M

last: Heuts

first: S

last: Apalategi

last: Frölich

last: Bergevoet

last: van den Oever

last: van Heeringen

last: van der Reijden

first: J

middle: H


title: Identification of transcription factors dictating blood cell development using a bidirectional transcription network-based computational framework [CAGEseq_THP1_GSK-LSD1]

overall_design: Comparative CAGE transcription start sites (CTSS) expression profiling analysis of CAGE-seq data for wildtype THP1 cells and GSK-LSD1 induced THP1 cells.


title: Trem2 deficiency does not alter virus control but impairs phagocytic activity during neurotropic coronavirus induced demyelination

city: Cleveland

first: Jihye

last: Kim

state: Ohio

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic

summary: Triggering receptor expressed on myeloid cells 2 (TREM2) plays a protective role in neurodegenerative diseases, including Alzheimer’s and demyelinating diseases. However, Trem2 functions can exacerbate tissue damage during viral respiratory or liver infections. We therefore investigated the role of TREM2 in a viral encephalomyelitis model associated with prominent Th1 responses and demyelination. To address our hypothesis, Wild type (WT) and  Trem2-/- mice were infected with a sublethal glia tropic murine coronavirus (MHV-JHM) was intracranially. Disease progression and survival were monitored daily. Immune response and demyelination in the spinal cord (SC) were determined by flow cytometry and immunofluorescences analysis. Expression of Inflammatory cytokines was measured with RT-PCR. Differential gene expression in sorted SC-derived microglia and infiltrated bone marrow-derived macrophages (BMDM) were determined by Nanostring, nCounter system, which directly captures and counts individual mRNA transcripts thereby omitting cDNA-based amplification. Upon infection, BMDM highly upregulated Trem2 mRNA compared to microglia, which showed a delayed increase coincident with demyelination. Although TREM2 deficiency did not alter disease onset and severity, it impaired clinical recovery during establishment of viral persistence associated with demyelination. Disease progression in Trem2-/- mice was not associated with altered virus control, leukocyte recruitment or overall inflammatory responses in the SC. However, there was a significant increase in degenerated myelin not associated with the myeloid markers IBA1 and/or CD68 in the lesions. Gene expression profiles of SC-derived microglia and BMDM using the Nanostring platform revealed that TREM2 deficiency resulted in the failure to upregulate genes associated with phagocytosis, including LPL and CD36. Overall our data using a virus infection model show that TREM2 deficiency does not affect viral control or T cell immunity but leads to impaired expression of select phagocytic pathway factors, ultimately resulting in failure to remove damaged myelin in demyelinated lesions. The results support that TREM2 dependent  removal of damaged myelin is independent of the initial insult or the inflammatory milieu, but rather regulated by sensing a dysregulated lipid environment.

overall_design: SC-derived microglia and SC-derived bone marrow derived monocytes (BMDM) from WT and Trem2-/- mice were analysed using Nanostring nCounter 'mouse nCounter Myeloid Innate Immune Panel ' panel.

first: Mihyun

last: Hwang

first: Carine

last: Savarin

first: Jennifer

last: Powers

first: Natasha

last: Towne

first: Cornelia

middle: C

last: Bergmann


title: BRD4 inhibitor GNE987 exerts anti-cancer effects by targeting C-Myc and S100A16 in Glioblastoma

city: Suzhou

first: Gen

last: Li

address: No. 92 Zhongnan Street

institute: Children's Hospital of Soochow University

summary: To investigate the function of GNE987 in the regulation of gene expression, we treated U87 cells with control (DMSO) or GNE987, respectively. We then performed gene expression profiling analysis using data obtained from RNA-seq of control and GNE987 treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for U87 cells treated with  control (DMSO) or GNE987 for 48h.

first: Liya

last: Ma

first: Li

last: Zhang