title: Expression data from proximal tubular cells of proximal tubular cell-specific KAT5 knockout mice

status: Public on Nov 19 2021

city: Shinjyuku-ku,

first: Akihito

last: Hishikawa

state: Tokyo

address: 35 Shinanomachi

institute: Keio University School of Medicine

summary:
Isolated proximal tubular cells from proximal tubular cell-specific KAT5 knockout mice for RNA extraction and hybridization on Affymetrix microarrays.
We sought to obtain the physiological significance of KAT5 in proximal tubular cells.

overall_design: Gene expression between proximal tubular cells of wild type mice and proximal tubular cell-specific KAT5 knockout mice were compared

first: Kaori

last: Hayashi


title: Biomarker Profile for Prediction of Response to SMAC Mimetic Monotherapy in Pediatric Precursor B-Cell Acute Lymphoblastic Leukemia

status: Public on Nov 18 2021

city: Ulm

first: Hans

middle: A

last: Kestler

address: Albert-Einstein-Allee 11

department: Research Group Bioinformatics and Systems Biology

country: Germany

institute: University of Ulm

summary:
SMAC Mimetics (SMs) are currently being evaluated in clinical trials. Biomarkers are urgently needed for prediction of patient response to SMs.
This study identified a characteristic gene expression pattern of SM sensitivity suitable for upfront identification of samples with high sensitivity to SMs.

overall_design: Differentially regulated genes between 8 SM-sensitive and 6 SM-insensitive BCP-ALL samples were identified using Human Genome U133 Plus 2.0 Arrays.

first: Lüder-Hinrich

last: Meyer

first: Klaus-Michael

last: Debatin


title: N6-methyladenosine methyltransferase METTL14-mediated autophagy in malignant development of oral squamous cell carcinoma

status: Public on Nov 17 2021

city: Guangzhou

first: Yue

last: Zhu

state: Guangdong

address: No. 56, Lingyuan West Road

country: China

institute: Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University

type: Expression profiling by high throughput sequencing

summary: N6-methyladenosine (m6A) is the most abundant internal mRNA modification in eukaryotes and is related to stability, localization, or translation efficiency in tumorigenesis. Autophagy plays an important role in the occurrence and development of tumours. However, the relationship between m6A and autophagy remains unclear. In this study, we used a rapamycin-induced autophagy model of oral squamous cell carcinoma (OSCC) cells, and observed increased m6A RNA methylation. When autophagy was activated, the methyltransferase-like 14 (METTL14) expression was upregulated and influenced the proliferation, migration, and invasiveness of OSCC cells. Through meRIP-seq and RNA-seq analysis, we found that METTL14 directly combined with eukaryotic translation initiation factor gamma 1 (eIF4G1) mRNA and decreased its RNA stability. According to the dual-luciferase reporter and mutagenesis assay, the mutated site 1 of exon 11 of eIF4G1 is the key target of METTL14. Knockdown of the main m6A binding protein YTHDF2 may rescue the shortened half-life of eIF4G1 mRNA induced by METTL14 overexpression. Furthermore, an in vivo tumour xenograft model confirmed that a high METTL14 expression can effectively reduce OSCC growth. Additionally, using clinical samples, we found that patients with advanced or moderately/poorly differentiated tumours exhibited lower METTL14 levels. Taken together, our results revealed that METTL14 mediated eIF4G1 expression via m6A modification and regulated autophagy levels and biological functions in OSCC. Our findings not only expand our understanding of the correlation between autophagy and RNA methylation in tumorigenesis but also present an opportunity to develop new therapeutic options.

overall_design: Total RNA was extracted from HSC3 and CAL33 cells treated with or without 100 nM rapamycin for three days, and the Magna Me-RIP m6A Kit (Merck Millipore, Burlington, MA, USA) with an anti-m6A antibody was used to perform immunoprecipitation. After immunoprecipitation, part of the target RNA was analysed using high-throughput sequencing (Epibiotek, Guangzhou, China)

first: Fang

last: Wang


title: MMP-9 drives melanomagenic transcription program through histone H3 tail proteolysis

city: Los Angeles

first: Suhn

middle: K

last: Rhie

state: CA

address: 1450 Biggy Street NRT 3504

department: Biochemistry and Molecular Medicine

country: USA

institute: University of Southern California

summary: Melanoma is a type of skin cancer that develops in pigment-producing melanocytes and often spreads to other parts of the body. Aberrant gene expression has been considered as a crucial step for increasing the risk of melanomagenesis, but how chromatin reorganization contributes to this pathogenic process is still not well understood. Here we report that matrix metalloproteinase 9 (MMP-9) localizes to the nucleus of melanoma cells and potentiates gene expression by proteolytically clipping histone H3 N-terminal tail (H3NT). From genome-wide studies, we discovered that growth regulatory genes are selectively targeted and activated by MMP-9-dependent H3NT proteolysis in melanoma cells. MMP-9 cooperates functionally with p300/CBP, because MMP-9 cleaves H3NT in a manner that is dependent on p300/CBP-mediated acetylation of H3K18. The functional significance of MMP-9-dependent H3NT proteolysis is further underscored by the fact that RNAi knockdown and small-molecule inhibition of MMP-9 and p300/CBP impede melanomagenic gene expression and melanoma tumor growth. Together, our data establish new functions and mechanisms for nuclear MMP-9 in promoting melanomagenesis and demonstrate how MMP-9-dependent H3NT proteolysis can be exploited to prevent and treat melanoma skin cancer.

overall_design: Effect of MMP-9 knockdown in melanoma cells.

first: Yonghwan

last: Shin

first: Sungmin

last: Kim

first: Nikhil

middle: B

last: Ghate

first: Woojin

last: An


title: The JAK2-STAT pathway epigenetically regulates tolerized genes during the first encounter to bacterial antigens

status: Public on Nov 23 2021

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Identification and characterization of potato anthocyanin synthesis and regulatory miRNA based on comparative transcriptome [miRNA-seq]

status: Public on Nov 20 2021

city: lanzhou

first: jinqiang

last: quan

address: No. 1 Yingmen Village, Anning District

department: College of Animal Science & Technology

institute: Gansu Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: The anthocyanin glycosides in potato tubers not only provide the plant with bright color and high nutritional value, but also have pharmacological effects such as antioxidant, hypotensive, lipid-lowering and immunity-boosting. However, the regulatory mechanism of anthocyanin in potato tubers is still unclear. In this study, twelve miRNA libraries, three of which are from the Red beauty (R-1, R-2 and R-3), three of which are from the Black kingkong (B-1, B-2 and B-3), three of which are from the Longshu No.7 (Y-1, Y-2 and Y-3) and three of which are from the LK77 (W-1, W-2 and W-3), were constructed and analyzed by high-throughput sequencing. A total of 167.3 M of clean reads were obtained. After the raw reads were subjected to quality control and filtering, 151,010,820 clean tags were obtained from the twelve libraries. The filtered reads were subsequently compared with the updated potato reference genome, and the vast majority of effective reads were successfully mapped. The mapped reads from the twelve libraries covered 77.10-84.48% of the potato genome, therefore, the analysis based on the genome was considered reliable. The lengths of the obtained miRNAs were further analysed to find that 64% of the miRNAs were concentrated at 21bp in length, followed by a higher number of miRNAs at 22bp and 24bp in length.

overall_design: Four kinds of potatoes (Black kingkong, Red beauty, Longshu No.7 and LK99) were planted at Yuzhong Experimental Station of Lanzhou County, Gansu Academy of Agricultural Sciences. They were planted on 22 April 2019 and harvested on 28 September. All conditions during planting were kept consistent for all four varieties, such as irrigation, light, temperature, etc. At harvest, the materials of each variety were randomly sampled, with 3 replicates for each sample, for anthocyanin determination and transcriptome sequencing.

first: Enfang

last: Qi


title: Identification and characterization of potato anthocyanin synthesis and regulatory genes based on comparative transcriptome [mRNA-seq]

summary: The anthocyanin glycosides in potato tubers not only provide the plant with bright color and high nutritional value, but also have pharmacological effects such as antioxidant, hypotensive, lipid-lowering and immunity-boosting. However, the regulatory mechanism of anthocyanin in potato tubers is still unclear. In this study, the content of anthocyanin was measured in four potato varieties (B, R, Y and W) and genes regulating anthocyanin synthesis in different potato varieties were identified by comparing transcriptomic approaches. The results showed that 82.6G of filtered data were obtained in 12 sequencing libraries, of which 82.23-87.66% of clean fragments were covered to the reference genome. In total, 42,793 genes were found in the twelve libraries of which 3765 were new genes. Finally, 3638 (B), 4295 (R) and 3594 (Y) DEGs were obtained in the three groups by the strict threshold screening (FDR<0.05 and |log2FC|>1), respectively. GO analysis showed that DEGs were mainly enriched in entries such as cell (GO:0005623), metabolic process (GO:0008152), catalytic activity (GO:0003824), etc. KEGG analysis revealed that metabolic pathways (ko01100), phenylalanine metabolism (ko00360), photosynthesis (ko00195) were significantly enriched. In addition, some genes related to anthocyanin synthesis (e.g. CHS, bHLH and MYB) were highly induced or repressed in different varieties. In conclusion, the results of this study provide insight into the genes regulating anthocyanin formation in potato and provide a scientific reference for breeding better quality potato varieties.


title: Cardiometabolic MicroRNAs are Associated with severeerity and 28-Day Intensive Care Unit Mortality in COVID-19 Patients

city: Wien

first: Andreas

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

summary:
Coronavirus disease 2019 (COVID-19) can lead to multiorgan damage and fatal outcomes. MicroRNAs (miRNAs) are detectable in blood, reflecting cell activation and tissue injury.
We performed small  RNA-Seq in healthy controls (N=11), non-severe (N=18) and severe (N=16) COVID-19 patients

overall_design: Small RNA sequencing profilles in plasma samples of severe and non-severe COVID_19 patients, as well as in healthy controls

first: Clemens

last: Gutmann

first: Kseniya

last: Khamina

first: Konstantinos

last: Theofilato

first: Sean

last: Burnap

first: Adam

last: Nabeebaccus

first: Matthew

last: Fish

first: Mark

middle: J

last: McPhail

first: Kevin

last: O'Gallagher

first: Lukas

middle: E

last: Schmidt

first: Christian

last: Cassel

first: Georg

last: Auzinger

first: Salvatore

last: Napoli

first: Salma

middle: F

last: Mujib

first: Francesca

last: Trovato

first: Barnaby

last: Sanderson

first: Blair

last: Merrick

first: Jonathan

middle: D

last: Edgeworth

first: Ajay

middle: M

last: Shah

first: Adrian

middle: C

last: Hayday

first: Ludwig

last: Traby

first: Matthias

last: Hackl

first: Sabine

last: Eichinger

first: Manu

last: Shankar-Hari

first: Manuel

last: Mayr


title: Identification and characterization of potato anthocyanin synthesis and regulatory miRNA based on comparative transcriptome

first: jinqiang

last: quan


title: An avian embryo patient-derived xenograft model for preclinical studies of human breast cancers.

city: LYON

first: Olivier

last: IMBAUD

state: Rhône-Alpes

address: Faculty of Medicine and Pharmacy - 3rd floor 8 Rockefeller Avenue

department: NeuroMyoGene Institut (INMG)

country: France

institute: UCBL | CNRS UMR 5310 | INSERM U1217

summary: Lack of preclinical patient-derived xenograft (PDX) cancer models in which to conduct large scale molecular studies seriously impairs the development of effective personalized therapies. We report here on an in vivo concept consisting of implanting human tumor cells in targeted tissues of an avian embryo, delivering therapeutics, evaluating their efficacy by measuring tumors using light sheet confocal microscopy, and conducting large scale RNAseq analysis to characterize therapeutic-induced changes in gene expression. The model was established to recapitulate triple negative breast cancer (TNBC) and validated using TNBC standards of care (SOCs) and an investigational therapeutic agent.

overall_design: Triple negative breast cancer cells (the MDA-MB-436 cell line) were transplanted into chicken embryos (AVI-cellDX). Two treatments were injected intravenously: 1-excipient (= control = 0.9% NaCl); 2-a mix of gemcitabine and carboplatin. We then performed whole RNASeq analyses. For each condition, the number of  significantly upregulated and downregulated transcripts as compared to control medium were homogeneously distributed. Each condition is in duplicates.

first: Loraine

last: Jarrosson

first: Clélia

last: Costechareyre

first: Fanny

last: Gallix

first: Séverine

last: Ciré

first: Fabien

last: Gay

last: Imbaud

first: Romain

last: Teinturier

first: Elisabetta

last: Marangoni

first: Karine

last: Aguéra

first: Céline

last: Delloye-Bourgeois

first: Valérie

last: Castellani


title: Dissecting systemic risk factors for NF1 optic glioma formation and growth in mice.

city: St Louis

first: David

last: Gutmann

state: MO

address: 660 S Euclid Ave

department: Neurology

institute: Washington University in St Louis

summary: Prior epidemiology studies have revealed a reduced incidence of brain tumors in children with T cell-mediated disorders, including asthma. Defining the molecular etiologies underlying how these T cell-mediated systemic conditions influence brain function and nervous system disease pathogenesis may also reveal new immunomodulatory treatment strategies for neurological disorders

overall_design: Examination of isolated spleen CD3+ T cells from Nf1OPG mice treated with PBS (control) and OVA (asthma induction)

first: Jit

last: Chatterjee

first: Olivia

last: Cobb

middle: H


title: Doxycycline-responsive transcriptome in the mouse inner medullary collecting duct cell line (mIMCD3)

city: Baltimore

first: Hyun Jun

last: Jung

state: MD

address: 720 Rutland Ave, Ross Research Building 1165B

department: Medicine (Nephrology)

institute: Johns Hopkins University School of Medicine

summary:
Purpose:  The goal of this study is to identify doxycycle-responsive genes in mouse kidney inner medullary collecting duct cell line mIMCD3. To explore compreshensive profile of doxycycline-mediated gene expression, transcriptomes of doxycycline-responsive genes at two different time points (3 days and 6 days) were profiled and analyzed.
Methods: Total RNAs were isolated from mIMCD3 cells treated with doxycycline or vehicle at different time points (3 days and 6 days). Four replicates for vehicle- or doxycycline-treated group were generated at each tested time point. cDNA libraries were prepared using a Nextera DNA library preparation protocol. The sequence reads from Illumina HiSeq3000 platform were qualified and quantified at the transcript level using Salmon (0.14.1). Differential expression analysis were performed using edgeR.
Results: mRNA profiles of mouse kidney inner medullary collecting duct mIMCD3 cells treated with doxycycline or vehicle (DMSO) for 3 days and 6 days were generated using an optimized RNA-Seq workflow. Transcript level quantification using a pseudo-alignment quantification method (Salmon) was performed to calculate transcript abundance in each sample. Then differential expression analysis identified the differentially expressed genes at each time point comparison (DOX vs vehicle).
Conclusions: This study revealed comprehensive transcriptomic changes of doxycycline-responsive gene expression in mouse kidney inner medullary collecting duct cells.

overall_design: Doxycycline-responsive transcriptome in mouse kidney inner medullary collecting duct cell line mIMCD3

first: Hyun

first: Paul

last: Welling


title: Astrocytes Tet1 regulates neuronal development and cognition through modulating GluA1 in mice

city: Houston

first: Ziyi

last: Li

state: TX

address: 1400 Pressler Street

institute: MD Anderson Cancer Center

type: Methylation profiling by high throughput sequencing

summary: Tet (Ten eleven translocation) mediated 5-hydroxymethylcytosine (5hmC) is highly enriched in the neuronal system and is involved in diverse biological processes and diseases. However, the function of 5hmC in astrocytes remains completely unknown. In the present study, we show that Tet1 deficiency alters astrocytes morphology and impairs neuronal function. Specific deletion of Tet1 in astrocytes impairs learning and memory ability of mice. Using 5hmC high-throughput DNA sequencing and RNA sequencing, we found the distribution feature of 5hmC in astrocytes and that Tet1 deficiency induces DNA hydroxymethylation regions (DhMRs) and alters gene expression. Mechanistically, we found that Tet1 deficiency leads to the abnormal Ca2+ signaling by regulating the expression of GluA1, which can be rescued by ectectopic expression of GluA1. Collectively, our findings suggest that Tet1 plays important functions by regulating astrocytes Ca2+ signaling.

overall_design: Brain tissues were collected from Tet1 KO and WT mice. 5hmC sequencing were performed on the collected tissues.


title: A New Murine Esophageal Organoid Culture Method and Organoid-Driven Model of Esophageal Squamous Cell Neoplasia

first: Jae-Il

last: Park

state: Texas

address: 6565 MD Anderson BLVD

department: Dept. of Experimental Radiation Oncology

institute: M.D. Anderson Cancer Center

summary: We sought to develop esophageal minimum essential organoid culture medium (E-MEOM) for culturing murine esophageal organoids (EOs) and establishing an early ESCC model. We formulated E-MEOM that is sufficient to grow EOs from a single cell with clonal expansion, maintenance, and passage. From the IHC and single cell RNA sequencing of EOs results, we found that EOs cultured in E-MEOM were histologically and functionally equivalent to the esophageal epithelium.

overall_design: single cell RNA sequencing from mouse esophageal organoids which were collected at day 8

first: Biyun

last: Zheng

first: Kyung-Pil

last: Ko

first: Moon

last: Kim

first: Jie

last: Zhang

first: Sohee

last: Jun

first: Xuefen

last: Fang

first: Xiaozhong

last: Wang

first: Bong-Jun

first: Wenyi

last: Luo

first: Youn-Sang

first: Christopher

middle: L

last: Cervantes

first: Jichao

last: Chen


title: Mouse mammary tumors and uminal cells

city: Macau

first: Heng

last: Sun

address: Avendia da Universidade, Taipa

department: Faculty of Health Sciences

country: Macau

institute: University of Macau


title: Single cell RNA-seq to study heterogeneity and tumorigenesis of Brca1-deficient mouse mammary tumors.

summary: Brca1 mutation predisposes women to early onset of breast and ovarian cancers.Through its diverse functions in DNA damage repair, cell cycle control, transcription regulation, ubiquitination and so on, BRCA1 acts as a very significant tumor suppressor and genomic safeguard. Brca1 deficiency induces severe cellular stress, when occurring in the mammary glands, it impairs the regular developmental process and eventually causes tumorigenesis due to accumulation of genome instability and other mechanisms. The Brca1-defiencient mouse mammary tumor were characterized with great  tumoral heterogeneity, which is in line with the human breast cancers carrying BRCA1 mutations. Here we studied the molecular complexicity of Brca1-deficient mouse mammary tumors vie single cell RNA sequencing.

overall_design: Luminal cells and tumor cells form mammary glands of control or Brca1-deficient mice were FACS-purified for single cell RNA-seq.

first: Chuxia

last: Deng


title: Dropseq to study heterogeneity and tumorigenesis of Brca1-deficient mouse mammary tumors.

summary: Brca1 mutation predisposes women to early onset of breast and ovarian cancers.Through its diverse functions in DNA damage repair, cell cycle control, transcription regulation, ubiquitination and so on, BRCA1 acts as a very significant tumor suppressor and genomic safeguard. Brca1 deficiency induces severe cellular stress, when occurring in the mammary glands, it impairs the regular developmental process and eventually causes tumorigenesis due to accumulation of genome instability and other mechanisms. The Brca1-defiencient mouse mammary tumor were characterized with great  tumoral heterogeneity, which is in line with the human breast cancers carrying BRCA1 mutations. Here we studied the molecular complexicity of Brca1-deficient mouse mammary tumors vie Dropseq.

overall_design: Mammary gland cells and mammary tumor cells form Brca1-deficient mice were isolated for dropseq.


title: Topoisomerases I and II facilitate the translocation of condensin DC in C. elegans [HiC]

status: Public on Nov 16 2021

city: New York

first: Ana

middle: Karina

last: Morao

state: New York

address: 29 Washington Place

department: Biology

institute: New York University

summary: Condensin complexes are evolutionarily conserved molecular motors from the structural maintenance of chromosomes (SMC) family, that use ATPase activity to translocate along DNA and form loops. Condensin and topoisomerase II (TOP-2) are essential for the structure and function of mitotic chromosomes. While condensin-mediated DNA looping is thought to direct TOP-2 chain-passing activity to separate sister chromatids, it is not known if TOP-2 in turn regulates loop formation. Here we used an X chromosome specific condensin that represses transcription for dosage compensation in C.elegans, to determine how DNA topology affects SMC translocation in vivo. We applied auxin-inducible degradation of topoisomerases I and II to determine their effect on condensin DC binding and function. We found that both topoisomerases colocalize with condensin DC and control its movement at different genomic scales. TOP-2 depletion hindered condensin DC spreading over long distances, resulting in accumulation around its X-specific recruitment sites and shorter Hi-C interactions. In contrast, TOP-1 depletion did not affect long-range spreading but resulted in accumulation of condensin DC within gene bodies, specially of highly expressed and long genes. Both TOP-1 and TOP-2 depletion resulted in X chromosome upregulation indicating that condensin DC translocation at both scales is required for its function in transcriptional repression. Together our work reveals distinct DNA topological requirements for two modes of condensin DC association with chromatin: long-range linear translocation that requires decatenation and unknotting of DNA and short-range binding to genes that requires resolution of transcription-induced supercoiling.

overall_design: Hi-C data in controls and topoisomerase II depleted conditions. Depletion was performed by Auxin inducible degradation. All experiments were performed in two biological replicates. L2/L3 larvae were used.

first: Jun

first: Daniel

last: Obaji

first: Siyu

first: Sevinc

last: Ercan


title: Transcriptomic profiling of DLE/SCLE/ACLE

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

summary: The microarray experiment was employed to evaluate the gene expressions in cutaneous lupus

overall_design: To investigate the specific gene regulations, microarray profiling was performed on RNA extracted from paraffin embedded skin biopsy samples.

first: Michelle

last: Kahlenberg


title: Topoisomerases I and II facilitate the translocation of condensin DC in C. elegans [RNA-seq]

overall_design: RNA-seq  in  controls and topoisomerases I and II depleted conditions. Depletion was performed by Auxin inducible degradation. All experiments were performed in two biological replicates. L2/L3 larvae were used for most experiments.


title: RNAseq of Brca1-deficient mouse mammary tumors

summary: Brca1 mutation predisposes women to early onset of breast and ovarian cancers.Through its diverse functions in DNA damage repair, cell cycle control, transcription regulation, ubiquitination and so on, BRCA1 acts as a very significant tumor suppressor and genomic safeguard. Brca1 deficiency induces severe cellular stress, when occurring in the mammary glands, it impairs the regular developmental process and eventually causes tumorigenesis due to accumulation of genome instability and other mechanisms. The Brca1-defiencient mouse mammary tumor were characterized with great  tumoral heterogeneity, which is in line with the human breast cancers carrying BRCA1 mutations. Here we studied the molecular complexicity of Brca1-deficient mouse mammary tumors vie RNA sequencing.

overall_design: 23 Brca1-deficient mouse mammary tumors were collected for RNA sequencing.


title: RB depletion is required for the continuous growth of tumors initiated by loss of RB

city: Vienna

first: Julia

last: Arand

address: Schwarzspanierstr. 16

institute: Medical University of Vienna

summary: The retinoblastoma (RB) tumor suppressor is functionally inactivated in a wide range of human tumors where this inactivation promotes tumorigenesis in part by allowing uncontrolled proliferation. RB has been extensively studied, but its mechanisms of action in normal and cancer cells remain only partly understood. Here we describe a new mouse model to investigate the consequences of RB loss and its re-activation in vivo. In these mice, induction of shRNA molecules targeting RB for knock-down results in the development of phenotypes similar to RB knock-out mice, including the development of pituitary and thyroid tumors. Re-expression of RB leads to cell cycle arrest in cancer cells and repression of transcriptional programs driven by E2F activity. Thus, continuous RB loss is required for the maintenance of tumor phenotypes initiated by loss of RB, and this new mouse model will provide a new platform to investigate RB function in vivo.

overall_design: We generated mice in which RB levels can be manipulated, using an inducible shRNA system with a miR-E-based, doxycycline-regulated (Tet-ON), GFP-linked shRNA at the Col1a1 locus. RNA seq was performed on pituitary samples after several weeks of RB KD and after different timepoints after reintroduction (long-term reintroduction & short-term reintroduction).

first: Alex

last: Doan

first: Julien

last: Sage


title: Transcriptomic Changes in Internode Explants of Stinging Nettle during Callogenesis

status: Public on Nov 15 2021

city: Hautcharage

first: Gea

last: Guerriero

state: Luxembourg

address: 5, rue Bommel, Z.A.E. Robert Steichen, L-4940

department: Environmental Research and Innovation Department

country: Luxembourg

institute: Luxembourg Institute of Science and Technology (LIST)

summary: Callogenesis, the process during which explants derived from differentiated plant tissues are subjected to a de-differentiation step characterized by the proliferation of an unorganized mass of cells, is fundamental to indirect organogenesis and the establishment of cell suspension cultures. There-fore, understanding how callogenesis takes place is helpful to plant tissue culture, as well as to plant biotechnology and bioprocess engineering. The common herbaceous plant stinging nettle (Urtica dioica L.) is a species producing cellulosic fibres (the bast fibres) and a whole array of phytochemicals of pharmacological and cosmeceutical use. It is thus of interest as a potential multi-purpose plant. In this study, callogenesis in internode explants of a nettle fibre clone (clone 13) was studied using RNA-Seq to understand which gene ontologies predominate at different time points. Callogenesis was induced with the plant growth regulators α-napthaleneacetic acid (NAA) and 6-benzyl aminopurine (BAP) after having determined their optimal concentrations. The process was studied over a period of 34 days, time point at which a well visible callus mass developed on the explants. The bioinformatic analysis of the transcriptomic dataset revealed specific gene ontologies charac-terizing each of the four time points investigated (0, 1, 10 and 34 days-D). The results show that while the advanced stage of callogenesis is characterized by the iron deficiency response triggered by the high levels of reactive oxygen species accumulated by the proliferating cell mass, the intermediate and early phases are dominated by ontologies related to immune response and cell wall loosening, respectively.

overall_design: Callogenesis study at different time points (0-1-10-34 days) in nettle internode explants incubazed on callus-inducing medium  supplemented with 3 mg/L NAA and 0.01 mg/L BAP in the dark.

first: Xu

last: Xuan

first: Legay

last: Sylvain

first: Berni

last: Roberto

first: Hausman

last: Jean-Francois

first: Guerriero

last: Gea


title: A comparison between two Escherichia coli K-12 MG1655 substrains possessing different swimming motility

city: Shenzhen

first: Conghui

last: You

address: 1068 Xueyuan Rd., Nanshan District

institute: Shenzhen University

summary: Substrains in Escherichia coli K-12 MG1655 can possess various swimming motility, which is mostly resulted from different expression levels of flhDC. Here, we studied the swimming motility of two MG1655 substrains, CY562 and CY570. Our results showed that CY562 had no insertion at the promoter region of flhDC and possessed no swimming motility. In contrast, CY570 had an IS-element insertion at the promoter region of flhDC and showed a hyper-motile phenotype. Transcriptomic data suggest that expression of flhDC and the other known flagella genes was much lower in CY562 than that in CY570. Moreover, CY562 possessed higher expression levels for genes involved in stress response, especially acid-stress response, than CY570. Consistently, CY562 showed a higher survival rate under acid stress than CY570. Our data indicate that there are mechanisms conversely regulating motility and stress response in E. coli.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design:
Determination of gene expression in E. coli K-12 MG1655 substrains CY562 and CY570.

Please note that each processed data file was generated from both replicates and is linked to the corresponding *-1 sample records.

first: Bingyu

last: Li


title: Inflammation and lymphocyte infiltration are associated with shorter survival in patients with high-grade glioma

city: Genève

first: Eliana

last: Marinari

address: Rue Michel-Servet 1

country: Switzerland

institute: UNIGE

summary: Glioma represents a serious health burden in terms of morbidity and mortality. The prognostic significance of the lymphoid and myeloid infiltrates in glioma is not clearly determined. Moreover, the characterization of different leukocyte subsets in the tumor microenvironment relies mainly on immunohistochemistry observations, and data about their association with prognosis are contradictory. Here, we performed acomprehensive study of both the tumor-infiltrating and circulating immune compartments of patients with high-grade glioma.  We identified prognostic tumor and peripheral immune signatures, which associate increased inflammation, immune infiltration and activation with shorter overall survival in high-grade glioma patients. Importantly, we confirmed our observations by flow cytometry analysis and validated the tumor-signature using the TCGA dataset. In addition, both tumor genotype and grade associated with the degree of glioma immune infiltration. Unlike in the majority of cancers, lymphocyte infiltration at the tumor site is anegative prognostic factor in glioma, suggesting the ambivalent pro-tumorigenic role of immune responses in glioma.

overall_design: Tumor biopsies  were collected from grade III–IV glioma patients at the time of surgery before and after chemoradiation. All patients were treated with standard treatment: surgery and chemoradiation. Patients were divided according to medial overall survival for differential expression analysis as described in the manuscript

first: Mathilde

last: Allard

first: Valérie

last: Dutoit

first: Pierre-Yves

last: Dietrich


title: Gene regulation changes driven by wild type and cancer-associated mutant variants of Myc as B-cells convert to Lymphoma-like cells

city: Uppsala

first: Gustav

last: Arvidsson

state: Uppsala

address: Husargatan 3

department: Department of Medical Sciences

country: Sweden

institute: Uppsala Universitet

summary: cMyc plays a major role in lymphoma development. In addition, missense mutations including T58A and T58I the substitution mutations augment cMyc activity during lymphoma development. In this study, we characterized lymphoma-associated gene expression changes as increasing levels of wild type or mutant cMyc proteins progressively drive conversion of B-cells to lymphoma-like cells. To this end we established a cell system in which primary mouse B-cells were transduced with constructs that over-express the anti-apoptotic proteins, BMI1 and BCLXL and allow variable expression of cMyc (wild type, T58A or T58I) from a doxycycline-regulated promoter. Increased cMyc expression is associated with cell cycle entry, increased cell size and increased cell proliferation. Generally, gene programs required for cell growth and proliferation are induced while specific functions associated with B-cells are repressed. Mutant cMyc proteins cause differential effects, relative to each other and to wild type cMyc, that are focused on particular aspects of the cMyc-induced program.

overall_design: Three genotypes (WT and two mutants) with seven treatment conditions each. Data in triplicates. 63 samples in total.

first: Amir

last: Nematollahi-Mahani

first: Anthony

middle: P

last: Wright


title: Mutation in Irf8 gene (Irf8R294C) impairs type I IFN mediated antiviral immune response by murine pDCs

status: Public on Nov 12 2021

city: NEW DELHI

first: Prafullakumar

last: Tailor

state: DELHI

address: Aruna Asaf Ali Road

country: India

institute: National Institute of Immunology

summary: The goal is to study the difference in transcriptomic profile (RNA seq) of pDCs from IRF8WT and IRF8R294C mice.

overall_design: pDC transcriptomic profile of IRF8WT and IRF8R294C mice.

first: Annesa

last: Das

first: Kuldeep

last: Singh Chauhan

first: Himanshu

last: Kumar


title: Genome-wide chromatin binding of Hdac2 in murine PDAC cells (ChIP-Seq)

status: Public on Nov 11 2021

city: Goettingen

first: Lukas

last: Krauß

state: Lower Saxony

address: Robert-Koch-Straße 40

department: Surgery-Department

institute: University Medicine Göettingen

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Hdac2 ChIP-seq were used to determine epigenetic differences between Hdac2 knockout versus Hdac2 wildtype pancreatic cancer cells.
DOI: 10.1158/0008-5472.can-20-3209

overall_design: Genomic DNA was extracted and genome-wide chromatin binding of Hdac2 was determined in a Hdac2 proficient vs Hdac2 deficient setting. DNA of 2 replicates per setting were harvested and analyzed. Input DNA of all samples was pooled and used as background for MACS2 peak calling. Called peaks were then differentially analyzed using DiffBind (Proficient vs deficient).

first: Krauß

last: Lukas

first: Schneider

last: Carolin

last: Günter

first: Klement

last: Christine

first: Öllinger

last: Rupert

first: Engleitner

last: Thomas

first: Rad

last: Roland


title: Osteopontin deficiency leads to the resolution of prostatic fibrosis and inflammation

city: Madison

first: Petra

last: Popovics

state: WI

department: Department of Urology

institute: University of Wisconsin-Madison

summary: The goals of this study is to determine transcriptomic changes in the mouse ventral prostate associated with E. coli-induced chronic inflammation and fibrosis and the alteration of this gene expression signature in osteopontin deficient mice.

overall_design: C57BL/J or osteopontin knockout (OPN-KO) male mice were transurethrally instilled with uropathogenic E. coli (UTI89), 2 times, 3 days apart. Control mice were instilled with saline.  Ventral prostate lobes were collected 8 weeks after the first instillation. Ventral lobes were thawed and the RNA was stabilized in RNAlater (Thermo Fisher Scientific) for 1 hour. Total RNA was isolated from ventral lobes using the Qiagen RNeasy Micro kit with on-column DNAse digestion (Germantown, MD). Library preparation, quality check, RNA sequencing and bioinformatics analysis were performed at the UW-Madison Biotechnology Center. RNA quantity was measured with NanoDrop and assayed on an Agilent 2100 Bioanalyzer. The cDNA library was prepared by the TruSeq Stranded Total RNA (Gold) Library Prep with after polyA enrichment and rRNA reduction. Libraries were quantified using Qubit DNA HS kit and assayed on Agilent Tapestation DNA 1000 system. Libraries were sequenced on a NovaSeq 6000 platform.

first: Chad

last: Vezina

first: William

last: Ricke


title: The strategy of a novel way to enhance bacterial motility

first: Conghui

last: You

summary: Bacterial motility shows a strong evolvable feature depending on the environment. Hyper-motile E. coli could be isolated by evolving non-motile E. coli due to the mutations that enhanced transcriptional expression of the master regulator of the flagellum biosynthesis, FlhDC. These hyper-motile isolates showed reduced growth fitness but with the molecular mechanisms unrevealed. Here we obtained a novel type of hyper-motile isolates by evolving a weakly-motile E. coli K12 strain on the soft agar plates. These isolates carried high accumulated FlhDC proteins and they shared one single point mutation of ClpXV78F. The V78F affected the ATP binding to ClpX via steric repulsive effect and the mutated ClpXP protease lost most of its ability to degraded FlhDC and some other of its known targets. The signal tag of FlhDC for ClpXP recognition was also characterized. Intriguingly, in the hyper-motile strains, the highly enhanced expression of the motility genes was accompanied by the reduced expression of stress resistance genes relating to the reduced fitness of these isolates. Hence, ClpX appeared to be a novel and hot locus during the evolution of bacterial motility and the molecular mechanism of the trade-off between motility and growth was proposed for the first time.

overall_design: Determination of gene expression in the wild type strain CY598 and its derivates CY706 (spontaneous clpX-V78F mutant), CY708 (spontaneous clpX-V78F mutant), CY1102 (manipulated clpX-V78F mutant), CY1166 (the CY708 strain with a wild-type clpX), and CY1179 (manipulated ∆clpX mutant).

first: Bingyu

last: Li


title: Methotrexate treatment of newly diagnosed RA patients is associated with DNA methylation differences at genes relevant for disease pathogenesis and pharmacological action

city: Oslo

first: Kari

last: Guderud

address: Kirkeveien 166

department: Medical Genetics

country: Norway

institute: University of Oslo

summary: Background: Methotrexate (MTX) is the first line treatment of rheumatoid arthritis (RA), and methylation changes in bulk T cells have been reported after treatment with MTX. We have investigated cell-type specific DNA methylation changes across the genome in naïve and memory CD4+ T cells before and after MTX treatment of RA patients. DNA methylation profiles of newly diagnosed RA patients (N=9) were assessed by reduced representation bisulfite sequencing. Results: We found that MTX treatment significantly influenced DNA methylation levels at multiple CpG sites in both cell populations. Interestingly, we identified differentially methylated sites annotated to two genes; TRIM15 and SORC2, previously reported to predict treatment outcome in RA patients when measured in bulk T cells. Furthermore, several of the genes, including STAT3, annotated to the significant CpG sites are relevant for RA susceptibility or the action of MTX.  Conclusion: We detected CpG sites that were associated with MTX treatment in CD4+ naïve and memory T cells isolated from RA patients. Several of these sites overlap genetic regions previously associated with RA risk and MTX treatment outcome.

first: Line

last: Sunde

first: Benedicte

last: Lie


title: Transcriptome Iso-Seq from Harpegnathos

status: Public on Nov 10 2021

city: Philadelphia

first: Emily

last: Shields

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: RNA from brain and fat body/ovary (combined) was sequenced to use in Harpegnathos annotation improvement.

overall_design: RNA was extracted from brain or from a combined sample of fat body and ovary.

first: E

first: R

last: Bonasio


title: TCR repertoire analysis reveals increased host CTL diversity induced by CD8a ALN-1

city: Gent

first: Bram

last: Van Den Eeckhout

address: Albert Baertsoenkaai 3

country: Belgium

institute: VIB-UGent

summary: Collectively, these data present evidence that the antitumor response mediated by CD8a ALN-1 correlates with clonal expansion and increased TCR repertoire diversity in the TDLN and the tumor tissue, implying epitope spreading.

overall_design: Treatment of mice with PBS, OVA alone and OVA + CD8a ALN-1. Isolation of TDLN and tumor tissue. FACS of CD8+ T cells. RNA isolation and TCR sequencing analysis.

first: Leander

last: Huyghe

first: Sandra

last: Van Lint

first: Elianne

last: Burg

first: Stéphane

last: Plaisance

first: Frank

last: Peelman

first: Anje

last: Cauwels

first: Gilles

last: Uzé

first: Niko

last: Kley

first: Sarah

last: Gerlo

first: Jan

last: Tavernier


title: RNA-seq of intestinal organoids after the first passage at day 5

city: Dresden

first: Francis

last: Stewart

address: Tatzberg 47-49

institute: BIOTEChnology Center TU Dresden

summary: The impact of MLL1 removal on intestinal organoids was evaluated in intestinal organoids from Mll1FC/+; RosaCreERT2/+ (control) and Mll1FC/FC; RosaCreERT2/+ (knockout) cultures after the first passage at day 5. Using 2x 100 bp reads, 50 million reads per sample with comparable unique mapped reads (74-81%) were obtained. To analyse differentially expressed genes, we applied DESeq2 analysis to the RNA-seq dataset. GO term analysis by DAVID at a false discovery rate (FDR) of 5% revealed that MLL1 was important for regulation of gene expression and differentiation.

overall_design: mRNA profiles of Mll1FC/+; RosaCreERT2/+ and Mll1FC/FC; RosaCreERT2/+ intestinal organoid cultures at passage 1 were generated by deep sequencing.

first: Neha

last: Goveas

first: Claudia

last: Waskow

first: Katrin

last: Arndt

first: Dimitra

last: Alexopoulou

first: Andreas

last: Dahl

first: Julian

last: Heuberger

first: Qinyu

last: Zhang

first: Walter

last: Birchmeier

first: Konstantinos

last: Anastassiadis

first: Andrea

last: Kranz


title: RNA-seq of intestinal organoids after the third passage at day 5

summary: The impact of MLL1 removal on intestinal organoids was evaluated in intestinal organoids from Mll1FC/+; RosaCreERT2/+ (control) and Mll1FC/FC; RosaCreERT2/+ (knockout) cultures after the third passage at day 5. Using 2x 100 bp reads, 50 million reads per sample with comparable unique mapped reads (68-87%) were obtained. To analyse differentially expressed genes, we applied DESeq2 analysis to the RNA-seq dataset. GO term analysis by DAVID at a false discovery rate (FDR) of 5% revealed that MLL1 was important for regulation of gene expression and differentiation.

overall_design: mRNA profiles of Mll1FC/+; RosaCreERT2/+ and Mll1FC/FC; RosaCreERT2/+ intestinal organoid cultures at passage 3 were generated by deep sequencing.


title: RNA-seq from Harpegnathos worker brains

first: Emily

last: Shields

summary: This RNA-seq was done separate from any annotation and used to calculate the % of reads mapping to features.

overall_design: Workers (inactive ovaries) were removed from the colony at 0, 3, 5, 9, 11, 31, 27, 28, 84, or 85 days and brains were dissected for transcriptome profiling.

first: E

first: R

last: Bonasio


title: Human tRF & tiRNA sequencing of SLE and LN patients

status: Public on Nov 09 2021

city: Nanjing

first: Yang

last: Ping

address: 321 Zhongshan Road

institute: nanjing drum tower hospital

summary: We first analyzed tsRNA signatures in SLE serum and identified that tRF-His-GTG-1 was significantly upregulated in SLE serum. The combination of tRF-His-GTG-1 and anti-dsDNA could serve as biomarkers for diagnosing SLE with a high AUC of 0.95 (95% CI=0.92-0.99), sensitivity (83.72%) and specificity (94.19%). Importantly, the non-invasive serum tRF-His-GTG-1 could also be used to distinguish SLE with LN or SLE without LN with AUC of 0.81 (95% CI, 0.73–0.88) and performance (sensitivity 66.27%, specificity 96.15%). Moreover, the serum tsRNA is mainly secreted via exosome and directly target signaling molecules that play crucial roles in regulating the immune system.

overall_design: We employed a strategy including the initial screening by sRNA sequencing and validation by qRT-PCR on an individual basis in 24 SLE without LN patients, 33 SLE with LN patients, and 23 healthy controls.

first: Xiaoshan

first: Shanshan

last: Chen

first: Zhiyang

last: Li

first: Shen

last: Han

first: Yanbo

last: Wang


title: Harpegnathos saltator RNA-seq and Iso-Seq

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

overall_design: Refer to individual Series


title: RNA-seq of sorted intestinal stem and Paneth cells

first: Francis

last: Stewart

summary: The impact of Mll1 removal on the intestinal stem cells and its direct effect on neighbouring Paneth cells was evaluated in sorted intestinal stem and Paneth cells from Mll1FC/+; Lgr5-eGFP-CreERT2/+ (control) and Mll1FC/FC; Lgr5-eGFP-CreERT2/+ (knockout) mice, 4 and 10 days after tamoxifen-induced mutagenesis. Using 75-base-pair reads, 30 million reads per sample with comparable unique mapped reads for stem (70-77%) and Paneth (60-76%) cells were obtained. To analyze differentially expressed genes, we applied DESeq2 analysis to the RNA-seq dataset. Analysis by DAVID and GSEA at a false discovery rate (FDR) of 5% was conducted.The stem cell transcriptome revealed that Mll1 knockout stem cells exhibited a decreased expression of several transcription factors and stem cell genes. Additionally, Mll1 ablation in stem cells had an impact on Paneth cells. Downregulation of Paneth cell specific markers indicated a loss of Paneth cell identity.

overall_design: mRNA profiles of sorted stem and Paneth cells from Mll1FC/+; Lgr5-eGFP-CreERT2 (control) and Mll1FC/FC; Lgr5-eGFP-CreERT2 (knockout) mice, 4 and 10 days after tamoxifen were generated by deep sequencing.

first: Neha

last: Goveas

first: Claudia

first: Katrin

first: A


title: RNA-seq of intestinal organoids after the first and third passages at day 5


title: DNA methylation analysis of ferroptotic multiple myeloma cells

status: Public on Nov 08 2021

city: Wilrijk

first: Emilie

last: Logie

state: Antwerp

address: Universiteitsplein 1

department: Biomedical Sciences

institute: University of Antwerp

summary: To investigate ferroptosis-dependent changes in DNA methylation, a genome wide DNA methylation profiling of ferroptotic (RSL3-treated) multiple myeloma cells (MM1S & MM1R) was performed using the 850K MethylationEPIC BeadChip Array. The ferroptotic DNA methylation signature was compared to myeloma cells pre-treated with the ferroptosis inhibitor ferrostatin-1 (FRSL3), which served as a negative control. In total, three biological replicates per treatment per cell line were included.

overall_design: Bisulphite converted DNA from  12 samples (i.e. 3 samples per cell line, per treatment) were hybridised to the Illumina Infinium 850k Human MethylationEPIC Array

first: Anne

last: Schepers

first: Wim

last: Vanden Berghe


title: Indoleamine 2,3-dioxygenase cannot inhibit Chlamydia trachomatis growth in HL-60 human neutrophil granulocytes

city: Debrecen

first: Szilard

last: Poliska

address: Egyetem ter 1.

department: Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

summary:
Neutrophil granulocytes are the major cells involved in the Chlamydia trachomatis (C.trachomatis)-mediated inflammation and histopathology. A key gene in human intracellular antichlamydial defense is the tryptophan degrading enzyme indoleamine 2,3-dioxygenase (IDO), which limits the growth of the tryptophan auxotroph Chlamydia. Despite its importance, the role of IDO in the intracellular defense against Chlamydia in neutrophils has not yet been characterized.
Affymetrix microarrays were used to obtain global gene expression data for monitoring the effect of C. trachomatis serovar D infection on the transcriptome of human neutrophil granulocytes.

overall_design: Three replicates of C. trachomatis-infected HL-60 samples were compared to three replicates of uninfected control HL-60 samples.

first: Dezso

last: Virok

first: Ferenc

last: Tömösi

first: Anita

last: Varga-Bogdanov

first: Bella

last: Bruszel

first: Zsuzsanna

last: Cseh

first: David

last: Kokai

first: Dóra

last: Paróczai

first: Valeria

last: Endresz

first: Tamas

last: Janaky

first: Katalin

last: Burián


title: Converging Effects of Three Different Endocrine Disrupters on Sox and Pou Gene Expression in Developing Rat Hippocampus: Possible Role of microRNA in Sex Differences

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

institute: ETH Zurich / University of Zurich

summary: Abstract. Transcriptomes of developing, early postnatal rat hippocampus were compared after gestational and lactational exposure to different environmental chemicals exhibiting endocrine activity (endocrine disrupters) at doses impairing memory in adult offspring: Aroclor 1254 (PCB mixture) and bisphenol A, 5 or 0.5 mg/kg administered in chow, and chlorpyrifos, 3 or 1 mg/kg injected subcutaneously. All three chemicals exhibited a common effect on Sox6, Sox11, Pou2f2/Oct2, and Pou3f2/Brn2 in male hippocampus at the higher dose level. Additional Sox and Pou genes were affected by two treatments. Real time RT PCR in samples not used for transcriptomics confirmed the transcriptomics data and showed a comparable expression change for bisphenol A also at the lower dose. No changes were seen in female hippocampus. In the case of Sox6, gene network analyses indicated that miR-24 may be involved in the sexual dimorphism. This miR, which represses Sox6 and is repressed by estrogen receptor-alpa in other tissues, was downregulated by all chemicals in male but not female hippocampus. Sox6 expression levels of individual hippocampus samples (FPKM) were inversely correlated with expression levels of Pvalb, a downstream target of Sox6 and marker of an interneuron subpopulation, but not with markers of Sox6-independent interneuron subpopulations, Nos1 and 5HT3aR, indicating a selective effect on a hippocampal interneuron subpopulation. Effects on interneuron development are further suggested, in males, by changes in Nrg1 and Erbb4 expression controlling interneuron migration. Our investigation disclosed genes involved in cell-autonomous regulation of developmental processes as potential targets of endocrine disrupters. If corroborated by additional studies, they may serve as markers of early developmental effects in regulatory test development.

overall_design: Overall design: Transcriptomics: Dorsal hippocampus (both sides) 1/sex and litter. Hippocampus of male offspring: Feeding control N=4, injection control N=5, Aroclor 1254 0.5 mg/kg body weight (Aro05) N=4, Aroclor 1254 5 mg/kg (Aro5) N=6, Bisphenol A 0.5 mg/kg (BPA05) N=4, Bisphenol A 5 mg/kg (BPA5) N=7, Chlorpyrifos 1 mg/kg (CPF1) N=4, Chlorpyrifos 3 mg/kg (CPF3) N=7. Hippocampus of female offspring from the same litters: Feeding control N=5, injection control N=5, Aro5 N=5, BPA5 N=4, CPF3 N=4 (lower dose groups not analyzed). Real time RT PCR N = 10-12 per group, cross-check with transcriptomics on samples not used for transcriptomics.

first: Walter

last: Lichtensteiger

first: Catherine

last: Bassetti-Gaille

first: Jelena

last: Georgijevic

first: Jesus

last: Tresguerres

first: Margret

last: Schlumpf


title: Changing the Waddington landscape to control mesendoderm competence

city: Cambridge

first: Sharad

last: Ramanathan

state: MA

address: 52 Oxford Street, Room 402

department: Molecular and Cellular Biology

institute: Harvard University


title: Changing the Waddington landscape to control mesendoderm competence -- ATAC-seq

summary: As pluripotent human embryonic stem cells progress towards one germ layer fate, they lose the ability to adopt alternative fates. It is unknown how the cells’ competence for these alternative fates changes along their developmental trajectory or if this competence can be modulated. Here, we show that a differentiating stem cell’s probability of adopting a mesendodermal fate when given the appropriate signal falls sharply at a specific point along the ectodermal trajectory, and we further demonstrate that this point can be moved using genetic perturbations. Using a low-dimensional reaction coordinate to monitor progression towards ectoderm, we can determine the probability that individual cells at different points along this path can transition to the mesendodermal fate upon BMP4 and Activin A signal exposure. Knowing this probability allows us to prospectively isolate and profile differentiating cells based on their mesendoderm competence. Analysis and validation of these RNA-seq and ATAC-seq profiles identified transcription factors that can independently control the cell’s mesendoderm competence and its progression along the ectodermal developmental trajectory. In the classical picture of a Waddington landscape, these effects correspond to altering the barrier between fates and changing the cell’s location on the landscape, respectively. The ability of the underlying gene regulatory network to modulate these two aspects of the developmental landscape could allow separate control of the dynamics of differentiation and tissue size proportions.

overall_design: ATAC-seq profiling of hESCs before and after they lose mesendoderm competence during ectoderm-differentiation, alongside a mesendoderm-derived outgroup to aid in the identification of fate-specific changes

first: James

middle: R

last: Valcourt

first: Roya

last: Huang

first: Sharmistha

last: Kundu

first: Divya

last: Venkatasubramanian

first: Robert

last: Kingston


title: Differential gene expression induced by Enzalutamide in a prostate cancer xenograft

status: Public on Nov 07 2021

city: Toronto

first: Lisanne

last: Mout

address: 101 College st

country: Canada

institute: University Health Network

summary: RNA-sequencing data of the prostate cancer xenograft PC346C-DCC-K model. Tumor bearing mice were treated daily with Enzalutamide (N=10, 60mg/kg) or placebo (N=5, vehicle) for a period of 7 days. Tumor were subsequently isolated and snap-frozen. Tumor tissue was lysed and homogenized in QIAzol (ref #79306, Qiagen, Hilden, Germany) using an Ultra-Turrax T25 (Janke & Kunkel, Staufen, Germany). Total RNA was isolated using the miRNA-easy mini kit (ref # 217004, Qiagen), and RNA quality was measured using the Bioanalyzer RNA 6000 Nano assay (ref #5067, Agilent, Santa Clara, California, USA). All RNA samples had a RIN value ≥7.  Library Prep was performed using the NEBNext Ultra Directional RNA Kit for Illumina according to the protocol "NEBNext Ultra Directional RNA Library Prep Kit for Illumina" (NEB #E7420S/L). Briefly, mRNA was isolated from total RNA using the oligo-dT magnetic beads. After mRNA fragmentation, cDNA synthesis was performed and used for ligation with adapters and PCR amplification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer. One sample was re-sequenced due high frequency of multi-mapped reads implicating inadequate depletion of ribosomal RNA. Paired-end RNA-Seq data of enzalutamide PDX samples (N = 15) was analyzed using UCSC human genome build hg38 and GENCODE annotation release v26 (GRCh38.p10) and mouse genome build mm10 (reference strain C57BL/6J) with GENCODE annotation release M15 (GRCm38.p5) for downstream disambiguation of human/mouse data. FASTQC (v0.11.5) was applied on the paired-end FASTQ files for quality control, both before and after running trimmomatic (v0.36), which removed TrueSeq adapter sequences. STAR (v2.5.3a) was used as aligner, with 2-pass mapping for each sample separately. AstraZeneca’s disambiguation algorithm (Python variant, 2013) for reads aligned to two species has been used to assess the best alignments and disambiguate the BAM files. Mapping quality plot was generated and checked based on sambamba Flagstat (v0.6.7) statistics. Count files, with the number of reads for each gene were created with subread FeatureCounts (v1.5.2) on the disambiguated BAM files. R (version 3.4.3) was used for further statistical analyses and data visualization. Differential expression analysis was performed with condition ‘enzalutamide treated’ (N = 10) versus ‘untreated’ (N = 5) using the DESeq2 package (v1.18.1) and the Wald-test. P values were adjusted using the Benjamini-Hochberg procedure. Gene set enrichment analysis (GSEA, v4.1.0) was performed using normalized gene expression values (count per million) of the individual tumor samples, with condition ‘enzalutamide treated’  versus ‘untreated’ and applied to the Molecular Signatures Database (MSigDB) hallmark gene set collection.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Fifteen tumor samples were analysed obtained from 10 Enzalutamide treated and 5 placebo control mice

first: Wesley

middle: S

last: van de Geer

first: Harmen

middle: G

last: van de Werken

first: Wytske

last: van Weerden


title: Changing the Waddington landscape to control mesendoderm competence -- RNA-seq

overall_design: RNA-seq profiling of hESCs before and after they lose mesendoderm competence during ectoderm-differentiation, alongside a mesendoderm-derived outgroup to aid in the identification of fate-specific changes


title: Single-cell RNA-seq of mouse colonic Th17 cells

status: Public on Nov 05 2021

city: Boston

first: Linglin

address: 60 Fenwood Road, HBTM 10016F

institute: Brigham and Women’s Hospital

summary: We generated droplet-based single-cell RNA-seq profiles of Th17 cells at homeostasis and during DSS-induced colitics from colon.

overall_design: We isolated and profiled the Th17 cells from the colon of mice with DSS-induced colitics and healthy controls.

first: Alexandra

last: Schnell

first: Meromit

last: Singer

first: Pratiksha

middle: I

last: Thakore

first: Danielle

last: Dionne

first: Toni

last: Delorey

first: Aviv

last: Regev

first: Vijay

last: Kuchroo


title: Single-cell clonotype tracing identifies a stem-like intestinal Th17 population that gives rise to pathogenic effector T cells during autoimmunity

summary: While intestinal Th17 cells are critical for maintaining tissue homeostasis, recent studies in both humans and mice have implicated their roles in the development of extra-intestinal autoimmune diseases such as multiple sclerosis. However, the mechanisms by which tissue Th17 cells mediate these dichotomous functions remain unknown. Here, we characterized the heterogeneity, plasticity, and migratory phenotypes of tissue Th17 cells in vivo by combining fate mapping with single-cell RNA sequencing to profile the transcriptomes and TCR clonotypes of over 84,000 Th17 cells at homeostasis and during CNS autoimmune inflammation. Inter- and intra-organ single-cell analyses revealed a homeostatic, stem-like TCF1+ IL-17+ SLAMF6+ population that traffics to the intestine where it is maintained by the microbiota, providing a ready-reservoir for the IL-23-driven generation of encephalitogenic GM-CSF+ IFNγ+ CXCR6+ T cells. Our study defines a direct relationship in vivo between IL-17+ non-pathogenic and GM-CSF+ and IFNγ+ pathogenic Th17 populations and provides, for the first time, a mechanism by which homeostatic intestinal Th17 cells direct extra-intestinal autoimmune disease.

overall_design: We generated droplet-based single-cell RNA-seq or scRNA/TCR-seq profiles for over 84,000 Th17 cells at homeostasis and during CNS autoimmune inflammation (EAE). A total of 80 samples were collected from multiple tissue sites and mice in 9 batches (32 samples were sequenced in individual channels, 48 samples were hashed per mouse and sequenced as 8 channels).

first: Orit

last: Rozenblatt-Rosen


title: Stem-like intestinal Th17 cells give rise to pathogenic effector T cells during autoimmunity


title: Population RNA-seq and ATAC-seq of SLAMF6+ and CXCR6+ Th17 cells

summary: To characterize and validate the functional roles of the splenic SLAMF6+ and CXCR6+ Th17 cells during EAE, we performed population RNA-seq and ATAC-seq for wild type mice, as well as population RNA-seq for Il17aCre Il23rfl/fl knockout mice.

overall_design: We isolated SLAMF6+ and CXCR6+ Th17 cells from the spleen during EAE for three independent experiments: (1) RNA-seq for cells from four Il17aCre tdTomato reporter mice; (2) ATAC-seq for cells from five Il17aCre tdTomato reporter mice. (3) RNA-seq for cells from four Il17aCre Il23rfl/fl (Il23r KO) vs. four Il17aCre Il23rWT (Il23r WT) mice.

first: Mathias

last: Pawlak


title: A colorectal cancer 3D bioprinting workflow as a platform for disease modelling and chemotherapeutic screening

city: Plovdiv

first: Yordan

last: Sbirkov

address: 15 A Vassil Aprilov Blvd

department: Medical Biology

country: Bulgaria

institute: Medical University of Plovdiv

summary: We have established an affordable, flexible and highly reproducible 3D bioprinted CRC model. Histological assessment of Caco-2 cells in 3D bioprints revealed the formation of glandular-like structures which show greater pathomorphological resemblance to tumours than monolayer cultures do. RNA expression profiles in 3D bioprinted cells were marked by upregulation of genes involved in cell adhesion, hypoxia, EGFR/KRAS signaling and downregulation of cell cycle programmes. Testing this 3D experimental platform with three of the most commonly used chemotherapeutics in CRC (5-fluoruracil, oxaliplatin and irinotecan), revealed overall increased resistance compared to 2D cell cultures. Lastly, we demonstrate that our workflow can be successfully extended to primary CRC samples. Thereby, we describe a novel accessible platform for disease modelling and drug testing, which may present an innovative approach in personalised therapeutic screening.

overall_design: Comparing biological duplicates of 2D monolayer cells to total of 6 bioprints (technical triplicates) in biological duplicates


title: CircPan3 Promotes the Ghrelin System and Chondrocyte Autophagy by Sponging miR-667-5p During Rat Osteoarthritis Pathogenesis [circRNA-Seq]

city: Guangzhou

first: li

middle: hao

last: yuan

address: International Biotech Island

institute: Forevergen Biosciences Co.,Ltd

summary: This study aimed to investigate the potential roles of circRNAs in regulating osteoarthritis (OA)-related ghrelin synthesis, autophagy induction, and the relevant molecular mechanisms.

overall_design: One IL-1β -treated chondrocytes sample and one control chondrocytes sample were used for circRNA and mRNA sequencing

first: Jing

last: Zeng

first: Zhenzhen

last: Zhang

first: Qing

last: Liao

first: Qijin

last: Lu

first: Jiemei

last: Liu

first: Lixia

last: Yuan

first: Gang


title: CircPan3 Promotes the Ghrelin System and Chondrocyte Autophagy by Sponging miR-667-5p During Rat Osteoarthritis Pathogenesis [RNA-seq]


title: Cell-type-specific chromatin occupancy by the pioneer factor Zelda drives key developmental transitions in Drosophila

first: Melissa

last: Harrison

email: mharrison3@wisc.edu, ykaur@wisc.edu, torreszelada@wisc.edu, mmfreund2@wisc.edu

address: 420 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin Madison

summary: During early Drosophila embryogenesis, the essential pioneer factor Zelda defines hundreds of cis-regulatory regions and in doing so reprograms the zygotic transcriptome. While Zelda is essential later in development, it is unclear how the ability of Zelda to define cis-regulatory regions is shaped by cell-type specific chromatin architecture established during differentiation. Asymmetric division of neural stem cells (neuroblasts) in the fly brain provide an excellent paradigm for investigating the cell-type specific functions of this pioneer factor. Zelda is expressed in neuroblasts, and we show that Zelda synergistically functions with Notch to maintain neuroblasts in an undifferentiated state. Zelda misexpression can reprogram progenitor cells to neuroblasts, but this capacity is limited by transcriptional repressors critical for progenitor commitment. Zelda genomic occupancy in neuroblasts is reorganized as compared to the embryo, despite sharing many target genes in these two developmental stages. This reorganization is likely driven by differences in chromatin accessibility and cofactor availability. We propose that Zelda regulates essential transitions in the neuroblasts and embryo through a shared gene regulatory network by defining cell-type specific enhancers.

overall_design: ChIP-seq of Zelda in type II neuroblasts was performed in duplicate using α-Zelda antibody (Harrison et al., 2011). As a control, a single replicate of Zelda ChIP-seq was performed on superfolder GFP-tagged Zelda using α-GFP antibody (Abcam, Cambridge, UK, Cat #ab290). All ChIP experiments were performed with input controls. ATAC-seq in type II neuroblasts was performed in duplicate. ATAC-seq using the time-release differentiation system was performed in duplicate or triplicate.

first: Elizabeth

last: Larson

first: Hideyuki

last: Komori

first: Tyler

last: Gibson

first: Cyrina

last: Ostgaard

last: Hamm

first: Jack

last: Schnell

first: Cheng-Yu

last: Lee


title: Genomic and transcriptomic profiles of human brain microvascular pericytes upon neural transdifferentiation

status: Public on Nov 04 2021

city: Sydney

first: Ramin

last: M Farahani

state: NSW

address: Westmead Hospital, Darcy Road

department: molecular biomedicine

country: Australia

institute: University of Sydney


title: Programmed genomic instability regulates neural transdifferentiation of human brain microvascular pericytes [DRIP-Seq]

summary: The observation that human microvascular pericytes transdifferentiate into neurons provided an opportunity to explore the endogenous molecular basis for lineage reprogramming. Here, we show that abrupt destabilization of the higher-order chromatin topology that chaperones lineage memory of pericytes is driven by transient global transcriptional arrest. This leads within minutes to localized decompression of the repressed competing higher-order chromatin topology and expression of pro-neural genes. Transition to neural lineage is completed by probabilistic induction of R-loops in key myogenic loci upon re-initiation of RNA polymerase activity, leading to depletion of the myogenic transcriptome and emergence of the neurogenic transcriptome.

overall_design: DRIP-seq profiles of Control, and transdifferentiating human primary brain pericytes sampled after 10 min in N2 medium, replicates: 1/group

last: Farahani


title: Programmed genomic instability regulates neural transdifferentiation of human brain microvascular pericytes [ChIP-Seq]

overall_design: H2AX ChIP-seq profiles of Control, and transdifferentiating human primary brain pericytes sampled after 10 min in N2 medium, replicates: 1/group


title: Type 1 innate lymphoid cells limit the antitumoral immune response

city: Marseille

first: Bertrand

last: Escaliere

address: 163 avenue de Luminy

institute: CIML

summary: In order to study the NK cell dependant immunoediting of carcinogen-induced fibrosarcomas, we studied the transcriptome of primary tumor grown in wt or NK cell deficient mice

overall_design: bulk mRNA sequencing of primary tumor cell lines grown in wt and NK cell deficient mice

first: Margaux

last: Vienne

first: Etiennot

last: Marion

first: Escalière

last: Bertrand

first: Galluso

last: Justine

first: Spinelli

last: Lionel

first: Guia

last: Sophie

first: Fenis

last: Aurore

first: Eric

last: Vivier

first: yann

last: Kerdiles


title: CircPan3 Promotes the Ghrelin System and Chondrocyte Autophagy by Sponging miR-667-5p During Rat Osteoarthritis Pathogenesis

first: li

last: yuan

overall_design: Refer to individual Series


title: The redox homeostasis of skeletal muscle cells regulates stage differentiation of Toxoplasma gondii

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

summary: Toxoplasma gondii is an obligatory intracellular parasite that causes persistent infections in birds and mammals including ~30% of the world’s human population. Differentiation from proliferative and metabolically active tachyzoites to largely dormant bradyzoites initiates the chronic phase of infection and occurs predominantly in brain and muscle tissues. Here we used murine skeletal muscle cells (SkMCs) to decipher host cellular factors that favor T. gondii bradyzoite formation in terminally differentiated and syncytial myotubes, but not in proliferating myoblast precursors. Genome-wide transcriptome analyses of T. gondii-infected SkMCs and non-infected controls identified ~6,500 genes which were differentially expressed (DEGs) in myotubes compared to myoblasts, largely irrespective of infection. On the other hand, genes related to central carbohydrate metabolism, to redox homeostasis, and to the Nrf2-dependent stress response pathway were enriched in both infected myoblast precursors and myotubes. Stable isotope-resolved metabolite profiling indicated increased fluxes into the oxidative branch of the pentose phosphate pathway (OxPPP) in infected myoblasts and into the TCA cycle in infected myotubes. High OxPPP activity in infected myoblasts was associated with increased NADPH/NADP+ ratio while myotubes exhibited higher ROS levels and lower expression of anti-oxidants and detoxification enzymes. Pharmacological reduction of ROS levels in SkMCs inhibited bradyzoite differentiation, while increased ROS induced bradyzoite formation. Thus, we identified a novel host cell-dependent mechanism that triggers stage conversion of T. gondii into persistent tissue cysts in its natural host cell type.

overall_design: High throughput RNA profiles from C2C12 myoblasts and myotubes infected with Toxoplasma gondii or left non-infected were generated by Illumina sequencing. Four experimental conditions with 3 biological replicates each were analysed.

first: Carsten

last: Lüder

first: M

middle: T

last: Rahman

first: Izabela

last: Swierzy

first: Bryan

last: Downie

first: Martin

last: Blume

first: Malcolm

last: McConville


title: Expression profiles of circular RNAs in ST cells uninfected or infected by PDCoV

city: NANJING

first: LIUYANG

last: Du

state: JIANGSU

address: WEIGANG NO.1

department: College of Veterinary Medicine

country: China

institute: Nanjing Agricultural University

summary: Circular RNAs (circRNAs) participate in regulating many biological processes. However, their roles in PDCoV pathogenicity are largely unknown. Here, we analyzed the expression profile of circRNAs in swine testicular (ST) cells uninfected or infected by PDCoV by high-throughput sequencing.

overall_design: Expression profiles of circular RNAs in ST cells infected or uninfected by PDCoV were generated by deep sequencing, in duplicates, using Illumina HiSeq X Ten.

first: Liuyang

first: Jinyan

last: Gu

first: Jiyong

last: Zhou


title: Expression profiles of microRNAs in ST cells uninfected or infected by PDCoV

summary: mircoRNAs (miRNAs) participate in regulating many biological processes. However, their roles in PDCoV pathogenicity are largely unknown. Here, we analyzed the expression profile of miRNAs in ST cells uninfected or infected by PDCoV by high-throughput sequencing

overall_design: Expression profiles of miRNAs in ST cells infected or uninfected by PDCoV were generated by deep sequencing, in duplicates, using Illumina Hiseq 2500.

first: Yu

last: Zhang


title: MIA SH3 Domain ER Export Factor 3 deficiency prevents neointimal formation by restoring BAT-like PVAT and decreasing VSMC proliferation and migration

status: Public on Nov 03 2021

city: Shanghai

first: Tao

last: Zhuang

address: 131 Dong’an Road

institute: Fudan University

summary: RNA-sequencing data of HASMC transfected with MIA3 siRNA or scramble siRNA.

overall_design: HASMCs were collected, RNA was isolated and libraries were prepared with phi29 to make DNA nanoball and sequenced on BGIseq500 platform.

last: Lei

first: Jianfei

last: Xu

first: Mengju

last: Li

first: Ting

last: Meng

first: Junli

last: Zuo


title: Programmed genomic instability regulates neural transdifferentiation of human brain microvascular pericytes [RNA-Seq]

first: Ramin

last: M Farahani

overall_design: RNA-seq profiles of Control, and transdifferentiating human primary brain pericytes sampled every 5 min, Technical replicates: 4/group

last: Farahani


title: The translational value of patient-derived primary melanoma cell cultures depends on the concentration of Tyrosine in the medium.

city: Leuven

first: Jasper

last: Wouters

address: ON IV Herestraat 49 - bus 602

institute: KU Leuven - VIB

summary: The use of patient-derived primary cell cultures in cancer preclinical assays, including drug screens and genotoxic studies, has increased in recent years. However, their translational value is constrained by several limitations, including variability that can be caused by the culture conditions. Here, we show that the medium composition commonly used to propagate primary melanoma cultures has limited their representability of their tumor of origin, their cellular plasticity and modified their sensitivity to therapy. We established and compared cultures from different melanoma patients propagated in parallel in low-tyrosine (Ham’s F10) or, in high-tyrosine (Ham’s F10 supplemented with tyrosine, RPMI/DMEM) media. Tyrosine is the precursor of melanin biosynthesis, a process particularly active in differentiated melanocytes and melanoma cells. Unexpectedly, we found that the high tyrosine concentrations promoted an early phenotypic drift towards either a mesenchymal-like or senescence-like phenotype, and prevented the establishment of cultures of melanoma cells harboring differentiated features, which we show are frequently present in human clinical biopsies. Moreover, the invasive phenotype emerging in these culture conditions appeared irreversible and, as expected, associated with intrinsic resistance to MAPKi. In sharp contrast, differentiated melanoma cell cultures retained their phenotypes upon propagation in low-tyrosine medium, and importantly their phenotypic plasticity, a key hallmark of melanoma cells. Our findings underline the importance of culturing melanoma cells in low-tyrosine-containing medium in order to preserve their phenotypic identity of origin and cellular plasticity.

overall_design: RNA-seq of primary cell cultures grown in Ham’s-F10 culture medium, Ham’s F10 supplemented with 100μM of tyrosine or RPMI1640.

first: Ahmad

last: Najem

first: Stein

last: Aerts

first: Ghanem

last: Ghanem


title: Programmed genomic instability regulates neural transdifferentiation of human brain microvascular pericytes [ATAC-Seq]

overall_design: ATAC-seq profiles of Control, and transdifferentiating human primary brain pericytes sampled every 2 min, Technical replicates: 2/group


title: Methylomes of macrophage-DC progenitors (MDPs), monocytes, common monocyte progenitors (cMoPs), common dendritic cell progenitors (CDPs), plasmacytoid dendritic cells (pDCs), and cDC CD8a+ as well as cDC CD11b+ dendritic cells

city: Augsburg

first: Stephen

last: Krämer

address: Alter Postweg 101

institute: University of Augsberg

summary: Dendritic cells (DCs) are critical immune regulators involved in autoimmune diseases, but exploiting them clinically requires a detailed picture on the mechanisms orchestrating their development. DNA methylation is attractive in this regard because it is reversible and as such allows therapeutic manipulation. Combining single cell transplantation assays with whole-genome methylation assessment and with mice expressing reduced DNA methyltransferase 1 levels, we show that conventional and plasmacytoid DCs arise from myeloid-restricted hematopoietic stem cells (HSCs), suggesting that both subsets can develop independently of the lymphoid pathway. DC commitment by these HSCs requires an intrinsically high methylation threshold to establish expression of DC genes, particularly the Flt3 cytokine receptor. Reducing methylation depleted DCs and ameliorated systemic lupus erythematosus in mice. These studies shed novel light on the DC origin, show how lineage- and subset-specific methylation dynamics regulate DC fate and provide a potential rationale for targeting DCs in autoimmunity by hypomethylating agents.

overall_design: Tagmentation-based whole-genome bisulfite sequencing (TWGBS) of MDPs (Lin- cKithi CD115+ Flt3+, 2 Replicates), Monocytes (CD11b+ Ly6Chi B220- CD5- CD8a- Ter119- SiglecF- Ly6G- FceRI-, 3 Replicates), cMoPs (Lin- cKithi CD115+ Flt3- CD11b- Ly6C+, 2 Replicates), CDPs (Lin- cKitlo CD115+ Flt3+, 4 replicates), pDCs (PDCA+ CD11cint, 3 replicates), cDC CD8a+ (MHC II+ CD11chi CD11b- CD8a+, 3 replicates) and cDC CD11b+ (MHC II+ CD11chi CD11b+ CD8a-, 3 replicates). Lineage markers (Lin): (B220, CD4, CD8a, CD3, CD19, CD11c, Ter119, NK1.1, expanded by antibodies to CD11b and Gr-1 for isolation of MDP and CDP or Ly-6G for cMoP isolation). For each replicate, four separate TWGBS libraries were prepared and pools of four libraries were sequenced on three separate HiSeq2000 lanes using the 125bp paired-end mode.

first: Sina

last: Stäble

first: Melinda

last: Czeh

first: Michael

last: Milsom

first: Matthias

last: Schlesner

first: Frank

last: Rosenbauer

first: Daniel

middle: B

last: Lipka


title: Treg transcriptomic profile in NSG, NSG+Thymus humanized mice and healthy donors (HD)

status: Public on Nov 02 2021

city: NEW HAVEN

first: Eric

last: Meffre

state: CT

address: 300 George street

country: USA

institute: Yale Univeristy

summary: RNA sequencing was performed on RNA extracted from human Treg cells from NSG, NSG+Thymus humanized mice and healthy donors

overall_design: RNA was extracted from batch-sorted human CD3+CD4+CD25hiCD127lo splenic Tregs isolated from humanized mice or blood Tregs from HDs

first: Jeff

middle: W

last: Chen


title: Prenatal Adversity Alters the Epigenetic Profile of the Prefrontal Cortex: Sexually Dimorphic Effects of Prenatal Alcohol Exposure and Food-related Stress

status: Public on Nov 01 2021

city: Vancouver

first: Alexandre

middle: A

last: Lussier

state: British Columbia

department: Department of Medical Genetics

institute: University of British Columbia

summary: Prenatal adversity or stress can have long-term consequences on developmental trajec-tories and health outcomes. Although the biological mechanisms underlying these effects are poorly understood, epigenetic modifications, such as DNA methylation, have the potential to link early-life environments to alterations in physiological systems, with long-term functional impli-cations. We investigated the consequences of two prenatal insults, prenatal alcohol exposure (PAE) and food-related stress, on DNA methylation profiles of the rat brain during early devel-opment. As these insults can have sex-specific effects on biological outcomes, we analyzed epige-nome-wide DNA methylation patterns in prefrontal cortex, a key brain region involved in cogni-tion, executive function, and behavior, of both males and females. We found sex-dependent and sex-concordant influences of these insults on epigenetic patterns. These alterations occurred in genes and pathways related to brain development and immune function, suggesting that PAE and food-related stress may reprogram neurobiological/physiological systems partly through central epigenetic changes, and may do so in a sex-dependent manner. Such epigenetic changes may re-flect the sex-specific effects of prenatal insults on long-term functional and health outcomes and may have important implications for understanding possible mechanisms underlying fetal alco-hol spectrum disorder and other neurodevelopmental disorders.

overall_design: DNA methylation data from meDIP-seq of 30 rat samples, spanning three prenatal treatment groups (control, pair-fed, prenatal alcohol exposed) and both sexes. Prefrontal cortex samples were collected on postnatal day 22 (PN22).  Each group/sex had n= 5. One sequencing run was performed for each sample (30 aligned bam files) and DNA methylation peaks were called using MACS2 following DNA processing (xls files).

first: Tamara

last: Bodnar

first: Michelle

last: Moksa

first: Martin

last: Hirst

last: Kobor

first: Joanne

last: Weinberg


title: Anti-tumor Effect of Apatinib and Relevant Mechanisms in Liposarcoma

city: Beijing

first: Chunyi

last: Hao

address: No. 52 Fucheng Road, Haidian District

department: Department of Hepato-Pancreato-Biliary Surgery

institute: Peking University Cancer Hospital & Institute

summary:
Purpose: Primary retroperitoneal liposarcomas (RLPSs) are rare heterogeneous tumors for which there are few effective therapies. Certain anti-angiogenic tyrosine kinase inhibitors have demonstrated efficacy against various solid tumors. The aims of this study were to investigate the effect of Apatinib against retroperitoneal liposarcoma cells and its underlying mechanism and to explore the anti-tumor efficacy of a combination of Apatinib and Epirubicin.
Methods: SW872 cells were treated with Apatinib(18μM) for 24 h. The RNAs of the control group and experimental group were stored in TRIzol reagent at -80 ℃. Then mRNA extraction and RNA sequencing were performed by Beijing Mygenostics Co. Ltd., Beijing, China. A Bioanalyzer 2100 System (Agilent Technologies, Santa Clara, CA, USA) was used to assay RNA integrity. An AMPureXP system (BeckmanCoulter, Brea, CA, USA) was used to perform PCR on the products. Quality-tested library preparations were sequenced on the Illumina Novaseq platform (Illumina, San Diego, CA, USA). There were three biological replicates per condition. Differential expression analysis of both groups was performed using DESeq2R v. 1.20.0. The Benjamini-Hochberg multiple hypothesis test correction was performed to obtain the false discovery rate (FDR). The criteria used to select the DEGs were |log2(FoldChange)| > 0.5 and FDR < 0.05. When log2(FoldChange) > 0, the gene was considered upregulated. When log2(FoldChange) < 0, the gene was considered downregulated. profiler package in R (R Core Team, Vienna, Austria) was used for GO function and KEGG pathway enrichment analyses of the DEGs. Histograms and bubble graphs were plotted with the ggplot2 package in R v. 3.4.3.
Results:To elucidate the mechanisms by which Apatinib inhibited liposarcoma cells, we used RNA-seq to evaluate relative genetic changes in the SW872 cells after being treated with Apatinib for 24 hs, and found 2,038 DEGs, including 1,059 significantly downregulated genes and 979 significantly upregulated genes. The output of the KEGG pathway enrichment analysis suggests that Apatinib might inhibit SW872 cell proliferation through p53, DNA replication, and other important signaling pathways. GO enrichment analysis was performed on the genes that were significantly altered after Apatinib application.High-throughput RNA sequencing showed that Apatinib downregulated the expression of TYMS and RRM2.
Conclusions:  Apatinib  showed strong efficacy against liposarcoma both in vitro and in vivo. Apatinib might inhibit liposarcoma cell proliferation through the RRM2/PI3K/AKT/mTOR signaling pathway and downregulate PD-L1 via the TYMS/STAT3 signaling pathway.

overall_design: mRNA profiles of untreated SW872 cells and SW872 cells treated with apatinib(18μM for 24 hours)

first: Lixuan

last: Cui

first: Xiuyun

last: Tian

first: Jianhui

last: Wu


title: Tbx1 regulates a cardiopharyngeal mesodermal niche in forming the heart and branchiomeric muscles [scRNA-Seq 4]

city: Bronx

first: Hiroko

last: Nomaru

state: NY

address: 1300 Morris Park ave

department: Genetics

institute: Albert Einstein College of Medicine

summary: The heart and branchiomeric muscles are formed from the cardiopharyngeal mesoderm (CPM) during mammalian embryogenesis.  The molecular mechanisms for lineage progression in the CPM in mammals remain elusive.  Here, we have used single cell RNA-seq and lineage analysis and identified a cardiopharyngeal niche containing multilineage primed cells termed multilineage progenitors (MLPs), which is maintained throughout maturation of the pharyngeal apparatus.  We found that MLP function is dependent on Tbx1, encoding a T-box transcription factor and the gene for 22q11.2 deletion syndrome.  TBX1 positively regulates novel MLP enriched genes such as Aplnr and Nrg1, as well as known CPM genes related to both BrM and cardiac muscle cell development.  Further, loss of Tbx1 results in ectopic expression of neuronal and other non-mesodermal specification genes such as Bdnf and Pax8, respectively, indicating that normal developmental regulation is disrupted.  Integration of the multi-omic data generated a TBX1 gene regulatory network, including Isl1, Pitx2, Foxc2, Six1/2 and Tcf21, that regulates CPM lineage progression from MLPs. Our finding suggests that TBX1 is a one of the key regulators in MLP to maintain CPM property and promote differentiation toward both BrM and cardiac muscle cells.

overall_design: Mesp1 gene expresses in early cardiac mesodermal cells. To capture mesodermal cell lineages,  sorted GFP positive cell from Mesp1-Cre/+;GFPflox/+ embryos at E8.0 to E10.5 embryos were used for scRNA-seq analysis.

first: Bernice

middle: E

last: Morrow

first: Deyou

last: Zheng

first: Yang

last: Liu


title: ANALYSIS OF THE GENETIC EXPRESSION PROFILES OF SENSITIVE AND MULTIPHARMACORRESISTANT Mycobacterium tuberculosis CLONES EXPOSED TO NEW COMPOUNDS

city: Monterrey

first: Katia

last: Penuelas-Urquides

state: Nuevo León

address: Calle 2 de abril 501, Col. Independencia

department: Molecular Biology Dept.

country: Mexico

institute: Instituto Mexicano del Seguro Social

summary: The aim of this study was to evaluate the effect of new compounds exposure on gene expression of sensitive and MDR clones of M. tuberculosis

overall_design: Sensitive and MDR M. tuberculosis clones were isolated, phenotypically, and genetically characterized, cultured to log phase and treated with the compounds; followed by total RNA isolation, reverse transcription and hybridization assays on Affymetrix genomic microarrays.

first: K

last: Peñuelas-Urquides

first: M

last: Bermúdez de León

first: B

last: Silva-Ramírez

first: F

last: Castorena-Torres

first: GM

last: Molina-Salinas

first: J

last: Castro-Garza

first: P

last: Becerril-Montes

first: E

last: Del Olmo-Fernández

first: A

last: San Feliciano-Martín

first: LA

last: González-Escalante

first: L

last: Villarreal-Treviño

first: S

last: Said-Fernández


title: HOTAIR Modulated Pathways in Early-Stage Breast Cancer Progression

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

summary: The long-non-coding HOX transcript antisense intergenic RNA (HOTAIR) was identified as significantly upregulated in breast ductal carcinoma in situ (DCIS).  The aim of this study was to characterize the phenotypic effects and signaling pathways modulated by HOTAIR in early-stage breast cancer progression. We determined that HOTAIR induces premalignant phenotypic changes by increasing cell proliferation, migration, invasion and in vivo growth in normal and DCIS breast cell lines. Transcriptomic studies (RNA-seq) identified the main signaling pathways modulated by HOTAIR which include bioprocesses related to cell migration, epithelial to mesenchymal transition, extracellular matrix remodeling and activation of HIF1A, AP1 and FGFR signaling pathways among others. Similar pathways were identified as activated in primary invasive breast carcinomas with HOTAIR over-expression. We conclude that HOTAIR over-expression behaves as a positive regulator of cell growth and migration both in normal and DCIS breast cells involved with early-stage breast cancer progression.

overall_design:
Normal breast epithelial cell lines MCF10A and DCIS (ductal carcinoma in situ) cell line DCIS.COM were stably transduced with pCDH-HOTAIR or pCDH-empty vector (as control)  and selected with 10µg/ml puromycin.
MCF10A and DCIS.COM stably transduced cells were used for RNA isolation from subconfluent plates using the RNeasy kit (Qiagen, CA, USA). RNA concentration and integrity were measured on an Agilent 2100 Bioanalyzer (Agilent Technologies). Only RNA samples with RNA integrity values (RIN) over 8.0 were considered for subsequent analysis.

first: C

last: Aldaz


title: Transcriptional profile of MRE deficient BLaER1 monocytes [RNA MRE]

city: Berkeley

first: Nir

last: Yosef

state: CA

address: 629 Soda Hall

institute: University of California, Berkeley

summary: We have identified a MORC3-regulated DNA element (MRE) that regulates the activation of IFNB1 upon loss of MORC3. To study the global transcriptional effects of the MRE, we deleted the MRE in STAT1–/– STAT2–/–  and STAT1–/– STAT2–/– MORC3–/– BLaER1 monocytes and performed RNA-seq.

overall_design: Monoclonal gene-deficient BLaER1 monocytes in two independent experiments.

first: Moritz

middle: M

last: Gaidt

first: Alyssa

last: Morrow

first: Marian

last: Fairgrieve

first: Russell

last: Vance


title: Transcriptional profile of MORC3 deficient BLaER1 monocytes [KO]

summary: We have identified MORC3 as a negative regulator of Type I Interferon (IFN), whose absence induces IFN and interferon-stimulated genes (ISGs). To study the global transcriptional effects of loss of MORC3, we deleted MORC3  in WT, IFNAR1–/– IFNAR2–/– and IFNB1–/– BLaER1 monocytes and performed RNA-seq.

overall_design: Monoclonal gene-deficient BLaER1 monocytes in three independent experiments.


title: Self-guarding of MORC3 enables virulence factor-triggered immunity

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

overall_design: Refer to individual Series


title: Affymetrix SNP array data for chicken responses to glycoconjugate vaccination against Campylobacter jejuni

city: Edmonton

first: Graham

last: Plastow

state: Alberta

address: 1400 College Plaza, 8215 - 112 Street

department: Agricultural, Food & Nutritional Science

institute: University of Alberta

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Campylobacter jejuni is a common cause of diarrheal disease worldwide. Human infection typically occurs through the ingestion of contaminated poultry products. We previously demonstrated that an attenuated Escherichia coli live vaccine strain expressing the C. jejuni N-glycan on its surface reduces the Campylobacter load in more than 50% of vaccinated leghorn and broiler birds to undetectable levels (responder birds), whereas the remainder of the animals were still colonized (non-responders). To understand the underlying mechanism, we conducted 3 larger scale vaccination and challenge studies using 135 broiler birds and found a similar responder/non responder effect. The submitted data were used for a genome-wide association study of the chicken responses to glycoconjugate vaccination against Campylobacter jejuni.

overall_design: In total, 134 chickens (88 responders and 46 non-responders) from three experiments were genotyped for the genome-wide association study.

first: Christine

last: Szymanski


title: ATAC-seq of MORC3 deficient BLaER1 monocytes [ATAC-seq]

summary: We have identified MORC3 as a negative regulator of Type I Interferon (IFN), whose absence induces IFN and interferon-stimulated genes (ISGs). To study the global effects of MORC3 on DNA accessibility, we deleted MORC3 in IFNAR1-/- IFNAR2-/- BLaER1 monocytes and performed ATAC-seq.


title: Effects of housekeeping sortase disruption on Bifidibacterium bifidum toranscriptome

city: Kunitachi

first: Eiji

last: Ishikawa

state: Tokyo

address: Izumi 5-11

country: Japan

institute: Yakult Central Institute

summary: To explore the molecular mechanism of B. bifidum adhesion, we compared transcriptomes among WT and non-adhesive mutants cultured in MRS or m-ILS medium.

overall_design: WT and three non-adahesive mutants (#1476, #1543, and #1649) growing exponentially in MRS or m-ILS medium were sampled at 3 hours after 5%(v/v) inoculation. Single experiment was performed for each sample.


title: Whole genome bisulfite sequencing analysis to measure the effect of EHMT2 (G9a, Bat8) on DNA methylation in the mouse embryo at 9.5 dpc

city: Grand Rapids

first: Piroska

last: Szabó

state: MI

address: 333 Bostwick ave NE

department: Epigenetics

institute: Van Andel Institute

summary: WGBS analysis was used to map DNA methylation in response to the mutation of Ehmt2 gene at the embryonic age of 9.5 days post coitum.

overall_design: One sample contains DNA from two Ehmt2 homozygous mutant embryos (one male and one female combined), and the control sample contains DNA from a wild type female embryo.

first: Szabó

last: Piroska

first: Pierce

last: Nicholas

first: Singh

last: Purima


title: RNAseq of mouse mammary luminal cells

city: Macau

first: Heng

last: Sun

address: Avendia da Universidade, Taipa

department: Faculty of Health Sciences

country: Macau

institute: University of Macau

summary: The mammary epithelia are mainly composed of two distinct lineages, the basal and luminal cells. In our MMTV-Cre; Brca1flox/flox mouse model, we found the Brca1 knockout mainly occurred in the luminal cells, which will lead the mammary tumorigenesis. To investigate the Brca1 deficiency mediated mammary tumorigenesis, we sorted the luminal cells from wild type mice and MMTV-Cre; Brca1flox/flox mice for RNAseq analysis.

overall_design: 5 mouse luminal cells samples were collected for RNA sequencing.

first: Chuxia

last: Deng


title: Transcriptional and anatomical diversity of medium spiny neurons in the primate striatum.

city: PITTSBURGH

first: William

middle: R.

last: Stauffer

state: PA

address: 3501 Fifth Ave

department: Neurobiology

institute: University of Pittsburgh

summary: The striatum is the interface between dopamine reward signals and cortico-basal ganglia circuits that mediate diverse behavioral functions. Medium spiny neurons (MSNs) constitute the vast majority of striatal neurons and are traditionally classified as direct- or indirect-pathway neurons. However, that traditional model does not explain the anatomical and functional diversity of MSNs. Here, we defined molecularly distinct MSN types in the primate striatum, including (1) dorsal striatum MSN types associated with striosome and matrix compartments, (2) ventral striatum types associated with the nucleus accumbens shell and olfactory tubercle, and (3) an MSN-like type restricted to mu-opioid receptor rich islands in the ventral striatum. These results lay the foundation for achieving cell type-specific transgenesis in the primate striatum and provide a blueprint for investigating circuit-specific processing.

overall_design: Single nuclei RNA profiles of rhesus macaque striatal regions, caudate, putamen, and ventral striatum.

first: Jing

last: He

first: Michael

last: Kleyman

first: Jianjiao

last: Chen

first: Aydin

last: Alikaya

first: Kathryn

last: Rothenhoefer

first: Bilge

last: Ozturk

first: Morgan

last: Wirthlin

first: Kenneth

last: Fish

first: Leah

last: Byrne

first: Andreas

last: Pfenning

first: Willam


title: Transcriptional effects of HSV-1-ICP0 and Ad5-E4ORF3 expression in BLaER1 monocytes [Virulence factors]

first: Nir

last: Yosef

summary: We have identified that the viral virulence factors ICP0 from HSV-1 and E4ORF3 from Adenovirus5 can activate the MORC3 pathway of innate immune sensing. To study the global transcriptional effects of virulence factor sensing, we overexpressed mCherry or these virulence factors from a doxycycline-inducible lentiviral construct in BLaER1 monocytes of various genotypes and performed RNA-seq.

overall_design: Monoclonal gene-deficient BLaER1 expressing mCherry or viral virulence factors in three independent experiments.

first: Moritz

last: Gaidt

first: Alyssa

last: Morrow

first: Marian

last: Fairgrieve

first: Russell

last: Vance


title: Single-cell RNA-seq analysis reveals reduction of B cells in the bone marrow promote fracture healing

city: shanghai

first: Renkai

last: Wang

address: 168 Changhai Road,

institute: changhai hospital

summary: Recent studies have identified B cells inhibit bone formation in rheumatoid arthritis by suppressing osteoblast differentiation. However, it remains unknown how B cells participate in the healing of fractures. Here we find that B cells decrease significantly during fracture healing and returned to normal levels after that by single-cell profiling. Furthermore, we found that exosomes derived from B cells inhibited the differentiation of osteoblasts and osteoclasts in vitro. Additionally, injection of these exosomes in mice delayed fracture healing. Thus, maintaining low B cell levels in the bone marrow microenvironment promotes fracture healing.

overall_design: scRNA profiles of fracture at different stage (control group, 30th day)

first: Hao

last: Tang